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

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 |