AI Qualifying Exam Reading List Associated with CS 776 - ADVANCED BIOINFORMATICS

For Fall 2009 and Later Exams

Topics

  1. Unsupervised Learning and Clustering: Expectation maximization (EM) methods, k-means clustering, hierarchical clustering, graph-based clustering.
    [DUDA00 (Chapter 10); MANN99 (Chapter 14)]
  2. Markov Chain Models: High-order Markov chains, inhomogeneous Markov chains.
    [DURB98, (Chapter 3)]
  3. Hidden Markov Models: Viterbi, Forward and Backward algorithms, Baum-Welch parameter estimation.
    [DURB98, (Chapters 3 and 5)]
  4. Pair Hidden Markov Models: Viterbi and Forward algorithms for pair HMMs, calculating alignments with pair HMMs, posterior probabilities and alignments.
    [DURB98, (Chapter 4)]
  5. Stochastic Context-Free Grammars: Chomsky hierarchy of transformational grammars, stochastic grammars, the Inside, Outside and CYK algorithms, Inside-Outside parameter estimation
    [DURB98, (Chapter 9)]

References

[DUDA00]
Duda, R., Hart, P. and Stork, D., Pattern Classification, 2nd Edition, John Wiley and Sons, 2000.

[DURB98]
Durbin, R., Eddy, S., Krogh, A. and Mitchison, G., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1998.

[MANN99]
Manning, C. and Schutze, H., Foundations of Statistical Natural Language Processing MIT Press, 1998.