PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

Modelling Genetic Variations using Fragmentation-Coagulation Processes
Yee Whye Teh, Charles Blundell and Lloyd Elliott
In: NIPS 2011, 12 Dec - 17 Dec 2011, Granada, Spain.


We propose a novel class of Bayesian nonparametric models for sequential data called fragmentation-coagulation processes (FCPs). FCPs model a set of sequences using a partition-valued Markov process which evolves by splitting and merging clusters. An FCP is exchangeable, projective, stationary and reversible, and its equilibrium distributions are given by the Chinese restaurant process. As opposed to hidden Markov models, FCPs allow for flexible modelling of the number of clusters, and they avoid label switching non-identifiability problems. We develop an efficient Gibbs sampler for FCPs which uses uniformization and the forward-backward algorithm. Our development of FCPs is motivated by applications in population genetics, and we demonstrate the utility of FCPs on problems of genotype imputation with phased and unphased SNP data.

EPrint Type:Conference or Workshop Item (Paper)
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Computational, Information-Theoretic Learning with Statistics
Learning/Statistics & Optimisation
ID Code:9399
Deposited By:Yee Whye Teh
Deposited On:16 March 2012