PPT-Markov Models for Gene Finding

BMICS 776 wwwbiostatwiscedubmi776 Spring 2020 Daifeng Wang daifengwangwiscedu These slides excluding thirdparty material are licensed under CC BYNC 40 by Mark Craven Colin Dewey Anthony . 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 Nimantha . Thushan. Baranasuriya. Girisha. . Durrel. De Silva. Rahul . Singhal. Karthik. . Yadati. Ziling. . Zhou. Outline. Random Walks. Markov Chains. Applications. 2SAT. 3SAT. Card Shuffling. Sai. Zhang. , . Congle. Zhang. University of Washington. Presented. . by . Todd Schiller. Software bug localization: finding the likely buggy code fragments. A . software. system. (. source code. Jean-Philippe Pellet. Andre . Ellisseeff. Presented by Na Dai. Motivation. Why structure . l. earning?. What are Markov blankets?. Relationship between feature selection and Markov blankets?. Previous work. 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. 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. . and Bayesian Networks. Aron. . Wolinetz. Bayesian or Belief Network. A probabilistic graphical model that represents a set of random variables and their conditional dependencies via a directed acyclic graph (DAG).. (part 2). 1. Haim Kaplan and Uri Zwick. Algorithms in Action. Tel Aviv University. Last updated: April . 18. . 2016. Reversible Markov chain. 2. A . distribution . is reversible . for a Markov chain if. (part 1). 1. Haim Kaplan and Uri Zwick. Algorithms in Action. Tel Aviv University. Last updated: April . 15 . 2016. (Finite, Discrete time) Markov chain. 2. A sequence . of random variables.  . Each . 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. . approaches. Genomics Lesson . 7_2. Hardison. 3/1/15. 1. 3. approaches . to gene predictions. Evidence-based. Transcribed regions. Align to mRNA sequence from the same species. Align to spliced ESTs from the same species. BMI/CS 776 . www.biostat.wisc.edu/bmi776/. Spring . 2018. Anthony Gitter. gitter@biostat.wisc.edu. These slides, excluding third-party material, are licensed . under . CC BY-NC 4.0. by Mark . Craven, Colin Dewey, and Anthony Gitter. Lecture 3. Gene Finding and Sequence Annotation. Objectives of this lecture. Introduce you to basic concepts and approaches of gene finding. Show you differences between gene prediction for prokaryotic and eukaryotic genomes. Fall 2012. Vinay. B . Gavirangaswamy. Introduction. Markov Property. Processes future values are conditionally dependent on the present state of the system.. Strong Markov Property. Similar as Markov Property, where values are conditionally dependent on the stopping time (Markov time) instead of present state..