CS379C: Computational Models of the Neocortex

Spring 2015


Invited Talks

  • March 30, Monday: Tom Dean, Introductory Remarks (HTML)

  • April 1, Wednesday: Tom Dean, Scalable Neuroscience (HTML)

  • April 6, Monday: Mario Galarreta (HTML)

  • April 8, Wednesday: Viren Jain (HTML)

  • April 13, Monday: Costas Anastassiou (HTML)

  • April 15, Wednesday: Peter Li, Deep Learning (HTML)

  • April 20, Monday: Surya Ganguli (HTML)

  • April 22, Wednesday: David Cox (HTML)

  • April 27, Monday: Ed Boyden (HTML)

  • April 29, Wednesday: Sebastian Seung (HTML)

  • May 4, Monday: Adam Marblestone (HTML)

  • May 6, Wednesday: Eric Jonas (HTML)

  • May 11, Monday: Davi Bock (HTML)

  • May 13, Wednesday: Alipasha Vaziri (PDF)

  • May 18, Monday: Clay Reid (HTML)

  • May 20, Wednesday: TBD

  • May 25, Monday: Memorial (no classes)

  • May 27, Wednesday: TBD

  • June 1, Monday: Wei-Chung Allen Lee (HTML)

  • June 3, Wednesday: TBD

Participants:

Speaker: Costas Anastassiou, Allen Institute for Brain Science
Date: April 13, 2015

Speaker: Davi Bock, HHMI Janelia Farm Campus
Date: May 11, 2015

Speaker: Ed Boyden, Massachusetts Institute of Technology
Date: April 27, 2015

Speaker: David Cox, Harvard University
Date: April 22, 2015

Speaker: Tom Dean, Google Research & Stanford University
Date: April 1 & 3, 2015

Speaker: Mario Galarreta, Google & Stanford University
Date: April 6, 2015

Speaker: Surya Ganguli, Stanford University
Date: April 20, 2015

Speaker: Viren Jain, Google Research
Date: April 8, 2015

Speaker: Eric Jonas, University of California Berkeley
Date: May 6, 2015

Speaker: Wei-chung Allen Lee, Harvard University
Date: May 27, 2015

Speaker: Peter Li, Google & Salk Institute
Date: April 15, 2015

Speaker: Clay Reid, Google & Allen Institute for Brain Science
Date: April 15, 2015

Speaker: Alipasha Vaziri, Max F. Perutz Laboratories
Date: May 11, 2015 [TENTATIVE]

Supplements:

Speaker: Michael Gazzaniga, University of California, Santa Barbara
Title: Gifford Lectures at Edinburgh University in 2009
Video: Available from Edinburgh here or the University’s YouTube channel.

Speaker: Eugene Izhikevich, Brain Corporation — formerly at The Neurosciences Institute, San Diego, CA
Papers: Izhikevich and Edelman [13]
Supplements: Supporting material for the PNAS paper including PDF is available here

Speaker: Eric Kandel, Columbia University
Video: Charlie Rose’s Brain Series (VIDEO)

Speaker: Henry Markram, Brain Mind Institute at EPFL
Title: Simulating the Brain: The Next Decisive Years
Video: Invited talk at the 2011 International Supercomputing Conference (ISC) (VIDEO)

Speaker: Dharmendra S. Modha, IBM, Almaden
Title: Towards Engineering the Mind by Reverse Engineering the Brain
Paper: Ananthanarayanan et al [3] (PDF) Video: Invited talk at the Krasnow Institute’s Decade of the Mind Symposium (VIDEO)

Speaker: Paul Rhodes, Evolved Machines
Title: Synthetic Neural Arrays That Wire Themselves
Video: Nvidia High Performance Computing (VIDEO)

Speaker: Robert Sapolsky, Stanford University
Title: Are Humans Just Another Primate?
Video: Invited lecture at the California Academy of Sciences (VIDEO)

References

[1]   A. Paul Alivisatos, Anne M. Andrews, Edward S. Boyden, Miyoung Chun, George M. Church, Karl Deisseroth, John P. Donoghue, Scott E. Fraser, Jennifer Lippincott-Schwartz, Loren L. Looger, Sotiris Masmanidis, Paul L. McEuen, Arto V. Nurmikko, Hongkun Park, Darcy S. Peterka, Clay Reid, Michael L. Roukes, Axel Scherer, Mark Schnitzer, Terrence J. Sejnowski, Kenneth L. Shepard, Doris Tsao, Gina Turrigiano, Paul S. Weiss, Chris Xu, Rafael Yuste, and Xiaowei Zhuang. Nanotools for neuroscience and brain activity mapping. ACS Nano, 7(3):1850–1866, 2013.

[2]   A. Paul Alivisatos, Miyoung Chun, George M. Church, Ralph J. Greenspan, Michael L. Roukes, , and Rafael Yuste. The brain activity map project and the challenge of functional connectomics. Neuron, 74, 2012.

[3]   Rajagopal Ananthanarayanan, Steven K. Esser, Horst D. Simon, and Dharmendra S. Modha. The cat is out of the bag: cortical simulations with 109 neurons, 1013 synapses. In Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, pages 63:1–63:12, 2009.

[4]   R.P.J. Barretto and M.J. Schnitzer. In vivo optical microendoscopy for imaging cells lying deep within live tissue. Cold Spring Harbor Protocols, 2012(10), 2012.

[5]   K.L. Briggman and D.D. Bock. Current opinion neurobiology. Volume electron microscopy for neuronal circuit reconstruction, 22:154–61, 2012.

[6]   K.L. Briggman, M. Helmstaedter, and W. Denk. Wiring specificity in the direction-selectivity circuit of the retina. Nature, 471:183–188, 2011.

[7]   E.M. Callaway. Transneuronal circuit tracing with neurotropic viruses. Current Opinion Neurobiology, 18(6):617–23, 2008.

[8]   D. D. Cox, A. M. Papanastassiou, D. Oreper, B. B. Andken, and J. J. DiCarlo. High-resolution three-dimensional microelectrode brain mapping using stereo microfocal x-ray imaging. Journal of Neurophysiology, 100(5):2966–2976, 2008.

[9]   James J. DiCarlo and David D. Cox. Untangling invariant object recognition. Trends in Cognitive Sciences, 11(8):333–341, 2007.

[10]   James J DiCarlo, Davide Zoccolan, and Nicole C Rust. How does the brain solve visual object recognition? Neuron, 73:415–34, 2012.

[11]   Michael Hawrylycz, Richard A. Baldock, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann E. Martone, Lydia Ng, Christopher Lau, Stephen D. Larson, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky, and Jyl Boline. Digital atlasing and standardization in the mouse brain. PLoS Computational Biology, 7, 2011.

[12]   Heng Huang, Savas Delikanli, Hao Zeng, Denise M. Ferkey, and Arnd Pralle. Remote control of ion channels and neurons through magnetic-field heating of nanoparticles. Nature Nanonotechnology, 5:602–606, 2010.

[13]   Eugene M. Izhikevich and Gerald M. Edelman. Large-scale model of mammalian thalamo-cortical systems. Proceedings of the National Academy of Science, 105(9):3593–3598, 2008.

[14]   Konrad Kording. Of toasters and molecular ticker tapes. PLoS Computational Biology, 7(12):e1002291, 2011.

[15]   Mo Li, W. H. P. Pernice, C. Xiong, T. Baehr-Jones, M. Hochberg, and H. X. Tang. Harnessing optical forces in integrated photonic circuits. Nature, 456:480–484, 2008.

[16]   Jesse D. Marshall and Mark J. Schnitzer. Optical strategies for sensing neuronal voltage using quantum dots and other semiconductor nanocrystals. ACS Nano, 7:4601–4609, 2013.

[17]   J.H. Marshel, T. Mori, K.J. Nielsen, and E.M. Callaway. Targeting single neuronal networks for gene expression and cell labeling in vivo. Neuron, 67(4):562–574, 2010.

[18]   Kristina D. Micheva and Stephen J. Smith. Array tomography: A new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron, 55(1):25–36, 2007.

[19]   Nancy A. O’Rourke, Nicholas C. Weiler, Kristina D. Micheva, and Stephen J. Smith. Deep molecular diversity of mammalian synapses: Why it matters and how to measure it. Nature Review Neuroscience, 10:365–379, 2012.

[20]   A.S. Sadek, R.B. Karabalin, J. Du, M.L. Roukes, C. Koch, and S.C. Masmanidis. Wiring nanoscale biosensors with piezoelectric nanomechanical resonators. Nano Letters, 10:1769–1773, 2010.

[21]   Susan Sunkin, Lydia Ng, Christopher Lau, Tim Dolbeare, Terri L. Gilbert, Carol L. Thompson, Michael Hawrylycz, and Chinh Dang. Allen brain atlas: an integrated spatio-temporal portal for exploring the central nervous system. Nucleic Acids Research, 41:996–1008, 2013.

[22]   B.A. Wandell and J.D. Yeatman. Biological development of reading circuits. Current Opinion Neurobiology, 23:261–268, 2013.

[23]   Brian A. Wandell, Serge O. Dumoulin, and Alyssa A. Brewer. Visual field maps in human cortex. Neuron, 56(2):366–383, 2007.

[24]   Anthony M. Zador, Joshua Dubnau, Hassana K. Oyibo, Huiqing Zhan, Gang Cao, and Ian D. Peikon. Sequencing the connectome. PLoS Biology, 10(10):e1001411, 2012.

[25]   Bradley Michael Zamft, Adam H. Marblestone, Konrad Kording, Daniel Schmidt, Daniel Martin-Alarcon, Keith Tyo, Edward S. Boyden, and George Church. Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing. PLoS ONE, 7(8):e43876, 2012.