PPT-Auto-Regressive HMM Recall the hidden Markov model (HMM)

a finite state automata with nodes that represent hidden states that is things we cannot necessarily observe but must infer from data and two sets of links transition probability that this state will follow from the previous state. Dr. Lawrence Kelley. Structural Bioinformatics Group. Imperial College London. SVYDAAAQLTADVKKDLRDSW. KVIGSDKKGNGVALMTTLFAD. NQETIGYFKRLGNVSQGMAND. KLRGHSITLMYALQNFIDQLD. NPDSLDLVCS. …….. Predict the 3D structure adopted by a user-supplied protein sequence. (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. Jeremy . Bolton, . Seniha. . Yuksel. , Paul . Gader. CSI. Laboratory . University of Florida. Highlights. Hidden Markov Models (HMMs) are useful tools for landmine detection in GPR imagery. Explicitly incorporating the Multiple Instance Learning (MIL) paradigm in HMM learning is intuitive and effective. 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, . Recall the hidden Markov model (HMM). a finite state automata with nodes that represent hidden states (that is, things we cannot necessarily observe, but must infer from data) and two sets of links. transition – probability that this state will follow from the previous state. 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. in Speech Recognition. Author. ：. Mark . Gales. 1. and Steve . Young. 2. Published. ：. 21 . Feb . 2008. . . Subjects. ：. Speech/audio/image/video . compression. Outline. Introduction. Architecture of an HMM-Based . Recall the hidden Markov model (HMM). a finite state automata with nodes that represent hidden states (that is, things we cannot necessarily observe, but must infer from data) and two sets of links. transition – probability that this state will follow from the previous state. James Pustejovsky. February . 27. , . 2018. Brandeis University. Slides . thanks to David . Blei. Set of states: . Process moves from one state to another generating a sequence of states : . Hidden Markov Models Teaching Demo The University of Arizona Tatjana Scheffler tatjana.scheffler@uni-potsdam.de Warm-Up: Parts of Speech Part of Speech Tagging = Grouping words into morphosyntactic types like noun, verb, etc.: Hidden Markov Models IP notice: slides from Dan Jurafsky Outline Markov Chains Hidden Markov Models Three Algorithms for HMMs The Forward Algorithm The Viterbi Algorithm The Baum-Welch (EM Algorithm) 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. Paul Newson and John Krumm. Microsoft Research. ACM SIGSPATIAL ’09. November 6. th. , 2009. Agenda. Rules of the game. Using a Hidden Markov Model (HMM). Robustness to Noise and Sparseness. Shared Data for Comparison.