Hidden Markov Models

Hidden Markov Models. Nucleotide frequencies in the human genome. CpG Islands. Written CpG to distinguish from a C ≡ G base pair). CpG dinucleotides are rarer than would be expected from the independent probabilities of C and G .

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Hidden Markov Models

Hidden Markov Models. Ankur Jain Y7073. What is Covered. Observable Markov Model Hidden Markov Model Evaluation problem Decoding Problem. Markov Models. Set of states: Process moves from one state to another generating a sequence of states :

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Markov Models and HMM in Genome Analysis

Journée Statistique et Santé Paris 5 – 5 mai 2006. Markov Models and HMM in Genome Analysis. Bernard PRUM. La genopole – Evry – France prum@genopole.cnrs.fr. Why Markov Models ?. A biological sequence : X = (X 1 , X 2 , … , X n ) where X k   A = { t , c , a , g }

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INTRODUCTION TO HIDDEN MARKOV MODELS HMM

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Hidden Markov Models

Hidden Markov Models. Outline. CG-islands The “Fair Bet Casino” Hidden Markov Model Decoding Algorithm Forward-Backward Algorithm Profile HMMs HMM Parameter Estimation Viterbi training Baum-Welch algorithm. CG -Islands.

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Hidden Markov Models

Hidden Markov Models. Adapted from Dr Catherine Sweeney-Reed’s slides. Summary. Introduction Description Central problems in HMM modelling Extensions Demonstration. Specification of an HMM. Description. N - number of states Q = {q 1 ; q 2 ; : : : ;q T } - set of states

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Hidden Markov Models

Hidden Markov Models. First Story!. Majid Hajiloo, Aria Khademi. Outline. This lecture is devoted to the problem of inference in probabilistic graphical models (aka Bayesian nets). The goal is for you to : Practice marginalization and conditioning Practice Bayes rule

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Hidden Markov Model (HMM) - Tutorial

Hidden Markov Model (HMM) - Tutorial. Credit: Prof. B.K.Shin ( Pukyung Nat’l Univ ) and Prof. Wilensky (UCB). Sequential Data. Often highly variable, but has an embedded structure Information is contained in the structure. More examples.

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Hidden Markov Models

Hidden Markov Models. Outline. CG -Islands The “Fair Bet Casino” Hidden Markov Model Decoding Algorithm Forward-Backward Algorithm Profile HMMs HMM Parameter Estimation Viterbi Training Baum-Welch Algorithm. Section 1: CG -Islands. CG -Islands.

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Hidden Markov Model (HMM) Tagging

Hidden Markov Model (HMM) Tagging. Using an HMM to do POS tagging HMM is a special case of Bayesian inference. Hidden Markov Model (HMM) Taggers. Goal: maximize P(word|tag) x P(tag|previous n tags) P(word|tag) word/lexical likelihood probability that given this tag, we have this word

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Hidden Markov Models

Hidden Markov Models. By Manish Shrivastava. A Simple Process. b. S1. b. a. S2. a. A simple automata. A Slightly Complicated Process. A colored ball choosing example :. Urn 1 # of Red = 100 # of Green = 0 # of Blue = 0. Urn 3 # of Red = 0 # of Green = 0 # of Blue = 100.

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Hidden Markov Models

Hidden Markov Models. Chris Brew. The Ohio State University. Introduction. Dynamic Programming Markov models as effective tools for language modelling How to solve three classic problems Calculate the probability of a corpus given a model Guess the sequence of states passed through

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Hidden Markov Models

Hidden Markov Models. Ellen Walker Bioinformatics Hiram College, 2008. State Machine to Recognize “AUG”. Final state. transition. Start state. Each character causes a transition to the next state. “AUG” anywhere in a string. “AUG” in frame. Deterministic Finite Automaton (DFA). States

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Sequence information, logos and Hidden Markov Models

Sequence information, logos and Hidden Markov Models. Morten Nielsen, CBS, BioCentrum, DTU. Information content. Information and entropy Conserved amino acid regions contain high degree of information (high order == low entropy)

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Hidden Markov Models

Hidden Markov Models. So far: considered systems for making a single decision (e.g. discriminant functions or estimation of class-conditional densities.) Now we consider: the problem of sequential decision making Example : Automatic Speech Recognition (ASR).

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Sequence classification & hidden Markov models

Bioinformatics, Models & algorithms, 8 th November 2005 Patrik Johansson, Dept. of Cell & Molecular Biology, Uppsala University. Sequence classification & hidden Markov models. A family of proteins share a similar structure but not necessarily sequence.

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Hidden Markov Models

Hidden Markov Models. A first-order Hidden Markov Model is completely defined by: A set of states. An alphabet of symbols. A transition probability matrix T=(t ij ) An emission probability matrix E=(e iX ). Linear Architecture. Loop Architecture. Wheel Architecture. Basic Ideas.

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Hidden Markov Models

Hidden Markov Models. Sean Callen Joel Henningsen. Example. Discovering average yearly temperature at a particular location on Earth over a series of years using observed size of tree growth rings. Possible states (hidden) – Hot (H) and Cold (C)

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Hidden Markov Models

Hidden Markov Models. Lecture 6, Thursday April 17, 2003. Review of Last Lecture. Lecture 6, Thursday April 17, 2003. Decoding. 1. 2. 2. 1. 1. 1. 1. …. 2. 2. 2. 2. …. K. …. …. …. …. x 1. K. K. K. K. …. x 2. x 3. x K. GIVEN x = x 1 x 2 ……x N

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Markov Models and HMM in Genome Analysis

Journée Statistique et Santé Paris 5 – 5 mai 2006. Markov Models and HMM in Genome Analysis. Bernard PRUM. La genopole – Evry – France prum@genopole.cnrs.fr. Why Markov Models ?. A biological sequence : X = (X 1 , X 2 , … , X n ) where X k   A = { t , c , a , g }

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Hidden Markov Models

Hidden Markov Models. and the Forward-Backward Algorithm. Please See the Spreadsheet. I like to teach this material using an interactive spreadsheet: http://cs.jhu.edu/~jason/papers/#tnlp02 Has the spreadsheet and the lesson plan I’ll also show the following slides at appropriate points.

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Hidden Markov Models

Hidden Markov Models. CBB 231 / COMPSCI 261. What is an HMM?. An HMM is a stochastic machine M =( Q ,  , P t , P e ) consisting of the following: a finite set of states , Q ={ q 0 , q 1 , ... , q m } a finite alphabet  ={ s 0 , s 1 , ... , s n }

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