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ICS-280 Spring 2005, Current Topics in Graphical Models with Focus on Genetic Linkage Analysis

Class Reference

  • Classroom: PSCB 220
  • Day: Wednesday
  • Time: 2:00 - 4:20pm
  • Instructor: Rina Dechter - dechter@ics.uci.edu

The seminar will focus on most recent research papers in graph-based reasoning and knowledge representation, as well as on exploring connection with focus on two application areas. Genetic Linkage Analysis and 2. Transportation Studies. Each student will be engaged in a research project and will be required to present relevant papers from the literature as well as their own findings. Students will also need to provide a final report for their research project.

Genetic analysis links

  1. SUPERLINK Homepage:
  2. [ PDF ] Exact Genetic Linkage Computations for General Pedigrees. M. Fishelson and D. Geiger. Bioinformatics, Volume 18 Suppl. 1: S189-S198 (July 2002). Also presented in ISMB2002 (August, 2002).
  3. [ PS ] Optimizing Exact Genetic Linkage Computations. M. Fishelson and D. Geiger Journal of Computational Biology Volume 11(2-3): 263-75 (2004). Also presented in RECOMB2003 (April, 2003).
  4. [ PDF ] Maximum Likelihood Haplotyping for General Pedigrees. M. Fishelson, N. Dovgolevsky and D. Geiger. Technical Report CS-2004-13. To appear in Human Heredity, 2005.
  5. [ PDF ] Maximum Likelihood Haplotyping for General Pedigrees. M. Fishelson, N. Dovgolevsky and D. Geiger. Human Heredity 610.
  6. Advanced Topics in Bioinformatics. Dan Geiger. Class notes from Technion, Israel Institute of Technology.
  7. Mathematical and Statistical Methods for Genetic Analysis . Kenneth Lange.
  8. An Introduction to Genetic Analysis . A.J.F. Griffiths et al.
  9. Cornelia de Lange syndrome is caused by mutations in NIPBL, the human homolog of Drosophila melanogaster Nipped-B . Ian D. Krantz et al.

Additional papers to be discussed

  1. [ PDF ] Bucket Elimination for Multiobjective Optimization Problems and its Application to Global Constraints. J. Larrosa and E. Rollon.
  2. [ PDF ] Affine Algebraic Decision Diagrams (AADDs) and their Application to Structured Probabilistic Inference. S. Sanner and D. McAllester. IJCAI-05.
  3. [ PDF ] Toward Good Elimination Orders for Symbolic SAT Solving. J. Huang and A. Darwiche. ICTAI-04.
  4. A Structure-Based Variable Ordering Heuristic for SAT. J. Huang and A. Darwiche. IJCAI-03.
  5. [ PDF ] New Advances in Inference by Recursive Conditioning. D. Allen and A. Darwiche. IJCAI-03.
  6. [ PDF ] Guiding Real-World SAT Solving with Dynamic Hypergraph Separator Decomposition. W. Li and P. van Beek. ICTAI-04.
  7. [ PDF ] Weighted Hypertree Decompositions and Optimal Query Plans. F. Scarcello, G. Greco and N. Leone. PODS-04.
  8. [ PDF ] Binary Decision Diagrams. B. Bollig, M. Sauerho, D. Sieling and I. Wegener.
  9. [ PDF ] Learning in Depth-First Search: A Unified Approach to Heuristic Search in Deterministic, Non-Deterministic, Probabilistic, and Game Tree Settings. B. Bonet and H. Geffner.
  10. [ PDF ] Solving Simple Planning Problems with More Inference and No Search. V. Vidal and H. Geffner.
  11. [ PDF ] An Algorithm better than AO*?. B. Bonet and H. Geffner.
  12. [ PDF ] Compiling Bayesian Networks with Local Structure. M. Chavira and A. Darwiche. IJCAI-05.
  13. [ PDF ] DPLL with a Trace: From SAT to Knowledge Compilation. J. Huang and A. Darwiche. IJCAI-05.
  14. [ PDF ] Sensitivity Analysis in Markov Networks. H. Chan and A. Darwiche. IJCAI-05.

Class presentations

Week Date Topic
Week 1 04/06 Robert Mateescu - Introduction to genetics. Brief discussion of Superlink algorithms. Slides from Advanced Topics in Bioinformatics: tutorials 1, 2; lecture 5.
Week 2 04/13 Robert Mateescu - Bayesian Network for Genetic Linkage. Superlink algorithms. Slides from Advanced Topics in Bioinformatics: lectures 5, 6, 7.
Rina Dechter - Decomposing a Relation into a Tree of Binary Relations.
Week 3 04/20 Bozhena Bidyuk - Bucket Elimination for Multiobjective Optimization Problems and its Application to Global Constraints
Optimizing Exact Genetic Linkage Computations
Max Welling - Introduction to Belief Propagation.
Week 4 04/27 Radu Marinescu - Exact Genetic Linkage Computations for General Pedigrees. Experimental results: MPE on genetic linkage files.
Alex Ihler - Nonparametric Belief Propagation for Self-Localization of Sensor Networks.
Week 5 05/04 Robert Mateescu - Iterative Join-Graph Propagation
A Simple Insight into Iterative Belief Propagationís Success
Week 6 05/11 Vibhav Gogate - Toward Good Elimination Orders for Symbolic SAT Solving;
Guiding Real-World SAT Solving with Dynamic Hypergraph Separator Decomposition.
James Worcester - A Structure-Based Variable Ordering Heuristic for SAT.
Vibhav Gogate and Robert Mateescu - Join-graphs and factor graphs; IBP and Arc Consistency.
Week 7 05/18  
Week 8 05/25  
Week 9 06/01  
Week 10 06/08