Nonparametric Bayesian sparse factor models with application to gene expression modeling

DOI10.1214/10-AOAS435zbMATH Open1223.62013arXiv1011.6293OpenAlexW1625086225MaRDI QIDQ641101FDOQ641101

Authors: Juan-Miguel Gracia 

Publication date: 21 October 2011

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: A nonparametric Bayesian extension of Factor Analysis (FA) is proposed where observed data $mathbfY$ is modeled as a linear superposition, $mathbfG$, of a potentially infinite number of hidden factors, $mathbfX$. The Indian Buffet Process (IBP) is used as a prior on $mathbfG$ to incorporate sparsity and to allow the number of latent features to be inferred. The model's utility for modeling gene expression data is investigated using randomly generated data sets based on a known sparse connectivity matrix for E. Coli, and on three biological data sets of increasing complexity.

Full work available at URL: https://arxiv.org/abs/1011.6293

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zbMATH Keywords

Markov chain Monte CarloIndian buffet process

Mathematics Subject Classification ID

Bayesian inference (62F15) Factor analysis and principal components; correspondence analysis (62H25) Numerical analysis or methods applied to Markov chains (65C40) Nonparametric inference (62G99)

Cites Work

• Infinite Sparse Factor Analysis and Infinite Independent Components Analysis
• High-dimensional sparse factor modeling: applications in gene expression genomics

Cited In (28)

• Compressed spectral screening for large-scale differential correlation analysis with application in selecting glioblastoma gene modules
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• Scaled Process Priors for Bayesian Nonparametric Estimation of the Unseen Genetic Variation
• A semiparametric approach to mixed outcome latent variable models: estimating the association between cognition and regional brain volumes
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• Posterior consistency of factor dimensionality in high-dimensional sparse factor models
• On the relation between the true and sample correlations under Bayesian modelling of gene expression datasets
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Uses Software

• PMA

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