In this work, we extend the sparse iterative covariance-based estimator (SPICE), by generalizing the formulation to allow for different norm constraints on the signal and noise parameters in the covariance model. For a given norm, the resulting extended SPICE method enjoys the same benefits as the regular SPICE method, including being hyper-parameter free, although the choice of norms are shown to govern the sparsity in the resulting solution. Furthermore, we show that solving the extended SPICE method is equivalent to solving a penalized regression problem, which provides an alternative interpretation of the proposed method and a deeper insight on the differences in sparsity between the extended and the original SPICE formulation. We examine the performance of the method for different choices of norms, and compare the results to the original SPICE method, showing the benefits of using the extended formulation. We also provide two ways of solving the extended SPICE method; one grid-based method, for which an efficient implementation is given, and a gridless method for the sinusoidal case, which results in a semi-definite programming problem.
Smoothing of noisy sample covariances is an important component in functional data analysis. We propose a novel covariance smoothing method based on penalized splines and associated software. The proposed method is a bivariate spline smoother that is designed for covariance smoothing and can be used for sparse functional or longitudinal data. We propose a fast algorithm for covariance smoothing using leave-one-subject-out cross validation. Our simulations show that the proposed method compares favorably against several commonly used methods. The method is applied to a study of child growth led…
We present a graph-based technique for estimating sparse covariance matrices and their inverses from high-dimensional data. The method is based on learning a directed acyclic graph (DAG) and estimating parameters of a multivariate Gaussian distribution based on a DAG. For inferring the underlying DAG we use the PC-algorithm and for estimating the DAG-based covariance matrix and its inverse, we use a Cholesky decomposition approach which provides a positive (semi-)definite sparse estimate. We present a consistency result in the high-dimensional framework and we compare our method with the Glass…
We propose an l1-regularized likelihood method for estimating the inverse covariance matrix in the high-dimensional multivariate normal model in presence of missing data. Our method is based on the assumption that the data are missing at random (MAR) which entails also the completely missing at random case. The implementation of the method is non-trivial as the observed negative log-likelihood generally is a complicated and non-convex function. We propose an efficient EM algorithm for optimization with provable numerical convergence properties. Furthermore, we extend the methodology to handle …
In high-dimensions, many variable selection methods, such as the lasso, are often limited by excessive variability and rank deficiency of the sample covariance matrix. Covariance sparsity is a natural phenomenon in high-dimensional applications, such as microarray analysis, image processing, etc., in which a large number of predictors are independent or weakly correlated. In this paper, we propose the covariance-thresholded lasso, a new class of regression methods that can utilize covariance sparsity to improve variable selection. We establish theoretical results, under the random design setti…
We consider the problem of estimating sparse graphs by a lasso penalty applied to the inverse covariance matrix. Using a coordinate descent procedure for the lasso, we develop a simple algorithm that is remarkably fast: in the worst cases, it solves a 1000 node problem (~500,000 parameters) in about a minute, and is 50 to 2000 times faster than competing methods. It also provides a conceptual link between the exact problem and the approximation suggested by Meinhausen and Buhlmann (2006). We illustrate the method on some cell-signaling data from proteomics.
We consider the problem of estimating high-dimensional covariance matrices of a particular structure, which is a summation of low rank and sparse matrices. This covariance structure has a wide range of applications including factor analysis and random effects models. We propose a Bayesian method of estimating the covariance matrices by representing the covariance model in the form of a factor model with unknown number of latent factors. We introduce binary indicators for factor selection and rank estimation for the low rank component combined with a Bayesian lasso method for the sparse compone…
In this paper we consider estimation of sparse covariance matrices and propose a thresholding procedure which is adaptive to the variability of individual entries. The estimators are fully data driven and enjoy excellent performance both theoretically and numerically. It is shown that the estimators adaptively achieve the optimal rate of convergence over a large class of sparse covariance matrices under the spectral norm. In contrast, the commonly used universal thresholding estimators are shown to be sub-optimal over the same parameter spaces. Support recovery is also discussed. The adaptive …
Covariance estimation for high-dimensional datasets is a fundamental problem in modern day statistics with numerous applications. In these high dimensional datasets, the number of variables p is typically larger than the sample size n. A popular way of tackling this challenge is to induce sparsity in the covariance matrix, its inverse or a relevant transformation. In particular, methods inducing sparsity in the Cholesky pa- rameter of the inverse covariance matrix can be useful as they are guaranteed to give a positive definite estimate of the covariance matrix. Also, the estimated sparsity pa…
High dimensional covariance estimation and graphical models is a contemporary topic in statistics and machine learning having widespread applications. An important line of research in this regard is to shrink the extreme spectrum of the covariance matrix estimators. A separate line of research in the literature has considered sparse inverse covariance estimation which in turn gives rise to graphical models. In practice, however, a sparse covariance or inverse covariance matrix which is simultaneously well-conditioned and at the same time computationally tractable is desired. There has been lit…
Covariance estimation is essential yet underdeveloped for analyzing multivariate functional data. We propose a fast covariance estimation method for multivariate sparse functional data using bivariate penalized splines. The tensor-product B-spline formulation of the proposed method enables a simple spectral decomposition of the associated covariance operator and explicit expressions of the resulting eigenfunctions as linear combinations of B-spline bases, thereby dramatically facilitating subsequent principal component analysis. We derive a fast algorithm for selecting the smoothing parameters…
Kronecker PCA involves the use of a space vs. time Kronecker product decomposition to estimate spatio-temporal covariances. In this work the addition of a sparse correction factor is considered, which corresponds to a model of the covariance as a sum of Kronecker products of low (separation) rank and a sparse matrix. This sparse correction extends the diagonally corrected Kronecker PCA of [Greenewald et al 2013, 2014] to allow for sparse unstructured "outliers" anywhere in the covariance matrix, e.g. arising from variables or correlations that do not fit the Kronecker model well, or from sourc…
This paper addresses the task of estimating a covariance matrix under a patternless sparsity assumption. In contrast to existing approaches based on thresholding or shrinkage penalties, we propose a likelihood-based method that regularizes the distance from the covariance estimate to a symmetric sparsity set. This formulation avoids unwanted shrinkage induced by more common norm penalties and enables optimization of the resulting non-convex objective by solving a sequence of smooth, unconstrained subproblems. These subproblems are generated and solved via the proximal distance version of the m…
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 …
In this article, we consider the problem of recovering the underlying trajectory when the longitudinal data are sparsely and irregularly observed and noise-contaminated. Such data are popularly analyzed with functional principal component analysis via the Principal Analysis by Conditional Estimation (PACE) method. The PACE method may sometimes be numerically unstable because it involves the inverse of the covariance matrix. We propose a sparse orthonormal approximation (SOAP) method as an alternative. It estimates the optimal empirical basis functions in the best approximation framework rather…
Statistical inference for sparse covariance matrices is crucial to reveal dependence structure of large multivariate data sets, but lacks scalable and theoretically supported Bayesian methods. In this paper, we propose beta-mixture shrinkage prior, computationally more efficient than the spike and slab prior, for sparse covariance matrices and establish its minimax optimality in high-dimensional settings. The proposed prior consists of beta-mixture shrinkage and gamma priors for off-diagonal and diagonal entries, respectively. To ensure positive definiteness of the resulting covariance matrix,…
This paper introduces a new data-driven methodology for estimating sparse covariance matrices of the random coefficients in logit mixture models. Researchers typically specify covariance matrices in logit mixture models under one of two extreme assumptions: either an unrestricted full covariance matrix (allowing correlations between all random coefficients), or a restricted diagonal matrix (allowing no correlations at all). Our objective is to find optimal subsets of correlated coefficients for which we estimate covariances. We propose a new estimator, called MISC, that uses a mixed-integer op…
Finite Gaussian mixture models are widely used for model-based clustering of continuous data. Nevertheless, since the number of model parameters scales quadratically with the number of variables, these models can be easily over-parameterized. For this reason, parsimonious models have been developed via covariance matrix decompositions or assuming local independence. However, these remedies do not allow for direct estimation of sparse covariance matrices nor do they take into account that the structure of association among the variables can vary from one cluster to the other. To this end, we in…
In this paper, we study a smoothness regularization method for a varying coefficient model based on sparse and irregularly sampled functional data which is contaminated with some measurement errors. We estimate the one-dimensional covariance and cross-covariance functions of the underlying stochastic processes based on a reproducing kernel Hilbert space approach. We then obtain least squares estimates of the coefficient functions. Simulation studies demonstrate that the proposed method has good performance. We illustrate our method by an analysis of longitudinal primary biliary liver cirrhosis…
Estimation of the covariance matrix of asset returns from high frequency data is complicated by asynchronous returns, market mi- crostructure noise and jumps. One technique for addressing both asynchronous returns and market microstructure is the Kalman-EM (KEM) algorithm. However the KEM approach assumes log-normal prices and does not address jumps in the return process which can corrupt estimation of the covariance matrix. In this paper we extend the KEM algorithm to price models that include jumps. We propose two sparse Kalman filtering approaches to this problem. In the first approach we d…
A new framework is developed to intrinsically analyze sparsely observed Riemannian functional data. It features four innovative components: a frame-independent covariance function, a smooth vector bundle termed covariance vector bundle, a parallel transport and a smooth bundle metric on the covariance vector bundle. The introduced intrinsic covariance function links estimation of covariance structure to smoothing problems that involve raw covariance observations derived from sparsely observed Riemannian functional data, while the covariance vector bundle provides a rigorous mathematical founda…
The well-known spatial sign covariance matrix (SSCM) carries out a radial transform which moves all data points to a sphere, followed by computing the classical covariance matrix of the transformed data. Its popularity stems from its robustness to outliers, fast computation, and applications to correlation and principal component analysis. In this paper we study more general radial functions. It is shown that the eigenvectors of the generalized SSCM are still consistent and the ranks of the eigenvalues are preserved. The influence function of the resulting scatter matrix is derived, and it is …
We propose a novel estimation approach for the covariance matrix based on the $l_1$-regularized approximate factor model. Our sparse approximate factor (SAF) covariance estimator allows for the existence of weak factors and hence relaxes the pervasiveness assumption generally adopted for the standard approximate factor model. We prove consistency of the covariance matrix estimator under the Frobenius norm as well as the consistency of the factor loadings and the factors. Our Monte Carlo simulations reveal that the SAF covariance estimator has superior properties in finite samples for low and h…
We study estimation and prediction of Gaussian processes with covariance model belonging to the generalized Cauchy (GC) family, under fixed domain asymptotics. Gaussian processes with this kind of covariance function provide separate characterization of fractal dimension and long range dependence, an appealing feature in many physical, biological or geological systems. The results of the paper are classified into three parts. In the first part, we characterize the equivalence of two Gaussian measures with GC covariance function. Then we provide sufficient conditions for the equivalence of two …
We offer a method to estimate a covariance matrix in the special case that \textit{both} the covariance matrix and the precision matrix are sparse --- a constraint we call double sparsity. The estimation method is maximum likelihood, subject to the double sparsity constraint. In our method, only a particular class of sparsity pattern is allowed: both the matrix and its inverse must be subordinate to the same chordal graph. Compared to a naive enforcement of double sparsity, our chordal graph approach exploits a special algebraic local inverse formula. This local inverse property makes computat…
We consider Bayesian inference of sparse covariance matrices and propose a post-processed posterior. This method consists of two steps. In the first step, posterior samples are obtained from the conjugate inverse-Wishart posterior without considering the sparse structural assumption. The posterior samples are transformed in the second step to satisfy the sparse structural assumption through the hard-thresholding function. This non-traditional Bayesian procedure is justified by showing that the post-processed posterior attains the optimal minimax rates. We also investigate the application of th…
Given n observations of a p-dimensional random vector, the covariance matrix and its inverse (precision matrix) are needed in a wide range of applications. Sample covariance (e.g. its eigenstructure) can misbehave when p is comparable to the sample size n. Regularization is often used to mitigate the problem. In this paper, we proposed an l1-norm penalized pseudo-likelihood estimate for the inverse covariance matrix. This estimate is sparse due to the l1-norm penalty, and we term this method SPLICE. Its regularization path can be computed via an algorithm based on the homotopy/LARS-Lasso algor…
In this paper, we consider estimating sparse inverse covariance of a Gaussian graphical model whose conditional independence is assumed to be partially known. Similarly as in [5], we formulate it as an $l_1$-norm penalized maximum likelihood estimation problem. Further, we propose an algorithm framework, and develop two first-order methods, that is, the adaptive spectral projected gradient (ASPG) method and the adaptive Nesterov's smooth (ANS) method, for solving this estimation problem. Finally, we compare the performance of these two methods on a set of randomly generated instances. Our comp…
The present paper concerns large covariance matrix estimation via composite minimization under the assumption of low rank plus sparse structure. In this approach, the low rank plus sparse decomposition of the covariance matrix is recovered by least squares minimization under nuclear norm plus $l_1$ norm penalization. This paper proposes a new estimator of that family based on an additional least-squares re-optimization step aimed at un-shrinking the eigenvalues of the low rank component estimated at the first step. We prove that such un-shrinkage causes the final estimate to approach the targe…
We propose a general framework for non-normal multivariate data analysis called multivariate covariance generalized linear models (McGLMs), designed to handle multivariate response variables, along with a wide range of temporal and spatial correlation structures defined in terms of a covariance link function combined with a matrix linear predictor involving known matrices. The method is motivated by three data examples that are not easily handled by existing methods. The first example concerns multivariate count data, the second involves response variables of mixed types, combined with repeate…
This paper is an extension of Parts I and Ia of a series about Nu-class generalized functions. We provide hand-generated algebraic expressions for integrals of single Matern-covariance functions, as well as for products of two Matern-covariance functions, for all odd-half-integer class parameters. These are useful both for IMSPE-optimal design software and for testing universality of Nu-class generalized-function properties, across covariance classes.
Estimation of a precision matrix (i.e., inverse covariance matrix) is widely used to exploit conditional independence among continuous variables. The influence of abnormal observations is exacerbated in a high dimensional setting as the dimensionality increases. In this work, we propose robust estimation of the inverse covariance matrix based on an $l_1$ regularized objective function with a weighted sample covariance matrix. The robustness of the proposed objective function can be justified by a nonparametric technique of the integrated squared error criterion. To address the non-convexity of…
Inference and Estimation in Missing Information (MI) scenarios are important topics in Statistical Learning Theory and Machine Learning (ML). In ML literature, attempts have been made to enhance prediction through precise feature selection methods. In sparse linear models, LASSO is well-known in extracting the desired support of the signal and resisting against noisy systems. When sparse models are also suffering from MI, the sparse recovery and inference of the missing models are taken into account simultaneously. In this paper, we will introduce an approach which enjoys sparse regression and…
We study the estimation of the covariance matrix $Σ$ of a $p$-dimensional normal random vector based on $n$ independent observations corrupted by additive noise. Only a general nonparametric assumption is imposed on the distribution of the noise without any sparsity constraint on its covariance matrix. In this high-dimensional semiparametric deconvolution problem, we propose spectral thresholding estimators that are adaptive to the sparsity of $Σ$. We establish an oracle inequality for these estimators under model miss-specification and derive non-asymptotic minimax convergence rates that are …
The thresholding covariance estimator has nice asymptotic properties for estimating sparse large covariance matrices, but it often has negative eigenvalues when used in real data analysis. To simultaneously achieve sparsity and positive definiteness, we develop a positive definite $\ell_1$-penalized covariance estimator for estimating sparse large covariance matrices. An efficient alternating direction method is derived to solve the challenging optimization problem and its convergence properties are established. Under weak regularity conditions, non-asymptotic statistical theory is also establ…
We propose a general framework for nonasymptotic covariance matrix estimation making use of concentration inequality-based confidence sets. We specify this framework for the estimation of large sparse covariance matrices through incorporation of past thresholding estimators with key emphasis on support recovery. This technique goes beyond past results for thresholding estimators by allowing for a wide range of distributional assumptions beyond merely sub-Gaussian tails. This methodology can furthermore be adapted to a wide range of other estimators and settings. The usage of nonasymptotic dime…
In this paper we first study a smooth optimization approach for solving a class of nonsmooth strictly concave maximization problems whose objective functions admit smooth convex minimization reformulations. In particular, we apply Nesterov's smooth optimization technique [Y.E. Nesterov, Dokl. Akad. Nauk SSSR, 269 (1983), pp. 543--547; Y. E. Nesterov, Math. Programming, 103 (2005), pp. 127--152] to their dual counterparts that are smooth convex problems. It is shown that the resulting approach has ${\cal O}(1/{\sqrtε})$ iteration complexity for finding an $ε$-optimal solution to both primal and…
Covariance function estimation is a fundamental task in multivariate functional data analysis and arises in many applications. In this paper, we consider estimating sparse covariance functions for high-dimensional functional data, where the number of random functions p is comparable to, or even larger than the sample size n. Aided by the Hilbert--Schmidt norm of functions, we introduce a new class of functional thresholding operators that combine functional versions of thresholding and shrinkage, and propose the adaptive functional thresholding estimator by incorporating the variance effects o…
We address the curse of dimensionality in dynamic covariance estimation by modeling the underlying co-volatility dynamics of a time series vector through latent time-varying stochastic factors. The use of a global-local shrinkage prior for the elements of the factor loadings matrix pulls loadings on superfluous factors towards zero. To demonstrate the merits of the proposed framework, the model is applied to simulated data as well as to daily log-returns of 300 S&P 500 members. Our approach yields precise correlation estimates, strong implied minimum variance portfolio performance and superior…
Many popular statistical models, such as factor and random effects models, give arise a certain type of covariance structures that is a summation of low rank and sparse matrices. This paper introduces a penalized approximation framework to recover such model structures from large covariance matrix estimation. We propose an estimator based on minimizing a non-likelihood loss with separable non-smooth penalty functions. This estimator is shown to recover exactly the rank and sparsity patterns of these two components, and thus partially recovers the model structures. Convergence rates under vario…
We propose a Bayesian methodology for estimating spiked covariance matrices with jointly sparse structure in high dimensions. The spiked covariance matrix is reparametrized in terms of the latent factor model, where the loading matrix is equipped with a novel matrix spike-and-slab LASSO prior, which is a continuous shrinkage prior for modeling jointly sparse matrices. We establish the rate-optimal posterior contraction for the covariance matrix with respect to the operator norm as well as that for the principal subspace with respect to the projection operator norm loss. We also study the poste…
We consider a more generalized spiked covariance matrix $Σ$, which is a general non-definite matrix with the spiked eigenvalues scattered into a few bulks and the largest ones allowed to tend to infinity. By relaxing the matching of the 4th moment to a tail probability decay, a {\it Generalized Four Moment Theorem} (G4MT) is proposed to show the universality of the asymptotic law for the local spectral statistics of generalized spiked covariance matrices, which implies the limiting distribution of the spiked eigenvalues of the generalized spiked covariance matrix is independent of the actual d…
Sparse principal component analysis (sPCA) has become one of the most widely used techniques for dimensionality reduction in high-dimensional datasets. The main challenge underlying sPCA is to estimate the first vector of loadings of the population covariance matrix, provided that only a certain number of loadings are non-zero. In this paper, we propose confidence intervals for individual loadings and for the largest eigenvalue of the population covariance matrix. Given an independent sample $X^i \in\mathbb R^p, i = 1,...,n,$ generated from an unknown distribution with an unknown covariance ma…
The generalized Ridge penalty is a powerful tool for dealing with overfitting and for high-dimensional regressions. The generalized Ridge regression can be derived as the mean of a posterior distribution with a Normal prior and a given covariance matrix. The covariance matrix controls the structure of the coefficients, which depends on the particular application. For example, it is appropriate to assume that the coefficients have a spatial structure in spatial applications. This study proposes an expectation-maximization algorithm for estimating generalized Ridge parameters whose covariance st…
High-dimensional statistical tests often ignore correlations to gain simplicity and stability leading to null distributions that depend on functionals of correlation matrices such as their Frobenius norm and other $\ell_r$ norms. Motivated by the computation of critical values of such tests, we investigate the difficulty of estimation the functionals of sparse correlation matrices. Specifically, we show that simple plug-in procedures based on thresholded estimators of correlation matrices are sparsity-adaptive and minimax optimal over a large class of correlation matrices. Akin to previous res…
