Date  
Topic 
Assignment 
Dec 1  (a) 
Introduction to biological and
linguistic sequences and strings; overview of main problems; course overview 
HW1.1 (due Dec.8) 
(b) 
Introduction to approximate matching;
edit distance, dynamic programming, local alignment 
Dec 2  (a) 
Chomsky hierarchy; weighted finitestate automata and transducers;
ngram language modeling 
HW 1.2 (due Dec.8) 
(b) 
Hidden Markov models; POStagging; Viterbi algorithm 
Dec 3  (a) 
Supervised and unsupervised sequence learning; Expectation
Maximization (EM) with forwardbackward algorithm; discriminative learning 

(b) 
Gene prediction 
Dec 4  (a) 
Protein and RNA secondary structure; Introduction to contextfree grammars 

(b) 
Contextfree parsing; Chomsky Normal Form; CYK parsing; Earley's
algorithm; Parser evaluation 
Dec 5  (a) 
"Mildly" contextsensitive grammars for pseudoknots and
crossserial dependencies (Will tentatively cover Dec.11) 

(b) 
Machine translation alignment; HMM alignment models; Transduction
grammars (Will tentatively cover Dec.18) 
Dec 8  (a) 
Deterministic exact string matching; a simple linear algorithm for
exact match 
HW 2.1 (due Dec.15) 
(b) 
KnuthMorrisPratt and BoyerMoore algorithms for exact match 
Dec 9  (a) 
AhoCorasick algorithm for sets of patterns; regular expression patterns 
HW 2.2 (due Dec.15) 
(b) 
Efficient approximate match: linear space, bounded approximate
matching and exclusion methods 
Dec 10  (a) 
Suffix trees 

(b) 
Suffix automata; suffix arrays; LempelZiv compression; Lowest
common ancestor retrieval 
Dec 11  (a) 
"Mildly" contextsensitive grammars for pseudoknots and
crossserial dependencies (Originally scheduled Dec.5) 

(b) 
High(er) accuracy contextfree parsing; Dependency grammars and parsing; efficient inference for
projective grammars; minimum spanning trees for nonprojective
dependency parsing 
Dec 12  (a) 
Topics in Contextfree parsing I: grammar induction and inference (Will tentatively cover Dec.17)
 
(b) 
Topics in Contextfree parsing II: finitestate approximations to contextfree grammars; pipelined systems; fast contextfree parsing with finitestate preprocessing 
Dec 15  (a) 
Introduction to multiple sequence alignments; families; profile
HMMs; Perceptron algorithm for learning profile models 
HW 3 (due Dec.19) 
(b) 
Aligning multiple sequences; minimum sumofpairs alignment;
higher dimensional dynamic programming; iterative pairwise alignment 
Dec 16  (a) 
Introduction to phylogenic tree building; ultrametric and additive
distance trees; distancebased tree construction; parsimony 

(b) 
Probabilistic models of phylogeny 
Dec 17  
Full course review; Topics in contextfree processing (Originally scheduled Dec.12) 


Dec 18  
Machine translation alignment; HMM alignment models; Transduction
grammars (Originally scheduled Dec.5) 


Dec 19  
Final exam 

