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Welcome to the Methods in Computational Neurobiology (PHYSL 317) Course Website. Here you can find information about prerequisites, get homework assignments with solutions, and browse the schedule for upcoming lectures.

Dr. Nelson's Lecture Schedule

DateLecture Number / TopicLinks
N/A0. Introduction to MATLABGuides / HW 0
1/261. Intro / RC circuits (notes)HW 1
2/22. Integrate-and-fire model (slides)HW 2
2/93. Hodgkin-Huxley model (reading) (figs)HW 3
2/164. Synaptic inputs, small networks (slides) HW 4
    QUIZ: Lectures 0-2
2/235. Simple behaviors, phototaxis (slides) HW 5
3/16. Real-world inputs, noise (slides)HW 6
3/87. Adaptive behavior, learning (slides)
    QUIZ: Lectures 3-5

Texts (recommended)

Nelson, M.E. (in press) Electrophysiological Models
In: Databasing the Brain: From Data to Knowledge.
(S. Koslow and S. Subramaniam, eds.) Wiley, New York.
[ preprint ]

Braitenberg, V (1984) Vehicles: Experiments in Synthetic Psychology,
The MIT Press.

Additional resources

Koch, C. and Segev, I (1998) Methods of Neuronal Modeling: From Ions to Networks. MIT Press, Cambridge MA

Dr. Anastasio's Lecture Schedule (also available as .pdf or .doc)

I. Lateral Inhibition - 3/15
  • Ratliff K, Knight BW, Graham W (1969) On tuning and amplification by lateral inhibition. Proc Natl Acad Sci 62:723-730
  • Didday RL (1976) A model of visuomotor mechanisms in the frog optic tectum. Math Biosci 30:169-180
  • Coombs S, Mogdans J, Halstead M, Montgomery J (1998) Transformations of peripheral inputs by the first-order lateral line brainstem nucleus. J Comp Physiol A 182: 609-626
II. Self-Organizing Feature Maps - 3/29
  • Malsburg CH von der (1973) Self-organization of orientation sensitive cells in the striate cortex. Kybernetik 14:85-100
  • Kohonen T (1982) Self-organized formation of topologically correct feature maps. Biol Cybern 43:59-69
  • Obermayer K, Ritter H, Schulten K (1990) A principle for the formation of the spatial structure of cortical feature maps. Proc Natl Acad Sci 87:8345-8349
III. Hopfield Networks - 4/5
  • Hopfield JJ (1982) Neural networks and physical systems with emergent collective abilities. Proc Natl Acad Sci 79:2554-2558
  • Hopfield JJ (1984) Neurons with graded response have collective properties like those of two-state neurons. Proc Natl Acad Sci 81:3088-3092
  • Rolls ET (1989) Functions of neuronal networks in the hippocampus and neocortex in memory. In: Byrne JH, Berry WO (Eds) Neural models of plasticity: experimental and theoretical approaches. Academic Press, San Diego, pp 240-265
IV. Back-Propagation - 4/12
  • Rumelhart DE, Hinton GE, Williams RJ (1986) Learning internal representations by error propagation. In: Rumelhart DE, McClelland JL, PDP Research Group (Eds) Parallel distributed processing: explorations in the microstructure of cognition: vol 1: foundations. MIT Press, Cambridge, pp 318-362
  • Anastasio TJ, Robinson DA (1989) the distributed representation of vestibulo-oculomotor signals by brain-stem neurons. Biol Cybern 61:79-88
  • Zipser D, Anderson RA (1988) A back-propagation programmed network that simulates response properties of a subset of posterior parietal neurons. Nature 331:679-684
V. Genetic Algorithms - 4/19
  • Holland JH (1992) Adaptation in natural and artificial systems. MIP Press, Cambridge, ch 1
  • Happel BL, Murre JMJ (1994) Design and evolution of modular neural network architectures. Neural Networks, 7:985-1004
  • Schaffer JD, Caruana RA, Eshelman LJ (1990) Using genetic search to exploit the emergent behavior of neural networks. Physica D 42:244-248
VI. Temporal Difference Learning - 4/26
  • Sutton RS (1988) Learning to predict by the methods of temporal differences. Machine Learning 3:9-44
  • Barto AG (1995) Adaptive critics and the basal ganglia. In: Houk JC, Davis JL, Beiser DG (Eds) Models of information processing in the basal ganglia. The MIT Press, Cambridge, ;; 215-232
  • Montague PR, Dayan P, Sejnowski TJ (1996) A framework for mesencephalic dopamine systems based on predictive Hebbian learning. J Neurosci 16:1936-1947
VII. Recurrent Back-Propagation - 5/5
  • Williams RJ, Zipser D (1989) A learning algorithm for continually running fully recurrent neural networks. Neural Comp 1:270-280
  • Anastasio TJ (1991) Neural network models of velocity storage in the horizontal vestibulo-ocular reflex. Biol Cybern 64:187-196
  • Zipser D (1991) Recurrent network model of the neural mechanisms of short-term active memory. Neural Comp 3:179-193
Suggested Textbooks
  • Beal R, Jackson T (1990) Neural computing: an introduction. Institute of Physics Publishing, Bristol, UK
  • Churchland PS, Sejnowski TJ (1992) The computational brain. MIT Press, Cambridge
  • Haykin S (1999) Neural networks: a comprehensive foundation. second edition. Prentice Hall, Upper Saddle River



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