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

2. 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

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

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

5. CISC841, F07, Liao

6. Viterbi decoding: find the most likely label sequenceIf
then no change,
else,
CISC841, F07, Liao

7. CISC841, F07, Liao

8. CISC841, F07, Liao

9. CISC841, F07, Liao