Accurate model selection is a fundamental requirement for statistical analysis. In many real-world applications of graphical modelling, correct model structure identification is the ultimate objective. Standard model validation procedures such as information theoretic scores and cross validation have demonstrated poor performance in the high dimensional setting. Specialised methods such as EBIC, StARS and RIC have been developed for the explicit purpose of high-dimensional Gaussian graphical model selection. We present a novel model score criterion, Graphical Neighbour Information. This method demonstrates oracle performance in high-dimensional model selection, outperforming the current state-of-the-art in our simulations. The Graphical Neighbour Information criterion has the additional advantage of efficient, closed-form computability, sparing the costly inference of multiple models on data subsamples. We provide a theoretical analysis of the method and benchmark simulations versus the current state of the art.
We characterize the sample size required for accurate graphical model selection from non-stationary samples. The observed data is modeled as a vector-valued zero-mean Gaussian random process whose samples are uncorrelated but have different covariance matrices. This model contains as special cases the standard setting of i.i.d. samples as well as the case of samples forming a stationary or underspread (non-stationary) processes. More generally, our model applies to any process model for which an efficient decorrelation can be obtained. By analyzing a particular model selection method, we deriv…
University of Illinois, Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
This paper addresses the problem of neighborhood selection for Gaussian graphical models. We present two heuristic algorithms: a forward-backward greedy algorithm for general Gaussian graphical models based on mutual information test, and a threshold-based algorithm for walk summable Gaussian graphical models. Both algorithms are shown to be structurally consistent, and efficient. Numerical results show that both algorithms work very well.
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].
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].
Local approximations are popular methods to scale Gaussian processes (GPs) to big data. Local approximations reduce time complexity by dividing the original dataset into subsets and training a local expert on each subset. Aggregating the experts' prediction is done assuming either conditional dependence or independence between the experts. Imposing the \emph{conditional independence assumption} (CI) between the experts renders the aggregation of different expert predictions time efficient at the cost of poor uncertainty quantification. On the other hand, modeling dependent experts can provide …
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…
Rice University（莱斯大学）；Baylor College of Medicine（贝勒医学院）
In neuroscience, researchers seek to uncover the connectivity of neurons from large-scale neural recordings or imaging; often people employ graphical model selection and estimation techniques for this purpose. But, existing technologies can only record from a small subset of neurons leading to a challenging problem of graph selection in the presence of extensive latent variables. Chandrasekaran et al. (2012) proposed a convex program to address this problem that poses challenges from both a computational and statistical perspective. To solve this problem, we propose an incredibly simple soluti…
Università Cattolica del Sacro Cuore（圣心天主教大学）；Università degli Studi di Torino（都灵大学）
This paper proposes a new algorithm for an automatic variable selection procedure in High Dimensional Graphical Models. The algorithm selects the relevant variables for the node of interest on the basis of mutual information. Several contributions in literature have investigated the use of mutual information in selecting the appropriate number of relevant features in a large data-set, but most of them have focused on binary outcomes or required high computational effort. The algorithm here proposed overcomes these drawbacks as it is an extension of Chow and Liu's algorithm. Once, the probabili…
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…
We consider the problem of estimating the topology of spatial interactions in a discrete state, discrete time spatio-temporal graphical model where the interactions affect the temporal evolution of each agent in a network. Among other models, the susceptible, infected, recovered ($SIR$) model for interaction events fall into this framework. We pose the problem as a structure learning problem and solve it using an $\ell_1$-penalized likelihood convex program. We evaluate the solution on a simulated spread of infectious over a complex network. Our topology estimates outperform those of a standar…
John A. Paulson School of Engineering and Applied Sciences, Harvard University（哈佛大学约翰·A·保尔森工程与应用科学学院）；Department of Electrical and Computer Engineering, Duke University（杜克大学电气与计算机工程系）
We consider the problem of model selection in Gaussian Markov fields in the sample deficient scenario. In many practically important cases, the underlying networks are embedded into Euclidean spaces. Using the natural geometric structure, we introduce the notion of spatially stationary distributions over geometric graphs. This directly generalizes the notion of stationary time series to the multidimensional setting lacking time axis. We show that the idea of spatial stationarity leads to a dramatic decrease in the sample complexity of the model selection compared to abstract graphs with the sa…
This thesis studies two problems in modern statistics. First, we study selective inference, or inference for hypothesis that are chosen after looking at the data. The motiving application is inference for regression coefficients selected by the lasso. We present the Condition-on-Selection method that allows for valid selective inference, and study its application to the lasso, and several other selection algorithms. In the second part, we consider the problem of learning the structure of a pairwise graphical model over continuous and discrete variables. We present a new pairwise model for grap…
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…
CMAP, CNRS, École polytechnique（应用数学中心、法国国家科学研究中心、巴黎综合理工学院）；Aramis project-team, Inria（Aramis项目组、法国国家信息与自动化研究所）；Institut du Cerveau et de la Moelle épinière, Sorbonne University, Inserm U1127, CNRS UMR 7225（脑与脊髓研究所、索邦大学、法国国家健康与医学研究院U1127、法国国家科学研究中心UMR 7225）；Hôpital Européen Georges-Pompidou AP-HP（乔治·蓬皮杜欧洲医院（巴黎公立医院集团））；Centre de Recherche des Cordeliers, Université de Paris, INSERM, Sorbonne Université（科德利耶研究中心、巴黎大学、法国国家健康与医学研究院、索邦大学）
Gaussian Graphical Models (GGM) are often used to describe the conditional correlations between the components of a random vector. In this article, we compare two families of GGM inference methods: nodewise edge selection and penalised likelihood maximisation. We demonstrate on synthetic data that, when the sample size is small, the two methods produce graphs with either too few or too many edges when compared to the real one. As a result, we propose a composite procedure that explores a family of graphs with an nodewise numerical scheme and selects a candidate among them with an overall likel…
We propose a method for inferring the conditional indepen- dence graph (CIG) of a high-dimensional discrete-time Gaus- sian vector random process from finite-length observations. Our approach does not rely on a parametric model (such as, e.g., an autoregressive model) for the vector random process; rather, it only assumes certain spectral smoothness proper- ties. The proposed inference scheme is compressive in that it works for sample sizes that are (much) smaller than the number of scalar process components. We provide analytical conditions for our method to correctly identify the CIG with hi…
High-dimensional Functional Graphical Model Structure Learning via Neighborhood Selection Approach
Booth School of Business, The University of Chicago（芝加哥大学布斯商学院）；Department of Statistics and Data Science, Cornell University（康奈尔大学统计与数据科学系）；Department of Data Sciences and Operations, Marshall School of Business, University of Southern California（南加州大学马歇尔商学院数据科学与运营系）
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…
École Polytechnique Fédérale de Lausanne (EPFL)（洛桑联邦理工学院 (EPFL)）
We consider the problem of estimating the underlying graph associated with a Markov random field, with the added twist that the decoding algorithm can iteratively choose which subsets of nodes to sample based on the previous samples, resulting in an active learning setting. Considering both Ising and Gaussian models, we provide algorithm-independent lower bounds for high-probability recovery within the class of degree-bounded graphs. Our main results are minimax lower bounds for the active setting that match the best known lower bounds for the passive setting, which in turn are known to be tig…
The problem of learning the structure of a high dimensional graphical model from data has received considerable attention in recent years. In many applications such as sensor networks and proteomics it is often expensive to obtain samples from all the variables involved simultaneously. For instance, this might involve the synchronization of a large number of sensors or the tagging of a large number of proteins. To address this important issue, we initiate the study of a novel graphical model selection problem, where the goal is to optimize the total number of scalar samples obtained by allowin…
Structure learning in random fields has attracted considerable attention due to its difficulty and importance in areas such as remote sensing, computational biology, natural language processing, protein networks, and social network analysis. We consider the problem of estimating the probabilistic graph structure associated with a Gaussian Markov Random Field (GMRF), the Ising model and the Potts model, by extending previous work on $l_1$ regularized neighborhood estimation to include the elastic net $l_1+l_2$ penalty. Additionally, we show numerical evidence that the edge density plays a role …
A challenging problem in estimating high-dimensional graphical models is to choose the regularization parameter in a data-dependent way. The standard techniques include $K$-fold cross-validation ($K$-CV), Akaike information criterion (AIC), and Bayesian information criterion (BIC). Though these methods work well for low-dimensional problems, they are not suitable in high dimensional settings. In this paper, we present StARS: a new stability-based method for choosing the regularization parameter in high dimensional inference for undirected graphs. The method has a clear interpretation: we use t…
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…
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…
Chandrasekaran, Parrilo and Willsky (2010) proposed a convex optimization problem to characterize graphical model selection in the presence of unobserved variables. This convex optimization problem aims to estimate an inverse covariance matrix that can be decomposed into a sparse matrix minus a low-rank matrix from sample data. Solving this convex optimization problem is very challenging, especially for large problems. In this paper, we propose two alternating direction methods for solving this problem. The first method is to apply the classical alternating direction method of multipliers to s…
We study a family of regularized score-based estimators for learning the structure of a directed acyclic graph (DAG) for a multivariate normal distribution from high-dimensional data with $p\gg n$. Our main results establish support recovery guarantees and deviation bounds for a family of penalized least-squares estimators under concave regularization without assuming prior knowledge of a variable ordering. These results apply to a variety of practical situations that allow for arbitrary nondegenerate covariance structures as well as many popular regularizers including the MCP, SCAD, $\ell_{0}…
Variable clustering is important for explanatory analysis. However, only few dedicated methods for variable clustering with the Gaussian graphical model have been proposed. Even more severe, small insignificant partial correlations due to noise can dramatically change the clustering result when evaluating for example with the Bayesian Information Criteria (BIC). In this work, we try to address this issue by proposing a Bayesian model that accounts for negligible small, but not necessarily zero, partial correlations. Based on our model, we propose to evaluate a variable clustering result using …
In neuroimaging data analysis, Gaussian graphical models are often used to model statistical dependencies across spatially remote brain regions known as functional connectivity. Typically, data is collected across a cohort of subjects and the scientific objectives consist of estimating population and subject-specific graphical models. A third objective that is often overlooked involves quantifying inter-subject variability and thus identifying regions or sub-networks that demonstrate heterogeneity across subjects. Such information is fundamental in order to thoroughly understand the human conn…
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 c…
Rice University（莱斯大学）；University of Wisconsin - Madison（威斯康星大学麦迪逊分校）
An undirected graphical model is a joint probability distribution defined on an undirected graph G*, where the vertices in the graph index a collection of random variables and the edges encode conditional independence relationships among random variables. The undirected graphical model selection (UGMS) problem is to estimate the graph G* given observations drawn from the undirected graphical model. This paper proposes a framework for decomposing the UGMS problem into multiple subproblems over clusters and subsets of the separators in a junction tree. The junction tree is constructed using a gr…
This paper considers the problem of networks reconstruction from heterogeneous data using a Gaussian Graphical Mixture Model (GGMM). It is well known that parameter estimation in this context is challenging due to large numbers of variables coupled with the degeneracy of the likelihood. We propose as a solution a penalized maximum likelihood technique by imposing an $l_{1}$ penalty on the precision matrix. Our approach shrinks the parameters thereby resulting in better identifiability and variable selection. We use the Expectation Maximization (EM) algorithm which involves the graphical LASSO …
Bayesian graphical models are a useful tool for understanding dependence relationships among many variables, particularly in situations with external prior information. In high-dimensional settings, the space of possible graphs becomes enormous, rendering even state-of-the-art Bayesian stochastic search computationally infeasible. We propose a deterministic alternative to estimate Gaussian and Gaussian copula graphical models using an Expectation Conditional Maximization (ECM) algorithm, extending the EM approach from Bayesian variable selection to graphical model estimation. We show that the …
We show that the two-stage adaptive Lasso procedure (Zou, 2006) is consistent for high-dimensional model selection in linear and Gaussian graphical models. Our conditions for consistency cover more general situations than those accomplished in previous work: we prove that restricted eigenvalue conditions (Bickel et al., 2008) are also sufficient for sparse structure estimation.
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 …
This paper presents a new algorithm for automatic variables selection. In particular, using the Graphical Models properties it is possible to develop a method that can be used in the contest of large dataset. The advantage of this algorithm is that can be combined with different forecasting models. In this research we have used the OLS method and we have compared the result with the LASSO method.
This paper presents the R package gRapHD for efficient selection of high-dimensional undirected graphical models. The package provides tools for selecting trees, forests and decomposable models minimizing information criteria such as AIC or BIC, and for displaying the independence graphs of the models. It has also some useful tools for analysing graphical structures. It supports the use of discrete, continuous, or both types of variables simultaneously.
A graphical model is a statistical model that is associated to a graph whose nodes correspond to variables of interest. The edges of the graph reflect allowed conditional dependencies among the variables. Graphical models admit computationally convenient factorization properties and have long been a valuable tool for tractable modeling of multivariate distributions. More recently, applications such as reconstructing gene regulatory networks from gene expression data have driven major advances in structure learning, that is, estimating the graph underlying a model. We review some of these advan…
We consider the problem of quantifying the quality of a model selection problem for a graphical model. We discuss this by formulating the problem as a detection problem. Model selection problems usually minimize a distance between the original distribution and the model distribution. For the special case of Gaussian distributions, the model selection problem simplifies to the covariance selection problem which is widely discussed in literature by Dempster [2] where the likelihood criterion is maximized or equivalently the Kullback-Leibler (KL) divergence is minimized to compute the model covar…
We propose estimation methods for change points in high-dimensional covariance structures with an emphasis on challenging scenarios with missing values. We advocate three imputation like methods and investigate their implications on common losses used for change point detection. We also discuss how model selection methods have to be adapted to the setting of incomplete data. The methods are compared in a simulation study and applied to a time series from an environmental monitoring system. An implementation of our proposals within the R-package hdcd is available via the Supplementary materials…
We introduce Graphical TREX (GTREX), a novel method for graph estimation in high-dimensional Gaussian graphical models. By conducting neighborhood selection with TREX, GTREX avoids tuning parameters and is adaptive to the graph topology. We compare GTREX with standard methods on a new simulation set-up that is designed to assess accurately the strengths and shortcomings of different methods. These simulations show that a neighborhood selection scheme based on Lasso and an optimal (in practice unknown) tuning parameter outperforms other standard methods over a large spectrum of scenarios. Moreo…
