https://rctn.org/w/api.php?action=feedcontributions&user=Edodds&feedformat=atomRedwoodCenter - User contributions [en]2024-03-28T08:31:55ZUser contributionsMediaWiki 1.39.4https://rctn.org/w/index.php?title=TCN&diff=9089TCN2017-11-13T07:48:51Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [December 13] <font color="##ff0000">Ryan Zarcone</font><br />
* [December 6] <font color="##ff0000">Danny Weitekamp</font><br />
* [November 29] <font color="##ff0000">Eric Weiss</font><br />
* [November 15] <font color="##ff0000">Bruno Olshausen</font> - Sara Sabour, Nicholas Frosst, and Geoffrey E. Hinton. "Dynamic Routing Between Capsules." [https://arxiv.org/abs/1710.09829]<br />
* [November 8] <font color="##ff0000">Charles Frye</font> - Jeffrey Pennington and Yasaman Bahri. "Geometry of Neural Network Loss Surfaces via Random Matrix Theory." [http://proceedings.mlr.press/v70/pennington17a/pennington17a.pdf]<br />
* [November 1] <font color="##ff0000">Shariq Mobin</font> - Matthew James Johnson <i>et al.</i> "Composing graphical models with neural networks for structured representations and fast inference." [http://papers.nips.cc/paper/6378-composing-graphical-models-with-neural-networks-for-structured-representations-and-fast-inference]<br />
* [October 25] <font color="##ff0000">Vasha DuTell</font> - Marius Pachitariu and Maneesh Sahani. "Visual motion computation in recurrent neural networks." [https://www.biorxiv.org/content/early/2017/01/09/099101]<br />
* [October 18] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar & Brent Doiron. "Slow dynamics and high variability in balanced cortical networks with clustered connections." [http://www.nature.com/neuro/journal/v15/n11/full/nn.3220.html?foxtrotcallback=true]<br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font> - Ingmar Kanitscheider & Ila Fiete. "Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems." [https://arxiv.org/abs/1609.09059]<br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=9075TCN2017-11-09T01:13:21Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [December 13] <font color="##ff0000">Ryan Zarcone</font><br />
* [December 6] <font color="##ff0000">James Arnemann</font><br />
* [November 29] <font color="##ff0000">Eric Weiss</font><br />
* [November 15] <font color="##ff0000">Bruno Olshausen</font> - Sara Sabour, Nicholas Frosst, and Geoffrey E. Hinton. "Dynamic Routing Between Capsules." [https://arxiv.org/abs/1710.09829]<br />
* [November 8] <font color="##ff0000">Charles Frye</font> - Jeffrey Pennington and Yasaman Bahri. "Geometry of Neural Network Loss Surfaces via Random Matrix Theory." [http://proceedings.mlr.press/v70/pennington17a/pennington17a.pdf]<br />
* [November 1] <font color="##ff0000">Shariq Mobin</font> - Matthew James Johnson <i>et al.</i> "Composing graphical models with neural networks for structured representations and fast inference." [http://papers.nips.cc/paper/6378-composing-graphical-models-with-neural-networks-for-structured-representations-and-fast-inference]<br />
* [October 25] <font color="##ff0000">Vasha DuTell</font> - Marius Pachitariu and Maneesh Sahani. "Visual motion computation in recurrent neural networks." [https://www.biorxiv.org/content/early/2017/01/09/099101]<br />
* [October 18] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar & Brent Doiron. "Slow dynamics and high variability in balanced cortical networks with clustered connections." [http://www.nature.com/neuro/journal/v15/n11/full/nn.3220.html?foxtrotcallback=true]<br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font> - Ingmar Kanitscheider & Ila Fiete. "Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems." [https://arxiv.org/abs/1609.09059]<br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=9073TCN2017-11-06T03:45:13Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [December 13] <font color="##ff0000">Ryan Zarcone</font><br />
* [December 6] <font color="##ff0000">James Arnemann</font><br />
* [November 29] <font color="##ff0000">Brian Cheung</font><br />
* [November 15] <font color="##ff0000">Bruno Olshausen</font> - Sara Sabour, Nicholas Frosst, and Geoffrey E. Hinton. "Dynamic Routing Between Capsules." [https://arxiv.org/abs/1710.09829]<br />
* [November 8] <font color="##ff0000">Charles Frye</font> - Jeffrey Pennington and Yasaman Bahri. "Geometry of Neural Network Loss Surfaces via Random Matrix Theory." [http://proceedings.mlr.press/v70/pennington17a/pennington17a.pdf]<br />
* [November 1] <font color="##ff0000">Shariq Mobin</font> - Matthew James Johnson <i>et al.</i> "Composing graphical models with neural networks for structured representations and fast inference." [http://papers.nips.cc/paper/6378-composing-graphical-models-with-neural-networks-for-structured-representations-and-fast-inference]<br />
* [October 25] <font color="##ff0000">Vasha DuTell</font> - Marius Pachitariu and Maneesh Sahani. "Visual motion computation in recurrent neural networks." [https://www.biorxiv.org/content/early/2017/01/09/099101]<br />
* [October 18] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar & Brent Doiron. "Slow dynamics and high variability in balanced cortical networks with clustered connections." [http://www.nature.com/neuro/journal/v15/n11/full/nn.3220.html?foxtrotcallback=true]<br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font> - Ingmar Kanitscheider & Ila Fiete. "Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems." [https://arxiv.org/abs/1609.09059]<br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=9072TCN2017-11-06T03:43:35Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [December 13] <font color="##ff0000">Ryan Zarcone</font><br />
* [December 6] <font color="##ff0000">James Arnemann</font><br />
* [November 29] <font color="##ff0000">Brian Cheung</font><br />
* [November 15] <font color="##ff0000">Bruno Olshausen</font><br />
* [November 8] <font color="##ff0000">Charles Frye</font> - Jeffrey Pennington and Yasaman Bahri. "Geometry of Neural Network Loss Surfaces via Random Matrix Theory." [http://proceedings.mlr.press/v70/pennington17a/pennington17a.pdf]<br />
* [November 1] <font color="##ff0000">Shariq Mobin</font> - Matthew James Johnson <i>et al.</i> "Composing graphical models with neural networks for structured representations and fast inference." [http://papers.nips.cc/paper/6378-composing-graphical-models-with-neural-networks-for-structured-representations-and-fast-inference]<br />
* [October 25] <font color="##ff0000">Vasha DuTell</font> - Marius Pachitariu and Maneesh Sahani. "Visual motion computation in recurrent neural networks." [https://www.biorxiv.org/content/early/2017/01/09/099101]<br />
* [October 18] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar & Brent Doiron. "Slow dynamics and high variability in balanced cortical networks with clustered connections." [http://www.nature.com/neuro/journal/v15/n11/full/nn.3220.html?foxtrotcallback=true]<br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font> - Ingmar Kanitscheider & Ila Fiete. "Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems." [https://arxiv.org/abs/1609.09059]<br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=9064TCN2017-10-30T19:16:00Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [December 13] <font color="##ff0000">Ryan Zarcone</font><br />
* [December 6] <font color="##ff0000">James Arnemann</font><br />
* [November 29] <font color="##ff0000">Brian Cheung</font><br />
* [November 15] <font color="##ff0000">Eric Dodds</font><br />
* [November 8] <font color="##ff0000">Charles Frye</font><br />
* [November 1] <font color="##ff0000">Shariq Mobin</font> - Matthew James Johnson <i>et al.</i> "Composing graphical models with neural networks for structured representations and fast inference." [http://papers.nips.cc/paper/6378-composing-graphical-models-with-neural-networks-for-structured-representations-and-fast-inference]<br />
* [October 25] <font color="##ff0000">Vasha DuTell</font> - Marius Pachitariu and Maneesh Sahani. "Visual motion computation in recurrent neural networks." [https://www.biorxiv.org/content/early/2017/01/09/099101]<br />
* [October 18] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar & Brent Doiron. "Slow dynamics and high variability in balanced cortical networks with clustered connections." [http://www.nature.com/neuro/journal/v15/n11/full/nn.3220.html?foxtrotcallback=true]<br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font> - Ingmar Kanitscheider & Ila Fiete. "Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems." [https://arxiv.org/abs/1609.09059]<br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=9063TCN2017-10-30T19:13:59Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [December 13] <font color="##ff0000">Ryan Zarcone</font><br />
* [December 6] <font color="##ff0000">James Arnemann</font><br />
* [November 29] <font color="##ff0000">Brian Cheung</font><br />
* [November 15] <font color="##ff0000">Eric Dodds</font><br />
* [November 8] <font color="##ff0000">Charles Frye</font><br />
* [November 1] <font color="##ff0000">Shariq Mobin</font> - Matthew James Johnson <i>et al.</i> "Composing graphical models with neural networks for structured representations and fast inference."<br />
* [October 25] <font color="##ff0000">Vasha DuTell</font> - Marius Pachitariu and Maneesh Sahani. "Visual motion computation in recurrent neural networks."<br />
* [October 18] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar & Brent Doiron. "Slow dynamics and high variability in balanced cortical networks with clustered connections." [http://www.nature.com/neuro/journal/v15/n11/full/nn.3220.html?foxtrotcallback=true]<br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font> - Ingmar Kanitscheider & Ila Fiete. "Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems." [https://arxiv.org/abs/1609.09059]<br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=9037TCN2017-10-13T00:47:19Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [December 13] <font color="##ff0000">Ryan Zarcone</font><br />
* [December 6] <font color="##ff0000">Charles Frye</font><br />
* [November 29] <font color="##ff0000">Brian Cheung</font><br />
* [November 15] <font color="##ff0000">Eric Dodds</font><br />
* [November 8] <font color="##ff0000">James Arnemann</font><br />
* [November 1] <font color="##ff0000">Shariq Mobin</font><br />
* [October 25] <font color="##ff0000">Vasha DuTell</font><br />
* [October 18] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar & Brent Doiron. "Slow dynamics and high variability in balanced cortical networks with clustered connections." [http://www.nature.com/neuro/journal/v15/n11/full/nn.3220.html?foxtrotcallback=true]<br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font> - Ingmar Kanitscheider & Ila Fiete. "Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems." [https://arxiv.org/abs/1609.09059]<br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=9034TCN2017-10-11T22:59:12Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [December 13] <font color="##ff0000">Ryan Zarcone</font><br />
* [December 6] <font color="##ff0000">Charles Frye</font><br />
* [November 29] <font color="##ff0000">Brian Cheung</font><br />
* [November 15] <font color="##ff0000">Eric Dodds</font><br />
* [November 8] <font color="##ff0000">James Arnemann</font><br />
* [November 1] <font color="##ff0000">Pratik Sachdeva</font><br />
* [October 25] <font color="##ff0000">Louis Kang</font><br />
* [October 18] <font color="##ff0000">Shariq Mobin</font><br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font> - Ingmar Kanitscheider & Ila Fiete. "Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems." [https://arxiv.org/abs/1609.09059]<br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=9011TCN2017-09-20T23:37:10Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [October 11] <font color="##ff0000">Vasha DuTell</font><br />
* [October 4] <font color="##ff0000">Mayur Mudigonda</font><br />
* [September 27] <font color="##ff0000">Spencer Kent</font> - Jiajun Wu, Joshua B. Tenenbaum, and Pushmeet Kohli. "Neural Scene De-rendering" [http://openaccess.thecvf.com/content_cvpr_2017/papers/Wu_Neural_Scene_De-Rendering_CVPR_2017_paper.pdf]<br />
* [September 13] <font color="##ff0000">Guy Isely</font> - Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8998TCN2017-09-07T20:59:10Z<p>Edodds: /* Fall 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [October 4] <font color="##ff0000">Vasha DuTell</font><br />
* [September 27] <font color="##ff0000">Mayur Mudigonda</font><br />
* [September 20] <font color="##ff0000">Spencer Kent</font><br />
* [September 13] <font color="##ff0000">Guy Isely</font> Saurabh Gupta, James Davidson, Sergey Levine, Rahul Sukthankar, and Jitendra Malik. "Cognitive Mapping and Planning for Visual Navigation." [https://arxiv.org/abs/1702.03920]<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8997TCN2017-09-07T20:04:02Z<p>Edodds: /* Topics in Computational Neuroscience */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2017)<br />
'''4pm-5pm''' almost every Wednesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2017===<br />
* [September 27] <font color="##ff0000">Vasha DuTell</font><br />
* [September 20] <font color="##ff0000">Mayur Mudigonda</font><br />
* [September 13] <font color="##ff0000">Spencer Kent</font><br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8996TCN2017-09-07T20:00:37Z<p>Edodds: /* Overview */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [September 12] <font color="##ff0000">Vasha DuTell</font><br />
* [September 5] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 29] <font color="##ff0000">Spencer Kent</font><br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8898TCN2017-08-14T19:35:34Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [September 12] <font color="##ff0000">Vasha DuTell</font><br />
* [September 5] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 29] <font color="##ff0000">Spencer Kent</font><br />
* [August 22] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8897TCN2017-08-11T17:40:40Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
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=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [September 5] <font color="##ff0000">Vasha DuTell</font><br />
* [August 29] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 22] <font color="##ff0000">Spencer Kent</font><br />
* [August 15] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan, Lingyun Zhang, and Garrison Cottrell. "Recursive ICA" [http://papers.nips.cc/paper/3018-recursive-ica.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8890TCN2017-07-31T23:12:56Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [September 5] <font color="##ff0000">Vasha DuTell</font><br />
* [August 29] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 22] <font color="##ff0000">Spencer Kent</font><br />
* [August 15] <font color="##ff0000">Dylan Paiton</font> - Honghao Shan and Garrison Cottrell. "Efficient Visual Coding: From Retina To V2" [https://arxiv.org/pdf/1312.6077.pdf]<br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8889TCN2017-07-30T00:16:59Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 29] <font color="##ff0000">Vasha DuTell</font><br />
* [August 22] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 15] <font color="##ff0000">Spencer Kent</font><br />
* [August 8] <font color="##ff0000">Guy Isely</font> - Max Jaderberg, Wojciech Marian Czarnecki, Simon Osindero, Oriol Vinyals, Alex Graves, David Silver, and Koray Kavukcuoglu. "Decoupled Neural Interfaces using Synthetic Gradients." [https://arxiv.org/abs/1608.05343]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8888TCN2017-07-29T02:07:13Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [September 5] <font color="##ff0000">Vasha DuTell</font><br />
* [August 29] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 22] <font color="##ff0000">Spencer Kent</font><br />
* [August 15] <font color="##ff0000">Guy Isely</font><br />
* [August 8] <font color="##ff0000">Charles Frye</font> - Günter Klambauer, Thomas Unterthiner, Andreas Mayr, and Sepp Hochreiter. "Self-Normalizing Neural Networks." [https://arxiv.org/abs/1706.02515]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8887TCN2017-07-28T21:17:19Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 29] <font color="##ff0000">Vasha DuTell</font><br />
* [August 22] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 15] <font color="##ff0000">Spencer Kent</font><br />
* [August 8] <font color="##ff0000">Charles Frye</font> - Günter Klambauer, Thomas Unterthiner, Andreas Mayr, and Sepp Hochreiter. "Self-Normalizing Neural Networks." [https://arxiv.org/abs/1706.02515]<br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8883TCN2017-07-25T23:03:08Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 29] <font color="##ff0000">Vasha DuTell</font><br />
* [August 22] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 15] <font color="##ff0000">Spencer Kent</font><br />
* [August 8] <font color="##ff0000">Charles Frye</font> <br />
* [August 1] <font color="##ff0000">Alex Anderson</font> - Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] Canceled<br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> - Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8882TCN2017-07-25T23:02:42Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 29] <font color="##ff0000">Vasha DuTell</font><br />
* [August 22] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 15] <font color="##ff0000">Spencer Kent</font><br />
* [August 8] <font color="##ff0000">Charles Frye</font> <br />
* [August 1] <font color="##ff0000">Alex Anderson</font> Rahul G. Krishnan, Uri Shalit, and David Sontag. "Structured Inference Networks for Nonlinear State Space Models." [https://arxiv.org/abs/1609.09869]<br />
* [July 25] <font color="##ff0000">Canceled</font><br />
* [July 18] Canceled for CRCNS course<br />
* [July 11] Canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8819TCN2017-06-27T22:35:38Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 29] <font color="##ff0000">Vasha DuTell</font><br />
* [August 22] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 15] <font color="##ff0000">Spencer Kent</font><br />
* [August 8] <font color="##ff0000">Alex Anderson</font> <br />
* [August 1] <font color="##ff0000">Charles Frye</font><br />
* [July 25] <font color="##ff0000">Eric Weiss</font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8818TCN2017-06-27T22:35:24Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 29] <font color="##ff0000">Vasha DuTell</font><br />
* [August 22] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 15] <font color="##ff0000">Spencer Kent</font><br />
* [August 8] <font color="##ff0000">Alex Anderson</font> <br />
* [August 1] <font color="##ff0000">Charles Frye</font><br />
* [July 25] <font color="##ff0000">Eric Weiss<\font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Everyone</font> Ravid Shwartz-Ziv and Naftali Tishby. "Opening the Black Box of Deep Neural Networks via Information." [https://arxiv.org/abs/1703.00810]<br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8802TCN2017-06-20T22:10:34Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson</font> <br />
* [July 25] <font color="##ff0000">Charles Frye</font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font> <br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit." [https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8801TCN2017-06-20T22:09:36Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson</font> <br />
* [July 25] <font color="##ff0000">Charles Frye</font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font> <br />
* [June 20] <font color="##ff0000">Sean Mackesey</font> - R. Ellen Ambrose, Brad E. Pfeiffer, and David J. Foster. "Reverse replay of hippocampal place cells is uniquely modulated by changing reward." Neuron 91.5 (2016): 1124-1136.<br />
* [June 13] <font color="##ff0000">Neha Wadia</font> - Dmitriy Aronov, Rhino Nevers, and David W. Tank. "Mapping of a non-spatial dimension by the hippocampal–entorhinal circuit."<br />
[https://www.nature.com/nature/journal/v543/n7647/pdf/nature21692.pdf]<br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font> - Plant neurobiology [https://www.researchgate.net/profile/Stefano_Mancuso/publication/6942772_Plant_neurobiology_an_integrated_view_of_plant_signaling/links/0fcfd5087fafc3b3df000000.pdf] [<br />
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047902/pdf/fpsyg-07-01505.pdf] [http://biorxiv.org/content/biorxiv/early/2017/03/30/122358.full.pdf]<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8789TCN2017-05-30T18:50:45Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson</font> <br />
* [July 25] <font color="##ff0000">Charles Frye</font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font><br />
* [June 20] <font color="##ff0000">Sean Mackesey</font><br />
* [June 13] <font color="##ff0000">Neha Wadia</font><br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font><br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8788TCN2017-05-30T18:50:21Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson</font> <br />
* [July 25] <font color="##ff0000">Charles Frye</font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font><br />
* [June 20] <font color="##ff0000">Sean Mackesey</font><br />
* [June 13] <font color="##ff0000">Neha Wadia</font><br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font><br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - Readings on (ab)uses of machine learning in policing [https://medium.com/@blaisea/physiognomys-new-clothes-f2d4b59fdd6a] [https://whitecollar.thenewinquiry.com/static/whitepaper.pdf] [<br />
http://www.americanrhetoric.com/speeches/robertoppenheimeratomicbomb.htm] etc<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8787TCN2017-05-30T18:48:05Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson</font> <br />
* [July 25] <font color="##ff0000">Charles Frye</font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font><br />
* [June 20] <font color="##ff0000">Sean Mackesey</font><br />
* [June 13] <font color="##ff0000">Neha Wadia</font><br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font><br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - TBA<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8780TCN2017-05-23T17:25:26Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson</font> <br />
* [July 25] <font color="##ff0000">Charles Frye</font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font><br />
* [June 20] <font color="##ff0000">Neha Wadia</font><br />
* [June 13] <font color="##ff0000">Sean Mackesey</font><br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font><br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - TBA<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8779TCN2017-05-22T21:53:16Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson</font> <br />
* [July 25] <font color="##ff0000">Neha Wadia</font><br />
* [July 18] canceled for CRCNS course<br />
* [July 11] canceled for CRCNS course<br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font><br />
* [June 20] <font color="##ff0000">Charles Frye</font><br />
* [June 13] <font color="##ff0000">Sean Mackesey</font><br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font><br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - TBA<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8778TCN2017-05-22T19:52:25Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson</font> <br />
* [July 25] <font color="##ff0000">Neha Wadia</font><br />
* [July 18] <font color="##ff0000">Chris Warner</font><br />
* [July 11] <font color="##ff0000">Yubei Chen</font><br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font><br />
* [June 20] <font color="##ff0000">Charles Frye</font><br />
* [June 13] <font color="##ff0000">Sean Mackesey</font><br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font><br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - TBA<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8777TCN2017-05-22T19:52:11Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [August 22] <font color="##ff0000">Vasha DuTell</font><br />
* [August 15] <font color="##ff0000">Mayur Mudigonda</font><br />
* [August 8] <font color="##ff0000">Spencer Kent</font><br />
* [August 1] <font color="##ff0000">Alex Anderson /font> <br />
* [July 25] <font color="##ff0000">Neha Wadia</font><br />
* [July 18] <font color="##ff0000">Chris Warner</font><br />
* [July 11] <font color="##ff0000">Yubei Chen</font><br />
* [July 4] Holiday<br />
* [June 27] <font color="##ff0000">Michael Fang</font><br />
* [June 20] <font color="##ff0000">Charles Frye</font><br />
* [June 13] <font color="##ff0000">Sean Mackesey</font><br />
* [June 6] <font color="##ff0000">Charles Garfinkle</font><br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - TBA<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8776TCN2017-05-22T19:29:12Z<p>Edodds: /* Summer 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [May 30] <font color="##ff0000">Jesse Livezey</font> - TBA<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8774TCN2017-05-09T22:30:39Z<p>Edodds: /* Topics in Computational Neuroscience */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Summer 2017===<br />
* [May 23] <font color="##ff0000">Jesse Livezey</font> - TBA<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8773TCN2017-05-09T22:29:16Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 16] <font color="##ff0000">Various?</font> - Redwood NIPS submissions 2017<br />
* [May 9] <font color="##ff0000">James Arnemann</font> - van den Oord et al. (2016) Wavenet: A Generative Model for Raw Audio. [https://deepmind.com/blog/wavenet-generative-model-raw-audio/]<br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8772TCN2017-05-02T22:12:47Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font> - Ashok Litwin-Kumar, Kameron Decker Harris, Richard Axel, Haim Sompolinsky, and L.F. Abbott. (2017) Optimal Degrees of Synaptic Connectivity.[http://www.sciencedirect.com/science/article/pii/S0896627317300545]<br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8771TCN2017-04-25T22:17:43Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Pratik Sachdeva</font><br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8768TCN2017-04-18T23:40:45Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Kata Slama</font> - József Fiser, Pietro Berkes, Gergő Orbán, Máté Lengyel. (2010) Statistically optimal perception and learning: from behavior to neural representations [http://www.sciencedirect.com/science/article/pii/S1364661310000045]<br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font> - Matthew Zeiler & Rob Fergus. (2012) Differentiable Pooling for Hierarchical Feature Learning. [https://arxiv.org/pdf/1207.0151.pdf ]<br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8752TCN2017-04-11T21:55:46Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Neha Wadia</font><br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font><br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font> - Discussion on computational complexity and regularization in machine learning<br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8749TCN2017-04-01T19:35:19Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Neha Wadia</font><br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font><br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font><br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font> - Jun-Yan Zhu, Taesung Park, Philip Isola, and Alexei A. Efros. (2017) "Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks." [https://arxiv.org/abs/1703.10593]<br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8748TCN2017-03-31T21:24:47Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Neha Wadia</font><br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font><br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font><br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font><br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8731TCN2017-03-18T00:30:34Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Neha Wadia</font><br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font><br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font><br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font><br />
* [Mar 28] <font color="##ff0000">Alex Anderson</font><br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8729TCN2017-03-14T22:11:53Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Neha Wadia</font><br />
* [Apr 18] <font color="##ff0000">Dylan Paiton</font><br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font><br />
* [Apr 4] <font color="##ff0000">Brian Cheung</font><br />
* [Mar 28] <font color="##ff0000">Alex Anderson</font><br />
* [Mar 21] <font color="##ff0000">Michael Fang</font><br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8728TCN2017-03-11T00:15:39Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Neha Wadia</font><br />
* [Apr 18] <font color="##ff0000">Brian Cheung</font><br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font><br />
* [Apr 4] <font color="##ff0000">Dylan Paiton</font><br />
* [Mar 28] <font color="##ff0000">Alex Anderson</font><br />
* [Mar 21] <font color="##ff0000">Michael Fang</font><br />
* [Mar 14] <font color="##ff0000">Ryan Zarcone</font> - Johannes Ballé, Valero Laparra, and Eero P. Simoncelli. (2017) "End-to-end Optimized Image Compression." ICLR 2017. [https://arxiv.org/pdf/1611.01704.pdf]<br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8720TCN2017-03-03T00:03:54Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Neha Wadia</font><br />
* [Apr 18] <font color="##ff0000">Brian Cheung</font><br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font><br />
* [Apr 4] <font color="##ff0000">Dylan Paiton</font><br />
* [Mar 28] <font color="##ff0000">Ryan Zarcone</font><br />
* [Mar 21] <font color="##ff0000">Michael Fang</font><br />
* [Mar 14] <font color="##ff0000">Alex Anderson</font><br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font> - Wiktor Młynarski and Josh McDermott. (2017) "Learning Mid-Level Auditory Codes from Natural Sound Statistics." [https://arxiv.org/pdf/1701.07138v3.pdf]<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8694TCN2017-02-27T00:49:26Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [May 9] <font color="##ff0000">James Arnemann</font><br />
* [May 2] <font color="##ff0000">Shariq Mobin</font><br />
* [Apr 25] <font color="##ff0000">Neha Wadia</font><br />
* [Apr 18] <font color="##ff0000">Brian Cheung</font><br />
* [Apr 11] <font color="##ff0000">Eric Weiss</font><br />
* [Apr 4] <font color="##ff0000">Dylan Paiton</font><br />
* [Mar 28] <font color="##ff0000">Ryan Zarcone</font><br />
* [Mar 21] <font color="##ff0000">Michael Fang</font><br />
* [Mar 14] <font color="##ff0000">Alex Anderson</font><br />
* [Mar 7] <font color="##ff0000">Eric Dodds</font><br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8682TCN2017-01-23T22:16:18Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. (2016) "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8681TCN2017-01-23T22:15:30Z<p>Edodds: /* Spring 2017 */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> - Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8680TCN2017-01-23T22:15:18Z<p>Edodds: /* Topics in Computational Neuroscience */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Spring 2017===<br />
* [Jan 19] <font color="##ff0000">Kata Slama</font> Jiefeng Jiang (江界峰), Christopher Summerfield and Tobias Egner. "Visual Prediction Error Spreads Across Object Features in Human Visual Cortex." [https://doi.org/10.1523/JNEUROSCI.1546-16.2016]<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8679TCN2017-01-23T22:12:09Z<p>Edodds: /* Time and Location */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''2pm-3pm''' almost every Tuesday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
Please note that we are on hiatus for a few weeks at the beginning of the Spring 2017 semester.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edoddshttps://rctn.org/w/index.php?title=TCN&diff=8678TCN2017-01-23T22:10:03Z<p>Edodds: /* Overview */</p>
<hr />
<div>== Topics in Computational Neuroscience ==<br />
<br />
For ideas about some interesting papers to discuss have look here [[TCN Paper Ideas]]<br />
<br />
=== Overview ===<br />
This journal club is aimed at graduate students from the neuroscience program, neuroscience related life sciences, as well as students from engineering, physics, and math programs with an interest in a computational approach to studying the brain. It provides a broad survey of literature from theoretical and computational neuroscience. Readings will combine both seminal works and recent theories. We meet for one session each week.<br />
<br />
It is possible to take this seminar for credit. If you would like to do so, please mention during journal club.<br />
<br />
If you have questions, please email the club organizer (Spring 2017) [mailto:edodds@berkeley.edu?Subject=Redwood%TCN%Journal%20Club Eric Dodds]<br />
<br />
=== Time and Location ===<br />
(Fall 2016)<br />
'''4pm-5pm''' every Monday in the Redwood Center conference room (560 Evans). Please sign up to the email list (below) for announcements on changes to meeting dates.<br />
<br />
=== Guidelines for Presenting Papers ===<br />
Each person that selects a paper should present, in about 15-30 minutes:<br />
* an executive summary<br />
* an outline of the key points, ideas, or contributions<br />
* relevant background information<br />
* a description of the key figures<br />
* what you took away from the paper<br />
* some potential questions for discussion<br />
* you are encouraged to use whatever method to present (slides, puppets, etc.)<br />
<br />
=== E-mail List ===<br />
<br />
To subscribe to the journal club email list, send an email to redwood_tcn+subscribe@lists.berkeley.edu. You will receive emails twice a week about papers that will be covered in the next meeting.<br />
<br />
===Fall 2016===<br />
<br />
* [Dec 12] <font color="##ff0000">James Golden</font> - JR Golden et al (2016). Conjectures Regarding the Nonlinear Geometry of Visual Neurons. [http://www.sciencedirect.com/science/article/pii/S0042698915003600]<br />
* [Dec 05] <font color="##ff0000">Sean Mackesey</font> - Kraus et al (2013). Hippocampal "Time Cells": Time Versus Path Integration [http://www.cell.com/neuron/abstract/S0896-6273(13)00317-6]<br />
* [Nov 28] <font color="##ff0000">Chris Warner</font> - Lazer et al. (2010). The coevolution of networks and political attitudes. [https://polisci.osu.edu/sites/polisci.osu.edu/files/_the%20coevolution%20of%20networks%20and%20political%20attitudes_.pdf]<br />
* [Nov 21] <font color="##ff0000">Kohta Ishikawa</font> - Do & Vetterli (2003). Framing pyramids. [https://infoscience.epfl.ch/record/33823/files/DoV03j-2.pdf]<br />
* [Nov 14] <font color="##ff0000">Charles Frye</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Nov 07] <font color="##ff0000">Petr Jezek</font> - Eslami et al (2016). Attend, Infer, Repeat: Fast Scene Understanding with Generative Models. [https://arxiv.org/pdf/1603.08575v3.pdf]<br />
* [Nov 04] <font color="##ff0000">Yubei Chen</font> - Wainwright & Jordan. (2008). Graphical models, exponential families, and variational inference. [http://bioinfo.au.tsinghua.edu.cn/member/mzhang/pgm/course.files/3_Supplementary_Reference.pdf]<br />
* [Oct 24] <font color="##ff0000">Ryan Zarcone</font> - Weiss et al (2007). Learning Compressed Sensing. [http://www.wisdom.weizmann.ac.il/~/vision/courses/2010_2/papers/allerton-final.pdf]<br />
* [Oct 17] <font color="##ff0000">Neha Wadia</font> - Rajan et al (2016). Recurrent network models of sequence generation and memory. [http://www.sciencedirect.com/science/article/pii/S0896627316001021]<br />
* [Oct 10] <font color="##ff0000">Eric Weiss</font> - Tutorial: Hyperdimensional Representations for Scene Analysis.<br />
* [Oct 03] <font color="##ff0000">Vasha Dutell</font> - Dong & Atick (1995). Temporal decorrelation: a theory of lagged and nonlagged responses in the lateral geniculate nucleus. [http://www.tandfonline.com/doi/abs/10.1088/0954-898X_6_2_003]<br />
* [Sep 26] <font color="##ff0000">Jesse Livezey</font> - Cheung et al (2016). The auditory representation of speech sounds in human motor cortex. [https://elifesciences.org/content/5/e12577]<br />
* [Sep 19] <font color="##ff0000">Brian Cheung</font> - Discussion: The Biological Plausibility of Backpropagation.<br />
* [Sep 12] <font color="##ff0000">Alex Anderson</font> - Jaderberg et al (2016). Decoupled neural interfaces using synthetic gradients. [https://arxiv.org/abs/1608.05343]<br />
* [Sep 05] <font color="##ff0000">Charles Garfinkle</font> - Palmer et al (2015). Predictive information in a sensory population. [http://www.pnas.org/content/112/22/6908.full]<br />
<br />
===Summer 2016===<br />
* [August 31] <font color="##ff0000">Spencer Kent</font> - Fu et al (2016). Occlusion boundary detection via deep exploration of context. [https://ps.is.tuebingen.mpg.de/publications/fu-cvpr-2016]<br />
* [August 17] <font color="#ff0000">Paxon Frady</font> - Glasser, M. F., et al. (2016) A Multi-modal parcellation of human cerebral cortex. [http://www.nature.com/nature/journal/v536/n7615/pdf/nature18933.pdf] and Huth, Alexander G., et al. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. [http://www.nature.com/nature/journal/v532/n7600/pdf/nature17637.pdf]<br />
* [August 10] <font color="#ff0000">Mayur Mudigonda</font> - Salimans, Tim, Diederik P. Kingma, and Max Welling (2015). Markov chain Monte Carlo and variational inference: Bridging the gap. [http://www.jmlr.org/proceedings/papers/v37/salimans15.pdf]<br />
* [August 3] <font color="#ff0000">Pratik Sachdeva</font> - Moreno-Bote, Rubén, et al. (2014). Information-limiting correlations. [http://www.nature.com/neuro/journal/v17/n10/pdf/nn.3807.pdf]<br />
* [July 26] <font color="#ff0000">Shariq Mobin</font> - Karklin, Yan, and Eero P. Simoncelli (2011). Efficient coding of natural images with a population of noisy linear-nonlinear neurons.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532291/pdf/nihms711099.pdf]<br />
* [July 20] <font color="#ff0000">Sean Mackesey</font> - Buzsáki, György (2010). Neural syntax: cell assemblies, synapsembles, and readers. [http://www.cell.com/neuron/pdf/S0896-6273(10)00765-8.pdf]<br />
* [July 13] <font color="#ff0000">Katarina Slama and Vasha DuTell</font> - Akam, Thomas, and Dimitri M. Kullmann (2010). Oscillations and filtering networks support flexible routing of information. [http://ac.els-cdn.com/S0896627310004770/1-s2.0-S0896627310004770-main.pdf?_tid=67abdb2c-448b-11e6-8094-00000aacb35d&acdnat=1467927801_0eb47d2d6165fef5d1a1ae39b1b927b2]<br />
* [July 6] <font color="#ff0000">Karl Zipser</font> - Bojarski, Mariusz, et al (2016). End to End Learning for Self-Driving Cars. [https://arxiv.org/pdf/1604.07316v1.pdf]<br />
* [June 29] <font color="#ff0000">Ian Robertson</font> - Hermans, M., & Van Vaerenbergh, T. (2015). Towards Trainable Media: Using Waves for Neural Network-Style Training. [http://arxiv.org/pdf/1510.03776v1.pdf]<br />
* [June 22] <font color="#ff0000">Group Discussion</font> - Jonas, Eric, and Konrad Kording. (2016) Could a neuroscientist understand a microprocessor? [http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf]<br />
* [June 15] <font color="#ff0000">Spencer Kent, Mayur Mudigonda, and Eric Weiss</font> - Kulkarni, Tejas D., et al (2015). Picture: A probabilistic programming language for scene perception. [https://mrkulk.github.io/www_cvpr15/1999.pdf]<br />
* [June 8] <font color="#ff0000">Jesse Livezey</font> - Bornschein, Jörg, Marc Henniges, and Jörg Lücke (2013). Are V1 simple cells optimized for visual occlusions? A comparative study. [http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1003062.PDF]<br />
* [June 1] <font color="#ff0000">Yubei Chen</font> - Y. Karklin & M. S. Lewicki (2003). Learning higher-order structures in natural images. [http://yan.karklin.com/pubs/Karklin-Lewicki-NCNS03.pdf]<br />
* [May 25] <font color="#ff0000">Eric Dodds</font> - Y. Karklin, C. Ekanadham, & E.P. Simoncelli (2012). Hierarchical spike coding of sound. [http://papers.nips.cc/paper/4780-hierarchical-spike-coding-of-sound.pdf]<br />
<br />
===Spring 2016===<br />
<br />
* [May 11] <font color="#ff0000">NIPS exchange</font><br />
<br />
* [May 04] <font color="#ff0000">Chris Warner</font> - MEJ Newman (2006). Finding Community Structure in Networks using the Eigenvectors of Matrices [http://arxiv.org/pdf/physics/0605087.pdf]<br />
<br />
* [Apr 27] <font color="#ff0000">Mr. (Alex) Anderson</font> - E Ahissar, A Arieli (2012). Seeing Via Miniature Eye Movements- A Dynamic Hypothesis for Vision [http://www.frontiersin.org/Journal/DownloadFile/1/91957/32594/1/21/fncom-06-00089_pdf]<br />
<br />
* [Apr 20] <font color="#ff0000">Charles Frye, Ryan Zarcone, Brian Cheung</font> - RM Neal, GE Hinton (1998). A View of the EM Algorithm That Justifies Incremental, Sparse, and Other Variants [http://ftp.cs.utoronto.ca/cs/ftp/pub/radford/emk.pdf]<br />
<br />
* [Apr 13] <font color="#ff0000">Kohta Ishikawa</font> - C Zetzsche, U Nuding (2009). Nonlinear and Higher-Order Approaches to the Encoding of Natural Scenes [http://www.tandfonline.com/doi/pdf/10.1080/09548980500463982]<br />
<br />
* [Apr 06] <font color="#ff0000">Spencer Kent</font> - IJ Goodfellow, J Pouget-Abadie, M Mirza, B Xu, D Warde-Farley, Y Bengio (2014). Generative Adversarial Nets [http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf]<br />
<br />
* [Mar 30] <font color="#ff0000">Guy Isley</font> - R Chaudhuri, A Bernacchia, XJ Wang (2014). A Diversity of Localized Timescales in Network Activity [http://elifesciences.org/content/3/e01239v1]<br />
<br />
* [Mar 23] <font color="#ff0000">Brian Cheung</font> - DJ Rezende, S Mohamed, I Danihelka, K Gregor, D Wierstra (2016). One-Shot Generalization in Deep Generative Models [http://arxiv.org/abs/1603.05106]<br />
<br />
* [Mar 16] <font color="#ff0000">Yubei Chen</font> - A Beck, M Teboulle (2009). A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems [http://www-ai.cs.uni-dortmund.de/LEHRE/VORLESUNGEN/LOPT/WS14/papers/FISTA.pdf]<br />
<br />
* [Mar 09] <font color="#ff0000">Sean Mackesey</font> - P Fries (2015). Rhythms for Cognition: Communication Through Coherence [http://www.sciencedirect.com/science/article/pii/S0896627315008235]<br />
<br />
* [Mar 02] <font color="#ff0000">Charles Garfinkle</font> - BB Ujfalussy, JK Makara, T Branco, M Lengyel (2015). Dendritic Nonlinearities are Tuned for Efficient Spike-Based Computations in Cortical Circuits [http://elifesciences.org/content/4/e10056v1#api_box]<br />
<br />
* [Feb 24] <font color="#ff0000">Eric Weiss</font> - TS Lee, D Mumford (2003). Hierarchical Bayesian Inference in the Visual Cortex [https://dash.harvard.edu/bitstream/handle/1/3637109/Mumford_HierarchBayesInfer.pdf]<br />
<br />
* [Feb 17] <font color="#ff0000">Paxon Frady</font> - C Eliasmith et al. (2012). A Large-Scale Model of the Functioning Brain [https://cs.uwaterloo.ca/~cdimarco/pdf/cogsci600/Eliasmith2013a.pdf]<br />
<br />
* [Feb 10] Cancelled - EECS Colloquium <br />
<br />
* [Feb 03] <font color="#ff0000">Charles Frye</font> - L Aitchison, M Lengyel (2014). The Hamiltonian Brain [http://arxiv.org/abs/1407.0973]<br />
<br />
* [Jan 21] <font color="#ff0000">Jesse Livezy and Andrew Berger</font> - S Shapero, M Zhu, J Hasler, C Rozell (2014). Optimal Sparse Approximations with Integrate and Fire Neurons [http://www.worldscientific.com/doi/abs/10.1142/S0129065714400012]<br />
<br />
* [Jan 14] <font color="#ff0000">Daniel Toker</font> - AK Seth, AB Barrett, L Barnett (2011). Causal Density and Integrated Information as Measures of Conscious Level [http://rsta.royalsocietypublishing.org/content/369/1952/3748.short]<br />
<br />
===Fall 2015===<br />
<br />
* [Dec 17] <font color="#ff0000">Charles Frye</font> - BM Lake, R Salakhutdinov, JB Tenenbaum (2015). Human-Level Concept Learning Through Probabilistic Program Induction [http://www.sciencemag.org/content/350/6266/1332.abstract]<br />
<br />
* [Dec 03] <font color="#ff0000">Omer Hazon</font> - D Soudry, I Hubara, R Meir (2014). Expectation Backpropagation [http://papers.nips.cc/paper/5269-expectation-backpropagation-parameter-free-training-of-multilayer-neural-networks-with-continuous-or-discrete-weights.pdf]<br />
<br />
* [Nov 26] Thanksgiving break<br />
<br />
* [Nov 19] <font color="#ff0000">Eric Dodds</font> - EC Smith, MS Lewicki (2006). Efficient Auditory Coding [http://www.nature.com/nature/journal/v439/n7079/full/nature04485.html]<br />
<br />
* [Nov 12] <font color="#ff0000">Vasha Dutell</font> - H Hosoya, A Hyvarinen (2015). A Hierarchical Statistical Model of Natural Images Explains Tuning Properties in V2 [http://www.jneurosci.org/content/35/29/10412.full]<br />
<br />
=== Summer 2014 ===<br />
<br />
* [June 19] Buzsaki & Mizuseki (2014). The log-dynamic brain: how skewed distributions affect network operations. [http://buzsakilab.com/content/PDFs/Mizuseki2014.pdf]<br />
<br />
* [June 12] Hukushima & Nemoto (1996). Exchange Monte Carlo method and application to spin glass simulations. [http://arxiv.org/pdf/cond-mat/9512035v1.pdf]<br />
<br />
* [June 5] Shi & Griffiths (2009). Neural implementation of hierarchical bayesian inference by importance sampling. [http://cocosci.berkeley.edu/tom/papers/neuralIS.pdf]<br />
<br />
* [May 29] Petersen & Crochet (2013). Synaptic computation and sensory processing in neocortical layer 2/3. [http://www.sciencedirect.com/science/article/pii/S0896627313002675]<br />
<br />
* [May 22] Laje R, Buonomano DV (2013) Robust timing and motor patterns by taming chaos in recurrent neural networks. Nat. Neurosci. 16:925-933 [http://www.neurobio.ucla.edu/~dbuono/PDFs/LajeBuonomano_NatNeurosci_13.pdf]<br />
<br />
=== Spring 2014 ===<br />
<br />
* [Jan 20] Sutskever 2012- Training Recurrent Neural Networks. [http://www.cs.utoronto.ca/~ilya/pubs/ilya_sutskever_phd_thesis.pdf]<br />
<br />
=== Fall 2013 ===<br />
<br />
* [Sep 18] Guillery & Sherman 2010 - Branched thalamic afferents: What are the messages that they relay to the cortex? [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657838/#!po=22.7273]<br />
<br />
=== Summer 2013 ===<br />
<br />
* [July 10] Curto & Itskov 2008 - Cell Groups Reveal Structure of Stimulus Space [http://www.math.unl.edu/~ccurto2/papers/cell-groups.pdf]<br />
<br />
=== Spring 2013 ===<br />
<br />
* [Apr 8] Burak et al. 2009 - Accurate Path Integration in Continuous Attractor Network Models of Grid Cells [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=Y&aulast=Burak&atitle=Accurate+path+integration+in+continuous+attractor+network+models+of+grid+cells&id=doi:10.1371/journal.pcbi.1000291&title=PLoS+Computational+Biology&volume=5&issue=2&date=2009&spage=e1000291&issn=1553-734X] [http://www.jneurosci.org/content/16/6/2112.full.pdf]<br />
<br />
* [Mar 27] Sreenivasan et al. 2011 - Grid cells generate an analog error-correcting code for singularly precise neural computation. [http://www.clm.utexas.edu/fietelab/Papers/nn.2901.pdf] <br />
<br />
* [Mar 20] Killian et al. - A map of visual space in the primate entorhinal cortex [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=NJ&aulast=Killian&atitle=A+map+of+visual+space+in+the+primate+entorhinal+cortex&id=doi:10.1038/nature11587&title=Nature&volume=491&issue=7426&date=2012&spage=761&issn=0028-0836]<br />
<br />
* [Mar 13] Doyle et al. 2011 - Architecture, constraints and behavior [http://www.pnas.org/content/108/suppl.3/15624.full.pdf+html]<br />
<br />
* [Mar 6] Grady 2006 - Random Walks for Image Segmentation [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704833&tag=1]<br />
<br />
* [Feb 27] Todorov 2012 - Parallels between sensory and motor information processing [http://scholar.google.com/scholar?hl=en&q=Parallels+between+sensory+and+motor+information+processing&btnG=&as_sdt=1%2C5&as_sdtp=]<br />
<br />
* [Feb 13] Sohl-Dickstein 2012 - The Natural Gradient by Analogy to Signal Whitening, and Recipes and Tricks for its Use [http://arxiv.org/pdf/1205.1828v1.pdf]<br />
<br />
* [Feb 06] Girosi 1998 - An Equivalence Between Sparse Approximation and Support Vector Machines [http://ucelinks.cdlib.org:8888/sfx_local?sid=google&auinit=F&aulast=Girosi&atitle=An+equivalence+between+sparse+approximation+and+support+vector+machines&id=doi:10.1162/089976698300017269&title=Neural+computation&volume=10&issue=6&date=1998&spage=1455&issn=0899-7667][http://18.7.29.232/bitstream/handle/1721.1/7289/AIM-1606.pdf?sequence=2]<br />
<br />
* [Jan 30] Zipser et al. 1996 - Contextual Modulation in Primary Visual Cortex [http://www.jneurosci.org/content/16/22/7376.full.pdf+html]<br />
Ayzenshtat et al. 2012 - Population Response to Natural Images in the Primary Visual Cortex Encodes Local Stimulus Attributes and Perceptual Processing [http://www.jneurosci.org/content/32/40/13971.full.pdf+html]<br />
<br />
* [Jan 23] Gillenwater et al. 2012 - Near-Optimal MAP Inference for Determinantal Point Processes [http://books.nips.cc/papers/files/nips25/NIPS2012_1264.pdf] [http://web.eecs.umich.edu/~kulesza/pubs/thesis.pdf]<br />
<br />
* [Jan 08] Cathart-Harris et al. 2012 - Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin [http://www.pnas.org/content/109/6/2138.long]<br />
<br />
=== Fall 2012 ===<br />
<br />
* [Aug 22] Maass et al. - Liquid State Computing [http://www.igi.tugraz.at/maass/psfiles/130.pdf] [http://www.igi.tugraz.at/maass/psfiles/186.pdf]<br />
<br />
* [Aug 29] Salakhutdinov & Hinton 2012 - An Efficient Learning Procedure for Deep Boltzmann Machines [http://www.mitpressjournals.org/doi/pdfplus/10.1162/NECO_a_00311]<br />
<br />
* [Sep 05] Coates & Ng 2011 - An Analysis of Single-Layer Networks in Unsupervised Feature Learning [http://www.stanford.edu/~acoates/papers/coatesleeng_aistats_2011.pdf]<br />
<br />
* [Sep 12] Quiroga 2012 - Concept Cells: The Building Blocks of Declarative Memory Functions [http://www.phys.psu.edu/~collins/RNI/Quian_Quiroga_concept_cell_review_2012.pdf]<br />
<br />
* [Oct 10] Moira & Bialek 2011 - Are Biological Systems Poised at Critcality? [http://www.sns.ias.edu/pitp/2012files/Are_Biological_Systems.pdf]<br />
<br />
* [Oct 17] Newman 2005 -Power laws, Pareto distributions and Zipfʼs law. [http://www-personal.umich.edu/~mejn/courses/2006/cmplxsys899/powerlaws.pdf]<br />
<br />
* [Nov 28] Todorov 2004 -Optimality Principles in Sensorimotor Control. [http://www.nature.com/neuro/journal/v7/n9/pdf/nn1309.pdf]<br />
<br />
=== [[Past TCN Papers]] ===<br />
<br />
===[[Suggestion Board]]===</div>Edodds