6.872/HST.950 Bio-Medical Computing
Fall 2004

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

(This class has, in the past, been taught during Spring semester. Beginning in Fall 2004, it will be taught only in the Fall semester each year.)

Class Meetings:

Tuesdays and Thursdays, 2:30-4:00pm, 32-144 (this is the "flat" classroom toward the Gates end of the Student Street in the Stata Center).
We may occasionally schedule additional class times to teach techniques relevant to homework or project assignments.


Peter Szolovits, PhD
MIT CSAIL Clinical Decision Making Group
Isaac S. Kohane, MD, PhD
Children's Hospital Informatics Program

Teaching Assistant:

Delin Shen, (dshen@mit.edu)   (617) 253-4679

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. It may also be available at the MIT Coop or other local bookstores.


The schedule below is still subject to some change. Please note that reading assignments are to have been read before the class to which they are relevant. Pointers to readings in parentheses are to optional or reference material that you may find useful but that is not required.

Some readings and assignments will 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 that will be given out in class. As soon as practical after class meetings, slides or notes from each class will be linked from the topic title.

Class Date Topic Lecturer Readings before class Assignments, notes, etc.
1 Sep. 9 Introduction: Nature of Modern Medicine and Medical Practice psz Read Chapters 1 & 2 of Shortliffe. (See references from the Institute of Medicine's "Quality Initiative".) Homework 1 handed out.
2 Sep. 14 Nature of Medical Data psz Read Chapters 9 & 10 of Shortliffe  
3 Sep. 16 Electronic Medical Records (see CCR description & readings)   Generic Data Modeling. Relational Database Theory. (If you need a refresher on Relational Databases, look at a SQL manual (for Oracle), and/or a chapter on Relational Theory.) Also see Post article.

Homework 1 due.
Homework 2 out.
(Rosh Hashana)

4 Sep. 21 Genomics in Medicine: What Can Bioinformatics Accomplish?


Human Genome Project, Human Variation, Microarrays and Functional Genomics, Classification, Shortliffe Chapter 18.  
5 Sep. 23 Fundamentals of Genes, Genomics, Proteomics, etc. Atul Butte Using bioinformatics in gene and drug discovery, Gene Ontology, Use and Analysis of Microarray Data Homework 2 due.
Homework 3 out.
6 Sep. 28 Microarray Analysis isk Self-organizing Maps, Gene-expression Monitoring, Relevance Networks, DNA Microarrays, B-cell Lymphoma  
7 Sep. 30 Population Genetics, SNPs and Haplotypes Marco Ramoni Array of Hope, Complex Traits, SNPs and the Human Genome, Minimal Haplotype Tagging Homework 3 due.
Homework 4 out.
8 Oct. 5 Building (Causal) Models from Experimental Data Marco Ramoni Gene Expression Dynamics, Gene-coexpression Network (Sukkot)
9 Oct. 7 Comparative Functional Genomics and Disease Alvin Kho Methods in Comparative Genomics, Tumorigenesis, Reduced Microarray Dimensional Space Homework 4 due.
Homework 5 out.
  Oct. 12 The Integrome: Research in the Genomic Era isk    
10 Oct. 14 Clinical Descriptions, Terminologies, Ontologies and Coding psz Chapter 6 of Shortliffe. Homework 5 due.
Homework 6 out.
11 Oct. 19 Patient data confidentiality and security psz Chapter 7 of Shortliffe and Privacy Confidentiality and EMR. Optional For the Record. See also the HIPAA Privacy Rule.  
12 Oct. 21 Enterprise Computing and Patient Identification psz Record Linkage Theory (later parts optional); Lisp code to compute SOUNDEX. Homework 6 due.
Homework 7 out.
13 Oct. 26 Decision Support: Bayesian psz Shortliffe Ch. 3, Uncertainty and Decisions in Medical Informatics  


Oct. 28 Decision Support: Expert Systems psz Shortliffe Ch. 16 Homework 7 due.
Homework 8 out.
15 Nov. 2 Surveillance for Detection of Emerging Diseases or Bioterrorist Attacks Ken Mandl Shortliffe Chapter 11  
16 Nov. 4 Connecting Patients, Providers and Payers John Halamka J.H. Congressional testimony 2004, PatientSite: Patient Centered .... See PatientSite demo. Final Project proposal due. (See old topics and ideas.)
17 Nov. 9 Telemedicine Hamish Fraser Chapter 14 of Shortliffe. Papers on Multi-Drug-Resistant TB and HIV treatment in developing countries Homework 8 due.
  Nov. 11 NO CLASS--Veterans Day Vacation
18 Nov. 16 Lifelong Personal Health Information Systems William Long Look at Guardian Angel description.  
19 Nov. 18 Patient Monitoring psz Shortliffe Chapters 12 & 13  
20 Nov. 23 The Real World: Incorporating Commercial Information Systems (Printable notes) Hoda Sayed-Friel, Medical Information Technology    
  Nov. 25 NO CLASS--Thanksgiving Vacation
21 Nov. 30 National Infrastructure for Data Sharing isk    
22 Dec. 2 Just-in-Time Clinical Information Octo Barnett    
23 Dec 7 Student Presentations

24 Dec 9 Student Presentations


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


Grades will be determined by a combination of three factors, with approximately the following contributions:

  1. Class participation (30%). Attendance and contributions to class discussions are a critical component of the class. Much of the material will be taught by guest lecturers who are uniquely knowledgeable about their fields and have the primary experience that can help inform engineering judgment. Many class meetings will also include discussions about the topic under study, for which it is essential that students be well prepared by having read the assigned material before class (and by being present).
  2. Homework assignments (30%). We plan to give a half-dozen homework assignments whose purpose is to ask students to explore some topic(s) presented in class more deeply or to learn and demonstrate specific skills related to class topics. Some of these will include programming tasks as well as thinking and writing. Homework will be announced in class and the assignments will be linked from the schedule, above. Note: With the exception of medical excuses, assignments will be penalized 50% if they are turned in up to two days late, and will receive no credit thereafter.
  3. Project(s) (40%). Students will work in groups of two or three on projects of their own choice related to the topic of the class. Grading will be based on both a written paper due at the end of the semester and oral class presentations on each project.


Homework assignments are to be completed by each student on his/her own effort. You may discuss problems and solution approaches with classmates, but you must write your own computer programs (when appropriate), calculate your own answers, and write your own text to be handed in without collaboration from other students. Staff will be happy to help out if you have serious problems with the homework, which is not our intent. Handing in any copied homework solution will earn an F for the entire semester class.

Projects, like efforts in the real world, will be collaborative and will require shared efforts with other students in the class. It will be important for everyone to contribute to the project(s) they work on. We will figure out an appropriate scheme for allocating credit for such collaborations (not on a zero-sum basis) as we define more clearly the nature of the project.

Last edited: 10/26/2004 by psz.