cs150: artificial intelligence in health informatics

Instructors

Kevin Small
Tufts Medical Center
35 Kneeland Ave., #724
Office Hours: after class*
ksmall@cs.tufts.edu

Byron Wallace
Tufts Medical Center
35 Kneeland Ave., #713
Office Hours: after class*
byron.wallace@gmail.com

* or by request

Announcements

11/23/11. here are the midterm solutions, for anyone who is interested.

11/21/11. here is a link to our class project's GitHub page.
10/25/11. the midterm is available. this is due next Wednesday.

11/2/11. Class is cancelled tomorrow.

10/7/11. homework 2 is available.

9/27/11. for those of you who haven't taken linear algebra in awhile, please consult Dr. Andrew Ng's linear algebra hand-out.

9/19/11. homework 1 is available.

9/14/11. please read and write a response to the Ledley & Lusted paper for Monday.

9/3/11. welcome to the class!

Syllabus

#	Date	Subject (click for slides)	Reading before class
1	9/7	Introduction and Administrivia: Biomedical Informatics
2	9/12	Clinical Reasoning & Probabilistic Inference I	Hersh, 2002 Tversky and Kahneman, 1974
3	9/14	Clinical Reasoning & Probabilistic Inference II	Owens and Sox, 2006²
4	9/19	Computational Models for Clinical Decision Making	Ledley and Lusted, 1959¹ Charniak, 1991²
5	9/21	Standards & Ontologies	Gorry, 1974¹
6	9/26	Pattern Classification	Stevens et al., 2000² Hammond and Cimino, 2006³
7	9/28	Classification Algorithms
8	10/3	Structured Classification	Rabiner, 1989
9	10/5	NLP & Biomedical Texts I	Nadkarni et al., 2011
10	10/12	NLP & Biomedical Texts II	Kim et al., 2011 Collins, 2002³
11	10/17/11	Information Retrieval in Health Informatics	Chapter 19, Shortliffe Muller et al., 2004³
12	10/19/11	Shared Task Presentations
13	10/24/11	Shared Task Presentations/Midterm Review
14	10/26/11	Class cancelled -- Work on take-home midterm
15	10/31/11	Mobile Health Systems	Reed and Shabot, 2006 (Chapter 17 in Shortliffe)
16	11/2/11	Data Mining in Medical Records
17	11/7/11	Guest Lecture: Issa Dahabreh on Mining for Causality
18	11/9/11	Class cancelled - Work on annotated bibliography
19	11/14/11	Guest Lecture: Carla Brodley on Content-based Image Retrieval
20	11/16/11	Machine Learning in Medical Imaging
21	11/21/11	Preliminary Presentations
22	11/28/11	Guest Lecture TBA
23	11/30/11	Guest Lecture TBA
24	12/5/11	Guest Lecture TBA
25	12/7/11	Guest Lecture TBA
25	12/12/11	Last Class

¹reaction paper due at beginning of class
²reading required, but not before specific class
³reference, peruse at your leisure/need

Assignments

homework 2. here is homework 1. please turn this in either in person on Wednesday, 9/28 or via e-mail by midnight on Friday, 9/30.

Readings

Hersh, W. R. (2002). Medical Informatics: Improving Health Care Through Information. The Journal of the American Medical Association, 288(16):155-158. (pdf)

Tversky, A. and Kahneman, D. (1974). Judgement Under Uncertainty: Heuristics and Biases. Science, 185(4157):1124-1131. (pdf)

Owens, D. and Sox H. (2006). Biomedical Decision Making: Probabilistic Clinical Reasoning, In Biomedical Informatics (Shortliffe and Cimino), Chapter 3, pages 80-129. (pdf)

Charniak, E. (1991). Bayesian Networks Without Tears AI Magazine 12(4):50-63. (pdf, local)

Ledley, R. S. and Lusted, L. B. (1959). Reasoning Foundations of Medical Diagnosis Science 130(3366):9-21. (pdf, local)

Gorry, G. A. (1974). Computer-assisted Clinical Decision Making Methods of Information in Medicine 12:45-51. (pdf)

Stevens, R., Goble, C. A. and Bechhofer S. (2000). Ontology-based Knowledge Representation for Bioinformatics Briefings in Bioinformatics 1(4):398-414. (pdf)

Hammond and Cimino (1974). In Biomedical Informatics (Shortliffe and Cimino), Chapter 7, pages 265-311. (pdf)

Nadkarni P. M., Ohno-Machado L. and Chapman W. W. (2011). Natural Language Processing: An Introduction. The Journal of the American Medical Informatics Association, 18:544-551. (pdf, local)

Kim J-D., Pyysalo S., Ohta T., Bossy R., Nguyen N. and Tsujii J. (2011). Overview of BioNLP Shared Task 2011. Proc. of the BioNLP Shared Task 2011 Workshop (ACL), pg. 1-6 (pdf)

Collins M. (2002). Discriminative Training Methods for Hidden Markov Models: Theory and Experiments with Perceptron Algorithms. Proc. of Empirical Methods on Natural Language Processing, pg. 1-8 (pdf)

Muller, Hans-Michael and Kenny, Eimear E., and Sternberg, Paul W. (2004). Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature. PLoS Medicine. (html)