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 the splitting and merging of their clusters. Our model can be thought of as a discrete analogue of the continuous fragmentation-coagulation process [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 accuracies comparable to other state-of-the-art genotype imputation methods.

The Mixed-Membership Stochastic Blockmodel~(MMSB) is proposed as one of the state-of-the-art Bayesian relational methods suitable for learning the complex hidden structure underlying the network data. However, the current formulation of MMSB suffers from the following two issues: (1), the prior information~(e.g. entities' community structural information) can not be well embedded in the modelling; (2), community evolution can not be well described in the literature. Therefore, we propose a non-parametric fragmentation coagulation based Mixed Membership Stochastic Blockmodel (fcMMSB). Our model performs entity-based clustering to capture the community information for entities and linkage-based clustering to derive the group information for links simultaneously. Besides, the proposed model infers the network structure and models community evolution, manifested by appearances and disappearances of communities, using the discrete fragmentation coagulation process (DFCP). By integrating the community structure with the group compatibility matrix we derive a generalized version of MMSB. An efficient Gibbs sampling scheme with Polya Gamma (PG) approach is implemented for posterior inference. We validate our model on synthetic and real world data.

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].