PPT-Spectral Algorithms for Learning HMMs and Tree HMMs for Epigenetics Data

Kevin C Chen Rutgers University joint work with Jimin Song Rutgers Palentir Kamalika Chaudhuri and Chicheng Zhang UCSD Human Genomewide Association Studies 12000 human disease SNPs known . Felzenszwalb Daniel P Huttenlocher Jon M Kleinberg AI Lab MIT Cambridge MA 02139 Computer Science Dept Cornell University Ithaca NY 14853 Abstract In applying Hidden Markov Models to the analysis of massive data streams it is often necessary to us Shabana. . Kazi. Mark Stamp. HMMs for Piracy Detection. 1. Intro. Here, we apply metamorphic analysis to software piracy detection. Very similar to techniques used in malware detection. But, problem is completely different . 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.). First we saw the finite state automaton. The rigid non-stochastic nature of these structures ultimately limited their usefulness to us as models of DNA. 1. 2. 3. 4. 5. 6. 7. 8. S. e. g. g. g. g. c. g. February 2011. Includes material from:. Dirk . Husmeier. , . Heng. Li. Hidden Markov models in Computational Biology. Overview. First part:. Mathematical context: Bayesian Networks. Markov models. Hidden Markov models. 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. biomolecular. sequence analysis. Nam-phuong Nguyen. Carl R. Woese Institute for Genomic Biology. University of Illinois at Urbana-Champaign. Human Microbiome. 10 times more bacteria cells than human cells. 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. Tandy Warnow. BioE. /CS 598AGB. Profile Hidden Markov Models. Basic tool in sequence analysis. Look more complicated than they really are. Used to model a family of sequences. Can be built from a multiple sequence alignment. Chuong. B. Do. CS262, Winter 2009. Lecture #8. Outline. I’ll cover two different topics today. pair-HMMs. conditional random fields (CRFs). Other resources. For more information on pair-HMMs, see the Durbin et al. book. Sushmita Roy. sroy@biostat.wisc.edu. Computational Network Biology. Biostatistics & Medical Informatics 826. Computer Sciences 838. https://compnetbiocourse.discovery.wisc.edu. Oct . 25. th. , 27. Toby O’Hara, HMMS. Derek Robertson, . TransForm. Toby O’Hara. GM. HMMS. Toby is General Manager of healthcare supply chain provider Healthcare Materials Management Services (HMMS) in London, Ontario. Prior to joining HMMS, Toby held positions at Baxter Corporation and Source Medical (Cardinal Health)..