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WELDON SCHOOL OF

BIOMEDICAL ENGINEERING

BIOMEDICAL SIGNAL PROCESSING


BME 595B - SPRING 2007

Time: Tuesday 1:30-2:45


Room: BMED 1083
Credits: 3

Professor: Michael G. Heinz, Ph.D.


Asst. Professor of Biomedical Engineering
Asst. Professor of Speech, Language, and Hearing Sciences
Office: G34C, Heavilon Hall
Phone: 496-6627
Email: mheinz@purdue.edu
Office Hours: Thursday 3-4 (BMED 3070), and by appointment

Teaching Assistant: Jayaganesh (Ganesh) Swaminathan


Email: jswamy@purdue.edu
Help Session: Tuesday 4:30-5:30 (BMED 1083)
Office Hours: Mon. and Wed. 4-5:30 (BMED 1084/1082)

Course Description: An introduction to the application of digital signal processing to practical


problems involving biomedical signals and systems. Topics include: examples of
biomedical signals; analysis of concurrent, coupled, and correlated processes;
filtering for removal of artifacts; event detection; analysis of waveshape and
waveform complexity; frequency domain characterization of signals and systems;
modeling biomedical signal-generating processes and systems; analysis of
nonstationary signals; pattern classification and diagnostic decision. MATLAB
will be used throughout to provide numerous opportunities for hands-on
application of the theory and techniques discussed to real-life biomedical signals.

Prerequisites: ECE 301 and ECE 302 (or permission of instructor). Familiarity with MATLAB.

Required Text: Rangayyan , R.M., Biomedical Signal Analysis : A Case-Study Approach,


Wiley-IEEE Press, 2001. (ISBN: 0471208116)

Required Software: MATLAB (see handout on options for accessing MATLAB)


MS Office (Word and PowerPoint)

Supplemental References:
1) Bruce, E., Biomedical Signal Processing and Signal Modeling, Wiley-
Interscience, 2000. (ISBN: 0471345407).
2) Oppenheim, A.V., Schafer, R.W., and Buck, J.R., Discrete-Time Signal
Processing, 2nd Edition, Prentice Hall, 1999. (ISBN: 0137549202).
3) Papoulis, A. and Pillai, S.U., Probability, Random Variables and Stochastic
Processes, 4th edition, McGraw-Hill Science, 2001. (ISBN: 0072817259).

BMED Building ■ 206 S. Intramural Drive ■ West Lafayette, IN 47907-2032


(765) 494-2995 ■ Fax: (765) 494-1193 ■ www.purdue.edu/BME
WebCT Vista:
Materials from the class will be posted on WebCT Vista, as well as grades. Announcements will be made
via regular email.

Grading: Problem Sets (5) 10%


Midterm Exam 20%
MATLAB Projects 40%
Final Project 30%

Problem Sets and Project Submissions:


Submitted work will consist of both written and electronic files. All assignments are due by the
beginning of class on the due date. No late assignments will be accepted (except in extenuating
circumstances, discussed with Dr. Heinz prior to the due date). Written material will consist of derived
solutions and/or MS Word (*.doc) text with inserted MATLAB figures (TIFFs recommended). Written
work should be handed in at the beginning of class. Electronic material will consist of your *.doc file,
and any scripts or functions you have written, as well as any *.wav files you have generated. The *.doc
file must have a list of every electronic file submitted with the assignment, with a brief description. Every
figure in your *.doc file should be generated by the code you submit, i.e., we should be able to run your
code and see your figures appear with no effort. All electronic files should be submitted as a ZIP file,
which should be emailed to Ganesh (jswamy@purdue.edu) prior to the start of class.

Access to MATLAB:
This course will require access to MATLAB and MS Office in order to complete the problem sets and
projects. It is each student’s responsibility to find a reliable environment in which to do the work for this
course. This should be worked out within the first week of class. MATLAB CDs are available from
ITAP for students to install (free of charge) on their own machine (laptop or at home – internet access
required to run license). MATLAB should also be available on all ITAP machines on campus. Three
MATLAB tutorials are posted on WebCT Vista for reference. Also, TA office hours and the weekly help
session are available to supplement you existing familiarity with MATLAB.

MATLAB Projects: (~3 weeks each)


Projects will be done in groups of two students, with individual project reports due from each student.
These projects will be done in MATLAB and will involve the implementation of signal processing
relevant to real-world biomedical problems. The MATLAB projects will be motivated by (and data will
be provided from) research projects from laboratories at Purdue, from primary papers from the literature,
or from the text book.

Project 1 (weeks 3-5): Evaluation of pitch coding in the human auditory brainstem using iterated rippled
noise. This project is motivated by ongoing research in the Auditory Electrophysiology Lab (Prof.
Krishnan in SLHS). The project will include stimulus design (iterated rippled noises with varying
pitch contours) as well as analysis of existing EEG data collected in response to iterated rippled
noises. Time-domain averaging will be used to remove noise and a short-term autocorrelation
algorithm will be used to extract the pitch contour and pitch strength from the averaged responses.

Project 2 (weeks 6-8): Simulation of Cochlear Implant Processing. Filter bank simulations of cochlear-
implant processing will be implemented to estimate how many frequency channels are needed to
understand speech (Shannon et al, 1995). The filter-bank analysis will then be extended to create
chimaeric sounds using the envelope from one sound (speech or music) and the fine-time structure
from another sound. This processing will be used to determine the salient types of information
(envelope or fine-time structure) required for the perception of speech and/or music as a function of
the number channels used (Smith et al., 2002).
Shannon, R.V., Zeng, F.G., Kamath, V., Wygonski, J., and Ekelid, M. “Speech recognition with
primarily temporal cues,” Science, 270, 303–304, 1995.
Smith Z.M., Delgutte B., Oxenham A.J. “Chimaeric sounds reveal dichotomies in auditory
perception,” Nature, 416, 87-90. 2002.
Project 3 (weeks 9-11): Detection of ectopic ECG beats. ECG data with normal and ectopic beats (data
provided with the textbook) will be used to develop an ectopic ECG beat detector. Signal processing
techniques will be used to filter the signals. Algorithms will be implemented to detect ECG
waveforms, analyze ECG waveform shape, and to classify ECG beats.

Final Project: (final 5 weeks)


An independent project applying signal processing to a research question of interest to each student. This
project can either be related to ongoing research in a lab or can be the replication of a published study.
The final projects are intended to be quite extensive as they will hopefully be in an area of direct interest
and familiarity to each student. Projects will be written up in a final report (with an abstract distributed to
the class) and will be presented to the class during the final exam period.

Statement on Collaborative Work:


The skills to be learned in this class rely on each student doing and understanding the assignments
themselves. However, collaboration is encouraged in ways that help to avoid students getting stuck and
not being able to complete an assignment (e.g., discussion of underlying concepts and theory, not
knowing the name of a specific MATLAB command, etc …). However, in no case should solutions,
code, or text be copied from another student. Each student is expected to write their own code, solutions,
and text. Violations of this expectation will receive 0 credit and may be referred to the BME department
and/or Dean of Students for disciplinary action.

Students with Disabilities


Students with disabilities must be registered with Adaptive Programs in the Office of the Dean of
Students before classroom accommodations can be provided. If you have a disability that requires
academic adjustments, please make an appointment with me to discuss your needs as soon as possible.
BME 595B Spring 2007 Lecture Schedule (Tentative)
Week Date Topic Assignments Reading

1 1/9 Review; Intro to Biomedical Signals PS 1 OUT Ch1


1/11 Concurrent, coupled, correlated processes Ch 2
2 1/16 Filtering for Artifact Removal PS 2 OUT Ch 3
1/18 Filtering for Artifact Removal PS 1 DUE
3 1/23 PROJECT 1 LECTURE (Swaminathan) PRJ 1 OUT
1/25 Filtering for Artifact Removal
4 1/30 Filtering for Artifact Removal PS 2 DUE
2/1 Event Detection Ch 4
5 2/6 Event Detection PS 3 OUT
2/8 PROJECT 2 LECTURE PRJ 1 DUE Shannon et al 1995;
PRJ 2 OUT Smith et al 2002
6 2/13 ARO – NO CLASS
2/15 Event Detection
7 2/20 Waveshape and waveform complexity PS 3 DUE Ch 5
2/22 Waveshape and waveform complexity PS 4 OUT
8 2/27 Waveshape and waveform complexity
3/1 Frequency domain characterization PRJ 2 DUE Ch 6
9 3/6 PROJECT 3 LECTURE PRJ 3 OUT
3/8 Frequency domain characterization PS 4 DUE
10 3/13 SPRING BREAK
3/15 SPRING BREAK
11 3/20 Frequency domain characterization
3/22 MIDTERM EXAM – IN CLASS
12 3/27 Modeling biomedical signals and systems Ch 7
3/29 Modeling biomedical signals and systems PRJ 3 DUE
13 4/3 Modeling biomedical signals and systems PS 5 OUT
4/5 Modeling biomedical signals and systems FINAL PROJECT
PROPOSAL DUE

14 4/10 Analysis of nonstationary signals Ch 8


4/12 Analysis of nonstationary signals
15 4/17 Pattern Classification, diagnostic decisions Ch 9
4/19 Pattern Classification, diagnostic decisions PS 5 DUE
16 4/24 Pattern Classification, diagnostic decisions
4/26 Pattern Classification, diagnostic decisions
17 4/30- EXAM WEEK PROJECT
PRESENTATIONS
5/4
5/3 FINAL PAPER
DUE

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