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The seminar will focus on recent advances in graphical models
reasoning and knowledge representation, as well as on exploring some
application areas. One such area is Genetic Linkage Analysis, which
involves both probabilistic information as well as constraints. In 2005
we explored the state of the art in applying Bayesian network
algorithms to Linkage analysis. Following a quick overview, we will
read recent papers, focusing on issues introduced by the recent
availability of Single Nucleotide Polymorphism (SNP) data and the
presence of Linkage disequilibrium (LD). Other application areas would
be welcomed. We will consider areas such as modeling human behavior and
environment in transportation system and the processing of or picture
databases.
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.
The topics we will discuss include:
- How to handle SNP data in
Linkage analysis. How to handle LD (Linkage disequilibrium).
- Sampling algorithms for linkage
analysis (MCMC methods by Elizabeth Thompson. The Morgan system)
- Cleaning data files: It is often
the case in many applications that parts of the data contain typos or
was corrupted in various ways. Such problem exists in linkage files.
Can this problem be modeled as a graphical model?
- Exploiting hypergraph structure.
In particular, looking into the significance of hypertree width vs
treewidth in capturing instance-based complexity of reasoning in
graphical models.
- Approximate and bounding
algorithms for posterior marginal (e.g., via belief propagation,
sampling and both)
- Using multiple heuristics during
search in graphical models
- Dynamic Temporal Bayesian
networks
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Relevant Papers
I. Linkage
- Eric S. Lander and Philip Green.
Construction of multilocus genetic linkage maps in humans.
Genetics. April 1987. PDF
- Goncalo R. Abecasis and Janis E.
Wigginton. Handling Marker-Marker Linkage Disequilibrium: Pedigree
Analysis with Clustered Markers, American Journal of Human
Genetics. Sept 2005. PDF
- 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. Download here
- 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
- 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. PDF
- 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. PDF
- Stephens, M and Scheet, P. Accounting
for Decay of Linkage Disequilibrium in Haplotype Inference and
Missing-Data Imputation, American Journal of Human Genetics. 2005. PDF
- 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). PDF
- 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). PS
- M. Fishelson, N. Dovgolevsky and
D. Geiger. Maximum Likelihood Haplotyping for General Pedigrees.
Technical Report CS-2004-13. To appear in Human Heredity, 2005. PDF
- M. Fishelson, N. Dovgolevsky and
D. Geiger. Maximum Likelihood Haplotyping for General Pedigrees.
Human Heredity 2004. PDF
- 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. PDF
II. Hypergraph analysis of graphical models (the hypertree width)
- Sathiamoorthy Subbarayan and
Henrik Reif Andersen, Backtracking Procedures for Hypertree,
HyperSpread and Connected Hypertree Decomposition of CSPs, IJCAI
2007. PDF
- Marko Samer and Stefan Szeider, Constraint
Satisfaction with Bounded Treewidth Revisited, CP 2006. PDF
- Francesco Scarcello, Gianluigi
Greco and Nicola Leone, Weighted Hypertree Decomposition and
Optimal Query Plans. PODS 2004. PDF
- Yong Gao and Joseph Culberson. Consistency
and Random Constraint Satisfaction Models. JAIR 2006. PDF
III. Inference
- Amir Globerson and Tommi
Jaakkola, Approximate inference using conditional entropy
decompositions, AISTATS 2007. PDF
- Timothee Cour and Jianbo Shi, Solving
Markov Random Fields with Spectral Relaxation, AISTATS 2007. PDF
- Joris Mooij, Bastian Wemmenhove,
Bert Kappen and Tommaso Rizzo, Loop
Corrected Belief Propagation, AISTATS 2007. PDF
- Edward Snelson and Zoubin
Ghahramani, Local and global sparse Gaussian process approximations.
AISTATS 2007. PDF
- Gregory Druck, Mukund Narasimhan
and Paul Viola. Learning A* underestimates: Using inference to
guide inference. AISTATS 2007. PDF
- 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. PDF
- M. J. Wainwright, and M. I.
Jordan. Graphical models, exponential families, and variational
inference. UC Berkeley, Dept. of Statistics, Technical Report 649.
September, 2003. PDF
Schedule:
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Week
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Date
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Topic
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1
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04/04
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(a) Visual-based experience (Ramesh
Jain, ppt), (b) In-house
competition overview (Vibhav Gogate), (c) Empirical results with
optimization-based AOBDD (Radu Marinescu) and (d) Overview of Linkage
Analysis (Rina Dechter)
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2
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04/11
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(a)
Continued Background on Linkage Analysis (Rina Dechter, ppt1, ppt2), (b)
Overview of the SampleSearch scheme (Vibhav Gogate, ppt)
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3
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04/18
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(a)
Overview of Linkage Analysis (Rina Dechter), (b) Continuous Time
Bayesian Networks (Guy Yosiphon) and (c) Finding hypertree width (Lars
Otten)
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4
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04/25
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(a)
Finding hypertree width (Lars Otten, pdf),
(b) Linkage Disequilibrium Mapping and HaploBlock (Rina Dechter, pdf) and (c) Mapping by Admixture
Linkage Disequilibrium (Rina Dechter, ppt)
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5
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05/02
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(a) Paper
by Yun Ju Sung, Elizabeth A. Thompson and Ellen M. Wijsman (Vibhav
Gogate, ppt), (b) Paper by Gonçalo Abecasis
and Janis Wigginton (Radu Marinescu, ppt)
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6
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05/09
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More
on Continuous time bayesian networks and possible connections to
stochastic grammars (Guy Yosiphon)
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7
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05/16
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(a)
More on Linkage analysis (Vibhav Gogate, ppt) and (b) Radio
advertisement (Google)
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8
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05/23
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9
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05/30
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10
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06/06
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11
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06/13
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