CISC 841 Bioinformatics (Fall 2007) Hybrid models

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Presentation transcript:

CISC 841 Bioinformatics (Fall 2007) Hybrid models Hidden Markov Support Vector Machines CISC841, F07, Liao

Label sequence learning Example: x is a transmembrane protein sequence, and y is the label sequence marking out where are the TMs, the inside and outside loops. CISC841, F07, Liao

Joint input/output space representation (x, y): Given a kernel: A dual form classifier can be built: F(x,y) = CISC841, F07, Liao

Joint label/observation features: Inter-label dependencies: At position t:  (x, y; t) For sequence/label pair (x, y): CISC841, F07, Liao

CISC841, F07, Liao

Viterbi decoding: find the most likely label sequence If then no change, else, CISC841, F07, Liao

CISC841, F07, Liao

CISC841, F07, Liao

CISC841, F07, Liao