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16
Sparse graphical models for exploring gene expression data
 Journal of Multivariate Analysis
, 2004
"... DMS0112069. Any opinions, findings, and conclusions or recommendations expressed in this material are ..."
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Cited by 202 (24 self)
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DMS0112069. Any opinions, findings, and conclusions or recommendations expressed in this material are
Decomposable Graphical Gaussian Model Determination
, 1999
"... We propose a methodology for Bayesian model determination in decomposable graphical gaussian models. To achieve this aim we consider a hyper inverse Wishart prior distribution on the concentration matrix for each given graph. To ensure compatibility across models, such prior distributions are obt ..."
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Cited by 107 (12 self)
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We propose a methodology for Bayesian model determination in decomposable graphical gaussian models. To achieve this aim we consider a hyper inverse Wishart prior distribution on the concentration matrix for each given graph. To ensure compatibility across models, such prior distributions are obtained by marginalisation from the prior conditional on the complete graph. We explore alternative structures for the hyperparameters of the latter, and their consequences for the model. Model determination is carried out by implementing a reversible jump MCMC sampler. In particular, the dimensionchanging move we propose involves adding or dropping an edge from the graph. We characterise the set of moves which preserve the decomposability of the graph, giving a fast algorithm for maintaining the junction tree representation of the graph at each sweep. As state variable, we propose to use the incomplete variancecovariance matrix, containing only the elements for which the correspondi...
Objective Bayesian model selection in Gaussian graphical models
, 2007
"... This paper presents a default modelselection procedure for Gaussian graphical models that involves two new developments. First, we develop a default version of the hyperinverse Wishart prior for restricted covariance matrices, called the hyperinverse Wishart gprior, and show how it corresponds t ..."
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Cited by 36 (4 self)
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This paper presents a default modelselection procedure for Gaussian graphical models that involves two new developments. First, we develop a default version of the hyperinverse Wishart prior for restricted covariance matrices, called the hyperinverse Wishart gprior, and show how it corresponds to the implied fractional prior for covariance selection using fractional Bayes factors. Second, we apply a class of priors that automatically handles the problem of multiple hypothesis testing implied by covariance selection. We demonstrate our methods on a variety of simulated examples, concluding with a real example analysing covariation in mutualfund returns. These studies reveal that the combined use of a multiplicitycorrection prior on graphs and fractional Bayes factors for computing marginal likelihoods yields better performance than existing Bayesian methods. Some key words: covariance selection; hyperinverse Wishart distribution; fractional Bayes factors; Bayesian model selection; multiple hypothesis testing.
Bayesian inference for nondecomposable graphical Gaussian models
 Sankhya, Ser. A
, 2003
"... In this paper we propose a method to calculate the posterior probability of a nondecomposable graphical Gaussian model. Our proposal is based on a new device to sample from Wishart distributions, conditional on the graphical constraints. As a result, our methodology allows Bayesian model selection w ..."
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Cited by 19 (0 self)
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In this paper we propose a method to calculate the posterior probability of a nondecomposable graphical Gaussian model. Our proposal is based on a new device to sample from Wishart distributions, conditional on the graphical constraints. As a result, our methodology allows Bayesian model selection within the whole class of graphical Gaussian models, including nondecomposable ones. 1 INTRODUCTION Let G be a conditional independence graph, describing the association structure of a vector of random variables, say X. A graphical model is a family of probability distributions P G which is Markov over G. In particular, when all the random variables in X are continuous, a graphical Gaussian model is obtained by assuming P G = N(¯; \Sigma G ), with \Sigma G positive definite and such that P G is Markov over G. For an introduction to graphical models, see for instance Lauritzen (1996) or Whittaker (1990). Typically the association structure of X is uncertain and, thus, has to be inferred from...
Bayesian analysis of matrix normal graphical models
 Biometrika
, 2009
"... We develop Bayesian analysis of matrixvariate normal data with conditional independence graphical structuring of the characterising variance matrix parameters. This leads to fully Bayesian analysis of matrix normal graphical models, including discussion of novel prior specifications, the resulting ..."
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Cited by 12 (4 self)
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We develop Bayesian analysis of matrixvariate normal data with conditional independence graphical structuring of the characterising variance matrix parameters. This leads to fully Bayesian analysis of matrix normal graphical models, including discussion of novel prior specifications, the resulting problems of posterior computation addressed using Markov chain Monte Carlo methods, and graphical model assessment that involves approximate evaluation of marginal likelihood functions under specified graphical models. Modelling and inference for spatial/image data via a novel class of Markov random fields that arise as natural examples of matrix normal graphical models is discussed. This is complemented by the development of a broad class of dynamic models for matrixvariate time series within which stochastic elements defining time series errors and structural changes over time are subject to graphical model structuring. Three examples illustrate these developments and highlight questions of graphical model uncertainty and comparison in matrix data contexts.
Bayesian covariance matrix estimation using a mixture of decomposable graphical models. Unpublished manuscript
, 2005
"... Summary. Estimating a covariance matrix efficiently and discovering its structure are important statistical problems with applications in many fields. This article takes a Bayesian approach to estimate the covariance matrix of Gaussian data. We use ideas from Gaussian graphical models and model sele ..."
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Cited by 12 (2 self)
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Summary. Estimating a covariance matrix efficiently and discovering its structure are important statistical problems with applications in many fields. This article takes a Bayesian approach to estimate the covariance matrix of Gaussian data. We use ideas from Gaussian graphical models and model selection to construct a prior for the covariance matrix that is a mixture over all decomposable graphs, where a graph means the configuration of nonzero offdiagonal elements in the inverse of the covariance matrix. Our prior for the covariance matrix is such that the probability of each graph size is specified by the user and graphs of equal size are assigned equal probability. Most previous approaches assume that all graphs are equally probable. We give empirical results that show the prior that assigns equal probability over graph sizes outperforms the prior that assigns equal probability over all graphs, both in identifying the correct decomposable graph and in more efficiently estimating the covariance matrix. The advantage is greatest when the number of observations is small relative to the dimension of the covariance matrix. Our method requires the number of decomposable graphs for each graph size. We show how to estimate these numbers using simulation and that the simulation results agree with analytic results when such results are known. We also show how
Inferring gene networks from discrete expression data
 Biostatistics
, 2013
"... The modeling of gene networks from transcriptional expression data is an important tool in biomedical research to reveal signaling pathways and to identify treatment targets. Current gene network modeling is primarily based on the use of Gaussian graphical models applied to continuous data, which gi ..."
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Cited by 6 (0 self)
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The modeling of gene networks from transcriptional expression data is an important tool in biomedical research to reveal signaling pathways and to identify treatment targets. Current gene network modeling is primarily based on the use of Gaussian graphical models applied to continuous data, which give a closedformmarginal likelihood. In this paper, we extend networkmodeling to discrete data, specifically data from serial analysis of gene expression, and RNAsequencing experiments, both of which generate counts of mRNA transcripts in cell samples.We propose a generalized linear model to fit the discrete gene expression data and assume that the log ratios of the mean expression levels follow a Gaussian distribution. We restrict the gene network structures to decomposable graphs and derive the graphs by selecting the covariance matrix of the Gaussian distribution with the hyperinverse Wishart priors. Furthermore, we incorporate prior network models based on gene ontology information, which avails existing biological information on the genes of interest. We conduct simulation studies to examine the performance of our discrete graphical model and apply the method to two real datasets for gene network inference.
Bayesian covariance selection
 ISDS Discussion Paper
, 2004
"... We present a novel structural learning method called HdBCS that performs covariance selection in a Bayesian framework for datasets with tens of thousands of variables. HdBCS is based on the intrinsic connection between graphical models on undirected graphs and graphical models on directed acyclic gr ..."
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Cited by 5 (1 self)
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We present a novel structural learning method called HdBCS that performs covariance selection in a Bayesian framework for datasets with tens of thousands of variables. HdBCS is based on the intrinsic connection between graphical models on undirected graphs and graphical models on directed acyclic graphs (Bayesian networks). We show how to produce and explore the corresponding association networks by Bayesian model averaging across the models identified. We illustrate the use of HdBCS with an example from a largescale gene expression study of breast cancer.
Handling Manipulated Evidence
, 2004
"... Bayesian Networks have been advocated as a useful tool to describe the relations of dependence/independence among random variables and relevant hypotheses in a crime case. Moreover, they have been applied to help the investigator structure the problem and weight the observed evidence, typically with ..."
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Cited by 1 (1 self)
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Bayesian Networks have been advocated as a useful tool to describe the relations of dependence/independence among random variables and relevant hypotheses in a crime case. Moreover, they have been applied to help the investigator structure the problem and weight the observed evidence, typically with respect to the hypothesis of guilt of a suspect. In this paper we describe a model to handle the possibility that one or more pieces of evidence have been manipulated in order to mislead the investigations. This method is based on causal inference models, although it is developed in a different, specific framework.