Asymptotic Bayesian structure learning using graph supports for Gaussian graphical models

The theory of Gaussian graphical models is a powerful tool for independence analysis between continuous variables. In this framework, various methods have been conceived to infer independence relations from data samples. However, most of them result in stepwise, deterministic, descent algorithms that are inadequate for solving this issue. More recent developments have focused on stochastic procedures, yet they all base their research on strong a priori knowledge and are unable to perform model selection among the set of all possible models. Moreover, convergence of the corresponding algorithms is slow, precluding applications on a large scale. In this paper, we propose a novel Bayesian strategy to deal with structure learning. Relating graphs to their supports, we convert the problem of model selection into that of parameter estimation. Use of non-informative priors and asymptotic results yield a posterior probability for independence graph supports in closed form. Gibbs sampling is then applied to approximate the full joint posterior density. We finally give three examples of structure learning, one from synthetic data, and the two others from real data.     

Improving on the maximum likelihood estimators of the means in Poisson decomposable graphical models

In this article we study the simultaneous estimation of the means in Poisson decomposable graphical models. We derive some classes of estimators which improve on the maximum likelihood estimator under the normalized squared losses. Our estimators are based on the argument in Chou [Simultaneous estimation in discrete multivariate exponential families, Ann. Statist. 19 (1991) 314-328.] and shrink the maximum likelihood estimator depending on the marginal frequencies of variables forming a complete subgraph of the conditional independence graph.     

Sparse graphical models for exploring gene expression data

We discuss the theoretical structure and constructive methodology for large-scale graphical models, motivated by their potential in evaluating and aiding the exploration of patterns of association in gene expression data. The theoretical discussion covers basic ideas and connections between Gaussian graphical models, dependency networks and specific classes of directed acyclic graphs we refer to as compositional networks. We describe a constructive approach to generating interesting graphical models for very high-dimensional distributions that builds on the relationships between these various stylized graphical representations. Issues of consistency of models and priors across dimension are key. The resulting methods are of value in evaluating patterns of association in large-scale gene expression data with a view to generating biological insights about genes related to a known molecular pathway or set of specified genes. Some initial examples relate to the estrogen receptor pathway in breast cancer, and the Rb-E2F cell proliferation control pathway.     

Conditional independence models for seemingly unrelated regressions with incomplete data

We consider normal ≡ Gaussian seemingly unrelated regressions (SUR) with incomplete data (ID). Imposing a natural minimal set of conditional independence constraints, we find a restricted SUR/ID model whose likelihood function and parameter space factor into the product of the likelihood functions and the parameter spaces of standard complete data multivariate analysis of variance models. Hence, the restricted model has a unimodal likelihood and permits explicit likelihood inference. In the development of our methodology, we review and extend existing results for complete data SUR models and the multivariate ID problem.     

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The IPSP algorithm is an efficient algorithm for computing maximum likelihood estimation of Gaussian graphical models. It first divides clique marginals of graphical models into several groups, and then it adjusts clique marginals in each group locally. This paper uses the IIPS algorithm on junction tree to replace local adjustment on each group in the IPSP algorithm and propose a resulting algorithm called IPSP-JT to reduce the complexity of the IPSP algorithm. Moreover, we give a graph with minimum edges used by IIPS to adjust locally, and we prove its existence and uniqueness and construct a local junction tree. Numerical experiments show that the IPSP-JT algorithm runs faster than the IPSP algorithm for large Gaussian graphical models.     

On the singularity of multivariate skew-symmetric models

In recent years, the skew-normal models introduced by Azzalini (1985) [1]-and their multivariate generalizations from Azzalini and Dalla Valle (1996) [4]-have enjoyed an amazing success, although an important literature has reported that they exhibit, in the vicinity of symmetry, singular Fisher information matrices and stationary points in the profile log-likelihood function for skewness, with the usual unpleasant consequences for inference. It has been shown (DiCiccio and Monti (2004) [23], DiCiccio and Monti (2009) [24] and Gómez et al. (2007) [25]) that these singularities, in some specific parametric extensions of skew-normal models (such as the classes of skew-t or skew-exponential power distributions), appear at skew-normal distributions only. Yet, an important question remains open: in broader semiparametric models of skewed distributions (such as the general skew-symmetric and skew-elliptical ones), which symmetric kernels lead to such singularities? The present paper provides an answer to this question. In very general (possibly multivariate) skew-symmetric models, we characterize, for each possible value of the rank of Fisher information matrices, the class of symmetric kernels achieving the corresponding rank. Our results show that, for strictly multivariate skew-symmetric models, not only Gaussian kernels yield singular Fisher information matrices. In contrast, we prove that systematic stationary points in the profile log-likelihood functions are obtained for (multi)normal kernels only. Finally, we also discuss the implications of such singularities on inference.     

High-Dimensional Mixed Graphical Models

While graphical models for continuous data (Gaussian graphical models) and discrete data (Ising models) have been extensively studied, there is little work on graphical models for datasets with both continuous and discrete variables (mixed data), which are common in many scientific applications. We propose a novel graphical model for mixed data, which is simple enough to be suitable for high-dimensional data, yet flexible enough to represent all possible graph structures. We develop a computationally efficient regression-based algorithm for fitting the model by focusing on the conditional log-likelihood of each variable given the rest. The parameters have a natural group structure, and sparsity in the fitted graph is attained by incorporating a group lasso penalty, approximated by a weighted lasso penalty for computational efficiency. We demonstrate the effectiveness of our method through an extensive simulation study and apply it to a music annotation dataset (CAL500), obtaining a sparse and interpretable graphical model relating the continuous features of the audio signal to binary variables such as genre, emotions, and usage associated with particular songs. While we focus on binary discrete variables for the main presentation, we also show that the proposed methodology can be easily extended to general discrete variables.     

Estimates of MM type for the multivariate linear model

We propose a class of robust estimates for multivariate linear models. Based on the approach of MM-estimation (Yohai 1987, [24]), we estimate the regression coefficients and the covariance matrix of the errors simultaneously. These estimates have both a high breakdown point and high asymptotic efficiency under Gaussian errors. We prove consistency and asymptotic normality assuming errors with an elliptical distribution. We describe an iterative algorithm for the numerical calculation of these estimates. The advantages of the proposed estimates over their competitors are demonstrated through both simulated and real data.     

Who's afraid of reduced-rank parameterizations of multivariate models? Theory and example

Reduced-rank restrictions can add useful parsimony to coefficient matrices of multivariate models, but their use is limited by the daunting complexity of the methods and their theory. The present work takes the easy road, focusing on unifying themes and simplified methods. For Gaussian and non-Gaussian (GLM, GAM, mixed normal, etc.) multivariate models, the present work gives a unified, explicit theory for the general asymptotic (normal) distribution of maximum likelihood estimators (MLE). MLE can be complex and computationally hard, but we show a strong asymptotic equivalence between MLE and a relatively simple minimum (Mahalanobis) distance estimator. The latter method yields particularly simple tests of rank, and we describe its asymptotic behavior in detail. We also examine the method's performance in simulation and via analytical and empirical examples.     

Selection of the Regularization Parameter in Graphical Models Using Network Characteristics

Gaussian graphical models represent the underlying graph structure of conditional dependence between random variables, which can be determined using their partial correlation or precision matrix. In a high-dimensional setting, the precision matrix is estimated using penalized likelihood by adding a penalization term, which controls the amount of sparsity in the precision matrix and totally characterizes the complexity and structure of the graph. The most commonly used penalization term is the L1 norm of the precision matrix scaled by the regularization parameter, which determines the trade-off between sparsity of the graph and fit to the data. In this article, we propose several procedures to select the regularization parameter in the estimation of graphical models that focus on recovering reliably the appropriate network structure of the graph. We conduct an extensive simulation study to show that the proposed methods produce useful results for different network topologies. The approaches are also applied in a high-dimensional case study of gene expression data with the aim to discover the genes relevant to colon cancer. Using these data, we find graph structures, which are verified to display significant biological gene associations. Supplementary material is available online.     

Robust Gaussian graphical modeling

A new Gaussian graphical modeling that is robustified against possible outliers is proposed. The likelihood function is weighted according to how the observation is deviated, where the deviation of the observation is measured based on its likelihood. Test statistics associated with the robustified estimators are developed. These include statistics for goodness of fit of a model. An outlying score, similar to but more robust than the Mahalanobis distance, is also proposed. The new scores make it easier to identify outlying observations. A Monte Carlo simulation and an analysis of a real data set show that the proposed method works better than ordinary Gaussian graphical modeling and some other robustified multivariate estimators.     

Asymptotic statistical equivalence for scalar ergodic diffusions

For scalar diffusion models with unknown drift function asymptotic equivalence in the sense of Le Cam's deficiency between statistical experiments is considered under long-time asymptotics. A local asymptotic equivalence result is established with an accompanying sequence of simple Gaussian shift experiments. Corresponding globally asymptotically equivalent experiments are obtained as compound experiments. The results are extended in several directions including time discretisation. An explicit transformation of decision functions from the Gaussian to the diffusion experiment is constructed. The authors acknowledge the financial support provided through the European Community's Human Potential Programme under contract HPRN-CT-2000-00100, DYNSTOCH     

Power of edge exclusion tests for graphical log-linear models

Asymptotic multivariate normal approximations to the joint distributions of edge exclusion test statistics for saturated graphical log-linear models, with all variables binary, are derived. Non-signed and signed square-root versions of the likelihood ratio, Wald and score test statistics are considered. Non-central chi-squared approximations are also considered for the non-signed versions of the test statistics. Simulation results are used to assess the quality of the proposed approximations. These approximations are used to estimate the overall power of edge exclusion tests. Power calculations are illustrated using data on university admissions.     

Regularized Estimation of Piecewise Constant Gaussian Graphical Models: The Group-Fused Graphical Lasso

The time-evolving precision matrix of a piecewise-constant Gaussian graphical model encodes the dynamic conditional dependency structure of a multivariate time-series. Traditionally, graphical models are estimated under the assumption that data are drawn identically from a generating distribution. Introducing sparsity and sparse-difference inducing priors, we relax these assumptions and propose a novel regularized M-estimator to jointly estimate both the graph and changepoint structure. The resulting estimator possesses the ability to therefore favor sparse dependency structures and/or smoothly evolving graph structures, as required. Moreover, our approach extends current methods to allow estimation of changepoints that are grouped across multiple dependencies in a system. An efficient algorithm for estimating structure is proposed. We study the empirical recovery properties in a synthetic setting. The qualitative effect of grouped changepoint estimation is then demonstrated by applying the method on a genetic time-course dataset. Supplementary material for this article is available online.     

The covariance structure and likelihood function for multivariate dyadic data

This paper extends the results in Li and Loken [A unified theory of statistical analysis and inference for variance component models for dyadic data, Statist. Sinica 12 (2002) 519-535] on the statistical analysis of measurements taken on dyads to the situations in which more than one attribute are measured on each dyad. Starting from the covariance structure for the univariate case obtained in Li and Loken (2002), the covariance structure for the multivariate case is derived based on the group symmetry induced by the assumed exchangeability in the units. Our primary objective is to document the Gaussian likelihood and the sufficient statistics for multivariate dyadic data in closed form, so that they can be referenced by researchers as they analyze those data. The derivation carried out can also serve as an example of multivariate extension of univariate models based on exchangeability.     

Modelling dependence

A new way of choosing a suitable copula to model dependence is introduced. Instead of relying on a given parametric family of copulas or applying the other extreme of modelling dependence in a nonparametric way, an intermediate approach is proposed, based on a sequence of parametric models containing more and more dependency aspects. In contrast to a similar way of thinking in testing theory, the method here, intended for estimating the copula, often requires a somewhat larger number of steps. One approach is based on exponential families, another on contamination families. An extensive numerical investigation is supplied on a large number of well-known copulas. The method based on contamination families is recommended. A Gaussian start in this approximation looks very promising.     

Asymptotic statistical equivalence for ergodic diffusions: the multidimensional case

Asymptotic local equivalence in the sense of Le Cam is established for inference on the drift in multidimensional ergodic diffusions and an accompanying sequence of Gaussian shift experiments. The nonparametric local neighbourhoods can be attained for any dimension, provided the regularity of the drift is sufficiently large. In addition, a heteroskedastic Gaussian regression experiment is given, which is also locally asymptotically equivalent and which does not depend on the centre of localisation. For one direction of the equivalence an explicit Markov kernel is constructed.     

A note on weak convergence of mean residual life of stationary mixing random variables

For a sequence of strictly stationary uniform or strong mixing we estimate the mean residual time of the marginal distribution from the first n observations. Under appropriate conditions it is shown that the estimate converges weakly to a well-defined Gaussian process even when the sample size is random.     

A decomposition of a linear model

In this paper we consider a general linear model in a continuous time. We propose a decomposition of the process which helps us to understand the structure of the model. Moreover, the sufficiency of the BLUE estimator of the expectation of the process can be characterized in terms of the Gaussian character of a component of the decomposition.     

How Many Ways Can One Draw A Graph?

Using results from extremal graph theory, we determine the asymptotic number of string graphs with n vertices, i.e., graphs that can be obtained as the intersection graph of a system of continuous arcs in the plane. The number becomes much smaller, for any fixed d, if we restrict our attention to systems of arcs, any two of which cross at most d times. As an application, we estimate the number of different drawings of the complete graph K_n with n vertices under various side conditions. Dedicated to Miklós Simonovits on his sixtieth birthday * Supported by NSF grant CR-00-98246, PSC-CUNY Research Award 62450-0031 and OTKA-T-032452. † Supported by OTKA-T-032452 and OTKA-T-038397.