Motivated by the task of clustering either $d$ variables or $d$ points into $K$ groups, we investigate efficient algorithms to solve the Peng-Wei (P-W) $K$-means semi-definite programming (SDP) relaxation. The P-W SDP has been shown in the literature to have good statistical properties in a variety of settings, but remains intractable to solve in practice. To this end we propose FORCE, a new algorithm to solve this SDP relaxation. Compared to the naive interior point method, our method reduces the computational complexity of solving the SDP from $\tilde{O}(d^7\logε^{-1})$ to $\tilde{O}(d^{6}K^{-2}ε^{-1})$ arithmetic operations for an $ε$-optimal solution. Our method combines a primal first-order method with a dual optimality certificate search, which when successful, allows for early termination of the primal method. We show for certain variable clustering problems that, with high probability, FORCE is guaranteed to find the optimal solution to the SDP relaxation and provide a certificate of exact optimality. As verified by our numerical experiments, this allows FORCE to solve the P-W SDP with dimensions in the hundreds in only tens of seconds. For a variation of the P-W SDP where $K$ is not known a priori a slight modification of FORCE reduces the computational complexity of solving this problem as well: from $\tilde{O}(d^7\logε^{-1})$ using a standard SDP solver to $\tilde{O}(d^{4}ε^{-1})$.
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.
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 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…
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 …
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 …
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…
University of Waterloo（滑铁卢大学）；University of Illinois at Urbana（伊利诺伊大学厄巴纳分校）
Mixtures of Gaussians, factor analyzers (probabilistic PCA) and hidden Markov models are staples of static and dynamic data modeling and image and video modeling in particular. We show how topographic transformations in the input, such as translation and shearing in images, can be accounted for in these models by including a discrete transformation variable. The resulting models perform clustering, dimensionality reduction and time-series analysis in a way that is invariant to transformations in the input. Using the EM algorithm, these transformation-invariant models can be fit to static data …
We consider joint estimation of multiple graphical models arising from heterogeneous and high-dimensional observations. Unlike most previous approaches which assume that the cluster structure is given in advance, an appealing feature of our method is to learn cluster structure while estimating heterogeneous graphical models. This is achieved via a high dimensional version of Expectation Conditional Maximization (ECM) algorithm (Meng and Rubin, 1993). A joint graphical lasso penalty is imposed on the conditional maximization step to extract both homogeneity and heterogeneity components across a…
Motivated by modern applications in which one constructs graphical models based on a very large number of features, this paper introduces a new class of cluster-based graphical models, in which variable clustering is applied as an initial step for reducing the dimension of the feature space. We employ model assisted clustering, in which the clusters contain features that are similar to the same unobserved latent variable. Two different cluster-based Gaussian graphical models are considered: the latent variable graph, corresponding to the graphical model associated with the unobserved latent va…
Università degli Studi di Genova（热那亚大学）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
Multivariate time series analysis is becoming an integral part of data analysis pipelines. Understanding the individual time point connections between covariates as well as how these connections change in time is non-trivial. To this aim, we propose a novel method that leverages on Hidden Markov Models and Gaussian Graphical Models -- Time Adaptive Gaussian Model (TAGM). Our model is a generalization of state-of-the-art methods for the inference of temporal graphical models, its formulation leverages on both aspects of these models providing better results than current methods. In particular,i…
Record linkage involves merging records in large, noisy databases to remove duplicate entities. It has become an important area because of its widespread occurrence in bibliometrics, public health, official statistics production, political science, and beyond. Traditional linkage methods directly linking records to one another are computationally infeasible as the number of records grows. As a result, it is increasingly common for researchers to treat record linkage as a clustering task, in which each latent entity is associated with one or more noisy database records. We critically assess per…
Gatsby Unit, University College London（伦敦大学学院盖茨比计算神经科学单元）
Current methods for learning graphical models with latent variables and a fixed structure estimate optimal values for the model parameters. Whereas this approach usually produces overfitting and suboptimal generalization performance, carrying out the Bayesian program of computing the full posterior distributions over the parameters remains a difficult problem. Moreover, learning the structure of models with latent variables, for which the Bayesian approach is crucial, is yet a harder problem. In this paper I present the Variational Bayes framework, which provides a solution to these problems. …
To better understand the spatial structure of large panels of economic and financial time series and provide a guideline for constructing semiparametric models, this paper first considers estimating a large spatial covariance matrix of the generalized $m$-dependent and $β$-mixing time series (with $J$ variables and $T$ observations) by hard thresholding regularization as long as ${\log J \, \cx^*(\ct)}/{T} = \Co(1)$ (the former scheme with some time dependence measure $\cx^*(\ct)$) or $\log J /{T} = \Co(1)$ (the latter scheme with some upper bounded mixing coefficient). We quantify the interpl…
Latent tree models are graphical models defined on trees, in which only a subset of variables is observed. They were first discussed by Judea Pearl as tree-decomposable distributions to generalise star-decomposable distributions such as the latent class model. Latent tree models, or their submodels, are widely used in: phylogenetic analysis, network tomography, computer vision, causal modeling, and data clustering. They also contain other well-known classes of models like hidden Markov models, Brownian motion tree model, the Ising model on a tree, and many popular models used in phylogenetics.…
The Hong Kong University of Science and Technology（香港科技大学）；Ant Financial Services Group（蚂蚁金融服务集团）；The Education University of Hong Kong（香港教育大学）
We present a novel method for hierarchical topic detection where topics are obtained by clustering documents in multiple ways. Specifically, we model document collections using a class of graphical models called hierarchical latent tree models (HLTMs). The variables at the bottom level of an HLTM are observed binary variables that represent the presence/absence of words in a document. The variables at other levels are binary latent variables, with those at the lowest latent level representing word co-occurrence patterns and those at higher levels representing co-occurrence of patterns at the l…
