6.872/HST.950 Medical Computing
Spring 2003

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

Class Meetings: Tuesdays and Thursdays, 11:00am-12:30pm, 36-112.


Peter Szolovits, PhD (psz@mit.edu)   MIT LCS 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

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

Schedule (tentative--subject to revision as we progress):

Class Date Topic Lecturer Readings before class Assignments
1 Feb. 4 Introduction: Nature of Modern Medicine and Medical Practice (S) (H) Peter Szolovits Read Chapters 1 & 2 of Shortliffe.  
2 Feb. 6 Nature of Medical Data: Where it is and Where it is Not (S) (H) Peter Szolovits Read Chapters 9 & 10 of Shortliffe  
3 Feb. 11 Genomics in Medicine: Centrality of Bioinformatics (S) Isaac Kohane Human Genome Project, Human Variation, Microarrays and Functional Genomics, Classification  
4 Feb. 13 Patient Identification (S) (H) Peter Szolovits Record Linkage Theory (optional) HW1 out
Other HW1 resources.
  Feb. 18 NO CLASS--Monday schedule of classes because of Presidents' Day
5 Feb. 20 Countering Bioterrorism (S) Ken Mandl Chapter 11 of Shortliffe HW1 due
6 Feb. 25 Workflow, Decision Support and Data Gathering (S) Isaac Kohane  Workflow, ethnography, communication, integration HW2 out
7 Feb. 27 Computing Support for the Enterprise (PDF) (Audio) John Glaser    
8 Mar. 4 Diagnosis, standards, codification (S) Peter Szolovits Chapters 6, 12 and 14 of Shortliffe  
9 Mar. 6 Patient data confidentiality and security (S) Peter Szolovits Chapter 7 of Shortliffe and Privacy Confidentiality and EMR. Optional For the Record.  
10 Mar. 11 Decreasing Variability in Health Care(S) Lucila Ohno-Machado   HW2 due
11 Mar. 13 Computerized Physician Order Entry: Using Technology To Improve Patient Safety (H) (PDF) David Bates    
12 Mar. 18 Integration and data sharing or medical data for quality improvement John Halamka    
13 Mar. 20 Telemedicine (S) Hamish Fraser Chapter 14 of Shortliffe  
  Mar. 25 & 27 NO CLASSES--MIT Spring Break HW3 out


Apr. 1 Genomic Medicine I: Population Genetics in the Post Genomic Era (S) Marco Ramoni Array of Hope, Complex Traits, SNPs and the Human Genome Please see HW3addendum
15 Apr. 3 Genomic Medicine II:
Expression Arrays, Gene Clustering and Distance Metrics (S)
Zoltan Szallasi Support Vector Machines HW3 due.
Final Project Discussion Board
16 Apr. 8 Decision analysis and decision support Peter Szolovits Chapters 15 and 16 of Shortliffe, Uncertainty in Medicine Sign up for final presentation
17 Apr. 10 Getting to Causality in Functional Genomics Zak Kohane Iyer99, Ramoni02 Project proposals due
18 Apr. 15 Advanced Expert Systems (S) Peter Szolovits Chapters 12 and 13 of Shortliffe  
19 Apr. 17 Patient Monitoring (S) Peter Szolovits    
  Apr. 22 NO CLASS--Patriots Day Vacation
20 Apr. 24 Genomic Medicine III:
Introduction to Genomics (PDF)
Atul Butte    
21 Apr. 29 Genomic Medicine IV:
Linking Genotypes and Phenotypes (S)
Peter Park    
22 May 1 Genomic Medicine V:
Reverse Engineering (S)
Zoltan Szallasi Genetic Networks (read chapter 5, page 23)  
23 May 6 Student Presentations

24 May 8 Student Presentations

25 May 13 Student Presentations  
26 May 15 Student Presentations


Legend for links in table:


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.  Of course 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.


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.

Fundamentals -- Links and Readings:

Conceptual Modeling & UML

Structured Query Language (SQL) and Relational Algebra