Artificial Neural Development - CMPSCI 691U

Announcements

• None.

Office Hours

In CS208, Thursdays 3:30-5:30 or by appointment.

Schedule

We meet MW 2:30-3:45 in LGRC 203.

• Sept 3: Course overview.
• Sept 5: Discuss: Quartz, S.R. and Sejnowski, T.J. (1997). `The neural basis of cognitive development: A constructivist manifesto', Behavioral and Brain Sciences 20, 537-596. Peer Commentary is optional.
• Sept 8: Discuss: Vaario, J., Onitsuka, A. and Shimohara, K. (1997). `Formation of neural structures', Proceedings of the Fourth European Conference on Articial Life, ECAL97, 214-223, MIT Press.
• Sept 10: Discuss: van Ooyen, A. (1994). `Activity-Dependent Neural Network Development' (Invited Review), Network: Computation in Neural Systems 5, 401-423.
• Sept 15: Discuss: Bi, G.Q. (2002). `Spatiotemporal specificity of synaptic plasticity: cellular rules and mechanisms', Biological Cybernetics 87, 319-332.
• Sept 17: Discuss: Rust, A.G., Adams R. and Bolouri H. (2000). `Evolutionary neural topiary: Growing and sculpting artificial neurons to order', Proceedings of the 7th International Conference on the Simulation and Synthesis of Living Systems (AlifeVII).
• Sept 22: Discuss: Kerszberg, M. and Changeux, J.P. (2003). `Molecular Models of Early Neural Development', in Modeling Neural Development, van Ooyen, A. (Ed), pp 1-26, MIT Press.
• Sept 24: Discuss: (chap 2 of ...) and homework: Describe/diagram basic physiology of single neuron at rest, chemistry of signal transmission, and operation of chemical synapse.
• Sept 29: No class
• Oct 1: Discuss: Marnellos, G. and Mjolsness, E.D. (2003). `Gene Network Models and Neural Development', in Modeling Neural Development, van Ooyen, A. (Ed), pp 27-48, MIT Press.
• Oct 6: Discuss: Hentschel, H.G.E. and Fine, A. (2003). `Early Dendritic and Axonal Morphgenesis', in Modeling Neural Development, van Ooyen, A. (Ed), pp 49-74, MIT Press.
• Oct 8: Discuss: Dellaert, F. and Beer, R.D. (1994). `Towards an Evolvable Model of Development for Autonomous Agent Synthesis,' in Artificial Life IV, Proceedings of the Fourth International Workshop on Synthesis and Simulation of Living Systems, Brooks, R. and Maes, P. (Eds), MIT Press.
• Oct 13: Holiday
• Oct 15: Double period for Sept 29 makeup.
  Discuss: van Pelt, J., Graham, B.P. and Uylings, H.B.M. (2003). `Formation of Dendritic Branching Patterns', in Modeling Neural Development, van Ooyen, A. (Ed), pp 75-94, MIT Press.
  Discuss: Kauffman, S.A. (1969). `Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets', in Journal of Theoretical Biology, vol 22, pp 437-467. I wrote a short program to simulate noiseless Boolean networks.
• Oct 20: Discuss: Goodhill, G.J. and Urbach, J.S. (2003). `Axon Guidance and Gradient Detection by Growth Cones', in Modeling Neural Development, van Ooyen, A. (Ed), pp 95-109, MIT Press.
• Oct 22: Discuss: Segev, R. and Ben-Jacob, E. (2000). `Generic Modeling of Chemotactic Based Self-Wiring of Neural Networks', in Neural Networks, vol 13, pp 185-199, Permagon.
• Oct 27: Discuss: van Ooyen, A., van Pelt, J., Corner, M.A. and Kater, S.B. (2003). `Activity-dependent neurite outgrowth: Implications for network development and neuronal morphology', in Modeling Neural Development, van Ooyen, A. (Ed), pp 111-132, MIT Press.
• Oct 29: Discuss: Ferree, T.C. and Lockery, S.R. (1999). `Computational rules for chemotaxis in the nematode C. elegans', in Journal of Computational Neuroscience, vol 6, pp 263-277.
• Nov 3: Discuss: Eglen, S.J., Galli-Resta, L. and Resse, B.E. (2003). `Theoretical models of retinal mosaic formation', in Modeling Neural Development, van Ooyen, A. (Ed), pp 133-150, MIT Press.
• Nov 5: Discuss: Abbott, L.F., Thoroughman, K.A., Prinz, A.A., Thirumalai, V. and Marder, E. (2003). `Activity-dependent modification of intrinsic and synaptic conductances in neurons and rhythmic networks', in Modeling Neural Development, van Ooyen, A. (Ed), pp 151-166, MIT Press.
• Nov 10: Discuss: Clarke, P.G.H. (2003). `Models of neuronal death in vertebrate development: From trophic interactions to network roles', in Modeling Neural Development, van Ooyen, A. (Ed), pp 167-182, MIT Press.
• Nov 12:
• Nov 17:
• Nov 19:
• Nov 24:
• Nov 26:
• Dec 1:
• Dec 3:
• Dec 8:
• Dec 10:

Prerequisites

This is primarily a reading course. I intend for it to be self contained, but some familiarity with artificial (or real) neural networks may be helpful. We will review some basic material, and launch into reading and discussing research papers as soon as possible.

Course Requirements

You must attend class and participate in the discussion. For each paper that we read, you will need to have prepared in advance of the class discussion a one page (max) `brief' that captures the main points, and identifies the strengths, and weaknesses of the method(s) or approach. There will be no midterm, but there will be a final exam. Timely attendance and participation (briefs & discussion) count for 70%, and the final exam counts for 30% of the final grade.

Late Policy

Each `brief' is due at the end of the class at which the paper is discussed. Preparing the brief prepares you for the discussion. Late papers will not be accepted. Plan ahead; do not be late to class.

Academic Honesty

Your work for the course needs to be the result of your individual effort. Talking with fellow classmates is of course an important and exciting part of the learning process, so you will need to use good judgement. If you are in doubt, feel free to ask. Be sure to attribute correctly those ideas that you borrow from others (written or spoken).