Course 4190.515: Bioinformatics (Machine Learning)
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School of Computer
Science and Engineering, Seoul National University
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Instructor |
- Prof. Byoung-Tak Zhang
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TA: |
- Jeong-Ho Chang, jhchang@scai.snu.ac.kr, Tel.: 880-1847, Room 301-419
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Classroom |
- 301-101
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Time |
Monday and Wednesday, 16:00-17:15
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- Textbook
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Bioinformatics: The Machine Learning
Approach, P. Baldi and S. Brunak,
A Bradford Book, The MIT Press,
1998
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- Requirements
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Two exams: 40 %, two projects: 40%, homeworks: 15%, class participation: 5%
Project 1: Gene finding with neural networks
Project 2: Protein modeling with hidden Markov models
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- Objectives
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- Understanding the current issues in bioinformatics
- Understanding the principles of important machine learning algorithms
- Understanding how to apply machine learning to biological data mining
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May 21, 2001 |
Deadline
for the draft term paper (NN only) |
June 4, 2001 |
Final
Exam |
June 18, 2001 |
Project
presentations |
June 25, 2001 |
Deadline
for the final term paper (NN + HMM) |
Week |
Topics |
Week 1 |
Introduction to Molecular Biology
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Week 2 |
Genomics, Proteomics, and Bioinformatics
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Week 3 |
Neural Networks: Theory(1)  Theory(2)
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Week 4 |
Neural Networks: Applications Assignment of Project 1
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Week 5 |
Probabilistic Framework, Bayesian Inference, Information Theory, Occam's Razor
Probabilistic Modeling and Inference |
Week 6 |
Introduction to Graphical Models and Bayesian Networks
(Nilsson - chapter 20, Mitchell - chapter 6)
- Reference - Artificial Intelligence: A New Synthesis, Nils J. Nilsson, Morgan Kaufmann, 1998.
Machine Learning, Tom Mitchell, McGraw-Hill, 1997.
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Week 7 |
Expectation-Maximization (EM) and Variants (Updated in 5.1)
Report Number 1 (in place of Mid Exam)
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Week 8 |
Hidden Markov Models (HMMs): Theory(1)  Theory(2)
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Week 9 |
Hidden Markov Models: Applications
Assignment of Project 2
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Week 10 |
Markov Chain Monte Carlo (MCMC), Gibbs Sampling, Metropolis Algorithms, Simulated Annealing
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Week 11 |
Evolutionary Computation, Importance Sampling, Active Learning, Constructive Learning
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Week 12 |
Latent Variable Models
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Week 13 |
Helmholts Machines
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Week 14 |
Final Exam
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Week 15 |
Project Presentations
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Week 16 |
Project Presentations
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Back to [SCAI Lab] [BTZhang's Home Page] [School of CSE]
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