6.872/HST.950 Medical Computing
Spring 2004

Medical science and practice in the age of automation and the genome: Present and Future

Class Meetings: Tuesdays and Thursdays, 11:00am-12:30pm, E25-111.
Note:  When the Stata Center opens (now scheduled for March 28), we plan to move to one of the new high-tech classrooms in Stata.  More news as it develops...


Peter Szolovits, PhD (psz@mit.edu)   MIT CSAIL Clinical Decision Making Group
Isaac Kohane, MD, PhD (isaac_kohane@harvard.edu)   Children's Hospital Informatics Program
Lucila Ohno-Machado, MD, PhD (machado@dsg.bwh.harvard.edu)   BWH Decision Systems Group

Teaching Assistant:

Delin Shen, (dshen@mit.edu)   (617) 253-3539

Class Secretary:

Fern DeOliveira, (fernd@mit.edu)   (617) 253-5860


Shortliffe EH, Perreault LE, Wiederhold G and Fagan LM, Medical Informatics: Computer Applications in Health Care and Biomedicine, 2nd Edition. Springer 2001.
Sold online at: Barnes & Noble, Amazon, Quantum, etc.

Schedule (very tentative--details will be filled in any may be modified as we progress)Readings link to files on our server that are not available to everyone on the Web.  You will need to enter a user name and password given out in class.

Class Date Topic Lecturer Readings before class Assignments
1 Feb. 3 Introduction: Nature of Modern Medicine and Medical Practice Peter Szolovits Read Chapters 1 & 2 of Shortliffe.  
2 Feb. 5 Nature of Medical Data Peter Szolovits Read Chapters 9 & 10 of Shortliffe HW1 assigned
3 Feb. 10 Genomics in Medicine: Centrality of Bioinformatics
(much smaller version w/ bad images)
Isaac Kohane Human Genome Project, Human Variation, Microarrays and Functional Genomics, Classification  
4 Feb. 12 Bioinformatics and its relation to Medicine? Atul Butte Using bioinformatics in gene and drug discovery, Gene Ontology, Use and Analysis of Microarray Data  
  Feb. 17 NO CLASS--Monday schedule of classes because of Presidents' Day Look over Shortliffe 4 and 5. CS people should find nothing new here, but familiar concepts applied to medicine.
5 Feb. 19 Population Genetics, SNPs and Haplotypes Marco Ramoni Array of Hope, Complex Traits, SNPs and the Human Genome, Minimal Haplotype Tagging HW1 due
6 Feb. 24 Microarray Analysis Isaac Kohane Self-organizing Maps, Gene-expression Monitoring, Relevance Networks, DNA Microarrays, B-cell Lymphoma  
7 Feb. 26 Extracting Causality from Experimental Data Isaac Kohane Gene Expression Dynamics, Gene-coexpression Network  
8 Mar. 2 Computing Support for the Enterprise John Glaser   HW2 assigned
9 Mar. 4 Clinical Descriptions, Terminologies, Ontologies, Coding and Diagnosis Peter Szolovits Chapters 6 and 3 of Shortliffe.  
10 Mar. 9 Patient data confidentiality and security Peter Szolovits Chapter 7 of Shortliffe and Privacy Confidentiality and EMR. Optional For the Record. See also the HIPAA Privacy Rule.  
11 Mar. 11 Clinical Systems: What Works and What We Wish Worked Barry Blumenfeld   HW2 due
12 Mar. 16 Enterprise Computing and Patient Identification Peter Szolovits Record Linkage Theory (later parts optional); Lisp code to compute SOUNDEX.  
13 Mar. 18 Genomic Databases Alberto Riva    
  Mar. 23 & 25 NO CLASSES--MIT Spring Break  


Mar. 30 Surveillance for Detection of Emerging Diseases or Bioterrorist Attacks Ken Mandl Shortliffe Chapter 11  
15 Apr. 1 Decision Support: Expert Systems Peter Szolovits Shortliffe Chapters 3 (if you didn't read it before) & 16 HW3 assigned
16 Apr. 6 Decision Support: Bayesian Peter Szolovits TBD  
17 Apr. 8 Patient Monitoring Peter Szolovits Shortliffe Chapters 12 & 13 HW3 due
18 Apr. 13 Telemedicine Hamish Fraser Chapter 14 of Shortliffe  
19 Apr. 15 Gene Regulation and Computation Voichita Marinescu   Sign up final presentation
  Apr. 20 NO CLASS--Patriots Day Vacation
20 Apr. 22 Clinical Decision Support Systems Octo Barnett    
21 Apr. 27 National Infrastructure for Data Sharing Isaac Kohane    
22 Apr. 29 Just-in-Time Clinical Information Octo Barnett   HW4 assigned
23 May 4 Student Presentations

24 May 6 Student Presentations

25 May 11 Student Presentations  
26 May 13 Student Presentations

HW3 and Project write-ups due

For those interested in last year's class material, you may follow this link.


We plan to give a handful of modest homework assignments to complement and reinforce material taught in the class.  Links to the assignments (and, eventually, solutions) will appear in the schedule above.  You must do the homework problems on your own.  You may ask for help and advice from classmates, but the final work that you turn in and all the words used to describe it must be your own. For late homeworks, each late day will cause the grade to step down one level. Homeworks late for more than 3 days won't be accepted.


The last four class sessions will be an opportunity for students to present the results of significant research projects done for the class.  We encourage you to team up (in teams of two or three students) to work on projects, and teams that span students with different interests, skills and approaches are encouraged.  Some reasonable illustrative project topics are listed here.  In addition, here is a list of project titles done in the past few years.

The presentation shall be no longer than 8, 12, or 15 minutes, for groups of 1, 2, or 3 students, respectively. The time constraints will be strictly applied, so please plan your presentation accordingly. The final paper shall be kept within 10 pages. Generally you can have an introduction to the problem you are attacking, a brief review of current state-of-the-art technologies, your methods, results, and some discussion. If you present in the first week, you don't have to have final result in the presentation but please give more details in the paper.

Fundamentals -- Links and Readings:

Conceptual Modeling & UML

Structured Query Language (SQL) and Relational Algebra

Record Linkage Theory (optional)