Sparse Gaussian Graphical Models with Discrete Optimization: Computational and Statistical Perspectives
Operations Research Center, Massachusetts Institute of Technology（麻省理工学院运筹学研究中心）；Sloan School of Management, Massachusetts Institute of Technology（麻省理工学院斯隆管理学院）
We consider the problem of learning a sparse graph underlying an undirected Gaussian graphical model, a key problem in statistical machine learning. Given $n$ samples from a multivariate Gaussian distribution with $p$ variables, the goal is to estimate the $p \times p$ inverse covariance matrix (aka precision matrix), assuming it is sparse (i.e., has a few nonzero entries). We propose GraphL0BnB, a new estimator based on an $\ell_0$-penalized version of the pseudo-likelihood function, while most earlier approaches are based on the $\ell_1$-relaxation. Our estimator can be formulated as a convex mixed integer program (MIP) which can be difficult to compute beyond $p\approx 100$ using off-the-shelf commercial solvers. To solve the MIP, we propose a custom nonlinear branch-and-bound (BnB) framework that solves node relaxations with tailored first-order methods. As a key component of our BnB framework, we propose large-scale solvers for obtaining good primal solutions that are of independent interest. We derive novel statistical guarantees (estimation and variable selection) for our estimator and discuss how our approach improves upon existing estimators. Our numerical experiments on real and synthetic datasets suggest that our BnB framework offers significant advantages over off-the-shelf commercial solvers, and our approach has favorable performance (both in terms of runtime and statistical performance) compared to the state-of-the-art approaches for learning sparse graphical models.
We characterize the effectiveness of a classical algorithm for recovering the Markov graph of a general discrete pairwise graphical model from i.i.d. samples. The algorithm is (appropriately regularized) maximum conditional log-likelihood, which involves solving a convex program for each node; for Ising models this is $\ell_1$-constrained logistic regression, while for more general alphabets an $\ell_{2,1}$ group-norm constraint needs to be used. We show that this algorithm can recover any arbitrary discrete pairwise graphical model, and also characterize its sample complexity as a function of…
University of Chicago（芝加哥大学）；Princeton University（普林斯顿大学）；Carnegie Mellon University（卡内基梅隆大学）
We present some nonparametric methods for graphical modeling. In the discrete case, where the data are binary or drawn from a finite alphabet, Markov random fields are already essentially nonparametric, since the cliques can take only a finite number of values. Continuous data are different. The Gaussian graphical model is the standard parametric model for continuous data, but it makes distributional assumptions that are often unrealistic. We discuss two approaches to building more flexible graphical models. One allows arbitrary graphs and a nonparametric extension of the Gaussian; the other u…
University of Edinburgh（爱丁堡大学）；Pharmatics Ltd（Pharmatics有限公司）
One of the fundamental tasks of science is to find explainable relationships between observed phenomena. One approach to this task that has received attention in recent years is based on probabilistic graphical modelling with sparsity constraints on model structures. In this paper, we describe two new approaches to Bayesian inference of sparse structures of Gaussian graphical models (GGMs). One is based on a simple modification of the cutting-edge block Gibbs sampler for sparse GGMs, which results in significant computational gains in high dimensions. The other method is based on a specific co…
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 …
Multivariate regression model is a natural generalization of the classical univari- ate regression model for fitting multiple responses. In this paper, we propose a high- dimensional multivariate conditional regression model for constructing sparse estimates of the multivariate regression coefficient matrix that accounts for the dependency struc- ture among the multiple responses. The proposed method decomposes the multivariate regression problem into a series of penalized conditional log-likelihood of each response conditioned on the covariates and other responses. It allows simultaneous esti…
We present an algorithm to identify sparse dependence structure in continuous and non-Gaussian probability distributions, given a corresponding set of data. The conditional independence structure of an arbitrary distribution can be represented as an undirected graph (or Markov random field), but most algorithms for learning this structure are restricted to the discrete or Gaussian cases. Our new approach allows for more realistic and accurate descriptions of the distribution in question, and in turn better estimates of its sparse Markov structure. Sparsity in the graph is of interest as it can…
In this paper we study the problem of exact recovery of the pure-strategy Nash equilibria (PSNE) set of a graphical game from noisy observations of joint actions of the players alone. We consider sparse linear influence games --- a parametric class of graphical games with linear payoffs, and represented by directed graphs of n nodes (players) and in-degree of at most k. We present an $\ell_1$-regularized logistic regression based algorithm for recovering the PSNE set exactly, that is both computationally efficient --- i.e. runs in polynomial time --- and statistically efficient --- i.e. has lo…
We focus on the problem of estimating the change in the dependency structures of two $p$-dimensional Gaussian Graphical models (GGMs). Previous studies for sparse change estimation in GGMs involve expensive and difficult non-smooth optimization. We propose a novel method, DIFFEE for estimating DIFFerential networks via an Elementary Estimator under a high-dimensional situation. DIFFEE is solved through a faster and closed form solution that enables it to work in large-scale settings. We conduct a rigorous statistical analysis showing that surprisingly DIFFEE achieves the same asymptotic conver…
This document aims to provide a review on learning with deep generative models (DGMs), which is an highly-active area in machine learning and more generally, artificial intelligence. This review is not meant to be a tutorial, but when necessary, we provide self-contained derivations for completeness. This review has two features. First, though there are different perspectives to classify DGMs, we choose to organize this review from the perspective of graphical modeling, because the learning methods for directed DGMs and undirected DGMs are fundamentally different. Second, we differentiate mode…
University of Michigan（密歇根大学）；Technicolor Research Center（特艺集团研究中心）
Gaussian graphical models (GGM) have been widely used in many high-dimensional applications ranging from biological and financial data to recommender systems. Sparsity in GGM plays a central role both statistically and computationally. Unfortunately, real-world data often does not fit well to sparse graphical models. In this paper, we focus on a family of latent variable Gaussian graphical models (LVGGM), where the model is conditionally sparse given latent variables, but marginally non-sparse. In LVGGM, the inverse covariance matrix has a low-rank plus sparse structure, and can be learned in …
Identifying context-specific entity networks from aggregated data is an important task, arising often in bioinformatics and neuroimaging. Computationally, this task can be formulated as jointly estimating multiple different, but related, sparse Undirected Graphical Models (UGM) from aggregated samples across several contexts. Previous joint-UGM studies have mostly focused on sparse Gaussian Graphical Models (sGGMs) and can't identify context-specific edge patterns directly. We, therefore, propose a novel approach, SIMULE (detecting Shared and Individual parts of MULtiple graphs Explicitly) to …
University of Virginia（弗吉尼亚大学）；Carnegie Mellon University（卡内基梅隆大学）
We study the estimation of the latent variable Gaussian graphical model (LVGGM), where the precision matrix is the superposition of a sparse matrix and a low-rank matrix. In order to speed up the estimation of the sparse plus low-rank components, we propose a sparsity constrained maximum likelihood estimator based on matrix factorization, and an efficient alternating gradient descent algorithm with hard thresholding to solve it. Our algorithm is orders of magnitude faster than the convex relaxation based methods for LVGGM. In addition, we prove that our algorithm is guaranteed to linearly conv…
We consider the problem of including additional knowledge in estimating sparse Gaussian graphical models (sGGMs) from aggregated samples, arising often in bioinformatics and neuroimaging applications. Previous joint sGGM estimators either fail to use existing knowledge or cannot scale-up to many tasks (large $K$) under a high-dimensional (large $p$) situation. In this paper, we propose a novel \underline{J}oint \underline{E}lementary \underline{E}stimator incorporating additional \underline{K}nowledge (JEEK) to infer multiple related sparse Gaussian Graphical models from large-scale heterogene…
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…
Estimating multiple sparse Gaussian Graphical Models (sGGMs) jointly for many related tasks (large $K$) under a high-dimensional (large $p$) situation is an important task. Most previous studies for the joint estimation of multiple sGGMs rely on penalized log-likelihood estimators that involve expensive and difficult non-smooth optimizations. We propose a novel approach, FASJEM for \underline{fa}st and \underline{s}calable \underline{j}oint structure-\underline{e}stimation of \underline{m}ultiple sGGMs at a large scale. As the first study of joint sGGM using the Elementary Estimator framework,…
DC Algorithm for Estimation of Sparse Gaussian Graphical Models
Graduate School of Science and Technology, University of Tsukuba（筑波大学理工学研究科）；Faculty of Engineering, Information and Systems, University of Tsukuba（筑波大学工学部信息系统学科）
The University of Electro-Communications（电气通信大学）；National Police Agency Info-Communications Bureau（警察厅信息通信局）
In this paper, we propose a Bayesian Graphical LASSO for correlated countable data and apply it to spatial crime data. In the proposed model, we assume a Gaussian Graphical Model for the latent variables which dominate the potential risks of crimes. To evaluate the proposed model, we determine optimal hyperparameters which represent samples better. We apply the proposed model for estimation of the sparse inverse covariance of the latent variable and evaluate the partial correlation coefficients. Finally, we illustrate the results on crime spots data and consider the estimated latent variables …
Berkeley AI Research（伯克利人工智能研究院）；Carnegie Mellon University（卡内基梅隆大学）
To operate effectively in the real world, agents should be able to act from high-dimensional raw sensory input such as images and achieve diverse goals across long time-horizons. Current deep reinforcement and imitation learning methods can learn directly from high-dimensional inputs but do not scale well to long-horizon tasks. In contrast, classical graphical methods like A* search are able to solve long-horizon tasks, but assume that the state space is abstracted away from raw sensory input. Recent works have attempted to combine the strengths of deep learning and classical planning; however…
National University of Singapore（新加坡国立大学）；Singapore University of Technology and Design（新加坡科技设计大学）
In this paper, we study high-dimensional estimation from truncated samples. We focus on two fundamental and classical problems: (i) inference of sparse Gaussian graphical models and (ii) support recovery of sparse linear models. (i) For Gaussian graphical models, suppose $d$-dimensional samples ${\bf x}$ are generated from a Gaussian $N(μ,Σ)$ and observed only if they belong to a subset $S \subseteq \mathbb{R}^d$. We show that $μ$ and $Σ$ can be estimated with error $ε$ in the Frobenius norm, using $\tilde{O}\left(\frac{\textrm{nz}(Σ^{-1})}{ε^2}\right)$ samples from a truncated $\mathcal{N}(μ,…
We analyze the sample complexity of learning graphical games from purely behavioral data. We assume that we can only observe the players' joint actions and not their payoffs. We analyze the sufficient and necessary number of samples for the correct recovery of the set of pure-strategy Nash equilibria (PSNE) of the true game. Our analysis focuses on directed graphs with $n$ nodes and at most $k$ parents per node. Sparse graphs correspond to ${k \in O(1)}$ with respect to $n$, while dense graphs correspond to ${k \in O(n)}$. By using VC dimension arguments, we show that if the number of samples …
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…
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…
Department of Statistics, University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校统计学系）
We consider a Bayesian framework for estimating a high-dimensional sparse precision matrix, in which adaptive shrinkage and sparsity are induced by a mixture of Laplace priors. Besides discussing our formulation from the Bayesian standpoint, we investigate the MAP (maximum a posteriori) estimator from a penalized likelihood perspective that gives rise to a new non-convex penalty approximating the $\ell_0$ penalty. Optimal error rates for estimation consistency in terms of various matrix norms along with selection consistency for sparse structure recovery are shown for the unique MAP estimator …
University of Warwick（华威大学）；The Netherlands Cancer Institute（荷兰癌症研究所）
In many applications, multivariate samples may harbor previously unrecognized heterogeneity at the level of conditional independence or network structure. For example, in cancer biology, disease subtypes may differ with respect to subtype-specific interplay between molecular components. Then, both subtype discovery and estimation of subtype-specific networks present important and related challenges. To enable such analyses, we put forward a mixture model whose components are sparse Gaussian graphical models. This brings together model-based clustering and graphical modeling to permit simultane…
Southeast University（东南大学）；Chinese Academy of Sciences（中国科学院）；Purple Mountain Laboratories（紫金山实验室）
Recently, graph-based models designed for downstream tasks have significantly advanced research on graph neural networks (GNNs). GNN baselines based on neural message-passing mechanisms such as GCN and GAT perform worse as the network deepens. Therefore, numerous GNN variants have been proposed to tackle this performance degradation problem, including many deep GNNs. However, a unified framework is still lacking to connect these existing models and interpret their effectiveness at a high level. In this work, we focus on deep GNNs and propose a novel view for understanding them. We establish a …
Institute for Mathematics and its Applications, University of Minnesota（明尼苏达大学数学及其应用研究所）；University of Florida（佛罗里达大学）；University of Michigan（密歇根大学）
High dimensional piecewise stationary graphical models represent a versatile class for modelling time varying networks arising in diverse application areas, including biology, economics, and social sciences. There has been recent work in offline detection and estimation of regime changes in the topology of sparse graphical models. However, the online setting remains largely unexplored, despite its high relevance to applications in sensor networks and other engineering monitoring systems, as well as financial markets. To that end, this work introduces a novel scalable online algorithm for detec…
University of Michigan（密歇根大学）；University of Southern California（南加州大学）
In this paper, we study the problem of inferring time-varying Markov random fields (MRF), where the underlying graphical model is both sparse and changes sparsely over time. Most of the existing methods for the inference of time-varying MRFs rely on the regularized maximum likelihood estimation (MLE), that typically suffer from weak statistical guarantees and high computational time. Instead, we introduce a new class of constrained optimization problems for the inference of sparsely-changing MRFs. The proposed optimization problem is formulated based on the exact $\ell_0$ regularization, and c…
Graphical model for factorization and completion of relatively high rank tensors by sparse sampling
D3 Center, Osaka University（大阪大学D3中心）；Department of Physics, Graduate School of Science, Osaka University（大阪大学理学研究生院物理学科）；Department of Systems Science, Graduate School of Informatics, Kyoto University（京都大学信息学研究生院系统科学学科）；RIKEN center for AIP（RIKEN AIP研究中心）
Gaussian Graphical Models (GGMs) have wide-ranging applications in machine learning and the natural and social sciences. In most of the settings in which they are applied, the number of observed samples is much smaller than the dimension and they are assumed to be sparse. While there are a variety of algorithms (e.g. Graphical Lasso, CLIME) that provably recover the graph structure with a logarithmic number of samples, they assume various conditions that require the precision matrix to be in some sense well-conditioned. Here we give the first polynomial-time algorithms for learning attractive …
Université Paris-Est（巴黎东大学）；Ecole des Ponts（国立桥路学校）
The edge structure of the graph defining an undirected graphical model describes precisely the structure of dependence between the variables in the graph. In many applications, the dependence structure is unknown and it is desirable to learn it from data, often because it is a preliminary step to be able to ascertain causal effects. This problem, known as structure learning, is hard in general, but for Gaussian graphical models it is slightly easier because the structure of the graph is given by the sparsity pattern of the precision matrix of the joint distribution, and because independence co…
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…
University of Southampton（南安普顿大学）；Cambridge University（剑桥大学）；University of Washington（华盛顿大学）；Harvard University（哈佛大学）
Hidden variables are ubiquitous in practical data analysis, and therefore modeling marginal densities and doing inference with the resulting models is an important problem in statistics, machine learning, and causal inference. Recently, a new type of graphical model, called the nested Markov model, was developed which captures equality constraints found in marginals of directed acyclic graph (DAG) models. Some of these constraints, such as the so called `Verma constraint', strictly generalize conditional independence. To make modeling and inference with nested Markov models practical, it is ne…
We study the problem of discovering functional dependencies (FD) from a noisy dataset. We focus on FDs that correspond to statistical dependencies in a dataset and draw connections between FD discovery and structure learning in probabilistic graphical models. We show that discovering FDs from a noisy dataset is equivalent to learning the structure of a graphical model over binary random variables, where each random variable corresponds to a functional of the dataset attributes. We build upon this observation to introduce AutoFD a conceptually simple framework in which learning functional depen…
Learning the relationships between various entities from time-series data is essential in many applications. Gaussian graphical models have been studied to infer these relationships. However, existing algorithms process data in a batch at a central location, limiting their applications in scenarios where data is gathered by different agents. In this paper, we propose a distributed sparse inverse covariance algorithm to learn the network structure (i.e., dependencies among observed entities) in real-time from data collected by distributed agents. Our approach is built on an online graphical alt…
DeepMind；University of Oxford（牛津大学）；University of Toronto（多伦多大学）；Vector Institute（向量研究所）
We present a framework for analysing agent incentives using causal influence diagrams. We establish that a well-known criterion for value of information is complete. We propose a new graphical criterion for value of control, establishing its soundness and completeness. We also introduce two new concepts for incentive analysis: response incentives indicate which changes in the environment affect an optimal decision, while instrumental control incentives establish whether an agent can influence its utility via a variable X. For both new concepts, we provide sound and complete graphical criteria.…
KTH Royal Institute of Technology（KTH皇家理工学院）；Georgia Institute of Technology（佐治亚理工学院）
We study multi-marginal optimal transport problems from a probabilistic graphical model perspective. We point out an elegant connection between the two when the underlying cost for optimal transport allows a graph structure. In particular, an entropy regularized multi-marginal optimal transport is equivalent to a Bayesian marginal inference problem for probabilistic graphical models with the additional requirement that some of the marginal distributions are specified. This relation on the one hand extends the optimal transport as well as the probabilistic graphical model theories, and on the o…
What is the optimal number of independent observations from which a sparse Gaussian Graphical Model can be correctly recovered? Information-theoretic arguments provide a lower bound on the minimum number of samples necessary to perfectly identify the support of any multivariate normal distribution as a function of model parameters. For a model defined on a sparse graph with $p$ nodes, a maximum degree $d$ and minimum normalized edge strength $κ$, this necessary number of samples scales at least as $d \log p/κ^2$. The sample complexity requirements of existing methods for perfect graph reconstr…
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…
