Jon Shlens

• A new tutorial on independent component analysis is (almost) available




• Code for CTW information and entropy estimation in neural data available at neuroanalysis.org

 Tutorials

• Tutorial on Independent Component Analysis [ not yet ]
  A complete introduction and discussion of independent component analysis. Builds on previous tutorial on principal component analysis. Version 1.0
• Tutorial on Principal Component Analysis [ PDF ]
  A full introduction, description, derivation, and discussion of principal component analysis. Concrete examples for intuition building, the mathematical relation to SVD, and new extensions of this algorithm. Version 3.01
• A Light Discussion and Derivation of Entropy [ PDF ]
  A light discussion of the underlying assumptions behind entropy followed by a rigorous but simple derivation of the formula for entropy. Version 1.0
• Notes on Kullback-Leibler Divergence and Likelihood [ PDF ]
  An intuitive discussion about where Kullback-Leibler divergence arises and its relationship to likelihood theory. Version 1.0
• Notes on Generalized Linear Models of Neurons [ PDF ]
  An introduction to the application of GLMs to model neurons and networks of neurons. Brief discussion and derivation of primary equations pertaining to maximum likelihood estimation. Version 1.5

 Publications

• Greg Field , Jeff Gauthier, Alexander Sher, Martin Greschner, Timothy Machado, Lauren Jepson, Jonathon Shlens, Deborah Gunning, Keith Mathieson, Wladyslaw Dabrowski, Liam Paninski, Alan Litke and E.J. Chichilnisky
  Functional connectivity in the retina at the resolution of photoreceptors
  Nature 2010: 467, 673-677. [ PDF ] [ supplement ] [ news & views ]
• Martin Greschner, Jonathon Shlens, Tina Bakolitsa, Greg Field , Jeff Gauthier, Lauren Jepson, Alexander Sher, Alan Litke and E.J. Chichilnisky
  Correlated firing among major ganglion cell types in primate retina
  Journal of Physiology, 2010, Oct 11. [ PDF ]
• Jonathon Shlens, Greg Field , Jeff Gauthier, Martin Greschner, Alexander Sher, Alan Litke and E.J. Chichilnisky
  The structure of large-scale synchronized firing in primate retina
  Journal of Neuroscience, 2009: 29, 5022-5031 . [ PDF ]
• Greg Field, Martin Greschner, Jeffrey Gauthier, Jonathon Shlens, Alexander Sher, Alan Litke and E.J. Chichilnisky
  High sensitivity rod photoreceptor input to blue-yellow color opponent pathway in primate retina
  Nature Neuroscience, 2009 12, 1150. [ PDF ]
• Jeff Gauthier, Greg Field , Alexander Sher, Martin Greschner, Jonathon Shlens, Alan Litke and E.J. Chichilnisky
  Receptive fields in primate retina are coordinated to sample visual space more uniformly
  PLoS Biology, 2009 7, e63. [ PDF ]
• Jeff Gauthier, Greg Field , Alexander Sher, Jonathon Shlens, Martin Greschner, Alan Litke and E.J. Chichilnisky
  Uniform signal redundancy of parasol and midget ganglion cells in primate retina
  Journal of Neuroscience, 2009: 29,4675-4680 . [ PDF ]
• Jonathon Shlens, Fred Rieke, E.J. Chichilnisky
  Synchronized firing in the retina
  Current Opinions in Neurobiology, 2008: 16, 396-402 . [ PDF ]
• Jonathan Pillow, Jonathon Shlens, Liam Paninski, Alexander Sher, Alan Litke, E.J. Chichilnisky and Eero Simoncelli
  Spatiotemporal correlations and visual signaling in a complete neuronal population
  Nature, 2008: 454:995-999 . [ PDF ]
• Jonathon Shlens, Matthew Kennel, Henry Abarbanel and E.J. Chichilnisky
  Estimating information rates in neural spike trains with confidence intervals
  Neural Computation, 2007: 19, 1683-1719 . [ PDF ]
• Greg Field, Alexander Sher, , Jeff Gauthier, Martin Greschner, Jonathon Shlens, Alan Litke and E.J. Chichilnisky
  Spatial properties and functional organization of small bistratifed cells in primate retina
  Journal of Neuroscience, 2007: 270 13261 . [ PDF ]
• Dumitru Petrusca, Matthew Grivich, Alexander Sher, Greg Field, Jeff Gauthier, Jonathon Shlens, E.J. Chichilnisky and Alan Litke
  Identification and characterization of a Y-like primate retinal ganglion cell type
  Journal of Neuroscience, 2007: 27) 11019 . [ PDF ]
• Jonathon Shlens, Greg Field, Jeff Gauthier, Matthew Grivich, Dumitru Petrusca, Alexander Sher, Alan Litke and E.J. Chichilnisky
  The structure of multi-neuron firing patterns in primate retina
  Journal of Neuroscience, 2006: 26, 8254-8266 . [ PDF ] [ Cover ] [ Preview ]
• Matthew Kennel, Jonathon Shlens, Henry Abarbanel and E.J. Chichilnisky
  Estimating entropy rates with Bayesian confidence intervals
  Neural Computation, 2005: 17, 1531-1576 . [ PDF ]