Scalable imputation of genetic data with a discrete fragmentation-coagulation process

Part of Advances in Neural Information Processing Systems 25 (NIPS 2012)

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Lloyd Elliott, Yee Teh


We present a Bayesian nonparametric model for genetic sequence data in which a set of genetic sequences is modelled using a Markov model of partitions. The partitions at consecutive locations in the genome are related by their clusters first splitting and then merging. Our model can be thought of as a discrete time analogue of continuous time fragmentation-coagulation processes [Teh et al 2011], preserving the important properties of projectivity, exchangeability and reversibility, while being more scalable. We apply this model to the problem of genotype imputation, showing improved computational efficiency while maintaining the same accuracies as in [Teh et al 2011].