'Emission probabilities' presentation slideshows

Patterns, Profiles, and Multiple Alignment

Patterns, Profiles, and Multiple Alignment. OUTLINE. Profiles and Sequence Logos Profile Hidden Markov Models Aligning Profiles Multiple Sequence Alignments by Gradual Sequence Adition Other Ways of Obtaining Multiple Alignments Sequence Pattern Discovery. OUTLINE.

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CS5263 Bioinformatics

CS5263 Bioinformatics. Lecture 12: Hidden Markov Models and applications. Project ideas. Implement an HMM including Viterbi decoding, posterior decoding and Baum-Welch learning Construct a model Generate sequences with the model Given labels, estimate parameters Given parameters, decode

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PART-OF-SPEECH TAGGING

PART-OF-SPEECH TAGGING. Topics of the next three lectures. Tagsets Rule-based tagging Brill tagger Tagging with Markov models The Viterbi algorithm. POS tagging: the problem. People/NNS continue/VBP to/TO inquire/VB the/DT reason/NN for/IN the/DT race /NN for/IN outer/JJ space/NN

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Probabilistic Sequence Alignment

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Maximal D-segments

Maximal D-segments. Maximal-scoring No subsegment has higher score No segment properly containing the segment satisfies the above No supersegment has higher score ? NOT TRUE (see next slide for example) Maximum allowed dropoff D < 0 No subsegment has score < D Score >= S Where S >= -D. D.

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2003. 12.04 Susie Jo Bio-Information System Laboratory BioSystem Dept., KAIST

Protein Family Classification Using AI Techniques (Profile-HMMs, SVM). 2003. 12.04 Susie Jo Bio-Information System Laboratory BioSystem Dept., KAIST. SOM. Intro. Table of Contents. Profile HMM. SVM-Fisher. Derive Function. Protein homology detection. CS774.

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Bioinformatics

Bioinformatics. Hidden Markov Models. Markov Random Processes. A random sequence has the Markov property if its distribution is determined solely by its current state. Any random process having this property is called a Markov random process .

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Hidden Markov Models

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Profile Hidden Markov Models

Profile Hidden Markov Models . Bioinformatics Fall-2004 Dr Webb Miller and Dr Claude Depamphilis Dhiraj Joshi Department of Computer Science and Engineering The Pennsylvania State University. Outline. Introduction to HMMs Profile HMMs

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Profile Hidden Markov Models

Profile Hidden Markov Models . Bioinformatics Fall-2004 Dr Webb Miller and Dr Claude Depamphilis Dhiraj Joshi Department of Computer Science and Engineering The Pennsylvania State University. Outline. Introduction to HMMs Profile HMMs

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Usage of profile HMMs in Bioinformatics

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Improving the Recognition of Interleaved Activities

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Phylogenetic HMMs

Phylogenetic HMMs.

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BINF6201/8201 Hidden Markov Models for Sequence Analysis 4 11-29-2011

BINF6201/8201 Hidden Markov Models for Sequence Analysis 4 11-29-2011. Choice of model topology. The structure (topology) and parameters together determine a HMM. The parameters of a HHM can be determined by the Baum-Welch algorithm and other optimization methods,

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Hidden Markov Models

Hidden Markov Models. Usman Roshan BNFO 601. Hidden Markov Models. Alphabet of symbols: Set of states that emit symbols from the alphabet: Set of probabilities State transition: Emission probabilities:. Loaded die problem. Loaded die automata. a FL. F. L. a FF. a LL. e F(i).

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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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CERN-INTC-2011-050 ; INTC-P-314 Properties of low-lying intruder states in 34 Al and 34 Si

CERN-INTC-2011-050 ; INTC-P-314 Properties of low-lying intruder states in 34 Al and 34 Si sequentially populated in beta-decay of 34 Mg. F. NEGOITA, N. Marginean et al. IFIN-HH , Bucharest, Romania S. GREVY, B. Blank , J. Giovinazzo et al. CENBG, Bordeaux, France

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TECHQM Charge to the Working Groups

TECHQM Charge to the Working Groups. Urs Achim Wiedemann CERN PH-TH. Wiedemann, NPB 588 (2000) 303. Radiation off produced parton. Parton undergoes Brownian motion :. Measures target average:. Two approximation schemes:. Harmonic oscillator approximation:.

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Study of octupole deformation in n-rich Ba isotopes populated via b decay

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Novel vertebrate homologues detected for two families of mechanosensitive channels.

1. 4. A Genomic Landscape of Ion Channels. Phylogenetic Trees with Evolutionary Distance combined. Novel vertebrate homologues detected for two families of mechanosensitive channels. HYUN JI KIM and MARK S. P. SANSOM

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