Machine Learning for Bioinformatics (COMP-766-02)

Winter Session, 2004

Course web page: http://www.mcb.mcgill.ca/~perkins/COMP76602/COMP76602.html
Location: Arts Building 210
Time: 10:35 am - 11:25 am, MWF

Office hours: Mon 11:45-12:45, Thu 1-2

Schedule

Lecture	Date	Topic	Handouts / Slides
1	Jan 5	Introduction	[lecture slides] [Course info in html] [Course info in ps]
Summarization / Unsupervised learning
2	Jan 7	Clustering	[lecture slides]
3	Jan 9	Clustering, Self-organizing maps	[lecture slides] Single-linkage clustering example 1 Complete-linkage clustering example 1 Group average clustering example 1 Single-linkage clustering example 2 Complete-linkage clustering example 2 Group average clustering example 2
4	Jan 12	Read and critique: Eisen, Spellman, Brown, Botstein (1998) "Cluster analysis and display of genome-wide expression patterns." PNAS Vol. 95 pp. 14863-14868.
5	Jan 14	Read and critique: Yeung, Haynor, Ruzzo (2001) "Validating clustering for gene expression data." Bioinformatics Vol. 17 No. 4 pp. 309-318
6	Jan 19	Basic statistics review, Principal components analysis	[lecture slides]
7	Jan 21	Gradient descent, Multi-dimensional scaling, Self-organizing maps	[lecture slides]
8	Jan 23	Read and critique: Landgrebe, Wurst, Welzl (2002) "Permutation-validated principal components analysis of microarray data" Genome Biology Vol. 3 No. 4
9	Jan 26	Read and critique: Grishin and Grishin (2002) "Euclidian space and grouping of biological objects" Bioinformatics Vol. 18 no. 11 pp. 1523-1533
10	Jan 28	Read and critique: Draghici and Potter (2003) "Predicting HIV drug resistance with neural networks" Bioinformatics Vol. 19 No. 1 pp. 98-107
Prediction
11	Jan 30	Prediction problems, Nearest neighbor	[lecture slides]
12	Feb 2	Nearest neighbor, Linear regression	[lecture slides]
13	Feb 4	Linear regression	[lecture slides]
14	Feb 6	Perceptrons (linear classification)	[lecture slides]
15	Feb 9	Read and critique: Huang and Li (2004) "Prediction of protein subcellular locations using fuzzy k-NN method" Bioinformatics Vol. 20 No. 1 pp. 21-28
16	Feb 11	Read and critique: Chuzhanov, Jones, Margetts (1998) "Feature selection for genetic sequence classification" Bioinformatics Vol. 14 No. 2 pp. 139-143
17	Feb 13	Read and critique: Wu, Schmidler, Hastie, Brutlag (1998) "Regression analysis of multiple protein structures" Journal of Computational Biology Vol. 5 No. 3 pp. 597-607
18	Feb 16	Logistic regression	[example logistic fit] [training to minimize sum squared error] [training to minimize cross-entropy]
19	Feb 18	Artificial neural networks	[training ANN with 2 hidden units]
20	Feb 20	Read and critique: Hatzigeorgiou (2002) "Translation initiation start prediction in human cDNAs with high accuracy" Bioinformatics Vol. 18 No. 2 pp. 343-350
spring break
21	Mar 3	Support vector machines 1	[lecture slides]
22	Mar 5	Support vector machines 2
23	Mar 8	Tree-structured predictors	[lecture slides]
24	Mar 10	Read and critique: Aliferis et al. (2002) "Machine learning models for lung cancer classification using array comparative genomic hybridization" Proc. AMIA Symposium 2002 pp. 7-11
Probabilistic Modeling
25	Mar 12	Review of probability theory 1	[lecture slides]
26	Mar 15	Review of probability theory 2
27	Mar 17	Maximum likelihood estimation of p.d.f.'s	[lecture slides]
28	Mar 22	Read and critique: Henikoff and Henikoff (1996) "Using substitution probabilities to improve position-specific scoring matrices" Computer Applications in the Biosciences Vol. 12 No. 2 pp. 135-143
29	Mar 24	Tests of statistical [in]dependence	[lecture slides]
30	Mar 26	Bayesian networks	[lecture slides]
31	Mar 29	Read and critique: Segal et a. (2002) "From Promoter Sequence to Expression: A Probabilistic Framework" RECOMB 2002
32	Mar 31	Learning Bayesian Networks 1	[lecture slides]
33	Apr 2	Learning Bayesian Networks 2