Syllabus for 15-883 Fall '17:
Computational Models of Neural Systems

Version of August 28, 2017
David S. Touretzky

Course web site:
Readings archive

1. Introduction to Computational Neuroscience

1.1 Brains and Computation [Mon. August 28] Slides: Course intro, and Brains and Computation

Required reading:
  • Churchland, P. S. (2002) Brain-Wise: Studies in Neurophilosophy, chapter 1, pp. 1-34. MIT Press.

Some quick Khan Academy lectures for people without a neuroscience background: Is Khan Academy too elementary for you? Want something meatier? How about a book chapter by Nobel Laureate Francis Crick? It's a bit dated now (dendritic spikes are no longer controversial), but still very good. This is an optional reading. Optional readings for people who want to explore the nature of computation more deeply:

1.2 Neurophysiology for Computer Scientists [Wed. August 30] Slides

No Class on Labor Day [Mon. September 4]

2. Cerebellum

Special resource (not required reading): Jaeger, D., Jorntell, H., and Kawato, M. (Eds.) Computation in the Cerebellum. Neural Networks, 47, November 2013. Special issue on the cerebellum.

2.1 Anatomy of the Cerebellum [Wed. September 6] slides

  • Ghez, C. and Thach, W. T. (2000) The cerebellum. In E. R. Kandel, J. H. Schwartz, and T. M. Jessell (Eds.), Principles of Neural Science, 4th edition, chapter 42, pp. 832-852. New York: Elsevier.

  • Glickstein, M. and Yeo, C. (1990) The cerebellum and motor learning. Journal of Cognitive Neuroscience, 2:69-80.

2.2 Table Lookup/Basis Function Models [Mon. September 11] slides

2.3 Cerebellar Forward and Inverse Models in Motor Control [Wed. September 13] slides

2.4 Cerebellar Timing and Classical Conditioning [Mon. September 18] slides

2.5 Dynamics of Parallel Fibers and Purkinje Cells [Wed. September 20] slides

3. The Hippocampus

3.1 Vectors, Matrices, and Associative Memory [Mon. September 25] Slides

3.2 Anatomy of the Hippocampal System [Wed. September 27] Slides

  • Johnston, D. and Amaral, D. G. (1998) Hippocampus. In G. M. Shepherd (ed.), The Synaptic Organization of the Brain, 4th edition, chapter 11, pp. 417-458. Oxford University Press. [Read pages 417-435 and 454-458. Skim the rest if you like.]

  • Amaral, D. G. (1993) Emerging principles of intrinsic hippocampal organization. Current Opinion in Neurobiology, 3:225-229.

  • [reference] contains a comprehensive summary of nearly 1600 known connections in the hippocampal formation and the parahippocampal region (presubiculum, parasubiculum, perirhinal and postrhinal cortex). It also has links to hippocampal anatomy sites, latest research news, and other resources.

  • [optional] Witter, M. P. (1993) Organization of the entorhinal-hippocampal system: a review of current anatomical data. Hippocampus, 3(special issue):33-44. [Very technical, but Figure 2 is worth looking at.]

3.3 Marr's Associative Memory Model, Part I [Mon. October 2] slides

  • Marr, D. (1971) Simple memory: A theory for archicortex. In L. M. Vaina (ed.), From the Retina to the Neocortex: Selected papers of David Marr, pp. 59-128. Includes commentaries by D. Willshaw and B. McNaughton. Paper originally appeared in Philosophical Transactions of the Royal Society of London B, 262:23-81. Read the commentaries first, then the paper. You need only read sections 0-3 of the paper.

3.4 Marr's Associative Memory Model, Part II [Wed. October 4] slides

3.5 Pattern Completion/Separation [Mon. October 9] slides

Midterm Exam [Wed. October 11]

3.6 Hippocampus as a Cognitive Map [Mon. October 16] slides

3.7 Entorhinal Grid Cells and Path Integration [Wed. October 18] slides

3.8 Theta, Gamma, and Working Memory [Mon. October 23] slides

4. Neural Basis of Learning and Memory

4.1 Synaptic Learning Rules [Wed. October 25] slides

4.2 Synaptic Plasticity and the NMDA receptor [Mon. October 30] slides

5. Conditioning and Reinforcement Learning

5.1 The Rescorla-Wagner Model and Its Descendants [Wed. November 1] slides

5.2 Predictive Hebbian Learning [Mon. November 6] slides

6. Basal Ganglia

6.1 Anatomy of the basal ganglia [Wed. November 8] slides

Society for Neuroscience Meeting, November 11-15 (no class)

6.2 Reinforcement learning models of the basal ganglia [Mon. November 20] slides

Start Work on Modeling Project

  • Standard modeling project

  • You can arrange your own modeling project by speaking with the instructor if you don't want to do the standard project.

No class on Wednesday, November 22 (day before Thanksgiving)

7. Cortical Representations

7.1 Coordinate Transformations In Parietal Cortex [Mon. November 27] slides

7.2 Probablistic Population Codes in Cortex [Wed. November 30] slides

8. Visual System

8.1 Low-Level Vision: Retina, LGN, and V1 [Mon. December 4] slides and more slides

8.2 Models of Object Recognition in Temporal Cortex [Wed. December 6] slides and more slides

Final Exam: TBA

The final exam will take place on Thursday, Dec. 14 from 1-4pm. Room TBA.

Modeling Projects are due Friday, Dec. 15 by 5:00 PM.

Dave Touretzky