Sparse graphical models for exploring gene expression data

DOI10.1016/J.JMVA.2004.02.009zbMATH Open1047.62104OpenAlexW2112814716MaRDI QIDQ1877000FDOQ1877000

Authors: Adrian Dobra, Chris Hans, Beatrix Jones, Joseph R. Nevins, Guang Yao, Mike West 

Publication date: 16 August 2004

Published in: Journal of Multivariate Analysis (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jmva.2004.02.009

Recommendations

• Bayesian structure learning in sparse Gaussian graphical models
• High-dimensional sparse factor modeling: applications in gene expression genomics
• Sparse estimation of conditional graphical models with application to gene networks
• A sparse conditional Gaussian graphical model for analysis of genetical genomics data
• Inferring sparse Gaussian graphical models with latent structure

zbMATH Keywords

Gene expressionGraphical modelsModel selectionBayesian regression analysisCompositional networksER pathwayEstrogen receptor gene and pathwayRb-E2F genes and pathwayTransitive gene expression pathways

Mathematics Subject Classification ID

Bayesian inference (62F15) Linear inference, regression (62J99) Applications of statistics to biology and medical sciences; meta analysis (62P10) Applications of graph theory (05C90)

Cites Work

• Parameter priors for directed acyclic graphical models and the characterization of several probability distributions
• Hyper Markov laws in the statistical analysis of decomposable graphical models
• A characterization of Markov equivalence classes for acyclic digraphs
• Sequential updating of conditional probabilities on directed graphical structures
• Title not available (Why is that?)
• Title not available (Why is that?)
• Some matrix-variate distribution theory: Notational considerations and a Bayesian application
• Dependency networks for inference, collaborative filtering, and data visualization
• Compatible Prior Distributions for Directed Acyclic Graph Models

Cited In (89)

• Sensitivity to hyperprior parameters in Gaussian Bayesian networks
• Objective methods for graphical structural learning
• Inferring sparse Gaussian graphical models with latent structure
• Enumerating the decomposable neighbors of a decomposable graph under a simple perturbation scheme
• Simplex factor models for multivariate unordered categorical data
• Sparse estimation of conditional graphical models with application to gene networks
• On Joint Estimation of Gaussian Graphical Models for Spatial and Temporal Data
• Graphical models for zero-inflated single cell gene expression
• Experiments in stochastic computation for high-dimensional graphical models
• Learning the structure of dynamic Bayesian networks from time series and steady state measurements
• Hierarchical normalized completely random measures for robust graphical modeling
• Gibbs ensembles for nearly compatible and incompatible conditional models
• A multilevel framework for sparse optimization with application to inverse covariance estimation and logistic regression
• High-dimensional sparse factor modeling: applications in gene expression genomics
• Bootstrap inference for network construction with an application to a breast cancer microarray study
• Network exploration via the adaptive LASSO and SCAD penalties
• Bayesian approaches for large biological networks
• GAP: a general framework for information pooling in two-sample sparse inference
• Gibbs posterior for variable selection in high-dimensional classification and data mining
• Estimation of Gaussian graphs by model selection
• An efficient algorithm for sparse inverse covariance matrix estimation based on dual formulation
• Robust Bayesian graphical modeling using Dirichlet \(t\)-distributions
• Bayesian graphical models for modern biological applications
• Sparse covariance matrix estimation by DCA-based algorithms
• Bayesian variable selection for high dimensional generalized linear models: convergence rates of the fitted densities
• Linear estimating equations for exponential families with application to Gaussian linear concentration models
• A localization approach to improve iterative proportional scaling in Gaussian graphical models
• Sparse estimation of high-dimensional inverse covariance matrices with explicit eigenvalue constraints
• Sparse factor model for co-expression networks with an application using prior biological knowledge
• Low-Order Conditional Independence Graphs for Inferring Genetic Networks
• Posterior convergence rates for estimating large precision matrices using graphical models
• Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks
• Bayesian selection of graphical regulatory models
• Modeling dependent gene expression
• Sparse pathway-based prediction models for high-throughput molecular data
• Gaussian graphical modeling for spectrometric data analysis
• Model free estimation of graphical model using gene expression data
• HdBCS
• Sparse seemingly unrelated regression modelling: applications in finance and econometrics
• On the relation between the true and sample correlations under Bayesian modelling of gene expression datasets
• The Hardness of Conditional Independence Testing and the Generalised Covariance Measure
• Bayesian sparse graphical models for classification with application to protein expression data
• Variable selection and dependency networks for genomewide data
• Bayesian model selection approach for coloured graphical Gaussian models
• Graphical models via joint quantile regression with component selection
• A sparse conditional Gaussian graphical model for analysis of genetical genomics data
• Multiple testing and error control in Gaussian graphical model selection
• Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data
• Structural learning of contemporaneous dependencies in graphical VAR models
• Building hyper Dirichlet processes for graphical models
• The use of unlabeled data in predictive modeling
• Graphical modeling for gene set analysis: a critical appraisal
• Bayesian graphical models for differential pathways
• Consistent Sparse Deep Learning: Theory and Computation
• Modeling Protein Expression and Protein Signaling Pathways
• Estimation of multiple networks in Gaussian mixture models
• Quantile graphical models: a Bayesian approach
• Bayesian structure learning in graphical models
• Information‐incorporated Gaussian graphical model for gene expression data
• Learning Gaussian graphical models with fractional marginal pseudo-likelihood
• Bayesian learning of Bayesian networks with informative priors
• A loss‐based prior for Gaussian graphical models
• Sparse covariance estimation in heterogeneous samples
• Maximum likelihood threshold and generic completion rank of graphs
• Efficient local updates for undirected graphical models
• Joint Gaussian graphical model estimation: a survey
• Bayesian learning of multiple directed networks from observational data
• Title not available (Why is that?)
• Bayesian graph selection consistency under model misspecification
• Singular Gaussian graphical models: Structure learning
• Understanding large text corpora via sparse machine learning
• A Bayesian hierarchical model for inference across related reverse phase protein arrays experiments
• Maximum likelihood thresholds via graph rigidity
• Rejoinder to ‘Dynamic dependence networks: Financial time series forecasting and portfolio decisions’
• High-dimensional undirected graphical models for arbitrary mixed data
• Discussion to: Bayesian graphical models for modern biological applications by Y. Ni, V. Baladandayuthapani, M. Vannucci and F.C. Stingo
• Identifying modularity structure of a genetic network in gene expression profile data
• Estimating Bayesian networks for high-dimensional data with complex mean structure and random effects
• Nonparametric Finite Mixture of Gaussian Graphical Models
• Graphical Model Inference with Erosely Measured Data
• Bayesian causal inference in probit graphical models
• Penalized estimation of the Gaussian graphical model from data with replicates
• Covariate-Assisted Bayesian Graph Learning for Heterogeneous Data
• A Gaussian graphical model approach to climate networks
• A BIRTH AND DEATH PROCESS FOR BAYESIAN NETWORK STRUCTURE INFERENCE
• Selection of the Regularization Parameter in Graphical Models Using Network Characteristics
• Finding the minimal set for collapsible graphical models
• Posterior convergence rates for high-dimensional precision matrix estimation using \(G\)-Wishart priors
• Block Structured Graph Priors in Gaussian Graphical Models

Uses Software

• Graphviz

This page was built for publication: Sparse graphical models for exploring gene expression data

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1877000)