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CS-295 Reasoning and Modeling with Graphical Models: Sampling and Parallel computation, Spring 2008

  • Link to CS 295 seminar offered in Spring 2007
  • Resources for Sampling.
    1. Monte Carlo Strategies in Scientific Computing” by J. S. Liu, Springer,
    2. E. Thompson Tutorial
    Resources for Parallel Processing.
    1. Ydo Wexler, Dan Geiger: Variational Upper Bounds for Probabilistic Phylogenetic Models. RECOMB 2007: 226-237,
    2. Ron Zohar, Dan Geiger: Estimation of flows in flow networks. European Journal of Operational Research 176(2): 691-706 (2007).
    3. Mark Silberstein, Dan Geiger, Assaf Schuster: A Distributed System for Genetic Linkage Analysis. GCCB 2006: 110-123.
    4. Dan Geiger, Christopher Meek, Ydo Wexler: A Variational Inference Procedure Allowing Internal Structure for Overlapping Clusters and Deterministic Constraints. J. Artif. Intell. Res. (JAIR) 27: 1-23 (2006).
    5. Class notes by Prof. Vishkin
    6. X. Wen and U. Vishkin  “Parallel computation for Graphical models PFGA-Based Prototype of a PRAM-On-Chip Processor”, 2007.
    7. M. Silberstein et al. "Efficient Sum Product computations on GPUs", 2008. PDF
    Resources for Inference.
    1. Mark Chavira and Adnan Darwiche “On Probabilistic Inference by Weighted Model Counting”  in Artificial Intelligence Journal (AIJ), 2008. 
    2. Joris Mooij “Understanding and improving Belief propagation, Phd thesis, 2008
    3. A. Ihler, John Fisher, A. Willskey Loopy belief propagation: Convergence and effects of message errors” JAIR 2005
    4. A Globerson and T Jaakola “Convergent Propagation algorithms via oriented Trees” 2007
    5. D Sontag and T. Jaakola “New Outer Bounds on the marginal polytope”
    6. Amir Globerson and Tommi Jaakkola, Approximate inference using conditional entropy decompositions, AISTATS 2007.
    7. Timothee Cour and Jianbo Shi, Solving Markov Random Fields with Spectral Relaxation, AISTATS 2007.
    8. Joris Mooij, Bastian Wemmenhove, Bert Kappen and Tommaso Rizzo, Loop Corrected Belief Propagation, AISTATS 2007.
    9. Edward Snelson and Zoubin Ghahramani, Local and global sparse Gaussian process approximations. AISTATS 2007.
    10. Gregory Druck, Mukund Narasimhan and Paul Viola. Learning A* underestimates: Using inference to guide inference. AISTATS 2007.
    11. M. J. Wainwright, T. Jaakkola and A. S. Willsky. A new class of upper bounds on the log partition function. IEEE Trans. on Information Theory, vol. 51, page 2313--2335, July 2005.
    12. M. J. Wainwright, and M. I. Jordan. Graphical models, exponential families, and variational inference. UC Berkeley, Dept. of Statistics, Technical Report 649. September, 2003.
    13. Paper on Graph cuts by Ramin Zabih
    14. Vladimir Kolmogorov and Ramin Zabih. "Graph Cut Algorithms for Binocular Stereo with Occlusions'', . In: Mathematical Models in Computer Vision: The Handbook, Springer-Verlag (2005).
    15. Vladimir Kolmogorov and Ramin Zabih. "What Energy Functions can be Minimized via Graph Cuts?'',  IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 26, no. 2 pages 147-159 (2004).
    Resources for Linkage Analysis.
    1.  Eric S. Lander and Philip Green. Construction of multilocus genetic linkage maps in humans. Genetics. April 1987.
    2. Goncalo R. Abecasis and Janis E. Wigginton. Handling Marker-Marker Linkage Disequilibrium: Pedigree Analysis with Clustered Markers, American Journal of Human Genetics. Sept 2005.
    3. P Stuart et al. Analysis of RUNX1 binding site and RAPTOR polymorphisms in psoriasis: no evidence for association despite adequate power and evidence for linkage. American Journal of Human Genetics. Sept 2006.
    4. Joshua T Burdick, Wei-Min Chen, Gonc¸alo R Abecasis and Vivian G Cheung, In silico method for inferring genotypes in pedigrees, Nature genetics.August 2006. Download here
    5. Gonçalo R. Abecasis, Stacey S. Cherny, William O. Cookson1 & Lon R. Cardon. Merlin—rapid analysis of dense genetic maps using sparse gene flow trees. Nature Genetics.Dec 2001.
    6. Scheet, P and Stephens, M A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase.  American Journal of Human Genetics. 2006.
    7. Stephens, M and Scheet, P. Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation, American Journal of Human Genetics. 2005.
    8. M. Fishelson and D. Geiger. Exact Genetic Linkage Computations for General Pedigrees.  Bioinformatics, Volume 18 Suppl. 1: S189-S198 (July 2002). Also presented in ISMB2002 (August, 2002).
    9. M. Fishelson and D. Geiger Optimizing Exact Genetic Linkage Computations.  Journal of Computational Biology Volume 11(2-3): 263-75 (2004). Also presented in RECOMB2003 (April, 2003).
    10. M. Fishelson, N. Dovgolevsky and D. Geiger. Maximum Likelihood Haplotyping for General Pedigrees. Technical Report CS-2004-13. To appear in Human Heredity, 2005.
    11. M. Fishelson, N. Dovgolevsky and D. Geiger. Maximum Likelihood Haplotyping for General Pedigrees. Human Heredity 2004.
    12. Yun Ju Sung, Elizabeth A. Thompson and Ellen M. Wijsman MCMC-Based Linkage Analysis for Complex Traits on General Pedigrees: Multipoint Analysis With a Two-Locus Model and a Polygenic Component, Genetic Epidemiology 2007.
    13. Hot topics: Essay on Computational Intelligence in Human Genetics Exciting