Stanford University CS270 / BIOMEDIN210 : Fundamental Methods - Syllabus Fall 2002

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	Syllabus	Text Document	25 Sep 2002
	Stanford Honor Code	HTML Document	30 Sep 2002

BMI 210 / CS 270 Introduction to Biomedical Informatics: Fundamental Methods Fall Quarter, 2002-2003 1 Thursday, 9/26/02 Introduction to the Course Professor Mark Musen Musen MA. “Modeling for Decision Support”, In: Bemmel van JH, Musen MA (eds.), Handbook of Medical Informatics, Springer-Verlag, Heidelberg, Germany, pp. 431-448, 1997. 2 Tuesday, 10/01/02 A Case Study: Internist-1/QMR Dr. Mor Peleg Miller RA, Pople HE, Myers JD. Internist-1, an experimental computer-based diagnostic consultant for general internal medicine. New England Journal of Medicine, 307:190-209, 1982. Pople HE. Heuristic Methods for Imposing Structure on Ill-Structured Problems: The Structuring of Medical Diagnostics, In: Artificial Intelligence in Medicine, ed. Peter Szolovits, AAAS Select Symposium 51, Westview Press, Boulder, Colorado, 1982. <a href=“http://medg.lcs.mit.edu/ftp/psz/AIM82/ch5.ht ml”>Article</a> Barnett GO, Cimino JJ, Hupp JA, Hoffer EP. DXplain. An evolving diagnostic decision-support system. JAMA, 3;258(1):67-74, 1987. 3 Thursday, 10/03/02 Controlled Terminologies Dr. Mor Peleg Cimino JJ. Desiderata for controlled medical vocabularies in the twenty-first century. Methods of Information in Medicine, 37(4-5):394-403, 1998. Lindberg DA, Humphreys BL, McCray AT. The Unified Medical Language System. Methods of Information in Medicine, 32(4):281-291, 1993. 4 Tuesday, 10/08/02 Frame-Based Representations Professor Mark Musen Noy NF, Musen MA, Mejino JL, Rosse C. (2002). Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy. Technical Report, Stanford Medical Informatics, Stanford University, 2002. <a href=“http://www.smi.stanford.edu/pubs/SMI_Reports /SMI-2002-0925.pdf”>Article</a> R. Davis, H. Shrobe, and P. Szolovits. What is a knowledge representation? AI Magazine, 14(1):17-33, 1993. <a href=“http://medg.lcs.mit.edu/ftp/psz/k- rep.html”>Article</a> 5 Thursday, 10/10/02 Description Logic Professor Mark Musen D. Nardi, R. J. Brachman. An introduction to description logics. In: The Description Logic Handbook, edited by F. Baader, D. Calvanese, D.L. McGuinness, D. Nardi, P.F. Patel- Schneider, Cambridge University Press, in press, pp. 5-20. Haimowitz IJ, Patil RS, and Szolovits P. Representing medical knowledge in a terminological language is difficult. In: Proceedings of the Symposium on Computer Applications in Medical Care, IEEE Computer Society Press, pp. 101–105, 1988. <a href=“http://medg.lcs.mit.edu/people/psz/Haimowitz _NIKL.html”>Article</a> 6 Tuesday, 10/15/02 Building Ontologies Professor Mark Musen Noy NF and McGuinness DL. Ontology development 101: A guide to creating your first ontology. Technical Report, Stanford Medical Informatics, Stanford University, 2001. <a href=“http://protege.stanford.edu/publications/ont ology_development/ontology101.pdf”>Article</a> Chandrasekaran B, Josephson JR, Benjamins VR. What are ontologies, and why do we need them? IEEE Intelligent Systems, 14(1):20–26, 1999. 7 Thursday, 10/17/02 Ontologies in Clinical Informatics Professor Mark Musen Rector AL, Glowinski AJ, Nowlan WA, Rossi-Mori A. Medical-concept models and medical records: An approach based on GALEN and PEN&PAD. Journal of the American Medical Informatics Association, 2 (1):19–35, 1995. <a href=“http://www.jamia.org/cgi/reprint/2/1/19.pdf” >Article</a> G. Schadow, D.C. Russler, C.N. Mead, and C.J. McDonald, “Integrating Medical Information And Knowledge in the HL7 RIM,” In: Proceedings of the AMIA Annual Symposium 2000, pp. 764-8. 8 Tuesday, 10/22/02 Ontologies in Bioinformatics Dr. Mor Peleg Baker PG, Goble CA, Bechhofer S, Paton NW, Stevens R, Brass A An ontology for bioinformatics applications. Bioinformatics, 15 (6):510-20, 1999. <a href=“http://bioinformatics.oupjournals.org/cgi/re print/15/6/510.pdf”>Article</a> Karp PD. An ontology for biological function based on molecular interactions. Bioinformatics, 16(3):269-85, 2000. <a href=“http://bioinformatics.oupjournals.org/cgi/re print/16/3/269.pdf”>Article</a> Stevens R, Goble CA, Bechhofer S. Ontology-based knowledge representation for bioinformatics. Brief Bioinformatics, 1(4):398- 414. Review, 2000. <a href=“http://www.iet.com/Projects/RKF/SME/ontology -based-knowledge-representation.pdf”>Article</a> The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics, 25 (1):25-29, 2000. <a href=“http://www.nature.com/cgi- taf/DynaPage.taf? file=/ng/journal/v25/n1/full/ng0500_25.html”>Artic le</a>&filetype=pdf 9 Thursday, 10/24/02 Rule-Based Systems I Professor Mark Musen Davis R, Buchanan BG, Shortliffe EH. Production rules as a representation for a knowledge based consultation program. Artificial Intelligence, 8:15–45, 1977. George Hripcsak, Paul D. Clayton, T. Allan Pryor, Peter Haug, Ove B. Wigertz, Johan van der Lei. The Arden Syntax for Medical Logic Modules. In: Proceedings of the Fourteenth Annual Symposium on Computer Applications in Medical Care; Washington, D.C. New York: IEEE Computer Society Press, pp. 200-204, November 4-7, 1990. 10 Tuesday, 10/29/02 Rule-Based Systems II Professor Mark Musen Compton P, Edwards G, Kang B, Lazarus L, Malor R, Menzies T, Preston P, Srinivasan A, Summut S. Ripple down rules: possibilities and limitations. In Boose JH, Gaines BR (eds.), Proceedings of the 6th Banff Knowledge Acquisition for Knowledge-based SystemsWorkshop, pp. 6-1–6-18, Banff, Alberta, Canada: AAAI, October 6-11, 1991. Clancey WJ. The epistemology of a rule-based expert system — a framework for explanation. Artificial Intelligence, 20: 215– 251, 1983. Clancey WJ. “Mycin’s Map”, In: Situated Cognition, On Human Knowledge and Computer Representations. Cambridge University Press, pp. 29-45, 1997. 11 Thursday, 10/31/02 Problem-Solving Methods Professor Mark Musen Chandrasekaran B, Johnson TR, Smith JW. Task- structure analysis for knowledge modelling. Comminications of the ACM, 35(9), pp. 124-137, 1992. McDermott J. Preliminary steps toward a taxonomy of problem-solving methods. In Marcus S, (ed.), Automating Knowledge Acquisition for Expert Systems, Kluwer Academic, Boston, pp. 225-256, 1988. 12 Tuesday, 11/05/02 Building Systems with Ontologies and PSMs Professor Mark Musen Musen MA. Ontology-oriented design and programming. In J. Cuena et al., (eds.), Knowledge Engineering and Agent Technology. IOS Press, Amsterdam, in press. <a href=“http://www- smi.stanford.edu/pubs/SMI_Reports/SMI-2000- 0833.pdf”>Article</a> Musen MA. Domain ontologies in software engineering: use of Protégé with the EON architecture. Methods of Information in Medicine 37:540-550, 1998. <a href=“http://www- smi.stanford.edu/pubs/SMI_Reports/SMI-97- 0657.pdf”>Article</a> 13 Thursday, 11/07/02 Cognitive Biases and Decision Making Professor Mark Musen Tversky A, Kahneman, D. Judgment under uncertainty: Heuristics and biases. Sience, 185:1124-1131, 1974. Johnson PE. What kind of expert should a system be? The Journal of Medicine and Philosophy 8:77-97, 1983. 14 Tuesday, 11/12/02 Midterm 15 Thursday, 11/14/02 Knowledge Acquisition Professor Mark Musen Schreiber AT, Wielinga B, Akkermans JM, van de Velde W, de Hoog R. CommonKADS: A comprehensive methodology for KBS development. IEEE Expert; 9 (6): 28-37, 1994. Berg M. Formal tools and medical practices: Getting computer-based decision techniques to work, in Bowker GC, Star SL, Turner W, Gasser L (eds.), Social Science, Technical Systems, and Cooperative Work, Beyond the Great Divide, Lawrence Erlbaum Associates, Hillsdale, N.J., Chapter 13, pp. 301-330, 1977. Gaines BR, and Shaw, MLG. Knowledge acquisition tools based on personal construct psychology. Knowledge Engineering Review 8:49–85, 1993. 16 Tuesday, 11/19/02 Ontology Management Dr. Natasha Noy Noy NF and Musen MA. PROMPT: Algorithm and tool for automated ontology merging and alignment. In: Proceedings of the Seventeenth National Conference on Artificial Intelligence (AAAI-2000), pp. 600-605, Austin, TX. <a href=“http://www- smi.stanford.edu/pubs/SMI_Reports/SMI-2000- 0831.pdf”>Article</a> Klein M. Combining and relating ontologies: an analysis of problems and solutions. In: Proceedings of the Workshop on Ontologies and Information Sharing, IJCAI'01, Seattle, USA, August 4-5, 2001. <a href=“http://www.cs.vu.nl/~mcaklein/papers/IJCAI01 -ws.pdf”>Article</a> 17 Thursday, 11/21/02 Methods for Simulation Dr. Mor Peleg Reddy VN, Liebman MN, Mavrovouniotis ML. Qualitative analysis of biochemical reaction systems. Computational Biology Medicine, 26(1):9-24, January 1996. Kuffner R, Zimmer R, Lengauer T. Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics, 16(9):825-36, September 2000. <a href=“http://bioinformatics.oupjournals.org/cgi/re print/16/9/825.pdf”>Article</a> Peleg M, Yeh I, Altman RB. Modelling biological processes using workflow and Petri net models. Bioinformatics,18(6):825-37, 2002. <a href=“http://bioinformatics.oupjournals.org/cgi/re print/18/6/825.pdf”>Article</a> 18 Tuesday, 11/26/02 Diagnostic Problem Solving I Professor Mark Musen Berner ES, Webster GD, Shugerman AA, Jackson JR, Algina J, Baker AL, Ball EV, Cobbs CG, Dennis VW, Frenkel EP, et al. Performance of four computer-based diagnostic systems. New England Journal of Medicine, 23;330(25):1792-6, June 1994. <a href=“http://content.nejm.org/cgi/content/full/330 /25/1792 Horrocks JC, McCann AP, Staniland JR, Leaper DJ, de Dombal FT. Computer-aided diagnosis: description of an adaptable system, and operational experience with 2,034 cases. British Medical Journal, 1;2(5804):5-9, April 1, 1972. McAdam WAF, Brock BM, Armitage T, Davenport P, de Dombal FT. Twelve years experience of computer-aided diagnosis in a District General Hospital. Annals of the Royal College of Surgeons of England, 72:140-6, 1990. 19 Thursday, 11/28/02 Thanksgiving 20 Tuesday, 12/03/02 Diagnostic Problem Solving II Professor Mark Musen Szolovits P and Pauker SG. Categorical and probabilistic reasoning in medical diagnosis. Artificial Intelligence, 11:115-144 (1978). ftp://medg.lcs.mit.edu/pub/psz/Szolovits- Pauker78.pdf”>Article</a> Szolovits P and Pauker SG. Categorical and Probabilistic Reasoning in Medicine Revisited. Artificial Intelligence 59:167-180, 1993. <a href=“http://medg.lcs.mit.edu/ftp/psz/Szolovits- Pauker93(Bobrow3).html”>Article</a> Patil RS, Szolovits P, Schwartz WB. Causal understanding of patient illness in medical diagnosis. In: Proceedings of the Seventh International Joint Conference on Artificial Intelligence, 2: 893-899. Vancouver, BC: AAAI, August 24–28, 1981. Shwe MA, Middleton B, Heckerman DE, Henrion M, Horvitz EJ, Lehmann HP, Cooper GF. Probabilistic Diagnosis Using a Reformulation of the INTERNIST- 1/QMR Knowledge Base I. The Probabilistic Model and Inference Algorithms. Methods of Information in Medicine, 30(4):241-255, 1991. Charniak E. Bayesian networks without tears. AI Magazine, 12(4):50-63, 1991. <a href=“http://www- psych.stanford.edu/~jbt/224/Charniak_91.pdf”>Artic le</a> 21 Thursday, 12/05/02 Therapeutic Problem Solving Professor Mark Musen Swartout WR. Explaining and justifying expert consulting programs. In: Proceedings of the Seventh International Joint Conference on Artificial Intelligence, 2:815–823. Vancouver, BC: AAAI, August 24–28, 1981. Van der Lei J, Musen MA. A model for critiquing based on automated medical records. Computers and Biomedical Research, 24:344–378, 1991. Coda Musen MA. Medical informatics: Searching for underlying components. Methods of Information in Medicine, 1:12-19, 2002. <a href=“http://www.smi.stanford.edu/pubs/SMI_Reports /SMI-2002-0916.pdf”>Article</a>