CPSC 689-603 Intelligent Neural Systems:
Spring 2004


NEWS: 1/6/05, 12:23PM (Thu)
  • [5/11] Final grades are online (you need username/password).
Read-Only Bulletin Board.: 1/6/05, 12:23PM (Thu)

Page last modified: 1/23/05, 08:42PM Sunday.

General Information Resources Reading List Weekly Schedule Lecture Notes

I. General Information


Dr. Yoonsuck Choe
Email: choe(a)tamu.edu
Office: HRBB 322B
Phone: 845-5466
Office hours: TBA


CPSC 625


MWF 12:40pm-1:30pm HRBB 126.


How does the brain generate intelligent (or complex) behavior? The focus of this course is to address this very question from various different perspectives. Select topics from computational vision, computational neuroscience, and cognitive science will be reviewed and critiqued. In the first few weeks, basic computational and mathematical preliminaries, as well as neuroscience basics will be covered. Afterwards, a selected collection of current research papers will be discussed. The course is designed to be open-ended to some degree, and a large portion of the time will be dedicated to discussion of the topics.


The goal of this course is to
  1. learn basic computational and mathematical tools for investigating the nervous system;
  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.


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.


  1. Assignments (30%20%): short programming assignment (10% each).
  2. Paper presentation (15%): each student will study and present a paper from the reading list. The term project may be loosely based on this paper.
  3. Paper comments (15%): 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.
  4. Term project intermediate report (10%)
  5. Term project (40%): 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.
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.)


  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.

III. Weekly Schedule and Class Notes

Under heavy construction
Notices and Dues
1 1/19 MLK Day (Holiday)      
1 1/21 Introduction     Three handouts were distributed. Ask the instructor for extra copies. slide01.pdf
1 1/23 Nervous system basics Handouts, and Stevens "The Neuron" in the paper packet     slide02.pdf
2 1/26 Intro wrap up Bell (1999; reading list) Paper comment#1 out (due 2/2) No class W/F slide03.pdf
2 1/28 No class     Make up (2/11 6-8pm HRBB302)
2 1/30 No class     Make up (2/11 6-8pm HRBB302)
3 2/2 Probability/ Bayesian Framework Knill et al. (1996; photocopy)   Paper comment#1 due;
slide04 will be distributed in class
3 2/4 Schneider (1999) Paper comment#2 assigned (due 2/9)   slide04.pdf
3 2/6 Bayesian vs. Info Theory Jepson and Feldman (1996; readling list); Ballard chapter 2 (pp46-51; handout)     slide05.pdf
4 2/9 Cognition/ Redundancy/ Learning Langlois and Garrouste (1997)   Paper comment#2 due slide06.pdf
4 2/11 Basic computational tools   Paper comment #3 announced (slide07 page2; due 2/13) Make-up class today 6-8pm HRBB302; 4 handouts plus the lecture notes (slide07) slide07.pdf
4 2/13 Computationalism Searle (1997; reading list; photocopy) Paper comment #4 announced (slide08 page1; due 2/18) Paper comment #3 due; Paper comment #1 grades slide08.pdf
5 2/16 Computationalism Searle (1997; reading list; photocopy)     slide08.pdf
5 2/18 Schema theory Arbib (1996; reading list; photocopy)   Paper comment #4 due slide09.pdf
5 2/20 Imitation Arbib (2003; pp606-611; photocopy)     slide10.pdf
6 2/23 Visual illusions Yu and Choe (2004)   Guest talk by Yingwei Yu
6 2/25 Interactive vision Churchland et al. (1994; readling list; photocopy) Paper comment #5 announced Paper comment #4 grades slide11.pdf
6 2/27 Action and Semantics Choe and Bhamidipati (2004; reading list; Bio-ADIT)   Paper comment #2 grades slide12.pdf
7 3/1 Thalamus Hill and Tononi (2003; reading list); Guillery and Sherman (2002; reading list)   Paper comment #5 due slide13.pdf
7 3/3 Thalamus and Analogy Choe (2003; reading list; IJCNN pp.1480-1485)     slide14.pdf
7 3/5 Analogy with Binary Spatter Code Kanerva (1998; reading list -- both)   slide16: project suggestions slide15.pdf
8 3/8 Evolutionary Agents Gomez and Miikkulainen (1998; reading list) Program Assignment Announced;
Paper presentation and project topics
8 3/10 Natural scene statistics Lee and Choe (2003; reading list; IJCNN pp.206-211), Barlow (2001)   Paper topics (prelim) due slide18.pdf
8 3/12 Dynamical systems Beer (2000; reading list)   Paper topics/presentation date preference due slide19.pdf
9 3/15 Spring Break     No class
9 3/17 Spring Break     No class
9 3/19 Spring Break     No class
10 3/22 Self-organization in the visual cortex Choe and Miikkulainen (Biol. Cyb. 2004)     slide20.pdf
10 3/24 Paper presentation 1 Helga and John Kocurek; Corlette    
10 3/26 Paper presentation 2 Whetzel; Meeks    
11 3/29 Paper presentation 3 Smith; Leiloglou   Program #1 due
11 3/31 Paper presentation 4 Dou; Song;Coker    
11 4/2 Paper presentation 5 Liu and Zhang; Wang    
12 4/5 Paper presentation 6 Sanders; Busse    
12 4/7 Paper presentation 7 Jung, Lim, and Shin    
12 4/9 Reading Day No Class    
13 4/12 Paper presentation 8 Dahms, Stoker, and Bethancourt    
13 4/14 Paper presentation 9 Misra, Annamala, and Isen    
13 4/16 Paper presentation (Corlette)
Self-organization in the visual cortex
Choe and Miikkulainen (Biol. Cyb. 2004)     slide20.pdf
14 4/19 Paper presentation (Corlette)
Self-organization in the visual cortex
Choe and Miikkulainen (Biol. Cyb. 2004)     slide20.pdf
14 4/21 Alternative essenses of AI Brooks (1998; reading list)     slide21.pdf
14 4/23 Active Vision Granlund (1998)   Project preliminary report due slide22.pdf
15 4/26 Rhythm recognition Buisson, J.-C., A rhythm recognition computer program to advocate interactivist perception, Cognitive Science, 28:75-87, 2004 [PDF] (demo)     slide23.pdf
15 4/28 Course wrap-up Summary and perspectives     slide24.pdf
15 4/30 Project presentation [1] Noah
[2]Navendu, Rajah, and Ciji;
[3] Fenghui and Yutu
16 5/3 Project presentation [4] Matt and Iason
(plus resources for further exploration)
  Last class day slide25.pdf
165/4Project presentation
(Redefined day: Tuesday)
[5] Dan
[6] John and Helga
 Redefined day: Tuesday class 
 5/10Final Presentation
[7] Jon and Brad
[8] Lingfeng
[9] Yantao and Jinding
[10] John (Meeks)
[11] Heejin, Jaehee, and Seongjin
[12] Deji
 Final Project Due (in class) 

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