'Gibbs sampling' presentation slideshows

Gibbs sampling in open-universe stochastic languages

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Mining Motifs from Biosequences

Mining Motifs from Biosequences. Computer Science Department National Chiao Tung University Yuh-Jyh Hu. Outline. Introduction to DNA Sequence Motif Prediction Characteristics of DNA Motif-finding Problem Issues of DNA Motif-finding Algorithms Examples and current research directions

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Computational Genomics and Proteomics

C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. Computational Genomics and Proteomics. Lecture 8 Motif Discovery. Outline Gene Regulation DNA Transcription factors Motifs What are they?

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Statistical NLP Winter 2009

Statistical NLP Winter 2009. Lecture 16: Unsupervised Learning II Roger Levy [thanks to Sharon Goldwater for many slides]. Supervised training. Standard statistical systems use a supervised paradigm. Training:. Labeled training data. Statistics. Machine learning system. Prediction

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Alignment by Bilingual Generation and Monolingual Derivation

Alignment by Bilingual Generation and Monolingual Derivation. Toshiaki Nakazawa and Sadao Kurohashi Kyoto University. Outline. Background & Related Work Model Overview Model Training Experiments Conclusion. Background.

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Motif finding

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Approximate Inference 2: Monte Carlo Markov Chain

Approximate Inference 2: Monte Carlo Markov Chain. MCMC. Limitations of LW: Evidence affects sampling only for nodes that are its descendants For nondescendants, the weights account for the effect of the evidence

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Probabilistic Models for Discovering E-Communities

Probabilistic Models for Discovering E-Communities. Ding Zhou, Eren Manavoglu, Jia Li, C. Lee Giles, Hongyuan Zha The Pennsylvania State University WWW 2006. Outline. Introduction Related Works Community-User-Topic Models Semantic Community Discovery Experiments Conclusion. Outline.

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End of Chapter 8

End of Chapter 8. Neil Weisenfeld March 28, 2005. Outline. 8.6 MCMC for Sampling from the Posterior 8.7 Bagging 8.7.1 Examples: Trees with Simulated Data 8.8 Model Averaging and Stacking 8.9 Stochastic Search: Bumping. MCMC for Sampling from the Posterior. Markov chain Monte Carlo method

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Biological Sequence Pattern Analysis

PLPTH 890 Introduction to Genomic Bioinformatics Lecture 16. Biological Sequence Pattern Analysis. Liangjiang (LJ) Wang ljwang@ksu.edu March 8, 2005. Outline. Basic concepts and biological problems. Regular expression for: Pattern matching (sequence motifs),

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Markov Chain Monte Carlo

Markov Chain Monte Carlo. Prof. David Page transcribed by Matthew G. Lee. Markov Chain. A Markov chain includes A set of states A set of associated transition probabilities

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Multi-User Diversity in Single-Radio OFDMA Ad Hoc Networks Based on Gibbs Sampling

Multi-User Diversity in Single-Radio OFDMA Ad Hoc Networks Based on Gibbs Sampling. Marzieh Veyseh J.J. Garcia-Luna-Aceves Hamid R. Sadjadpour. Motivation. Channel 1. Channel 1. Concurrency Frequency Code Space. Channel 3. fc3. fc4. fc5. fc1. fc2. Code 1. Channel 1. Code 3.

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Genome evolution: a sequence-centric approach

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Advisor: Hsin-Hsi Chen Reporter: Y.H Chang 2008-03-21

Efficient Topic-based Unsupervised Name Disambiguation Yang Song, Jian Huang, Isaac G. Councill, Jia Li, C. Lee Giles JCDL2007. Advisor: Hsin-Hsi Chen Reporter: Y.H Chang 2008-03-21. Outline. Introductoin Related Work Method Topic-based PLSA (Probabilistic Latent Semantic Analysis)

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Gibbs sampling for motif finding

Gibbs sampling for motif finding. Yves Moreau. Overview. Markov Chain Monte Carlo Gibbs sampling Motif finding in cis -regulatory DNA Biclustering microarray data. Markov Chain Monte-Carlo. Markov chain with transition matrix T. A C G T

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Parsing Arabic Dialects

Parsing Arabic Dialects. Progress Report (- Week 2-). Overview. Baselines Infrastructure Sentence Transduction Treebank Transduction Grammar Transduction Issues. - Dialect -. - MSA -. Small UAC. Big UAC. Parsing Arabic Dialects: The Problem. Treebank. ??????? ???? ???????. ?.

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CHAPTER 16 M ARKOV C HAIN M ONTE C ARLO

Slides for Introduction to Stochastic Search and Optimization ( ISSO ) by J. C. Spall. CHAPTER 16 M ARKOV C HAIN M ONTE C ARLO. Organization of chapter in ISSO Background on MCMC Metropolis-Hastings algorithm Numerical example of Metropolis-Hastings Gibbs sampling

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Multiple Species Gene Finding using Gibbs Sampling

Multiple Species Gene Finding using Gibbs Sampling. Sourav Chatterji Lior Pachter University of California, Berkeley. Multiple Species Comparative Gene Finding (with Alignment). McAuliffe et al. (2004), Siepel et al. (2004). Multiple Species Comparative Gene Finding (with Alignment).

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Gibbs Sampling

Gibbs Sampling. Qianji Zheng Oct. 5 th , 2010. Outline. Motivation & Basic Idea Algorithm Example Applications Why Gibbs Works. Gibbs Sampling: Motivation.

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Lecture 15

Lecture 15. Sampling. Approximate Inference. Motivation comes from EM, where in the E-step we need to do inference which is often intractable.

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