12 Hidden Markov Model

12 Hidden Markov Model - 1 Introduction to Bioinformatics/...

Info iconThis preview shows pages 1–8. Sign up to view the full content.

View Full Document Right Arrow Icon
1 Introduction to Bioinformatics/ Elements of Bioinformatics Hidden Markov Model
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
2 References Mount D.W. (2004) Bioinformatics: Sequence and Genome Analysis. 2 nd ed. Cold Spring Harbor Lab. Press, N.Y. Chapter 5. • Eddy SR (2004) What is a hidden Markov model? Nature Biotechnology 22: 1315-1316. • Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
Background image of page 2
3 Markov chain • To model the dynamic change of a random variable over time • System is in any one of a finite set of states at a given time but may switch from a state to another with a certain probability • The probability of a state depends only on the preceding state.
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
4 • Examples of Markov chain: – Traffic light: – Weather: Markov chain red red / amber green amber Weather today Sunny Rainy Cloudy Weather Sunny 0.5 0.15 0.35 yesterday Rainy 0.1 0.2 0.7 Cloudy 0.4 0.4 0.2 Observation sequence: Sunny cloudy sunny rainy cloudy sunny …
Background image of page 4
5 Hidden Markov model: The urn and ball urn1 urn2 urn3 a 11 a 22 a 33 a 12 a 23 a 21 a 32 a 31 a 13 11 12 13 14 () P b P b P Y G R b P b B = = = = 21 22 23 24 P b P b P Y G R b P b B = = = = 31 32 33 34 P b P b P Y G R b P b B = = = = Observation sequence: State (urn) sequence is hidden.
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
6 Hidden Markov model (HMM) • Set of states • Each state generates an observation (emission probabilities) • State sequence follows a Markov chain (state transition probabilities) • Initial state probabilities • Try to infer the hidden state sequence from the observation sequence
Background image of page 6
7 Algorithms associated with HMMs
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 8
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 07/29/2010 for the course BIOC BIOC1805 taught by Professor Dr.brianwong during the Summer '09 term at HKU.

Page1 / 20

12 Hidden Markov Model - 1 Introduction to Bioinformatics/...

This preview shows document pages 1 - 8. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online