Related papers: Identifying Heritable Communities of Microbiome by…
In this paper we propose weighted symmetric binary matrix factorization (wSBMF) framework to detect overlapping communities in bipartite networks, which describe relationships between two types of nodes. Our method improves performance by…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
In microbiome studies, it is often of great interest to identify clusters or partitions of microbiome profiles within a study population and to characterize the distinctive attributes of each resulting microbial community. While raw counts…
We propose a method for simultaneously detecting shared and unshared communities in heterogeneous multilayer weighted and undirected networks. The multilayer network is assumed to follow a generative probabilistic model that takes into…
The prediction of the variance-covariance matrix of the multivariate normal distribution is important in the multivariate analysis. We investigated Bayesian predictive distributions for Wishart distributions under the Kullback-Leibler…
We are interested in the distribution of Wishart samples after forgetting their scaling factors. We call such a distribution a projective Wishart distribution. We show that projective Wishart distributions have strong links with the…
Using modern technology, it is now common to survey microbial communities by sequencing DNA or RNA extracted in bulk from a given environment. Comparative methods are needed that indicate the extent to which two communities differ given…
In this work, we consider the weighted difference of two independent complex Wishart matrices and derive the joint probability density function of the corresponding eigenvalues in a finite-dimension scenario using two distinct approaches.…
Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…
This paper proposes a hierarchical Bayesian multitask learning model that is applicable to the general multi-task binary classification learning problem where the model assumes a shared sparsity structure across different tasks. We derive a…
Discovering overlapping community structures is a crucial step to understanding the structure and dynamics of many networks. In this paper we develop a symmetric binary matrix factorization model (SBMF) to identify overlapping communities.…
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…
The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…
Neutral models which assume ecological equivalence between species provide null models for community assembly. In Hubbell's Unified Neutral Theory of Biodiversity (UNTB), many local communities are connected to a single metacommunity…
WISDoM (Wishart Distributed Matrices) is a new framework for the quantification of deviation of symmetric positive-definite matrices associated to experimental samples, like covariance or correlation matrices, from expected ones governed by…
There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with…
Based on a student research project this article gives a short review on Wishart processes. A Wishart procces is a matrix valued continuous time stochastic process with a marginal Wishart distribution. The Wishart distribution is a matrix…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
Local community detection consists of finding a group of nodes closely related to the seeds, a small set of nodes of interest. Such group of nodes are densely connected or have a high probability of being connected internally than their…
Variational Inference is a powerful tool in the Bayesian modeling toolkit, however, its effectiveness is determined by the expressivity of the utilized variational distributions in terms of their ability to match the true posterior…