HMMs-1 - Hidden Markov Models(Part 1 BMI/CS 576...

Info icon This preview shows pages 1–4. Sign up to view the full content.

View Full Document Right Arrow Icon
Hidden Markov Models (Part 1) BMI/CS 576 www.biostat.wisc.edu/bmi576.html Mark Craven [email protected] Fall 2011 A simple HMM A T C G A T C G given say a T in our input sequence, which state emitted it?
Image of page 1

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

View Full Document Right Arrow Icon
The hidden part of the problem we’ll distinguish between the observed parts of a problem and the hidden parts in the Markov models we’ve considered previously, it is clear which state accounts for each part of the observed sequence in the model above, there are multiple states that could account for each part of the observed sequence – this is the hidden part of the problem Simple HMM for gene finding Figure from A. Krogh, An Introduction to Hidden Markov Models for Biological Sequences GCTAC AAAAA TTTTT CTACG CTACA CTACC CTACT start A T C G A T C G A T C G start
Image of page 2
The parameters of an HMM since we’ve decoupled states and characters, we might also have emission probabilities e k ( b ) = P ( x i = b | " i = k ) a kl = P ( " i = l | " i # 1 = k ) probability of emitting character b in state k probability of a transition from state k to l represents a path (sequence of states) through the model as in Markov chain models, we have transition probabilities ! A simple HMM with emission parameters 0.8 ) A ( 2 e 13 a probability of emitting character A in state 2 probability of a transition from state 1 to state 3 0.4 A 0.4 C 0.1 G 0.2 T 0.3 A 0.1 C 0.4 G 0.4 T 0.1 A 0.2 C 0.3 G 0.3 T 0.2 begin end 0.5 0.5 0.2 0.8 0.6 0.1 0.9 0.2 0 5 4 3 2 1 A 0.4 C 0.1 G 0.1 T 0.4
Image of page 3

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

View Full Document Right Arrow Icon
Image of page 4
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern