Bayesian graphical compositional regression for microbiome data
From MaRDI portal
Abstract: An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group heterogeneities among samples and the existence of potential confounding variables that, when ignored, increase the chance of false discoveries and reduce the power for identifying true differences. We propose a probabilistic framework to overcome these issues by combining three ideas: (i) a phylogenetic tree-based decomposition of the cross-group comparison problem into a series of local tests, (ii) a graphical model that links the local tests to allow information sharing across taxa, and (iii) a Bayesian testing strategy that incorporates covariates and integrates out the within-group variation, avoiding potentially unstable point estimates. We derive an efficient inference algorithm based on numerical integration and junction-tree message passing, conduct extensive simulation studies to investigate the performance of our approach, and compare it to state-of-the-art methods in a number of representative settings. We then apply our method to the American Gut data to analyze the association of dietary habits and human's gut microbiome composition in the presence of covariates, and illustrate the importance of incorporating covariates in microbiome cross-group comparison.
Recommendations
- Regression analysis for microbiome compositional data
- A Bayesian model of microbiome data for simultaneous identification of covariate associations and prediction of phenotypic outcomes
- A logistic normal multinomial regression model for microbiome compositional data analysis
- Bayesian compositional regression with structured priors for microbiome feature selection
- Kernel-penalized regression for analysis of microbiome data
Cites work
- A Bayesian analysis of tree-structured statistical decision problems
- A Dirichlet-Tree Multinomial Regression Model for Associating Dietary Nutrients with Gut Microorganisms
- A logistic normal multinomial regression model for microbiome compositional data analysis
- A phylogenetic scan test on a Dirichlet-tree multinomial model for microbiome data
- Analysis of Distributional Variation Through Graphical Multi-Scale Beta-Binomial Models
- Approximate Bayesian model selection with the deviance statistic
- scientific article; zbMATH DE number 4121482 (Why is no real title available?)
- MIMIX: a Bayesian mixed-effects model for microbiome data from designed experiments
- Mixtures of g Priors for Bayesian Variable Selection
- On the hyper-dirichlet type 1 and hyper-liouville distributions
- Optimal predictive model selection.
- Probabilistic graphical models.
- Probabilistic multi-resolution scanning for two-sample differences
- Two-sample Bayesian nonparametric hypothesis testing
- Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis
Cited in
(20)- A phylogenetic scan test on a Dirichlet-tree multinomial model for microbiome data
- A Bayesian model of microbiome data for simultaneous identification of covariate associations and prediction of phenotypic outcomes
- Bayesian multivariate sparse functional principal components analysis with application to longitudinal microbiome multiomics data
- Correction to: ``A Bayesian model of microbiome data for simultaneous identification of covariate associations and prediction of phenotypic outcomes
- Dirichlet-tree multinomial mixtures for clustering microbiome compositions
- A hierarchical Bayesian approach for detecting global microbiome associations
- A Bayesian framework for identifying consistent patterns of microbial abundance between body sites
- Compositional mediation analysis for microbiome studies
- Regression analysis for microbiome compositional data
- Differential Markov random field analysis with an application to detecting differential microbial community networks
- Generalized linear models with linear constraints for microbiome compositional data
- Statistical models and computational algorithms for discovering relationships in microbiome data
- Hypothesis testing for phylogenetic composition: a minimum-cost flow perspective
- Robust Shape Matrix Estimation for High-Dimensional Compositional Data with Application to Microbial Inter-Taxa Analysis
- Compositional Graphical Lasso Resolves the Impact of Parasitic Infection on Gut Microbial Interaction Networks in a Zebrafish Model
- Microbiome Subcommunity Learning with Logistic-Tree Normal Latent Dirichlet Allocation
- A Dirichlet-Tree Multinomial Regression Model for Associating Dietary Nutrients with Gut Microorganisms
- A Common Atoms Model for the Bayesian Nonparametric Analysis of Nested Data
- Bayesian modeling of interaction between features in sparse multivariate count data with application to microbiome study
- A tree-based model for addressing sparsity and taxa covariance in microbiome compositional count data
This page was built for publication: Bayesian graphical compositional regression for microbiome data
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5130601)
