Yueyang Alice Li

92 Pages·2011·0.31 MB·English

Medical Data Mining: Improving Information
Accessibility using Online Patient Drug Reviews
by
Yueyang Alice Li
S.B., Massachusetts Institute of Technology (2010)
Submitted to the Department of Electrical Engineering and Computer
Science
in partial fulfillment of the requirements for the degree of
Master of Engineering in Electrical Engineering and Computer Science
at the
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
February 2011
(cid:13)c Massachusetts Institute of Technology 2011. All rights reserved.
Author ..............................................................
Department of Electrical Engineering and Computer Science
January 4, 2011
Certified by..........................................................
Dr. Stephanie Seneff
Senior Research Scientist
Thesis Supervisor
Accepted by.........................................................
Dr. Christopher J. Terman
Chairman, Masters of Engineering Thesis Committee
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Medical Data Mining: Improving Information Accessibility
using Online Patient Drug Reviews
by
Yueyang Alice Li
Submitted to the Department of Electrical Engineering and Computer Science
on January 4, 2011, in partial fulfillment of the
requirements for the degree of
Master of Engineering in Electrical Engineering and Computer Science
Abstract
We address the problem of information accessibility for patients concerned about
pharmaceutical drug side effects and experiences. We create a new corpus of online
patient-provided drug reviews and present our initial experiments on that corpus.
We detect biases in term distributions that show a statistically significant associa-
tion between a class of cholesterol-lowering drugs called statins, and a wide range
of alarming disorders, including depression, memory loss, and heart failure. We also
develop an initial language model for speech recognition in the medical domain, with
transcribed data on sample patient comments collected with Amazon Mechanical
Turk. Our findings show that patient-reported drug experiences have great potential
to empower consumers to make more informed decisions about medical drugs, and
our methods will be used to increase information accessibility for consumers.
Thesis Supervisor: Dr. Stephanie Seneff
Title: Senior Research Scientist
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Acknowledgments
I would like to express my sincere gratitude to Stephanie Seneff for acting as my
advisor. Her invaluable expertise and generous guidance were instrumental to the
completion of this thesis, and her eternal enthusiasm kept me motivated throughout
the year.
It has been a pleasure being part of the Spoken Language Systems group. Special
thanks goes to JingJing Liu for her knowledgeable insight and collaboration in the
classificationexperiments, toJimGlassforhiskindencouragement, andtoVictorZue
for his advice on grad school and life beyond. I would especially like to thank Scott
Cyphers who was always willing to answer my endless questions about the Galaxy
system. Many thanks to everyone in the group for making it such an enjoyable and
welcome place to work.
I would also like to acknowledge Tommi Jaakkola for his patient and illuminating
instruction on machine learning, and Regina Barzilay for first introducing me to NLP.
This work would not have been possible without Victor Costan, who gave me massive
help whenever I ran into difficulties with Ruby on Rails. I also deeply appreciate
my friends and colleagues at CSAIL, for most enjoyable discussions and treasured
memories.
Finally, I am indebted to my wonderful family for their unconditional love and
support.
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Bibligraphic Note
Portions of this thesis are based on the paper entitled “Automatic Drug Side Effect
Discovery from Online Patient-Submitted Reviews - Focus on Statin Drugs” with
Stephanie Seneff and JingJing Liu, which was submitted to the Proceedings of the
49th Annual Meeting of the Association for Computational Linguistics.
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Contents
1 Introduction 17
1.1 Vision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.2 Contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.3 Thesis Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2 Related Work 23
2.1 Term Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.1.1 Medical Knowledge Resources . . . . . . . . . . . . . . . . . . 24
2.1.2 Statistical Approaches . . . . . . . . . . . . . . . . . . . . . . 25
2.2 Medical Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
2.2.1 Dialogue Systems . . . . . . . . . . . . . . . . . . . . . . . . . 26
2.2.2 Health Surveillance . . . . . . . . . . . . . . . . . . . . . . . . 28
2.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3 Data 31
3.1 Data Collection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.1.1 Data Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.1.2 Data Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.2 Example Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.3 Spelling Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4 Automatic Discovery of Side Effects: Focus on Cholesterol-Lowering
Drugs 39
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4.1 Side Effects of Cholesterol-lowering Drugs: Brief Literature Review . 40
4.1.1 Statin Drugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4.1.2 Non-Statin Cholesterol-Lowering Drugs . . . . . . . . . . . . . 42
4.2 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.3 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.3.1 Log Likelihood Statistic . . . . . . . . . . . . . . . . . . . . . 44
4.3.2 Pointwise Mutual Information . . . . . . . . . . . . . . . . . . 45
4.3.3 Set Operations . . . . . . . . . . . . . . . . . . . . . . . . . . 46
4.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
4.4.1 Cholesterol-lowering vs Blood-pressure-lowering Drugs . . . . 46
4.4.2 Statins vs Non-statins . . . . . . . . . . . . . . . . . . . . . . 47
4.4.3 Gender Differences . . . . . . . . . . . . . . . . . . . . . . . . 50
4.4.4 Lipophilic vs Hydrophilic Statins . . . . . . . . . . . . . . . . 51
4.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
4.5.1 Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
4.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
5 Speech Recognition Experiments 55
5.1 Collection of Spoken Questions Data . . . . . . . . . . . . . . . . . . 55
5.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
5.2.1 Trigram Language Model . . . . . . . . . . . . . . . . . . . . . 57
5.2.2 Data Sparsity . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
5.3 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
6 Additional Preliminary Experiments 63
6.1 Multi-word Term Identification . . . . . . . . . . . . . . . . . . . . . 63
6.1.1 Term Frequency . . . . . . . . . . . . . . . . . . . . . . . . . . 64
6.1.2 Part of Speech Filter . . . . . . . . . . . . . . . . . . . . . . . 65
6.1.3 Association Measures . . . . . . . . . . . . . . . . . . . . . . . 66
6.1.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
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