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14
The hidden life of latent variables: Bayesian learning with mixed graph models
, 2008
"... Directed acyclic graphs (DAGs) have been widely used as a representation of conditional independence in machine learning and statistics. Moreover, hidden or latent variables are often an important component of graphical models. However, DAG models suffer from an important limitation: the family of D ..."
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Cited by 13 (4 self)
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Directed acyclic graphs (DAGs) have been widely used as a representation of conditional independence in machine learning and statistics. Moreover, hidden or latent variables are often an important component of graphical models. However, DAG models suffer from an important limitation: the family of DAGs is not closed under marginalization of hidden variables. This means that in general we cannot use a DAG to represent the independencies over a subset of variables in a larger DAG. Directed mixed graphs (DMGs) are a representation that includes DAGs as a special case, and overcomes this limitation. This paper introduces algorithms for performing Bayesian inference in Gaussian and probit DMG models. An important requirement for inference is the characterization of the distribution over parameters of the models. We introduce a new distribution for covariance matrices of Gaussian DMGs. We discuss and illustrate how several Bayesian machine learning tasks can benefit from the principle presented here: the power to model dependencies that are generated from hidden variables, but without necessarily modelling such variables explicitly.
Wishart distributions for decomposable covariance graph models, Ann. Statist
, 2010
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Marginal loglinear parameters for graphical markov models. arXiv preprint arXiv:1105.6075, 2011. RA Fisher. On the interpretation of χ2 from contingency tables, and the calculation of p
"... Marginal loglinear (MLL) models provide a flexible approach to multivariate discrete data. MLL parametrizations under linear constraints induce a wide variety of models, including models defined by conditional independences. We introduce a subclass of MLL models which correspond to Acyclic Direct ..."
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Cited by 10 (3 self)
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Marginal loglinear (MLL) models provide a flexible approach to multivariate discrete data. MLL parametrizations under linear constraints induce a wide variety of models, including models defined by conditional independences. We introduce a subclass of MLL models which correspond to Acyclic Directed Mixed Graphs (ADMGs) under the usual global Markov property. We characterize for precisely which graphs the resulting parametrization is variation independent. The MLL approach provides the first description of ADMG models in terms of a minimal list of constraints. The parametrization is also easily adapted to sparse modelling techniques, which we illustrate using several examples of real data.
Sequences of regressions and their independences
, 2012
"... Ordered sequences of univariate or multivariate regressions provide statistical modelsfor analysingdata fromrandomized, possiblysequential interventions, from cohort or multiwave panel studies, but also from crosssectional or retrospective studies. Conditional independences are captured by what we ..."
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Cited by 9 (2 self)
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Ordered sequences of univariate or multivariate regressions provide statistical modelsfor analysingdata fromrandomized, possiblysequential interventions, from cohort or multiwave panel studies, but also from crosssectional or retrospective studies. Conditional independences are captured by what we name regression graphs, provided the generated distribution shares some properties with a joint Gaussian distribution. Regression graphs extend purely directed, acyclic graphs by two types of undirected graph, one type for components of joint responses and the other for components of the context vector variable. We review the special features and the history of regression graphs, prove criteria for Markov equivalence anddiscussthenotion of simpler statistical covering models. Knowledgeof Markov equivalence provides alternative interpretations of a given sequence of regressions, is essential for machine learning strategies and permits to use the simple graphical criteria of regression graphs on graphs for which the corresponding criteria are in general more complex. Under the known conditions that a Markov equivalent directed acyclic graph exists for any given regression graph, we give a polynomial time algorithm to find one such graph.
Computing Maximum Likelihood Estimates in Recursive . . .
, 2008
"... In recursive linear models, the multivariate normal joint distribution of all variables exhibits a dependence structure induced by a recursive (or acyclic) system of linear structural equations. These linear models have a long tradition and appear in seemingly unrelated regressions, structural equat ..."
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Cited by 8 (4 self)
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In recursive linear models, the multivariate normal joint distribution of all variables exhibits a dependence structure induced by a recursive (or acyclic) system of linear structural equations. These linear models have a long tradition and appear in seemingly unrelated regressions, structural equation modelling, and approaches to causal inference. They are also related to Gaussian graphical models via a classical representation known as a path diagram. Despite the models ’ long history, a number of problems remain open. In this paper, we address the problem of computing maximum likelihood estimates in the subclass of ‘bowfree ’ recursive linear models. The term ‘bowfree ’ refers to the condition that the errors for variables i and j be uncorrelated if variable i occurs in the structural equation for variable j. We introduce a new algorithm, termed Residual Iterative Conditional Fitting (RICF), that can be implemented using only least squares computations. In contrast to existing algorithms, RICF has clear convergence properties and finds parameter estimates in closed form whenever possible.
A Localization Approach to Improve Iterative Proportional Scaling in Gaussian Graphical Models
, 2008
"... We discuss an efficient implementation of the iterative proportional scaling procedure in the multivariate Gaussian graphical models. We show that the computational cost can be reduced by localization of the update procedure in each iterative step by using the structure of a decomposable model obtai ..."
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We discuss an efficient implementation of the iterative proportional scaling procedure in the multivariate Gaussian graphical models. We show that the computational cost can be reduced by localization of the update procedure in each iterative step by using the structure of a decomposable model obtained by triangulation of the graph associated with the model. Some numerical experiments demonstrate the competitive performance of the proposed algorithm. 1
Robust Graphical Modeling with tDistributions
"... Graphical Gaussian models have proven to be useful tools for exploring network structures based on multivariate data. Applications to studies of gene expression have generated substantial interest in these models, and resulting recent progress includes the development of fitting methodology involvin ..."
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Cited by 1 (0 self)
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Graphical Gaussian models have proven to be useful tools for exploring network structures based on multivariate data. Applications to studies of gene expression have generated substantial interest in these models, and resulting recent progress includes the development of fitting methodology involving penalization of the likelihood function. In this paper we advocate the use of the multivariate t and related distributions for more robust inference of graphs. In particular, we demonstrate that penalized likelihood inference combined with an application of the EM algorithm provides a simple and computationally efficient approach to model selection in the tdistribution case. 1
Sparse Matrix Decompositions and Graph Characterizations
"... The question of when zeros (i.e., sparsity) in a positive definite matrix A are preserved in its Cholesky decomposition, and vice versa, was addressed by Paulsen et al. [19] [see Journ. of Funct. Anal., 85, 151178]. In particular, they prove that for the pattern of zeros in A to be retained in the ..."
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The question of when zeros (i.e., sparsity) in a positive definite matrix A are preserved in its Cholesky decomposition, and vice versa, was addressed by Paulsen et al. [19] [see Journ. of Funct. Anal., 85, 151178]. In particular, they prove that for the pattern of zeros in A to be retained in the Cholesky decomposition of A, the pattern of zeros in A has to necessarily correspond to a chordal (or decomposable) graph associated with a specific type of vertex ordering. This result therefore yields a characterization of chordal graphs in terms of sparse positive definite matrices. It has also proved to be extremely useful in probabilistic and statistical analysis of Markov random fields where zeros in positive definite correlation matrices are intimately related to the notion of stochastic independence. Now, consider a positive definite matrix A and its Cholesky decomposition given by A = LDLT, where L is lower triangular with unit diagonal entries, and D a diagonal matrix with positive entries. In this paper, we prove that a necessary and sufficient condition for zeros (i.e., sparsity) in a positive definite matrix A to be preserved in its associated Cholesky matrix L, and in addition also preserved in the inverse of the Cholesky matrix L−1, is that the pattern of zeros corresponds to a cochordal or homogeneous graph associated with a specific type of vertex ordering. We proceed to provide a second characterization of this class of graphs in terms of determinants of submatrices that correspond to cliques in the graph. These results add to the growing body of literature in the field of sparse matrix decompositions, and also prove to be critical ingredients in the probabilistic analysis of an important class of Markov random fields.
Proportional Scaling in Gaussian Graphical Models
, 2008
"... scholarly and technical work on a noncommercial basis. Copyright and all rights therein are maintained by the authors or by other copyright holders, notwithstanding that they have offered their works here electronically. It is understood that all persons copying this information will adhere to the ..."
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scholarly and technical work on a noncommercial basis. Copyright and all rights therein are maintained by the authors or by other copyright holders, notwithstanding that they have offered their works here electronically. It is understood that all persons copying this information will adhere to the terms and constraints invoked by each author’s copyright. These works may not be reposted without the explicit permission of the copyright holder. A Localization Approach to Improve Iterative