THEORETICAL NEUROSCIENCE

COURSE MATERIAL


Course CA6 (previously "CA1")
Course homepage: 
French/ English version.

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General and useful references: see below.

Specific material for the Course CA6, Academic year 2008/2009
(last update: Jan. 21, 2009)

Class 0, September Friday 26th 2008: Introduction to Computational Neuroscience.
Special day, compulsary for all the students registered at the Cogmaster. Open to the other students, but not compulsary. ENS, 29, rue d'Ulm, amphi Jules Ferry
9h30-10h15 Intro to computational neuroscience
Presentation of the M1 Course C06
Presentation of the M2 Course-seminar
10h15-10h40 Presentation of the M2 Course CA6
10h40-11h: pause
11h-12h Short illustrative talks:
11h-11h20: "Matching law"
11h20-11h40: " Rescorla-Wagner learning rule"
11h40-12h: "Reinforcement learning"
12h-14h Students choose a paper and read it (and eat...)
14h-15h30: paper presentations and discussion
Papers: see here.

 

Class 1, Oct 2: Biophysics of Neuron, I.

pdf presentation: slides

Access to papers here.

Class 2, Oct 9: Biophysics of Neuron, II

pdf presentations: slides

Hodgkin-Huxley model

pdf presentations: slides

Access to papers here.

Class 3, Oct 16: Biophysics of synapses and short term plasticity

pdf presentations: Biophysics of synapses, slides
Physiology of the Synapse, short term plasticity slides

Recommended papers:
Mochida, Few, Scheuer and Catterall, Neuron 2008
Cheng and Augustine ('Preview' on Mochida et al paper).
More papers here.

Class 4, Oct 23: Single cell neural coding

pdf presentation: slides

Recommended papers:
de Ruyter and Bialek, 1988
Newsome et al. 1989
Salzman et al. 1990
Britten et al. 1992
Chichilnisky 2001.

Class 5, Nov. 6: Learning and synaptic plasticity
Introduction
Different kinds of learning: supervised, unsupervised and reward learning.
D. O. Hebb and synaptic plasticity
Course material on LTP and LTD.
Learning associations
Supervised learning by the Perceptron: capacity, information storage.
Hertz, Krogh, and Palmer (1991) (see general references below), Chap. 5.
Hebbian learning with binary synapses: the Willshaw model.
Willshaw, D J, Buneman, O P Longuet-Higgins, H C (1969). Non-holographic associative memory. Nature, 222, 960-962.
Course material

Class 6, Nov. 13: Learning II
The Purkinje-Perceptron
Papers and Lecture notes here
Unsupervised learning
Hebbian unsupervised learning and neural coding - the Oja model
Lecture notes on Oja's model: here (pdf file)
E. Oja, A simplified neuron model as a principal components analyzer, J. Math. Biol. 15 (1982) 267-273.
Hertz, Krogh, and Palmer (1991) (see general references below), Chap. 8.2 pp. 199-210
From unsupervised learning to optimal information processing (infomax)
Papers:
Linsker, R. (1988), "An application of the principle of maximum information preservation to linear systems", NIPS 1988 (http://books.nips.cc/nips01.html)
R. Linsker, From Basic Network Principles to Neural Architecture (series), Proc. Nat'l Academy of Sciences USA, Vol. 83, Oct.-Nov. 1986, pp. 7508-7512, 8390-8394, 8779-8783.
van Hateren, Biol. Cybernetics 1992, "A theory of maximizing sensory information".
van Hateren, J. Comp. Physiology, 1992, "Theoretical predictions of spatiotemporal receptive fields of fly LMCs, and experimental validation".
Dan, Atick and Reid (1996), "Efficient Coding of Natural Scenes in the Lateral Geniculate Nucleus: Experimental Test of a Computational Theory", The Journal of Neuroscience, Vol.16 (10) pp. 3351-3362


Class 7, Nov. 20: Rate models, I
Lecture slides here

Papers (access here):

Visual receptors and retinal interaction
H. K. Hartline - Nobel Lecture, December 12, 1967 (full text)

Enhancement of flicker by lateral inhibition
Ratliff F, Knight BW, Toyoda JI, Hartline HK, Science 1967;158:392-393

Inhibitory interaction in the retina of Limulus
Hartline, H. K., and Ratliff, F.,
in: Handbook of Sensory Physiology: Physiology of Photoreceptor Organs (M. G. F. Fuortes, Ed.), Berlin: Springer-Verlag, 1972, pp. 382-447


Class 8, Nov. 27: Rate models, II
Lecture slides here

Papers:
Decision making : Machens 2005, Wang 2008 (here)
Pattern formation in visual cortex: Bressloff, Review 1999 (here; see in particular Chapter 4.6)


Class 9, Dec. 4: Anatomy; Putative organization principles of the connectivity.

pdf presentation: lecture-Anatomy.pdf

The neocortical microcircuit as a tabula rasa
Nir Kalisman, Gilad Silberberg, and Henry Markram
PNAS, January 18, 2005, vol. 102 no. 3, pp 880-885 ( full text from PNAS web site)  

Highly Nonrandom Features of Synaptic Connectivity in Local Cortical Circuits
Sen Song, Per Jesper Sjöström, Markus Reig, Sacha Nelson, Dmitri B. Chklovskii
PLOS Biology, Volume 3, Issue 3, March  2005 (paper freely available online)

Pyramidal cell communication within local networks in layer 2/3 of rat neocortex
Carl Holmgren, Tibor Harkany, BjöSvennenfors and Yuri Zilberter
J Physiol (2003), 551.1, pp. 139-153 (paper from J Physiol web site)

Cortical rewiring and information storage
D. B. Chklovskii, B. W. Mel & K. Svoboda
Nature 431, 782 - 788 (14 October 2004) (full text from Nature web site

Connectivity optimization and the positioning of cortical areas
Vitaly A. Klyachko and Charles F. Stevens,
PNAS, June 24, 2003 Vol. 100, no. 13 pp. 7937-7941 (full text from PNAS web site)  

Nonoptimal Component Placement, but Short Processing Paths, due to Long-Distance Projections in Neural Systems
Marcus Kaiser and Claus C. Hilgetag
PLOS Biology, Volume 2, Issue 7, July  2006 (paper freely available online)

Students: click here.
 


Class 10, Dec. 11: Guest lecture by Michael Berry (Princeton University)

"Dynamics and Computations in the Retina".

Class 11, Dec. 18: Oscillations, synchronization and all that.

pdf presentation: click here.

Class 13, Jan. 15: Coding: Optimization of nonlinear transfer function - Population Coding
Laughlin 1987, "Form and function in retinal processing" (click here).
"Information theoretic approach to neural coding and parameter estimation: a perspective" (click here).
Population coding: Fisher and Shannon informations (click here for a low quality copy of a set of slides)
S. Seung and H. Sompolinsky, PNAS 90 pp:10749-10753, 1993 (click here)
N. Brunel and J.-P. Nadal, Neural Computation, Vol. 10 issue 7 (October 1, 1998) pp. 1731-1757 (click here)


More course material will be available very soon



Problem sets


First problem set (on Integrate-and-Fire models)

Second problem set (on conductance-based synapses and shunting inhibition)

Third problem set (on supervised learning)

Fourth problem set (on unsupervised Hebbian learning and coding)

Fifth problem set (on rate models)

Sixth problem set (ring model)

Seventh problem set (synchronization of spiking neurons)

Eighth problem set (memory: network with stochastic binary synapses)



Archive, specific material for this Course:

Back to Course homepage: French/ English version

GENERAL REFERENCES

 

All the following books are available at the RISC library.
Most of them are also available at the library of Institut Henri Poincaré.

 

* Computational neuroscience books

 

Abbott and Dayan, "Theoretical Neuroscience" (MIT Press, 2001)

A nice overview of the field of computational neuroscience, at a level comparable to that of the course.

 

Tuckwell, "Introduction to Theoretical Neurobiology", Vols. I & II (Cambridge U. Press, 1988)

A more mathematical treatment, with narrower scope and emphasis on single-neuron dynamics and statistics of neural activity.

 

Koch, "Biophysics of Computation" (Oxford U. Press, 1999)

A detailed presentation of computational aspects of single-neuron behavior, closer to biology than Tuckwell's book (but more restricted in topics also).

 

Hertz, Krogh, and Palmer, "Introduction to the Theory of Neural Computation" (Addison-Wesley, 1991 - now from: Perseus Book Group and Westview Press)

A good reference book on memory models in the perspective of statistical physics (and on many other neural network models). This book is more advanced mathematically than the three other and a good resource for learning useful statistical physics techniques.

 

Rieke, Warland, de Ruyter van Steveninck, and Bialek, "Spikes" (MIT Press, 1997)

A nice introduction to the statistical and information theoretic approach to neural coding, with a title length inversely proportional to the number of authors.

 

* General neurobiology books:

 

Nicholls, Martin, Wallace, and Fuchs, "From Neurons to Brain" (Sinauer Associates, 2001, 4th ed.)

A readable and well-balanced introductory survey of neurobiology.

 

Kandel, Schwartz, and Jessel, "Principles of Neural Science" (McGraw-Hill, 4th edition, 2000)

Another successful neurobiology survey text.

 

Hubel, "Eye, Brain, and Vision" (Scientific American Library, 1988 and 1995)

A delightful introduction to visual processing by the brain, at an undergraduate/interested general reader level.

 

Johnston and Wu, "Foundations of Cellular Neurophysiology" (MIT Press, 1995)

A comprehensive introduction to the biophysics of neurons, with a quantitative leaning.

 

Fain, "Molecular and Cellular Physiology of Neurons" (Harvard University Press, 1999)

A nice very read on the physiology of single neurons and synapses, at an introductory level, with a lovely final part on sensory transduction.

 

 

* Periodicals:

 

A number of journals are devoted to computational neuroscience; these include Neural Computation, The Journal of Computational Neuroscience, Network: Computation in Neural Systems, Biological Cybernetics, Neural Networks. Other general or topical science journals also publish computational neuroscience articles; prominently, Nature, Nature Neuroscience, Science, Neuron, PNAS, PloS (free, online), The Journal of Physiology, The Journal of Neuroscience, The Journal of Neurophysiology, Cerebral Cortex, Vision Research, Trends in Neurosciences, Current Opinion in Neurobiology.



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