CPSC 689-603 Computations in Neural and Biological Systems:
Spring 2005

Syllabus

I. General Information

Instructor:

Dr. Yoonsuck Choe
Email: choe(a)tamu.edu
Office: HRBB 322B
Phone: 845-5466
Office hours: 1-2pm, MWF

Prerequisite/Restrictions:

CPSC 625, or consent of instructor.

Lectures:

MWF 11:30am-12:20pm HRBB115.

Introduction:

Goal:

1. learn basic computational and mathematical tools for investigating computations in neural and biological systems;
2. get acquaninted with diverse computational approaches to the understanding of brain function; and
3. explore how the seemingly disjoint topics can be integrated in a unique synthesis.

Textbook:

• Required: Dana Ballard, "Introduction to Natural Computation", MIT Press, 1997.
• Required: paper collection compiled by the instructor. Most of the papers are available online.
• Optional, but highly recommended: Michael A. Arbib (Editor), "The Handbook of Brain Theory and Neural Networks", Second Edition, MIT Press, 2002
• Optional: Pfeifer and Scheier, "Understanding Intelligence", MIT Press, 1999.

Administrative Trivia:

1. Computer accounts: if you do not have a unix account, ask for one on the CS web page.
2. We will use Matlab(tm) (there is also an excellent open source clone called GNU/Octave). Matlab is installed on all SunOS machines (and also on the Windows machines -- I've got to check).

Topics to be covered:

See the Weekly Schedule section for more details.

• nervous system overview
• computational tools and basic theoretical concepts
• natural sensory statistics and neural coding,
• visual illusions and their neural mechanisms,
• inhibition and disinhibition in neural systems,
• self-organization in neural networks,
• connectivity analysis in biological networks,
• active approach and analogy,
• understanding the behavior of dynamical agents,
• evolutionary computation,
• time in perception and cognition, and
• semantics and the role of action in perception and cognition.

Grading:

1. Assignments (30%20%): short programming assignment (10% each).
2. Paper comments (20%): for the reading assignments each week, a brief (one paragraph) comment/critique must be submitted. Occasionally, the instructor will ask a specific question or ask the student to comment on a particular aspect of the paper.
3. Paper presentation (10%): each student will study and present a paper from the reading list. The term project may be loosely based on this paper.
4. Term project (30%): 6-7 page term paper (double spaced) describing the project, and project demo and a presentation (20 minutes + 5 minutes Q/A). The project can either be done individually or as a team of two to three.
5. Take-home midterm (10%)

Grading will be on the absolute scale. The cutoff for an `A' will be at most 90% of total score, 80% for a `B', 70% for a `C', and 60% for a `D'. However, these cutoffs might be lowered at the end of the semester to accomodate the actual distribution of grades.

Academic Policy:

The TAMU student rules (http://student-rules.tamu.edu/), Part I Rule 20 will be strictly enforced.

Students with Disabilities:

The Americans with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Department of Student Life: Services for Students with Disabilities in Room 126 of the Koldus Building, or call 845-1637. (The source of this passage is TAMU Phil320 Syllabus.)

Resources:

1. Neural Networks: Sharewares and Freewares (Thanks to Subru)
2. Thalamus slices
3. Neuroscience Tutorial at The Washington University School of Medicine. (Thanks to Barani)
4. Research resources page
5. Ganeral reading list (u: p: ): includes short blurb about how to find, read, and critique others' work. This list is not the course reading list.

• Lecture notes (in PDF format): all notes will be uploaded in this directory.
• It is your responsibility to download, print, and bring the notes to the class. Notes will be available 24 hours before each class.
• See the 2005 Spring TAMU Calendar for breaks, etc. May 4th is the last class day (note that it is Tuesday).
• This is a very rough draft: More detail will be available as we go along.