In this paper, we propose a class of Bayes estimators for the covariance matrix of graphical Gaussian models Markov with respect to a decomposable graph $G$. Working with the $W_{P_G}$ family defined by Letac and Massam [Ann. Statist. 35 (2007) 1278--1323] we derive closed-form expressions for Bayes estimators under the entropy and squared-error losses. The $W_{P_G}$ family includes the classical inverse of the hyper inverse Wishart but has many more shape parameters, thus allowing for flexibility in differentially shrinking various parts of the covariance matrix. Moreover, using this family avoids recourse to MCMC, often infeasible in high-dimensional problems. We illustrate the performance of our estimators through a collection of numerical examples where we explore frequentist risk properties and the efficacy of graphs in the estimation of high-dimensional covariance structures.
Undirected graphs are often used to describe high dimensional distributions. Under sparsity conditions, the graph can be estimated using $\ell_1$-penalization methods. We propose and study the following method. We combine a multiple regression approach with ideas of thresholding and refitting: first we infer a sparse undirected graphical model structure via thresholding of each among many $\ell_1$-norm penalized regression functions; we then estimate the covariance matrix and its inverse using the maximum likelihood estimator. We show that under suitable conditions, this approach yields consis…
Covariance graphical lasso applies a lasso penalty on the elements of the covariance matrix. This method is useful because it not only produces sparse estimation of covariance matrix but also discovers marginal independence structures by generating zeros in the covariance matrix. We propose and explore two new algorithms for solving the covariance graphical lasso problem. Our new algorithms are based on coordinate descent and ECM. We show that these two algorithms are more attractive than the only existing competing algorithm of Bien and Tibshirani (2011) in terms of simplicity, speed and stab…
KU Leuven（鲁汶大学）；Leuven Statistics Research Center (LStat)（鲁汶统计研究中心）；Université Paris Descartes（巴黎笛卡尔大学）；CNRS（法国国家科学研究中心）；Université Paris-Sud（巴黎南大学）；INRA（法国国家农业研究院）
Gaussian graphical models are widely utilized to infer and visualize networks of dependencies between continuous variables. However, inferring the graph is difficult when the sample size is small compared to the number of variables. To reduce the number of parameters to estimate in the model, we propose a non-asymptotic model selection procedure supported by strong theoretical guarantees based on an oracle inequality and a minimax lower bound. The covariance matrix of the model is approximated by a block-diagonal matrix. The structure of this matrix is detected by thresholding the sample covar…
We consider the sparse inverse covariance regularization problem or graphical lasso with regularization parameter $ρ$. Suppose the co- variance graph formed by thresholding the entries of the sample covariance matrix at $ρ$ is decomposed into connected components. We show that the vertex-partition induced by the thresholded covariance graph is exactly equal to that induced by the estimated concentration graph. This simple rule, when used as a wrapper around existing algorithms, leads to enormous performance gains. For large values of $ρ$, our proposal splits a large graphical lasso problem int…
We develop a new estimator of the inverse covariance matrix for high-dimensional multivariate normal data using the horseshoe prior. The proposed graphical horseshoe estimator has attractive properties compared to other popular estimators, such as the graphical lasso and graphical Smoothly Clipped Absolute Deviation (SCAD). The most prominent benefit is that when the true inverse covariance matrix is sparse, the graphical horseshoe provides estimates with small information divergence from the true sampling distribution. The posterior mean under the graphical horseshoe prior can also be almost …
Toyota Technological Institute at Chicago（芝加哥丰田理工学院）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
This paper considers the problem of estimating multiple related Gaussian graphical models from a $p$-dimensional dataset consisting of different classes. Our work is based upon the formulation of this problem as group graphical lasso. This paper proposes a novel hybrid covariance thresholding algorithm that can effectively identify zero entries in the precision matrices and split a large joint graphical lasso problem into small subproblems. Our hybrid covariance thresholding method is superior to existing uniform thresholding methods in that our method can split the precision matrix of each in…
The precision matrix that encodes conditional linear dependency relations among a set of variables forms an important object of interest in multivariate analysis. Sparse estimation procedures for precision matrices such as the graphical lasso (Glasso) gained popularity as they facilitate interpretability, thereby separating pairs of variables that are conditionally dependent from those that are independent (given all other variables). Glasso lacks, however, robustness to outliers. To overcome this problem, one typically applies a robust plug-in procedure where the Glasso is computed from a rob…
University of California, Santa Barbara（加州大学圣巴巴拉分校）
Building on a recent framework for distributionally robust optimization, we consider estimation of the inverse covariance matrix for multivariate data. We provide a novel notion of a Wasserstein ambiguity set specifically tailored to this estimation problem, leading to a tractable class of regularized estimators. Special cases include penalized likelihood estimators for Gaussian data, specifically the graphical lasso estimator. As a consequence of this formulation, the radius of the Wasserstein ambiguity set is directly related to the regularization parameter in the estimation problem. Using t…
The graphical lasso (glasso) is a widely-used fast algorithm for estimating sparse inverse covariance matrices. The glasso solves an L1 penalized maximum likelihood problem and is available as an R library on CRAN. The output from the glasso, a regularized covariance matrix estimate a sparse inverse covariance matrix estimate, not only identify a graphical model but can also serve as intermediate inputs into multivariate procedures such as PCA, LDA, MANOVA, and others. The glasso indeed produces a covariance matrix estimate which solves the L1 penalized optimization problem in a dual sense; ho…
We consider the problem of estimating multiple related but distinct graphical models on the basis of a high-dimensional data set with observations that belong to distinct classes. A motivating example occurs in the analysis of gene expression data for tissue samples with and without cancer. In this case, we might wish to estimate a gene expression network for the normal tissue and a gene expression network for the tumor tissue. We expect the two gene expression networks to be similar but not identical to each other, and so more accurate estimation of these two networks may be possible using a …
Anomalies and outliers are common in real-world data, and they can arise from many sources, such as sensor faults. Accordingly, anomaly detection is important both for analyzing the anomalies themselves and for cleaning the data for further analysis of its ambient structure. Nonetheless, a precise definition of anomalies is important for automated detection and herein we approach such problems from the perspective of detecting sparse latent effects embedded in large collections of noisy data. Standard Graphical Lasso-based techniques can identify the conditional dependency structure of a colle…
In this paper, we introduce a new directed graphical model from Gaussian data: the Gaussian graphical interaction model (GGIM). The development of this model comes from considering stationary Gaussian processes on graphs, and leveraging the equations between the resulting steady-state covariance matrix and the Laplacian matrix representing the interaction graph. Through the presentation of conceptually straightforward theory, we develop the new model and provide interpretations of the edges in the graphical model in terms of statistical measures. We show that when restricted to undirected grap…
This paper studies iteration convergence of Kronecker graphical lasso (KGLasso) algorithms for estimating the covariance of an i.i.d. Gaussian random sample under a sparse Kronecker-product covariance model and MSE convergence rates. The KGlasso model, originally called the transposable regularized covariance model by Allen ["Transposable regularized covariance models with an application to missing data imputation," Ann. Appl. Statist., vol. 4, no. 2, pp. 764-790, 2010], implements a pair of $\ell_1$ penalties on each Kronecker factor to enforce sparsity in the covariance estimator. The KGlass…
We introduce the Poisson Log-Normal Graphical Model for count data, and present a normality transformation for data arising from this distribution. The model and transformation are feasible for high-throughput microRNA (miRNA) sequencing data and directly account for known overdispersion relationships present in this data set. The model allows for network dependencies to be modeled, and we provide an algorithm which utilizes a one-step EM based result in order to allow for a provable increase in performance in determining the network structure. The model is shown to provide an increase in perf…
A precision matrix is the inverse of a covariance matrix. In this paper, we study the problem of estimating the precision matrix with a known graphical structure under high-dimensional settings. We propose a simple estimator of the precision matrix based on the connection between the known graphical structure and the precision matrix. We obtain the rates of convergence of the proposed estimators and derive the asymptotic normality of the proposed estimator in the high-dimensional setting when the data dimension grows with the sample size. Numerical simulations are conducted to demonstrate the …
We consider estimation of covariance matrices and their inverses (a.k.a. precision matrices) for high-dimensional stationary and locally stationary time series. In the latter case the covariance matrices evolve smoothly in time, thus forming a covariance matrix function. Using the functional dependence measure of Wu [Proc. Natl. Acad. Sci. USA 102 (2005) 14150-14154 (electronic)], we obtain the rate of convergence for the thresholded estimate and illustrate how the dependence affects the rate of convergence. Asymptotic properties are also obtained for the precision matrix estimate which is bas…
Brain networks has attracted the interests of many neuroscientists. From functional MRI (fMRI) data, statistical tools have been developed to recover brain networks. However, the dimensionality of whole-brain fMRI, usually in hundreds of thousands, challenges the applicability of these methods. We develop a hierarchical graphical model (HGM) to remediate this difficulty. This model introduces a hidden layer of networks based on sparse Gaussian graphical models, and the observed data are sampled from individual network nodes. In fMRI, the network layer models the underlying signals of different…
Several methods have been recently proposed for estimating sparse Gaussian graphical models using $\ell_{1}$ regularization on the inverse covariance matrix. Despite recent advances, contemporary applications require methods that are even faster in order to handle ill-conditioned high dimensional modern day datasets. In this paper, we propose a new method, G-AMA, to solve the sparse inverse covariance estimation problem using Alternating Minimization Algorithm (AMA), that effectively works as a proximal gradient algorithm on the dual problem. Our approach has several novel advantages over exis…
We propose a scalable, efficient and statistically motivated computational framework for Graphical Lasso (Friedman et al., 2007b) - a covariance regularization framework that has received significant attention in the statistics community over the past few years. Existing algorithms have trouble in scaling to dimensions larger than a thousand. Our proposal significantly enhances the state-of-the-art for such moderate sized problems and gracefully scales to larger problems where other algorithms become practically infeasible. This requires a few key new ideas. We operate on the primal problem an…
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…
In a Gaussian graphical model, the conditional independence between two variables are characterized by the corresponding zero entries in the inverse covariance matrix. Maximum likelihood method using the smoothly clipped absolute deviation (SCAD) penalty (Fan and Li, 2001) and the adaptive LASSO penalty (Zou, 2006) have been proposed in literature. In this article, we establish the result that using Bayesian information criterion (BIC) to select the tuning parameter in penalized likelihood estimation with both types of penalties can lead to consistent graphical model selection. We compare the …
Large-scale precision matrix estimation is of fundamental importance yet challenging in many contemporary applications for recovering Gaussian graphical models. In this paper, we suggest a new approach of innovated scalable efficient estimation (ISEE) for estimating large precision matrix. Motivated by the innovated transformation, we convert the original problem into that of large covariance matrix estimation. The suggested method combines the strengths of recent advances in high-dimensional sparse modeling and large covariance matrix estimation. Compared to existing approaches, our method is…
University of California, Irvine（加利福尼亚大学欧文分校）；University of California, Los Angeles（加利福尼亚大学洛杉矶分校）
We consider the problem of estimating the inverse covariance matrix by maximizing the likelihood function with a penalty added to encourage the sparsity of the resulting matrix. We propose a new approach based on the split Bregman method to solve the regularized maximum likelihood estimation problem. We show that our method is significantly faster than the widely used graphical lasso method, which is based on blockwise coordinate descent, on both artificial and real-world data. More importantly, different from the graphical lasso, the split Bregman based method is much more general, and can be…
High dimensional covariance estimation and graphical models is a contemporary topic in statistics and machine learning having widespread applications. An important line of research in this regard is to shrink the extreme spectrum of the covariance matrix estimators. A separate line of research in the literature has considered sparse inverse covariance estimation which in turn gives rise to graphical models. In practice, however, a sparse covariance or inverse covariance matrix which is simultaneously well-conditioned and at the same time computationally tractable is desired. There has been lit…
We consider the problem of Graphical lasso with an additional $\ell_{\infty}$ element-wise norm constraint on the precision matrix. This problem has applications in high-dimensional covariance decomposition such as in \citep{Janzamin-12}. We propose an ADMM algorithm to solve this problem. We also use a continuation strategy on the penalty parameter to have a fast implemenation of the algorithm.
We study ridge estimation of the precision matrix in the high-dimensional setting where the number of variables is large relative to the sample size. We first review two archetypal ridge estimators and note that their utilized penalties do not coincide with common ridge penalties. Subsequently, starting from a common ridge penalty, analytic expressions are derived for two alternative ridge estimators of the precision matrix. The alternative estimators are compared to the archetypes with regard to eigenvalue shrinkage and risk. The alternatives are also compared to the graphical lasso within th…
Graphical Lasso (GL) is a popular method for learning the structure of an undirected graphical model, which is based on an $l_1$ regularization technique. The objective of this paper is to compare the computationally-heavy GL technique with a numerically-cheap heuristic method that is based on simply thresholding the sample covariance matrix. To this end, two notions of sign-consistent and inverse-consistent matrices are developed, and then it is shown that the thresholding and GL methods are equivalent if: (i) the thresholded sample covariance matrix is both sign-consistent and inverse-consis…
We consider the problem of constructing nonparametric undirected graphical models for high-dimensional functional data. Most existing statistical methods in this context assume either a Gaussian distribution on the vertices or linear conditional means. In this article we provide a more flexible model which relaxes the linearity assumption by replacing it by an arbitrary additive form. The use of functional principal components offers an estimation strategy that uses a group lasso penalty to estimate the relevant edges of the graph. We establish statistical guarantees for the resulting estimato…
We consider the problem of covariance matrix estimation in the presence of latent variables. Under suitable conditions, it is possible to learn the marginal covariance matrix of the observed variables via a tractable convex program, where the concentration matrix of the observed variables is decomposed into a sparse matrix (representing the graphical structure of the observed variables) and a low rank matrix (representing the marginalization effect of latent variables). We present an efficient first-order method based on split Bregman to solve the convex problem. The algorithm is guaranteed to…
The interactions between microbial taxa in microbiome data has been under great research interest in the science community. In particular, several methods such as SPIEC-EASI, gCoda, and CD-trace have been proposed to model the conditional dependency between microbial taxa, in order to eliminate the detection of spurious correlations. However, all those methods are built upon the central log-ratio (CLR) transformation, which results in a degenerate covariance matrix and thus an undefined inverse covariance matrix as the estimation of the underlying network. Jiang et al. (2021) and Tian et al. (…
The sparse inverse covariance estimation problem is commonly solved using an $\ell_{1}$-regularized Gaussian maximum likelihood estimator known as "graphical lasso", but its computational cost becomes prohibitive for large data sets. A recent line of results showed--under mild assumptions--that the graphical lasso estimator can be retrieved by soft-thresholding the sample covariance matrix and solving a maximum determinant matrix completion (MDMC) problem. This paper proves an extension of this result, and describes a Newton-CG algorithm to efficiently solve the MDMC problem. Assuming that the…
The dependency structure of multivariate data can be analyzed using the covariance matrix $Σ$. In many fields the precision matrix $Σ^{-1}$ is even more informative. As the sample covariance estimator is singular in high-dimensions, it cannot be used to obtain a precision matrix estimator. A popular high-dimensional estimator is the graphical lasso, but it lacks robustness. We consider the high-dimensional independent contamination model. Here, even a small percentage of contaminated cells in the data matrix may lead to a high percentage of contaminated rows. Downweighting entire observations,…
We propose to learn latent graphical models when data have mixed variables and missing values. This model could be used for further data analysis, including regression, classification, ranking etc. It also could be used for imputing missing values. We specify a latent Gaussian model for the data, where the categorical variables are generated by discretizing an unobserved variable and the latent variables are multivariate Gaussian. The observed data consists of two parts: observed Gaussian variables and observed categorical variables, where the latter part is considered as partially missing Gau…
We consider estimation of undirected Gaussian graphical models and inverse covariances in high-dimensional scenarios by penalizing the corresponding precision matrix. While single $L_1$ (Graphical Lasso) and $L_2$ (Graphical Ridge) penalties for the precision matrix have already been studied, we propose the combination of both, yielding an Elastic Net type penalty. We enable additional flexibility by allowing to include diagonal target matrices for the precision matrix. We generalize existing algorithms for the Graphical Lasso and provide corresponding software with an efficient implementation…
The graphical lasso \citep{FHT2007a} is an algorithm for learning the structure in an undirected Gaussian graphical model, using $\ell_1$ regularization to control the number of zeros in the precision matrix ${\BΘ}={\BΣ}^{-1}$ \citep{BGA2008,yuan_lin_07}. The {\texttt R} package \GL\ \citep{FHT2007a} is popular, fast, and allows one to efficiently build a path of models for different values of the tuning parameter. Convergence of \GL\ can be tricky; the converged precision matrix might not be the inverse of the estimated covariance, and occasionally it fails to converge with warm starts. In th…
We present the path-sum formulation for exact statistical inference of marginals on Gaussian graphical models of arbitrary topology. The path-sum formulation gives the covariance between each pair of variables as a branched continued fraction of finite depth and breadth. Our method originates from the closed-form resummation of infinite families of terms of the walk-sum representation of the covariance matrix. We prove that the path-sum formulation always exists for models whose covariance matrix is positive definite: i.e.~it is valid for both walk-summable and non-walk-summable graphical mode…
Florida State University（佛罗里达州立大学）；University of South Florida（南佛罗里达大学）
Complex analyses involving multiple, dependent random quantities often lead to graphical models - a set of nodes denoting variables of interest, and corresponding edges denoting statistical interactions between nodes. To develop statistical analyses for graphical data, especially towards generative modeling, one needs mathematical representations and metrics for matching and comparing graphs, and subsequent tools, such as geodesics, means, and covariances. This paper utilizes a quotient structure to develop efficient algorithms for computing these quantities, leading to useful statistical tool…
Finding an unconstrained and statistically interpretable reparameterization of a covariance matrix is still an open problem in statistics. Its solution is of central importance in covariance estimation, particularly in the recent high-dimensional data environment where enforcing the positive-definiteness constraint could be computationally expensive. We provide a survey of the progress made in modeling covariance matrices from two relatively complementary perspectives: (1) generalized linear models (GLM) or parsimony and use of covariates in low dimensions, and (2) regularization or sparsity f…
Directed graphical models specify noisy functional relationships among a collection of random variables. In the Gaussian case, each such model corresponds to a semi-algebraic set of positive definite covariance matrices. The set is given via parametrization, and much work has gone into obtaining an implicit description in terms of polynomial (in-)equalities. Implicit descriptions shed light on problems such as parameter identification, model equivalence, and constraint-based statistical inference. For models given by directed acyclic graphs, which represent settings where all relevant variable…
We propose the use of a robust covariance estimator based on multivariate Winsorization in the context of the Tarr-Muller-Weber framework for sparse estimation of the precision matrix of a Gaussian graphical model. Likewise Croux-Ollerer's precision matrix estimator, our proposed estimator attains the maximum finite sample breakdown point of 0.5 under cellwise contamination. We conduct an extensive Monte Carlo simulation study to assess the performance of ours and the currently existing proposals. We find that ours has a competitive behavior, regarding the the estimation of the precision matri…
Gaussian graphical models (GGMs) are probabilistic tools of choice for analyzing conditional dependencies between variables in complex systems. Finding changepoints in the structural evolution of a GGM is therefore essential to detecting anomalies in the underlying system modeled by the GGM. In order to detect structural anomalies in a GGM, we consider the problem of estimating changes in the precision matrix of the corresponding Gaussian distribution. We take a two-step approach to solving this problem:- (i) estimating a background precision matrix using system observations from the past with…
To model high dimensional data, Gaussian methods are widely used since they remain tractable and yield parsimonious models by imposing strong assumptions on the data. Vine copulas are more flexible by combining arbitrary marginal distributions and (conditional) bivariate copulas. Yet, this adaptability is accompanied by sharply increasing computational effort as the dimension increases. The approach proposed in this paper overcomes this burden and makes the first step into ultra high dimensional non-Gaussian dependence modeling by using a divide-and-conquer approach. First, we apply Gaussian m…
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…
We study the problem of estimating from data, a sparse approximation to the inverse covariance matrix. Estimating a sparsity constrained inverse covariance matrix is a key component in Gaussian graphical model learning, but one that is numerically very challenging. We address this challenge by developing a new adaptive gradient-based method that carefully combines gradient information with an adaptive step-scaling strategy, which results in a scalable, highly competitive method. Our algorithm, like its predecessors, maximizes an $\ell_1$-norm penalized log-likelihood and has the same per itera…
This paper introduces the Sylvester graphical lasso (SyGlasso) that captures multiway dependencies present in tensor-valued data. The model is based on the Sylvester equation that defines a generative model. The proposed model complements the tensor graphical lasso (Greenewald et al., 2019) that imposes a Kronecker sum model for the inverse covariance matrix by providing an alternative Kronecker sum model that is generative and interpretable. A nodewise regression approach is adopted for estimating the conditional independence relationships among variables. The statistical convergence of the m…
Multichannel electroencephalograms (EEGs) have been widely used to study cortical connectivity during acquisition of motor skills. In this paper, we introduce copula Gaussian graphical models on spectral domain to characterize dependence in oscillatory activity between channels. To obtain a simple and robust representation of brain connectivity that can explain the most variation in the observed signals, we propose a framework based on maximizing penalized likelihood with Lasso regularization to search for the sparse precision matrix. To address the optimization problem, graphical Lasso, Ledoi…
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 …
Lawrence Berkeley National Lab（劳伦斯伯克利国家实验室）；Stanford University（斯坦福大学）；University of Florida（佛罗里达大学）
Sparse high dimensional graphical model selection is a popular topic in contemporary machine learning. To this end, various useful approaches have been proposed in the context of $\ell_1$-penalized estimation in the Gaussian framework. Though many of these inverse covariance estimation approaches are demonstrably scalable and have leveraged recent advances in convex optimization, they still depend on the Gaussian functional form. To address this gap, a convex pseudo-likelihood based partial correlation graph estimation method (CONCORD) has been recently proposed. This method uses coordinate-wi…
We investigate the relationship between the structure of a discrete graphical model and the support of the inverse of a generalized covariance matrix. We show that for certain graph structures, the support of the inverse covariance matrix of indicator variables on the vertices of a graph reflects the conditional independence structure of the graph. Our work extends results that have previously been established only in the context of multivariate Gaussian graphical models, thereby addressing an open question about the significance of the inverse covariance matrix of a non-Gaussian distribution.…
Many modern spatial models express the stochastic variation component as a basis expansion with random coefficients. Low rank models, approximate spectral decompositions, multiresolution representations, stochastic partial differential equations and empirical orthogonal functions all fall within this basic framework. Given a particular basis, stochastic dependence relies on flexible modeling of the coefficients. Under a Gaussianity assumption, we propose a graphical model family for the stochastic coefficients by parameterizing the precision matrix. Sparsity in the precision matrix is encourag…
