Machine Learning for Bioinformatics (COMP-766-02)

Winter Session, 2004

Taught by: Theodore J. Perkins
Office: McGill Centre for Bioinformatics (Click "Contact" and "MCB Directions" for info on how to find the centre.)
Email: perkins@mcb.mcgill.ca
Phone: 398-7071 x 09317

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

(The schedule will grow more definite as we proceed.)

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