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Modelling Genetic Variations using Fragmentation-Coagulation Processes
Yee Whye Teh · Charles Blundell · Lloyd T Elliott

Tue Dec 13 08:45 AM -- 02:59 PM (PST) @ None #None

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.

Author Information

Yee Whye Teh (University of Oxford, DeepMind)

I am a Professor of Statistical Machine Learning at the Department of Statistics, University of Oxford and a Research Scientist at DeepMind. I am also an Alan Turing Institute Fellow and a European Research Council Consolidator Fellow. I obtained my Ph.D. at the University of Toronto (working with Geoffrey Hinton), and did postdoctoral work at the University of California at Berkeley (with Michael Jordan) and National University of Singapore (as Lee Kuan Yew Postdoctoral Fellow). I was a Lecturer then a Reader at the Gatsby Computational Neuroscience Unit, UCL, and a tutorial fellow at University College Oxford, prior to my current appointment. I am interested in the statistical and computational foundations of intelligence, and works on scalable machine learning, probabilistic models, Bayesian nonparametrics and deep learning. I was programme co-chair of ICML 2017 and AISTATS 2010.

Charles Blundell (DeepMind)
Lloyd T Elliott (University of Oxford)

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