MATH 3104: Assignments 3 and 4 (Neural Decoding)
Prof. Geoffrey Goodhill, Semester 1, 2021
Since both assignments 3 and 4 relate to the same coding problem they are presented together here. Each
is marked out of 14 marks and is worth 8.75% of the total mark for the course overall. Both assignments
are due by 4pm on Tuesday April 13th.
What you hand in must be your own unique work. For each assignment you should hand in the following:
• Fully-worked answers to the analysis questions below.
• One copy of the Matlab code (EXTENSIVELY COMMENTED, and making clear which lines of code
address each question).
• The results of running your program as asked for below.
Please note that your code should ALWAYS deal with the general case, i.e. numbers should be obtained
from the relevant data structures rather than being hard-coded. Also make sure that all plots have the
correct axis labels and show the correct range of values.
Assignment 3
1. (Written question.) Imagine you are getting married outdoors tomorrow in a town called Black Stump
in western Queensland. On average it rains only 5 days a year in Black Stump. However tomorrow
the Bureau of Meteorology (BoM) predicts rain at Black Stump. Historically, assume that when it
actually rains, the BoM correctly forecasts rain 90% of the time. Also when it doesn’t rain, the BoM
incorrectly forecasts rain 10% of the time. Calculate the probability that it will rain on your wedding,
and hence assess whether it’s worth trying to rent a marquee. (Note that comments on the accuracy
of the BoM in the real world are not required.) [2 marks]
2. (Written question.) Consider the case of Bayesian inference, i.e. minimizing∫
L(s, sbayes)P (s|r)ds
for the case L = (s− sbayes)2. By differentiating wrt sbayes, show the optimal estimate in this case is
sbayes =
∫
sP (s|r)ds
[2 marks]
3. Download the Matlab function generatetrains.m from Blackboard. This generates a set of Poisson
spike trains for multiple presentations of several different stimuli (i.e. a slightly generalized version
of the program you were asked to write for the previous assignment). Read the comments in the
program carefully.
NOTE: For any cases where the ML or MAP estimates are ambiguous (i.e. two stimuli have the same
probability), pick the smaller stimulus (this is an arbitrary choice for concreteness).
Use generatetrains.m to generate a spike train array for the case of 5 stimuli, where each stimulus
presentation is 1 second long, the mean firing rates produced by the 5 stimuli are 10, 20, 30, 40 and
50 spikes/sec respectively, and each stimulus is presented 100 times (we will vary this later). Use a
time bin of 1 ms, and a seed of 1. Required: code (0 marks - preparatory for the following questions)
4. Define an array spikeSums which has 2 dimensions of size ‘numberOfStimuli’ and
‘max(numStimPres)’ respectively, and fill it with the number of spikes in each of the spike trains you
created in question 1. You may find the matlab command sum useful for this. Determine maxN, the
maximum number of spikes occuring in any train. Required: code (2 marks)
5. Define an array pns (of size numberOfStimuli by maxN+1), and fill it with the probability of observing
a particular number of spikes given that a particular stimulus was presented (using the spikeSums
array from Q2). Remember to account for the possibility that no spikes might occur in a given stim-
ulus presentation. Plot pns using plot(0:maxN,pns). This will have 5 lines, so include a legend.
Required: code, plot (3 marks)
6. Define a vector mlEstimate of length maxN+1. Fill this vector such that the m+1th element contains the
maximum likelihood estimate of the stimulus that was presented, given that m spikes were observed
(note that the ML estimate is a stimulus value, not a probability). Plot mlEstimate against spike
number. NOTE: You may find that there are numbers of spikes which were generated by none of
the spike trains (for example, it is likely that none of the spike trains generated 0 spikes). For these
values, set mlEstimate to NaN. Required: code, plot (5 marks)
Assignment 4
1. (Written question). Consider two binary variables X and Y having the following joint probability distri-
bution:
X\Y 0 1
0 1/3 1/3
1 0 1/3
Evaluate the following entropies: H(X), H(Y ), H(X|Y ), H(Y |X), H(X,Y ), and the mutual informa-
tion Im(X,Y ). (3 marks).
2. (Written question.) Fill in the missing steps in the derivation of the entropy of spike trains in the section
‘Direct calculation of Poisson entropy’ from the notes for the Entropy Maximisation lecture. (2 marks).
3. Using the same Matlab code as for Assignment 3, define a vector mapEstimate of length maxN+1, and
fill it with the maximum a posteriori estimate of the stimulus that was presented given that a particular
number of spikes was observed. Plot mapEstimate. As with mlEstimate, for spike numbers that
weren’t observed, set mapEstimate to NaN. Make sure your plot shows the correct values for the
number of spikes. Required: code, plot (5 marks)
4. Now increase the number of times stimulus 3 is presented to 400, regenerate the spike train array,
and plot mlEstimate and mapEstimate. Explain the differences you see from the case when all stimuli
were presented the same number of times. Required: plots, explanation (2 marks)
5. With all stimuli presented 100 times, estimate the entropy in the spike count response, H, the noise
entropy, Hnoise, and from those, calculate the mutual information between spike count and stimulus,
I = H − Hnoise (you may find it helpful to recall that P (r) =
∑
s P (r|s)P (s)). Recalculate this for
stimulus presentations times T of 1, 2, 3, 4, 5, 6 and 7 seconds. What happens to I, as the stimulation
time is varied? How does I at these different times compare to the entropy of the stimulus distribution,
Hstim = −
∑
s P (s) log2 P (s)? Discuss. Required: code, values of I at the requested T values,
discussion (2 marks)


















































































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