Hierarchical Dirichlet process

Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they may control, making it a valuable downstream analysis tool in chromatin conformation studies.

16p viaristotle 29-01-2022 10 0   Download

We propose a new hierarchical Bayesian n-gram model of natural languages. Our model makes use of a generalization of the commonly used Dirichlet distributions called Pitman-Yor processes which produce power-law distributions more closely resembling those in natural languages. We show that an approximation to the hierarchical Pitman-Yor language model recovers the exact formulation of interpolated Kneser-Ney, one of the best smoothing methods for n-gram language models.

8p hongvang_1 16-04-2013 40 1   Download

Department of Cognitive and Linguistic Sciences Brown University Providence, RI, USA correction, the approximation is poor for hierarchical models, which are commonly used for NLP applications. We derive an improved O(1) formula that gives exact values for the expected counts in non-hierarchical models. For hierarchical models, where our formula is not exact, we present an efficient method for sampling from the HDP (and related models, such as the hierarchical PitmanYor process) that considerably decreases the memory footprint of such models as compared to the naive implementation. ...

4p hongphan_1 15-04-2013 49 1   Download