EE434

Biomedical Signal Processing

Spring 2011
Final
Due date: June 10th, 2011, midnight
Instructions: This is a take-home test. Complete the questions, and return your work as a single
PDF document by e-mail before the due date and time. Clearly explain your methodology and
justify your answers. Sharing of ideas is encouraged, but sharing of results and/or text is not. Your
name on your test is a testimony that you have neither received nor given any unauthorized
assistance. Correct answers to wrong questions are not creditable.

Question 1: (15 pts) Consider the Hodgkin-Huxley action potential model, and explain how the
following changes would affect the action potentials generated by an external current.
a) (5 pts) Half of the Na+ channels on the axonal membrane are inhibited.
b) (5 pts) Half of the K+ channels on the axonal membrane are inhibited.
d) (5 pts) The axon has been placed in a lower Na+ environment.

Question 2: (25 pts) Stochastic models of molecular evolution on nucleotide sequences characterize
the probability of replacing a base X at a site with another base Y in t units of time by a matrix P(t)
of probabilities PX→Y(t) determined by
⎡ PA→ A (t ) PA→G (t ) PA→T (t ) PA→C (t ) ⎤
⎢ P (t ) P
G →G (t ) PG →T (t ) PG →C (t )⎥⎥
P (t ) = ⎢ G → A = exp(Qt )
⎢ PT → A (t ) PT →G (t ) PT →T (t ) PT →C (t ) ⎥
⎢ ⎥
⎣ PC → A (t ) PC →G (t ) PC →T (t ) PC →C (t ) ⎦
where Q is the associated rate matrix. The rate matrix presumed by the Kimura’s two-parameter
model is given by
⎡− α − 2 β α β β ⎤
⎢ α − α − 2β β β ⎥⎥
Q=⎢
⎢ β β − α − 2β α ⎥
⎢ ⎥
⎣ β β α − α − 2β⎦
where α and β are the transition and the transversion rates respectively.
a) (10 pts) Compute and plot the curves of PA→G(t), PC→A(t), and PT→T(t) using α = 1.0 and β = 0.5
for t 0 [0, 1].
b) (10 pts) Repeat above using α = 2.0 and β = 1.0.
c) (5 pts) What can you say about the limit values and the speed of convergence of P(t) as t goes to
infinity between the two cases above?

Question 3: (30 pts) Carry out a SAM analysis on the dataset GDS3542 available for download at
the GEO data server, and identify the differentially expressed genes between
a) (10 pts) the baseline and at 12 hours,
b) (10 pts) the baseline and at 24 hours, and
c) (10 pts) the baseline and at 72 hours
with around one falsely discovered gene.
(Hint: The GEO data server can be found at the address http://www.ncbi.nlm.nih.gov/gds.
Make sure to download the tab-delimited dataset SOFT file and delete all the comment lines until
the one beginning with “ID_REF.” The SAM analysis can be carried out using the TIGR MeV
suite available for download at the internet address http://www.tm4.org/mev/. Provide both the
delta graph as well as a table view of the differentially expressed genes in all cases as part of your
answer.)

Question 4: (30 points) Prepare a report on one of the papers provided in the Suggested Reading
list. Your report must be 2 A4 pages, double spaced and with 2 cm margins. It also must include the
following sections in addition to your name along with the title and the authors of the paper:
• Introduction (a brief account of the subject matter and its significance)
• Problem Description (specifics of the subject matter including, if applicable, the various
objectives)
• Discussion (a summary of the proposed methods in the literature concluding with a perspective
on the future developments in the field)