CIS 6930/4930, Introduction to Computational Neuroscience, Fall 2008

Place:CSE; E121
Time:Tuesday 8,9 (3:00-4:55 p.m.) and Thursday 9 (4:05-4:55 p.m.)

Prof. Arunava Banerjee
Office: CSE E336.
Phone: 392-1476.
Office hours: Wednesday 2:00 p.m.-4:00 p.m. or by appointment.


Textbook: Theoretical Neuroscience, Dayan and Abbott, MIT Press, ISBN 0-262-04199-5.
Neuroscience Reference: Fundamental Neuroscieence, Zigmond, Bloom, Landis, Roberts, and Squire, Academic Press, ISBN 0-12-780870-1.

The goal of Computational Neuroscience is to acquire a formal understanding of how the brain (or any part thereof) works. The central dogma is that there are computational principles lurking in the dynamics of systems of neurons in the brain that we can harness to create better machines for such disparate tasks as computer vision, audition, language processing etc (note that in all these cases human beings far surpass the best known solutions).

This course is aimed at giving an overview of the field. In addition to particular issues, we shall take a tour through some essential neurobiology and a couple of mathematical areas. The targeted audience is students who wish to conduct research in this field, although any body interested in acquainting themselves with the area is welcome to attend. Although there will be a text that we shall (loosely) follow (Theoretical Neuroscience by Dayan & Abbott; available as an e-book thru the UF library system), a large portion of the course will involve material from disparate sources (other books, articles etc.)

Please return to this page at least once a week to check updates in the table below

Evaluation: There will be no exams in this course. The final grade will be based on a series of written assignments, and programming projects.

Course Policies:

Academic Dishonesty: See for Academic Honesty Guidelines. All academic dishonesty cases will be handled through the University of Florida Honor Court procedures as documented by the office of Student Services, P202 Peabody Hall. You may contact them at 392-1261 for a "Student Judicial Process: Guide for Students" pamphlet.

Students with Disabilities: Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation.

List of Topics covered
Week Topic Additional Reading Assignment
Aug 24 - Aug 30 Basic Neurobiology. Powerpoint Slides.
Aug 31 - Sep 06
  • Paper on "in vivo" recording.
  • Paper on "slice" recording.
  • Paper on "culture" recording.
  • Paper on "fmri" recording.
  • Neuro Electronics. Powerpoint slides can be found here.
Sep 7 - Sep 13 Neuro Electronics continued.
Sep 14 - Sep 20 Reduced models of the neuron.
  • Which Model to Use for Cortical Spiking Neurons? By E. M. Izhikevich Link here.
  • Alex found this hardware implementations of the above models. Link here
  • Scholerpedia article on the FitzHugh-Nagumo Model: Link here.
Sep 21 - Sep 27
  • System Identification
  • Volterra Weiner Series
  • Stimulus Reconstruction
  • Spike triggered averaging
Sep 28 - Oct 04
  • Point set topology
  • Metric spaces
  • Read more about Brouwer's Fixed point theorem here
Oct 05 - Oct 11
  • Vector Spaces
  • Banach and Hilbert Spaces
  • Fourier Series
Oct 12 - Oct 18
  • Finished Fourier Series and Fourier Transform
  • Started Information Theory
Oct 19 - Oct 25 Information theory continued
Oct 26 - Nov 01
  • Artificial Neural Networks
  • perceptron (delta) learning rule
  • Error backpropagation
Nov 02 - Nov 08
  • Hopfield Nets
  • Dynamical Systems Theory
Nov 09 - Nov 15
  • Dynamical Systems Theory continued.
  • Stability analysis
Nov 16 - Nov 22
  • Dynamical Systems Theory continued.
  • Topological Conjugacy, Sensitive dependence, chaos etc.
Nov 23 - Nov 29
  • (Thanksgiving)
Nov 30 - Dec 06
  • The phase space dynamics of recurrent systems of spiking neurons
  • Sensitivity analysis
  • Stochastic processes.