Homework #2: Neural Encoding and Decoding
Due Date: Wednesday, February 2, 2005 (at the beginning of class)
 
This homework is based on the list of textbook exercises for Chapters 1 and 2 that can 
be downloaded from: http://people.brandeis.edu/~abbott/book/exercises.html
 
Download the exercises and solve the following problems using Matlab. 
Turn in a hard-copy containing: 
(1) your answers to any questions asked in each exercise, 
(2) any figures, plots, or graphs supporting your answers, and 
(3) printouts of your Matlab programs. 
Also email your Matlab program files to Scott (scotths@cs.washington.edu).




Please staple your hard copies, and when emailing files, make sure to use the subject 
line "528-hw2 lastname, firstname". 
 
1. (20 points) Exercise #1 in Chapter 1 (Read page 30 of the text for ideas)
2. (20 points) Exercise #8 in Chapter 1 (Meet the eminent H1 neuron in the fly!)
3. (20 points) Exercise #9 in Chapter 1 (Get to know the H1 neuron)
4. (20 points) Exercise #2 in Chapter 2 (Imitate the H1 neuron!)
5. (20 points) Compute the covariance matrix and its eigenmodes for the fly data in (2) 
 above and make a scatter plot of the projections of the spike-triggered stimuli onto 
 the two leading eigenmodes.  Find the threshold (nonlinear decision) functions as 
 defined in class, both with respect to the two leading eigenmodes separately, and 
 jointly, i.e., the two-dimensional threshold function. Can the two-dimensional 
 distribution of projections be approximated by the product of the one-dimensional 
 distributions (i.e. do the two features contribute independently?). 
 Suggested background reading: Lecture slides and the paper by Arcas, Fairhall, and 
 Bialek on the class website: 
 http://www.cs.washington.edu/education/courses/528/05wi/AgueraFairhallBialek2001.pdf 
 For this problem, assume all spikes are “isolated” (in the terminology of the paper) 
 and use all spikes for your analysis.