We consider the problem of estimating high-dimensional Gaussian graphical models corresponding to a single set of variables under several distinct conditions. This problem is motivated by the task of recovering transcriptional regulatory networks on the basis of gene expression data {containing heterogeneous samples, such as different disease states, multiple species, or different developmental stages}. We assume that most aspects of the conditional dependence networks are shared, but that there are some structured differences between them. Rather than assuming that similarities and differences between networks are driven by individual edges, we take a node-based approach, which in many cases provides a more intuitive interpretation of the network differences. We consider estimation under two distinct assumptions: (1) differences between the K networks are due to individual nodes that are perturbed across conditions, or (2) similarities among the K networks are due to the presence of common hub nodes that are shared across all K networks. Using a row-column overlap norm penalty function, we formulate two convex optimization problems that correspond to these two assumptions. We solve these problems using an alternating direction method of multipliers algorithm, and we derive a set of necessary and sufficient conditions that allows us to decompose the problem into independent subproblems so that our algorithm can be scaled to high-dimensional settings. Our proposal is illustrated on synthetic data, a webpage data set, and a brain cancer gene expression data set.
Virginia Polytechnic Institute and State University（弗吉尼亚理工大学）；Bradley Department of Electrical and Computer Engineering（布拉德利电气与计算机工程系）
Graphical models are widely used in scienti fic and engineering research to represent conditional independence structures between random variables. In many controlled experiments, environmental changes or external stimuli can often alter the conditional dependence between the random variables, and potentially produce significant structural changes in the corresponding graphical models. Therefore, it is of great importance to be able to detect such structural changes from data, so as to gain novel insights into where and how the structural changes take place and help the system adapt to the new…
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…
Rice University（莱斯大学）；Baylor College of Medicine（贝勒医学院）
Knowledge of functional groupings of neurons can shed light on structures of neural circuits and is valuable in many types of neuroimaging studies. However, accurately determining which neurons carry out similar neurological tasks via controlled experiments is both labor-intensive and prohibitively expensive on a large scale. Thus, it is of great interest to cluster neurons that have similar connectivity profiles into functionally coherent groups in a data-driven manner. In this work, we propose the clustered Gaussian graphical model (GGM) and a novel symmetric convex clustering penalty in an …
Khoury College of Computer Sciences（科瑞计算机学院）；Northeastern University（东北大学）；National University of Singapore（新加坡国立大学）
Graphical model selection in Markov random fields is a fundamental problem in statistics and machine learning. Two particularly prominent models, the Ising model and Gaussian model, have largely developed in parallel using different (though often related) techniques, and several practical algorithms with rigorous sample complexity bounds have been established for each. In this paper, we adapt a recently proposed algorithm of Klivans and Meka (FOCS, 2017), based on the method of multiplicative weight updates, from the Ising model to the Gaussian model, via non-trivial modifications to both the …
We explore the algebraic structure of the solution space of convex optimization problem Constrained Minimum Trace Factor Analysis (CMTFA), when the population covariance matrix $Σ_x$ has an additional latent graphical constraint, namely, a latent star topology. In particular, we have shown that CMTFA can have either a rank $ 1 $ or a rank $ n-1 $ solution and nothing in between. The special case of a rank $ 1 $ solution, corresponds to the case where just one latent variable captures all the dependencies among the observables, giving rise to a star topology. We found explicit conditions for bo…
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.
Princeton University（普林斯顿大学）；Charles H. Dyson School of Applied Economics and Management（查尔斯·H·戴森应用经济与管理学院）；University of Chicago（芝加哥大学）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
We propose a partially linear additive Gaussian graphical model (PLA-GGM) for the estimation of associations between random variables distorted by observed confounders. Model parameters are estimated using an $L_1$-regularized maximal pseudo-profile likelihood estimator (MaPPLE) for which we prove $\sqrt{n}$-sparsistency. Importantly, our approach avoids parametric constraints on the effects of confounders on the estimated graphical model structure. Empirically, the PLA-GGM is applied to both synthetic and real-world datasets, demonstrating superior performance compared to competing methods.
University of Helsinki（赫尔辛基大学）；Åbo Akademi University（奥博学术大学）
We propose a Bayesian approximate inference method for learning the dependence structure of a Gaussian graphical model. Using pseudo-likelihood, we derive an analytical expression to approximate the marginal likelihood for an arbitrary graph structure without invoking any assumptions about decomposability. The majority of the existing methods for learning Gaussian graphical models are either restricted to decomposable graphs or require specification of a tuning parameter that may have a substantial impact on learned structures. By combining a simple sparsity inducing prior for the graph struct…
We derive an efficient method to perform clustering of nodes in Gaussian graphical models directly from sample data. Nodes are clustered based on the similarity of their network neighborhoods, with edge weights defined by partial correlations. In the limited-data scenario, where the covariance matrix would be rank-deficient, we are able to make use of matrix factors, and never need to estimate the actual covariance or precision matrix. We demonstrate the method on functional MRI data from the Human Connectome Project. A matlab implementation of the algorithm is provided.
High-dimensional graphical models are often estimated using regularization that is aimed at reducing the number of edges in a network. In this work, we show how even simpler networks can be produced by aggregating the nodes of the graphical model. We develop a new convex regularized method, called the tree-aggregated graphical lasso or tag-lasso, that estimates graphical models that are both edge-sparse and node-aggregated. The aggregation is performed in a data-driven fashion by leveraging side information in the form of a tree that encodes node similarity and facilitates the interpretation o…
A new Bayesian modeling method is proposed by combining the maximization of the marginal likelihood with a momentum-space renormalization group transformation for Gaussian graphical models. Moreover, we present a scheme for computint the statistical averages of hyperparameters and mean square errors in our proposed method based on a momentumspace renormalization transformation.
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…
We consider the problem of learning high-dimensional Gaussian graphical models. The graphical lasso is one of the most popular methods for estimating Gaussian graphical models. However, it does not achieve the oracle rate of convergence. In this paper, we propose the graphical nonconvex optimization for optimal estimation in Gaussian graphical models, which is then approximated by a sequence of convex programs. Our proposal is computationally tractable and produces an estimator that achieves the oracle rate of convergence. The statistical error introduced by the sequential approximation using …
We propose {graphical sure screening}, or GRASS, a very simple and computationally-efficient screening procedure for recovering the structure of a Gaussian graphical model in the high-dimensional setting. The GRASS estimate of the conditional dependence graph is obtained by thresholding the elements of the sample covariance matrix. The proposed approach possesses the sure screening property: with very high probability, the GRASS estimated edge set contains the true edge set. Furthermore, with high probability, the size of the estimated edge set is controlled. We provide a choice of threshold f…
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…
Gaussian Graphical Models (GGMs) are popular tools for studying network structures. However, many modern applications such as gene network discovery and social interactions analysis often involve high-dimensional noisy data with outliers or heavier tails than the Gaussian distribution. In this paper, we propose the Trimmed Graphical Lasso for robust estimation of sparse GGMs. Our method guards against outliers by an implicit trimming mechanism akin to the popular Least Trimmed Squares method used for linear regression. We provide a rigorous statistical analysis of our estimator in the high-dim…
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 …
Consider jointly Gaussian random variables whose conditional independence structure is specified by a graphical model. If we observe realizations of the variables, we can compute the covariance matrix, and it is well known that the support of the inverse covariance matrix corresponds to the edges of the graphical model. Instead, suppose we only have noisy observations. If the noise at each node is independent, we can compute the sum of the covariance matrix and an unknown diagonal. The inverse of this sum is (in general) dense. We ask: can the original independence structure be recovered? We a…
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 …
This paper studies the partial estimation of Gaussian graphical models from high-dimensional empirical observations. We derive a convex formulation for this problem using $\ell_1$-regularized maximum-likelihood estimation, which can be solved via a block coordinate descent algorithm. Statistical estimation performance can be established for our method. The proposed approach has competitive empirical performance compared to existing methods, as demonstrated by various experiments on synthetic and real datasets.
Graphical models with bi-directed edges (<->) represent marginal independence: the absence of an edge between two vertices indicates that the corresponding variables are marginally independent. In this paper, we consider maximum likelihood estimation in the case of continuous variables with a Gaussian joint distribution, sometimes termed a covariance graph model. We present a new fitting algorithm which exploits standard regression techniques and establish its convergence properties. Moreover, we contrast our procedure to existing estimation methods.
We develop a new method called Discriminated Hub Graphical Lasso (DHGL) based on Hub Graphical Lasso (HGL) by providing prior information of hubs. We apply this new method in two situations: with known hubs and without known hubs. Then we compare DHGL with HGL using several measures of performance. When some hubs are known, we can always estimate the precision matrix better via DHGL than HGL. When no hubs are known, we use Graphical Lasso (GL) to provide information of hubs and find that the performance of DHGL will always be better than HGL if correct prior information is given and will seldo…
This paper addresses the problem of scalable optimization for L1-regularized conditional Gaussian graphical models. Conditional Gaussian graphical models generalize the well-known Gaussian graphical models to conditional distributions to model the output network influenced by conditioning input variables. While highly scalable optimization methods exist for sparse Gaussian graphical model estimation, state-of-the-art methods for conditional Gaussian graphical models are not efficient enough and more importantly, fail due to memory constraints for very large problems. In this paper, we propose …
Purdue University（普渡大学）；Massachusetts Institute of Technology（麻省理工学院）；Stony Brook University（石溪大学）
In this paper, we present $\ell_{1,p}$ multi-task structure learning for Gaussian graphical models. We analyze the sufficient number of samples for the correct recovery of the support union and edge signs. We also analyze the necessary number of samples for any conceivable method by providing information-theoretic lower bounds. We compare the statistical efficiency of multi-task learning versus that of single-task learning. For experiments, we use a block coordinate descent method that is provably convergent and generates a sequence of positive definite solutions. We provide experimental valid…
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 consider the task of estimating a Gaussian graphical model in the high-dimensional setting. The graphical lasso, which involves maximizing the Gaussian log likelihood subject to an l1 penalty, is a well-studied approach for this task. We begin by introducing a surprising connection between the graphical lasso and hierarchical clustering: the graphical lasso in effect performs a two-step procedure, in which (1) single linkage hierarchical clustering is performed on the variables in order to identify connected components, and then (2) an l1-penalized log likelihood is maximized on the subset …
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…
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 …
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…
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 …
Gaussian graphical models (GGMs) are widely used for statistical modeling, because of ease of inference and the ubiquitous use of the normal distribution in practical approximations. However, they are also known for their limited modeling abilities, due to the Gaussian assumption. In this paper, we introduce a novel variant of GGMs, which relaxes the Gaussian restriction and yet admits efficient inference. Specifically, we impose a bipartite structure on the GGM and govern the hidden variables by truncated normal distributions. The nonlinearity of the model is revealed by its connection to rec…
The Chinese University of Hong Kong（香港中文大学）；City University of Hong Kong（香港城市大学）
Tensor Gaussian graphical models (GGMs), interpreting conditional independence structures within tensor data, have important applications in numerous areas. Yet, the available tensor data in one single study is often limited due to high acquisition costs. Although relevant studies can provide additional data, it remains an open question how to pool such heterogeneous data. In this paper, we propose a transfer learning framework for tensor GGMs, which takes full advantage of informative auxiliary domains even when non-informative auxiliary domains are present, benefiting from the carefully desi…
In this paper, learning of tree-structured Gaussian graphical models from distributed data is addressed. In our model, samples are stored in a set of distributed machines where each machine has access to only a subset of features. A central machine is then responsible for learning the structure based on received messages from the other nodes. We present a set of communication efficient strategies, which are theoretically proved to convey sufficient information for reliable learning of the structure. In particular, our analyses show that even if each machine sends only the signs of its local da…
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.
We introduce the truncated Gaussian graphical model (TGGM) as a novel framework for designing statistical models for nonlinear learning. A TGGM is a Gaussian graphical model (GGM) with a subset of variables truncated to be nonnegative. The truncated variables are assumed latent and integrated out to induce a marginal model. We show that the variables in the marginal model are non-Gaussian distributed and their expected relations are nonlinear. We use expectation-maximization to break the inference of the nonlinear model into a sequence of TGGM inference problems, each of which is efficiently s…
In this paper, we propose a semiparametric approach, named nonparanormal skeptic, for efficiently and robustly estimating high dimensional undirected graphical models. To achieve modeling flexibility, we consider Gaussian Copula graphical models (or the nonparanormal) as proposed by Liu et al. (2009). To achieve estimation robustness, we exploit nonparametric rank-based correlation coefficient estimators, including Spearman's rho and Kendall's tau. In high dimensional settings, we prove that the nonparanormal skeptic achieves the optimal parametric rate of convergence in both graph and paramet…
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…
We address the task of identifying densely connected subsets of multivariate Gaussian random variables within a graphical model framework. We propose two novel estimators based on the Ordered Weighted $\ell_1$ (OWL) norm: 1) The Graphical OWL (GOWL) is a penalized likelihood method that applies the OWL norm to the lower triangle components of the precision matrix. 2) The column-by-column Graphical OWL (ccGOWL) estimates the precision matrix by performing OWL regularized linear regressions. Both methods can simultaneously identify highly correlated groups of variables and control the sparsity i…
Distributed Gaussian process (DGP) is a popular approach to scale GP to big data which divides the training data into some subsets, performs local inference for each partition, and aggregates the results to acquire global prediction. To combine the local predictions, the conditional independence assumption is used which basically means there is a perfect diversity between the subsets. Although it keeps the aggregation tractable, it is often violated in practice and generally yields poor results. In this paper, we propose a novel approach for aggregating the Gaussian experts' predictions by Gau…
Knowing when a graphical model is perfect to a distribution is essential in order to relate separation in the graph to conditional independence in the distribution, and this is particularly important when performing inference from data. When the model is perfect, there is a one-to-one correspondence between conditional independence statements in the distribution and separation statements in the graph. Previous work has shown that almost all models based on linear directed acyclic graphs as well as Gaussian chain graphs are perfect, the latter of which subsumes Gaussian graphical models (i.e., …
We provide a correction to the expression for scoring Gaussian directed acyclic graphical models derived in Geiger and Heckerman [Ann. Statist. 30 (2002) 1414-1440] and discuss how to evaluate the score efficiently.
University of Virginia（弗吉尼亚大学）；Southeast University（东南大学）；University of Michigan（密歇根大学）
Graphical models are commonly used to represent conditional dependence relationships between variables. There are multiple methods available for exploring them from high-dimensional data, but almost all of them rely on the assumption that the observations are independent and identically distributed. At the same time, observations connected by a network are becoming increasingly common, and tend to violate these assumptions. Here we develop a Gaussian graphical model for observations connected by a network with potentially different mean vectors, varying smoothly over the network. We propose an…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；The University of Chicago Booth School of Business（芝加哥大学布斯商学院）
Graphs from complex systems often share a partial underlying structure across domains while retaining individual features. Thus, identifying common structures can shed light on the underlying signal, for instance, when applied to scientific discoveries or clinical diagnoses. Furthermore, growing evidence shows that the shared structure across domains boosts the estimation power of graphs, particularly for high-dimensional data. However, building a joint estimator to extract the common structure may be more complicated than it seems, most often due to data heterogeneity across sources. This man…
Estimation of Gaussian graphical models is important in natural science when modeling the statistical relationships between variables in the form of a graph. The sparsity and clustering structure of the concentration matrix is enforced to reduce model complexity and describe inherent regularities. We propose a model to estimate the sparse Gaussian graphical models with hidden clustering structure, which also allows additional linear constraints to be imposed on the concentration matrix. We design an efficient two-phase algorithm for solving the proposed model. We develop a symmetric Gauss-Seid…
This paper introduces a novel approach to embed flow-based models with hierarchical structures. The proposed framework is named Variational Flow Graphical (VFG) Model. VFGs learn the representation of high dimensional data via a message-passing scheme by integrating flow-based functions through variational inference. By leveraging the expressive power of neural networks, VFGs produce a representation of the data using a lower dimension, thus overcoming the drawbacks of many flow-based models, usually requiring a high dimensional latent space involving many trivial variables. Aggregation nodes …
Gaussian graphical models are widely used to represent conditional dependence among random variables. In this paper, we propose a novel estimator for data arising from a group of Gaussian graphical models that are themselves dependent. A motivating example is that of modeling gene expression collected on multiple tissues from the same individual: here the multivariate outcome is affected by dependencies acting not only at the level of the specific tissues, but also at the level of the whole body; existing methods that assume independence among graphs are not applicable in this case. To estimat…
Graphical model has been widely used to investigate the complex dependence structure of high-dimensional data, and it is common to assume that observed data follow a homogeneous graphical model. However, observations usually come from different resources and have heterogeneous hidden commonality in real-world applications. Thus, it is of great importance to estimate heterogeneous dependencies and discover subpopulation with certain commonality across the whole population. In this work, we introduce a novel regularized estimation scheme for learning nonparametric mixture of Gaussian graphical m…
The time-evolving precision matrix of a piecewise-constant Gaussian graphical model encodes the dynamic conditional dependency structure of a multivariate time-series. Traditionally, graphical models are estimated under the assumption that data is drawn identically from a generating distribution. Introducing sparsity and sparse-difference inducing priors we relax these assumptions and propose a novel regularized M-estimator to jointly estimate both the graph and changepoint structure. The resulting estimator possesses the ability to therefore favor sparse dependency structures and/or smoothly …
Oregon State University（俄勒冈州立大学）；University of Massachusetts, Amherst（马萨诸塞大学阿默斯特分校）；Mount Holyoke College（曼荷莲学院）
The Collective Graphical Model (CGM) models a population of independent and identically distributed individuals when only collective statistics (i.e., counts of individuals) are observed. Exact inference in CGMs is intractable, and previous work has explored Markov Chain Monte Carlo (MCMC) and MAP approximations for learning and inference. This paper studies Gaussian approximations to the CGM. As the population grows large, we show that the CGM distribution converges to a multivariate Gaussian distribution (GCGM) that maintains the conditional independence properties of the original CGM. If th…
