Graphical models provide a framework for exploration of multivariate dependence patterns. The connection between graph and statistical model is made by identifying the vertices of the graph with the observed variables and translating the pattern of edges in the graph into a pattern of conditional independences that is imposed on the variables' joint distribution. Focusing on Gaussian models, we review classical graphical models. For these models the defining conditional independences are equivalent to vanishing of certain (partial) correlation coefficients associated with individual edges that are absent from the graph. Hence, Gaussian graphical model selection can be performed by multiple testing of hypotheses about vanishing (partial) correlation coefficients. We show and exemplify how this approach allows one to perform model selection while controlling error rates for incorrect edge inclusion.
Gaussian Graphical Model selection problem is considered. Concentration graph is identified by multiple decision procedure based on individual tests. Optimal unbiased individual tests are constructed. It is shown that optimal tests are equivalent to sample partial correlation tests. Associated multiple decision procedure is compared with standard procedure.
In many large scale multiple testing applications, the hypotheses often have a known graphical structure, such as gene ontology in gene expression data. Exploiting this graphical structure in multiple testing procedures can improve power as well as aid in interpretation. However, incorporating the structure into large scale testing procedures and proving that an error rate, such as the false discovery rate (FDR), is controlled can be challenging. In this paper, we introduce a new general approach for large scale multiple testing, which can aid in developing new procedures under various setting…
Model selection for Gaussian concentration graph is based on multiple testing of pairwise conditional independence. In practical applications partial correlation tests are widely used. However it is not known whether partial correlation test is uniformly most powerful for pairwise conditional independence testing. This question is answered in the paper. Uniformly most powerful unbiased test of Neymann structure is obtained. It turns out, that this test can be reduced to usual partial correlation test. It implies that partial correlation test is uniformly most powerful unbiased one.
We propose a new family of combinatorial inference problems for graphical models. Unlike classical statistical inference where the main interest is point estimation or parameter testing, combinatorial inference aims at testing the global structure of the underlying graph. Examples include testing the graph connectivity, the presence of a cycle of certain size, or the maximum degree of the graph. To begin with, we develop a unified theory for the fundamental limits of a large family of combinatorial inference problems. We propose new concepts including structural packing and buffer entropies to…
Testing (conditional) independence of multivariate random variables is a task central to statistical inference and modelling in general - though unfortunately one for which to date there does not exist a practicable workflow. State-of-art workflows suffer from the need for heuristic or subjective manual choices, high computational complexity, or strong parametric assumptions. We address these problems by establishing a theoretical link between multivariate/conditional independence testing, and model comparison in the multivariate predictive modelling aka supervised learning task. This link all…
This paper develops a new statistical inference theory for the precision matrix of high-frequency data in a high-dimensional setting. The focus is not only on point estimation but also on interval estimation and hypothesis testing for entries of the precision matrix. To accomplish this purpose, we establish an abstract asymptotic theory for the weighted graphical Lasso and its de-biased version without specifying the form of the initial covariance estimator. We also extend the scope of the theory to the case that a known factor structure is present in the data. The developed theory is applied …
Ron et al (1998) introduced a rich family of models for discrete longitudinal data, called acyclic probabilistic finite automata. These may be described as context-specific graphical models, since they are represented as directed multigraphs that embody context-specific conditional independence relations. Here we develop the methodology from a statistical modelling perspective. We show how likelihood ratio tests may be constructed using standard contingency table methods, and indicate how these may be used in model selection. We also show that the models generalize certain subclasses of conven…
Gaussian graphical model is a graphical representation of the dependence structure for a Gaussian random vector. It is recognized as a powerful tool in different applied fields such as bioinformatics, error-control codes, speech language, information retrieval and others. Gaussian graphical model selection is a statistical problem to identify the Gaussian graphical model from a sample of a given size. Different approaches for Gaussian graphical model selection are suggested in the literature. One of them is based on considering the family of individual conditional independence tests. The appli…
We study the problem of identifying the set of \emph{active} variables, termed in the literature as \emph{variable selection} or \emph{multiple hypothesis testing}, depending on the pursued criteria. For a general \emph{robust setting} of non-normal, possibly dependent observations and a generalized notion of \emph{active set}, we propose a procedure that is used simultaneously for the both tasks, variable selection and multiple testing. The procedure is based on the \emph{risk hull minimization} method, but can also be obtained as a result of an empirical Bayes approach or a penalization stra…
In many large multiple testing problems the hypotheses are divided into families. Given the data, families with evidence for true discoveries are selected, and hypotheses within them are tested. Neither controlling the error-rate in each family separately nor controlling the error-rate over all hypotheses together can assure that an error-rate is controlled in the selected families. We formulate this concern about selective inference in its generality, for a very wide class of error-rates and for any selection criterion, and present an adjustment of the testing level inside the selected famili…
Structure discovery in graphical models is the determination of the topology of a graph that encodes conditional independence properties of the joint distribution of all variables in the model. For some class of probability distributions, an edge between two variables is present if and only if the corresponding entry in the precision matrix is non-zero. For a finite sample estimate of the precision matrix, entries close to zero may be due to low sample effects, or due to an actual association between variables; these two cases are not readily distinguishable. %Fisher provided a hypothesis test…
This paper studies the estimation of high dimensional Gaussian graphical model (GGM). Typically, the existing methods depend on regularization techniques. As a result, it is necessary to choose the regularized parameter. However, the precise relationship between the regularized parameter and the number of false edges in GGM estimation is unclear. Hence, it is impossible to evaluate their performance rigorously. In this paper, we propose an alternative method by a multiple testing procedure. Based on our new test statistics for conditional dependence, we propose a simultaneous testing procedure…
The Gaussian graphical model is routinely employed to model the joint distribution of multiple random variables. The graph it induces is not only useful for describing the relationship between random variables but also critical for improving statistical estimation precision. In high-dimensional data analysis, despite an abundant literature on estimating this graph structure, tests for the adequacy of its specification at a global level is severely underdeveloped. To make progress, this paper proposes a novel goodness-of-fit test that is computationally easy and theoretically tractable. Under t…
When dealing with the problem of simultaneously testing a large number of null hypotheses, a natural testing strategy is to first reduce the number of tested hypotheses by some selection (screening or filtering) process, and then to simultaneously test the selected hypotheses. The main advantage of this strategy is to greatly reduce the severe effect of high dimensions. However, the first screening or selection stage must be properly accounted for in order to maintain some type of error control. In this paper, we will introduce a selection rule based on a selection statistic that is independen…
Recombinant Inbred Lines derived from divergent parental lines can display extensive segregation distortion and long-range linkage disequilibrium (LD) between distant loci. These genomic signatures are consistent with epistatic selection during inbreeding. Epistatic interactions affect growth and fertility traits or even cause complete lethality. Detecting epistasis is challenging as multiple testing approaches are under-powered and true long-range LD is difficult to distinguish from drift. Here we develop a method for reconstructing an underlying network of genomic signatures of high-dimensio…
Transfer learning for high-dimensional Gaussian graphical models (GGMs) is studied with the goal of estimating the target GGM by utilizing the data from similar and related auxiliary studies. The similarity between the target graph and each auxiliary graph is characterized by the sparsity of a divergence matrix. An estimation algorithm, Trans-CLIME, is proposed and shown to attain a faster convergence rate than the minimax rate in the single study setting. Furthermore, a debiased Trans-CLIME estimator is introduced and shown to be element-wise asymptotically normal. It is used to construct a m…
Functional brain networks are well described and estimated from data with Gaussian Graphical Models (GGMs), e.g. using sparse inverse covariance estimators. Comparing functional connectivity of subjects in two populations calls for comparing these estimated GGMs. Our goal is to identify differences in GGMs known to have similar structure. We characterize the uncertainty of differences with confidence intervals obtained using a parametric distribution on parameters of a sparse estimator. Sparse penalties enable statistical guarantees and interpretable models even in high-dimensional and low-sam…
Evidence synthesis models that combine multiple datasets of varying design, to estimate quantities that cannot be directly observed, require the formulation of complex probabilistic models that can be expressed as graphical models. An assessment of whether the different datasets synthesised contribute information that is consistent with each other, and in a Bayesian context, with the prior distribution, is a crucial component of the model criticism process. However, a systematic assessment of conflict suffers from the multiple testing problem, through testing for conflict at multiple locations…
We establish bounds on the KL divergence between two multivariate Gaussian distributions in terms of the Hamming distance between the edge sets of the corresponding graphical models. We show that the KL divergence is bounded below by a constant when the graphs differ by at least one edge; this is essentially the tightest possible bound, since classes of graphs exist for which the edge discrepancy increases but the KL divergence remains bounded above by a constant. As a natural corollary to our KL lower bound, we also establish a sample size requirement for correct model selection via maximum l…
We present a comprehensive study of graphical log-linear models for contingency tables. High dimensional contingency tables arise in many areas such as computational biology, collection of survey and census data and others. Analysis of contingency tables involving several factors or categorical variables is very hard. To determine interactions among various factors, graphical and decomposable log-linear models are preferred. First, we explore connections between the conditional independence in probability and graphs; thereafter we provide a few illustrations to describe how graphical log-linea…
Discussion of "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].
Discussion of "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].
We propose a comprehensive Bayesian approach for graphical model determination in observational studies that can accommodate binary, ordinal or continuous variables simultaneously. Our new models are called copula Gaussian graphical models (CGGMs) and embed graphical model selection inside a semiparametric Gaussian copula. The domain of applicability of our methods is very broad and encompasses many studies from social science and economics. We illustrate the use of the copula Gaussian graphical models in the analysis of a 16-dimensional functional disability contingency table.
Methods for selecting loglinear models were among Steve Fienberg's research interests since the start of his long and fruitful career. After we dwell upon the string of papers focusing on loglinear models that can be partly attributed to Steve's contributions and influential ideas, we develop a new algorithm for selecting graphical loglinear models that is suitable for analyzing hyper-sparse contingency tables. We show how multi-way contingency tables can be used to represent patterns of human mobility. We analyze a dataset of geolocated tweets from South Africa that comprises 46 million latit…
Multivariate density estimation and graphical models play important roles in statistical learning. The estimated density can be used to construct a graphical model that reveals conditional relationships whereas a graphical structure can be used to build models for density estimation. Our goal is to construct a consolidated framework that can perform both density and graph estimation. Denote $\bm{Z}$ as the random vector of interest with density function $f(\bz)$. Splitting $\bm{Z}$ into two parts, $\bm{Z}=(\bm{X}^T,\bm{Y}^T)^T$ and writing $f(\bz)=f(\bx)f(\by|\bx)$ where $f(\bx)$ is the densit…
We consider the estimation and inference of graphical models that characterize the dependency structure of high-dimensional tensor-valued data. To facilitate the estimation of the precision matrix corresponding to each way of the tensor, we assume the data follow a tensor normal distribution whose covariance has a Kronecker product structure. A critical challenge in the estimation and inference of this model is the fact that its penalized maximum likelihood estimation involves minimizing a non-convex objective function. To address it, this paper makes two contributions: (i) In spite of the non…
We propose a new class of semiparametric exponential family graphical models for the analysis of high dimensional mixed data. Different from the existing mixed graphical models, we allow the nodewise conditional distributions to be semiparametric generalized linear models with unspecified base measure functions. Thus, one advantage of our method is that it is unnecessary to specify the type of each node and the method is more convenient to apply in practice. Under the proposed model, we consider both problems of parameter estimation and hypothesis testing in high dimensions. In particular, we …
We present a new method for post-selection inference for L1 (lasso)-penalized likelihood models, including generalized regression models. Our approach generalizes the post-selection framework presented in Lee et al (2014). The method provides p-values and confidence intervals that are asymptotically valid, conditional on the inherent selection done by the lasso. We present applications of this work to (regularized) logistic regression, Cox's proportional hazards model and the graphical lasso.
We propose a novel class of time-varying nonparanormal graphical models, which allows us to model high dimensional heavy-tailed systems and the evolution of their latent network structures. Under this model, we develop statistical tests for presence of edges both locally at a fixed index value and globally over a range of values. The tests are developed for a high-dimensional regime, are robust to model selection mistakes and do not require commonly assumed minimum signal strength. The testing procedures are based on a high dimensional, debiasing-free moment estimator, which uses a novel kerne…
We consider tests of significance in the setting of the graphical lasso for inverse covariance matrix estimation. We propose a simple test statistic based on a subsequence of the knots in the graphical lasso path. We show that this statistic has an exponential asymptotic null distribution, under the null hypothesis that the model contains the true connected components. Though the null distribution is asymptotic, we show through simulation that it provides a close approximation to the true distribution at reasonable sample sizes. Thus the test provides a simple, tractable test for the significa…
We consider the problem of inferring the conditional independence graph (CIG) of a multivariate stationary dicrete-time Gaussian random process based on a finite length observation. Using information-theoretic methods, we derive a lower bound on the error probability of any learning scheme for the underlying process CIG. This bound, in turn, yields a minimum required sample-size which is necessary for any algorithm regardless of its computational complexity, to reliably select the true underlying CIG. Furthermore, by analysis of a simple selection scheme, we show that the information-theoretic…
Discussion of "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].
Discussion of "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].
Discussion of "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].
Discussion of "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].
Graphical model selection is a seemingly impossible task when many pairs of variables are never jointly observed; this requires inference of conditional dependencies with no observations of corresponding marginal dependencies. This under-explored statistical problem arises in neuroimaging, for example, when different partially overlapping subsets of neurons are recorded in non-simultaneous sessions. We call this statistical challenge the "Graph Quilting" problem. We study this problem in the context of sparse inverse covariance learning, and focus on Gaussian graphical models where we show tha…
California Institute of Technology（加州理工学院）；Massachusetts Institute of Technology（麻省理工学院）
Rejoinder to "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].
The topic of this paper is modeling and analyzing dependence in stochastic social networks. Using a latent variable block model allows the analysis of dependence between blocks via the analysis of a latent graphical model. Our approach to the analysis of the graphical model then is based on the idea underlying the neighborhood selection scheme put forward by Meinshausen and Bühlmann (2006). However, because of the latent nature of our model, estimates have to be used in lieu of the unobserved variables. This leads to a novel analysis of graphical models under uncertainty, in the spirit of Rose…
This paper deals with the Bayesian estimation of high dimensional Gaussian graphical models. We develop a quasi-Bayesian implementation of the neighborhood selection method of Meinshausen and Buhlmann (2006) for the estimation of Gaussian graphical models. The method produces a product-form quasi-posterior distribution that can be efficiently explored by parallel computing. We derive a non-asymptotic bound on the contraction rate of the quasi-posterior distribution. The result shows that the proposed quasi-posterior distribution contracts towards the true precision matrix at a rate given by th…
Center for Pervasive Communications and Computing（普适通信与计算中心）；University of California, Irvine（加利福尼亚大学欧文分校）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；Laboratory for Information and Decision Systems（信息与决策系统实验室）；Massachusetts Institute of Technology（麻省理工学院）
We consider the problem of high-dimensional Gaussian graphical model selection. We identify a set of graphs for which an efficient estimation algorithm exists, and this algorithm is based on thresholding of empirical conditional covariances. Under a set of transparent conditions, we establish structural consistency (or sparsistency) for the proposed algorithm, when the number of samples n=omega(J_{min}^{-2} log p), where p is the number of variables and J_{min} is the minimum (absolute) edge potential of the graphical model. The sufficient conditions for sparsistency are based on the notion of…
This paper studies graphical model selection, i.e., the problem of estimating a graph of statistical relationships among a collection of random variables. Conventional graphical model selection algorithms are passive, i.e., they require all the measurements to have been collected before processing begins. We propose an active learning algorithm that uses junction tree representations to adapt future measurements based on the information gathered from prior measurements. We prove that, under certain conditions, our active learning algorithm requires fewer scalar measurements than any passive al…
We consider the problem of estimating the graph structure associated with a discrete Markov random field. We describe a method based on $\ell_1$-regularized logistic regression, in which the neighborhood of any given node is estimated by performing logistic regression subject to an $\ell_1$-constraint. Our framework applies to the high-dimensional setting, in which both the number of nodes $p$ and maximum neighborhood sizes $d$ are allowed to grow as a function of the number of observations $n$. Our main results provide sufficient conditions on the triple $(n, p, d)$ for the method to succeed …
In order to make graphical Gaussian models a viable modelling tool when the number of variables outgrows the number of observations, model classes which place equality restrictions on concentrations or partial correlations have previously been introduced in the literature. The models can be represented by vertex and edge coloured graphs. The need for model selection methods makes it imperative to understand the structure of model classes. We identify four model classes that form complete lattices of models with respect to model inclusion, which qualifies them for an Edwards-Havránek model sele…
We consider multivariate centered Gaussian models for the random vector $(Z^1,\ldots, Z^p)$, whose conditional structure is described by a homogeneous graph and which is invariant under the action of a permutation subgroup. The following paper concerns with model selection within colored graphical Gaussian models, when the underlying conditional dependency graph is known. We derive an analytic expression of the normalizing constant of the Diaconis-Ylvisaker conjugate prior for the precision parameter and perform Bayesian model selection in the class of graphical Gaussian models invariant by th…
Testing properties of trees in graphical models with covariance queries
IMTECH and Departament de Matemàtiques, Universitat Politècnica de Catalunya, Barcelona, Spain and Department of Economics and Business, Pompeu Fabra University, Barcelona, Spain（IMTECH 和 巴塞罗那理工大学数学系及巴塞罗那庞培法华大学经济与商业系，西班牙巴塞罗那）；LPSM, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France（巴黎索邦大学LPSM，法国巴黎，4 Place Jussieu, 75005）；ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain（ICREA，西班牙巴塞罗那Lluís Companys 23号，08010；巴塞罗那庞培法华大学经济与商业系，西班牙巴塞罗那；巴塞罗那经济学院）；Department of Economics and Business, Pompeu Fabra University, Barcelona, Spain（巴塞罗那庞培法华大学经济与商业系，西班牙巴塞罗那；巴塞罗那经济学院）；Barcelona School of Economics；Department of Economics and Business, Pompeu Fabra University, Barcelona, Spain；Barcelona School of Economics
