Bayesian network marker selection via the thresholded graph Laplacian Gaussian prior

DOI10.1214/18-BA1142MaRDI QIDQ2297232zbMATHWikidataFDO

Authors Qingpo Cai, Jian Kang, Tianwei Yu

Publication date 18 February 2020

Published in Bayesian Analysis (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1810.00274

zbMATH Keywords

generalized linear modelposterior consistencygene networknetwork marker selectionthresholded graph Laplacian Gaussian prior

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Probabilistic graphical models (62H22) Generalized linear models (logistic models) (62J12)

Abstract: Selecting informative nodes over large-scale networks becomes increasingly important in many research areas. Most existing methods focus on the local network structure and incur heavy computational costs for the large-scale problem. In this work, we propose a novel prior model for Bayesian network marker selection in the generalized linear model (GLM) framework: the Thresholded Graph Laplacian Gaussian (TGLG) prior, which adopts the graph Laplacian matrix to characterize the conditional dependence between neighboring markers accounting for the global network structure. Under mild conditions, we show the proposed model enjoys the posterior consistency with a diverging number of edges and nodes in the network. We also develop a Metropolis-adjusted Langevin algorithm (MALA) for efficient posterior computation, which is scalable to large-scale networks. We illustrate the superiorities of the proposed method compared with existing alternatives via extensive simulation studies and an analysis of the breast cancer gene expression dataset in the Cancer Genome Atlas (TCGA).

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Cited in

(7)

• Gene-gene interaction analysis incorporating network information via a structured Bayesian approach
• Gaussian graphical modeling for spectrometric data analysis
• A graph Laplacian prior for Bayesian variable selection and grouping
• Bayesian Inferences on Neural Activity in EEG-Based Brain-Computer Interface
• Bayesian Spatial Blind Source Separation via the Thresholded Gaussian Process
• Bayesian hierarchical models for high-dimensional mediation analysis with coordinated selection of correlated mediators
• Bayesian Nonlinear Tensor Regression with Functional Fused Elastic Net Prior

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Uses Software

• GOstats
• Algorithm 447
• BMSS
• Hint

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