PPT-Hidden Markov Models (HMMs)

Steven Salzberg CMSC 828H Univ of Maryland Fall 2010 2 What are HMMs used for Real time continuous speech recognition HMMs are the basis for all the leading products Eukaryotic and prokaryotic gene finding HMMs are the basis of GENSCAN Genie VEIL GlimmerHMM TwinScan etc. T state 8712X action or input 8712U uncertainty or disturbance 8712W dynamics functions XUW8594X w w are independent RVs variation state dependent input space 8712U 8838U is set of allowed actions in state at time brPage 5br Policy action is function (1). Brief . review of discrete time finite Markov . Chain. Hidden Markov . Model. Examples of HMM in Bioinformatics. Estimations. Basic Local Alignment Search Tool (BLAST). The strategy. Important parameters. Van Gael, et al. ICML 2008. Presented by Daniel Johnson. Introduction. Infinite Hidden Markov Model (. iHMM. ) is . n. onparametric approach to the HMM. New inference algorithm for . iHMM. Comparison with Gibbs sampling algorithm. 1. 2. K. …. 1. 2. K. …. 1. 2. K. …. …. …. …. 1. 2. K. …. x. 1. x. 2. x. 3. x. K. 2. 1. K. 2. Example: The Dishonest Casino. A casino has two dice:. Fair die. P(1) = P(2) = P(3) = P(5) = P(6) = 1/6. First – a . Markov Model. State. . : . sunny cloudy rainy sunny ? . A Markov Model . is a chain-structured process . where . future . states . depend . only . on . the present . state, . Steven Salzberg. CMSC 828H, Univ. of Maryland . Fall 2010. 2. What are HMMs used for?. Real time continuous speech recognition (HMMs are the basis for all the leading products). Eukaryotic and prokaryotic gene finding (HMMs are the basis of GENSCAN, Genie, VEIL, GlimmerHMM, TwinScan, etc.). Using PFAM database’s profile HMMs in MATLAB Bioinformatics Toolkit. Presentation by: . Athina. . Ropodi. University of Athens- Information Technology in Medicine and Biology . outline. Introduction. February 10, 2010. Hidden Markov models in Computational Biology. Overview. First part:. Mathematical context: Bayesian Networks. Markov models. Hidden Markov models. Second part:. Worked example: the occasionally crooked casino. notes for. CSCI-GA.2590. Prof. Grishman. Markov Model . In principle each decision could depend on all the decisions which came before (the tags on all preceding words in the sentence). But we’ll make life simple by assuming that the decision depends on only the immediately preceding decision. Sushmita Roy. sroy@biostat.wisc.edu. Computational Network Biology. Biostatistics & Medical Informatics 826. Computer Sciences 838. https://compnetbiocourse.discovery.wisc.edu. Oct 25. th. 2016. Mark Stamp. 1. HMM. Hidden Markov Models. What is a hidden Markov model (HMM)?. A machine learning technique. A discrete hill climb technique. Where are . HMMs. used?. Speech recognition. Malware detection, IDS, etc., etc.. Jurafsky. Outline. Markov Chains. Hidden Markov Models. Three Algorithms for HMMs. The Forward Algorithm. The . Viterbi. Algorithm. The Baum-Welch (EM Algorithm). Applications:. The Ice Cream Task. Part of Speech Tagging. Kevin C. Chen. Rutgers University. joint work with . Jimin. Song (Rutgers/. Palentir. ), . Kamalika. Chaudhuri and . Chicheng. Zhang (UCSD). Human Genome-wide Association Studies. ~12,000 human disease SNPs known . Hidden Markov Models. Hidden Markov Models for Time Series. Walter Zucchini. An Introduction to Statistical Modeling. o. f Extreme Values. Stuart Coles. Coles (2001), Zucchini (2016). Nonstationary GEV models.