CPSC 644-600 Cortical Networks:
Spring 2010


NEWS: 5/10/10, 01:51PM (Mon)
  • [5/10] Final grades posted: grades page
  • [4/22] Project presentation order will be discussed today.
  • [4/22] slide29 uploaded (we will not cover this in class).
  • [4/22] slide28 uploaded (we will not cover this in class).
  • [4/18] slide27 uploaded.
  • [4/15] slide26 uploaded.
  • [4/15] slide25 uploaded.
  • [4/07] hw1 and hw2 grades posted: grades page.
  • [4/07] slide23 and slide24 uploaded.
  • [4/06] slide22 uploaded.
  • [3/25] slide20 and slide21 uploaded. Print and bring to class. (slide19 was uploaded too, but we will not cover it in the class.)
  • [3/23] slide17 and slide18 uploaded. Print and bring to class.
  • [3/10] slide15 uploaded. Print and bring to class.
  • [3/08] slide14 uploaded. Print and bring to class.
  • [3/04] Slight chance of running late to class on next Tuesday due to a seminar in ECE I'm giving.
  • [3/04] Weekly schedule reorganized to reflect current topics.
  • [3/04] slide13 uploaded. Print and bring to class.
  • [3/02] Homework 2 announced: topic selection due 3/9/2010. Full results due 4/01/2010.
  • [3/01] slide12 uploaded. Print and bring to class.
  • [2/13] slide11 uploaded. Print and bring to class.
  • [2/10] slide10 uploaded. Print and bring to class.
  • [2/08] slide09 uploaded. Print and bring to class.
  • [1/29] slide07 and slide08 uploaded. Print and bring to class.
  • [1/28] Homework 1 posted (due 2/9/2010, in class).
  • [1/28] Quiz on Tuesday (2/2/2010).
  • [1/27] slide05 and slide06 uploaded. Print and bring to class.
  • [1/25] slide04 uploaded. Print and bring to class.
  • [1/20] slide03 uploaded. Print and bring to class. See reading material as well (see slide03 for pointers).
  • [1/18] syllabus, slide01, and slide02 uploaded. Print and bring to class.
  • [1/18] Course web page goes online
  • -----------------------
  • Links: Lectures, Documents, News archive
Read-Only Bulletin Board.: 1/18/10, 04:11PM (Mon)

Page last modified: 1/26/10, 04:56PM Tuesday.

General Information Resources Reading List Weekly Schedule Lecture Notes Course Material

I. General Information


Dr. Yoonsuck Choe
Email: choe(a)tamu.edu
Office: HRBB 322B (or HRBB 507, if I'm not in 322B)
Phone: 845-5466
Office hours: 4pm-5pm, TR



CPSC 420, 625, 636, or 633 (or equivalent) and graduate classification; or consent of instructor.


TR 5:30–6:45pm HRBB 104.


From the course catalog: The architecture of the mammalian cerebral cortex; its modular organization and its network for distributed and parallel processing; cortical networks in perception and memory; neuronal microstructure and dynamical simulation of cortical networks; the cortical network as a proven paradigm for the design of cognitive machines.

About this semester: This course will provide necessary background for modeling the structure (anatomy), function (physiology), and growth (development) of neurons, neuronal circuits, and neuronal networks. Various computational concepts, techniques, and tools necessary for modeling neural systems will be introduced. A selected set of latest papers in the field of computational neuroscience and neuroinformatics will be surveyed.


Administrative Trivia:

  1. Computer accounts: if you do not have a unix account, ask for one on the CS web page.
  2. Programming languages permitted: C/C++, Java, or Matlab (or octave), and must be executable on CS unix hosts or any windows system in the departmental lab.

Topics to be covered:

See the Weekly Schedule section for more details.


  1. Quiz (one or two): 10%
  2. Paper commentaries (3 to 4, each one paragraph long): 20%
  3. Programming assignments/exercises (about 3): 10% each = 30%
  4. Term project: proposal, presentation, final report 40%
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 Integrity Statement:

AGGIE HONOR CODE: An Aggie does not lie, cheat, or steal or tolerate those who do.

Upon accepting admission to Texas A&M University, a student immediately assumes a commitment to uphold the Honor Code, to accept responsibility for learning, and to follow the philosophy and rules of the Honor System. Students will be required to state their commitment on examinations, research papers, and other academic work. Ignorance of the rules does not exclude any member of the TAMU community from the requirements or the processes of the Honor System.

For additional information please visit: http://www.tamu.edu/aggiehonor/

Local Course Policy:

Americans with Disabilities Act notice:

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 Cain Hall or call 845-1637.


  1. Research resources page
  2. 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.
  3. eLearningTools.tamu.edu

III. Weekly Schedule and Class Notes

Notices and Dues
1 1/19 Introduction Course overview, Terminology     slide01.pdf
1 1/21 Introduction, Neuron Terminology, Shepherd: Chapter 2     slide02.pdf
2 1/26 Neuron: Computational models Dayan and Abbott: Chapter 5, Appendix A.4     slide04.pdf
2 1/28 Neuron: Computational models Dayan and Abbott: Chapter 5, Appendix A.4 Homework 1 announced   slide05.pdf
3 2/2 Thalamus Shepherd: Chapter 8     slide07.pdf
3 2/4 Thalamus Model Choe (2004) [PDF]     slide08.pdf
4 2/9 Neuron: Plasticity Dayan and Abbott: Chapter 8   Homework 1 due slide09.pdf
4 2/11 Neuron: Plasticity; Neural encoding Dayan and Abbott: Chapter 8; Dayan and Abbott: Chapter 1     slide09.pdf
5 2/16 Neural Encoding; Visual System: Computation Dayan and Abbott: Chapter 1; Miikkulainen et al. (2005) Chapters 1,2,3     slide10.pdf
5 2/18 Visual System: Development Miikkulainen et al. [eBook]: Chapter 4, 5     slide11.pdf
6 2/23 Visual System: Development Miikkulainen et al.: Chapters 4 and 5     slide11.pdf
6 2/25 Visual System: Development Miikkulainen et al.: Chapters 4 and 5     slide11.pdf
7 3/2 Delay Compensation Lim and Choe (2006) [PDF] Homework 2 announced   slide12.pdf
7 3/4 Delay Compensation; Neocortex Lim and Choe (2006) [PDF]; Shepherd: Chapter 12; Douglas and Martin (2004) [PDF]     slide12.pdf
8 3/9 Basal Ganglia; Motor System Shepherd: Chapter 9; Choe and Smith (2006) [PDF]   Homework 2 topic due slide14.pdf
8 3/11 Motor System: Decoding Internal State Choe and Smith (2006) [PDF]     slide15.pdf
9 3/16 Spring break        
9 3/18 Spring break        
10 3/23 Motor System: RF Development; Motor System: Response Tuning Reto Wyss et al. (2006) [PDF]; Emilio Salinas (2006) [PDF]     slide17.pdf
10 3/25 Natural Images: Response Statistics and Salience, Statistical Structure Choe and Sarma (2006) [PDF]; Xiuwen Liu and DeLiang Wang (2002) [PDF]     slide20.pdf
11 3/30 Guest lecture Gary Wan (TAMU library), on utilizing library resources      
11 4/1 Guest lecture Huei-Fang Yang (TAMU CSE), on neuronal morphology reconstruction   Homework 2 due  
12 4/6 Neuron Morphology De Schutter: Chapter 6 and 7     slide22.pdf
12 4/8 Neuron Morphology: Statistical Description Ascoli et al. (2001) [PDF]     slide23.pdf
13 4/13 Network Analysis: Complexity Sporns and Tononi (2002) [PDF]; Sporns et al. (2004) [PDF]     slide24.pdf
13 4/15 Network Analysis: Shortest Path; Network Dynamics Kaiser and Hilgetag (2006) [PDF]; Thiel et al. (2003) [PDF]     slide25.pdf
14 4/20 Systems Neuroscience Van Hemmen and Sejnowski: Chapters 1, 13, and 19     slide27.pdf
14 4/22 Dynamics Heinz Von Foerster     slide28.pdf
15 4/27 Project Presentation        
15 4/29 Project Presentation        

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