Bayesian Estimation of Large Precision Matrix Based on Cholesky Decomposition

This paper considers the ridge-type shrinkage estimation of the large dimensional precision matrix. The asymptotic optimal shrinkage coefficients and the theoretical loss are derived. Data-driven estimators for the shrinkage coefficients are also conducted based on the asymptotic results from random matrix theory. The new method is distribution-free and no assumption on the structure of the covariance matrix or the precision matrix is required. The proposed method also applies to situations where the dimension is larger than the sample size. Finally, numerical studies using simulated data and real data demonstrate that the proposed estimator performs better than the existing competitors in a wide range of settings.

ABSTRACTWe propose a penalized likelihood method to fit the linear discriminant analysis model when the predictor is matrix valued. We simultaneously estimate the means and the precision matrix, which we assume has a Kronecker product decomposition. Our penalties encourage pairs of response category mean matrix estimators to have equal entries and also encourage zeros in the precision matrix estimator. To compute our estimators, we use a blockwise coordinate descent algorithm. To update the optimization variables corresponding to response category mean matrices, we use an alternating minimization algorithm that takes advantage of the Kronecker structure of the precision matrix. We show that our method can outperform relevant competitors in classification, even when our modeling assumptions are violated. We analyze three real datasets to demonstrate our method’s applicability. Supplementary materials, including an R package implementing our method, are available online.

Large-scale precision matrix estimation is of fundamental importance yet challenging in many contemporary applications for recovering Gaussian graphical models. In this paper, we suggest a new approach of innovated scalable efficient estimation (ISEE) for estimating large precision matrix. Motivated by the innovated transformation, we convert the original problem into that of large covariance matrix estimation. The suggested method combines the strengths of recent advances in high-dimensional sparse modeling and large covariance matrix estimation. Compared to existing approaches, our method is scalable and can deal with much larger precision matrices with simple tuning. Under mild regularity conditions, we establish that this procedure can recover the underlying graphical structure with significant probability and provide efficient estimation of link strengths. Both computational and theoretical advantages of the procedure are evidenced through simulation and real data examples.

Estimation of the covariance matrix and its inverse, the precision matrix, in high-dimensional situations is of great interest in many applications. In this paper, we focus on the estimation of a class of sparse precision matrices which are assumed to be approximately inversely closed for the case that the dimensionality p can be much larger than the sample size n, which is fundamentally different from the classical case that p <; n. Different in nature from state-of-the-art methods that are based on penalized likelihood maximization or constrained error minimization, based on the truncated Neumann series representation, we propose a computationally efficient precision matrix estimator that has a computational complexity of O (p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ). We prove that the proposed estimator is consistent in probability and in L <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> under the spectral norm. Moreover, its convergence is shown to be rate-optimal in the sense of minimax risk. We further prove that the proposed estimator is model selection consistent by establishing a convergence result under the entry-wise ∞-norm. Simulations demonstrate the encouraging finite sample size performance and computational advantage of the proposed estimator. The proposed estimator is also applied to a real breast cancer data and shown to outperform existing precision matrix estimators.

Accurate estimation of large covariance and precision matrices is an essential prerequisite of portfolio selection and financial risk management. Among factor-based covariance estimators, high-frequency data provides additional information but also introduces noise, which could degrade the estimation of betas. In this paper, we propose a new Mixed-frequency and FActor-based (MFACE) combining high-frequency (intraday) data and low-frequency (daily) betas. We apply approximate factor structure to construct the high-dimensional minimum variance portfolio. We establish the consistency and obtain the convergence rate of the covariance estimator and the corresponding precision matrix estimator. A comprehensive simulation study investigates the estimation accuracy under different combinations of intrady sampling frequency, intraday sample size and daily sample size. Out-of-sample forecasts demonstrate that our estimator explains the daily volatility of the equally-weighted portfolio pretty well. The minimum variance portfolio that embodies low-frequency betas also achieves the minimum risk at relatively low cost among several estimators.

In many engineering applications, estimation of covariance and precision matrices is of great importance, helping researchers understand the dependency and conditional dependency between variables of interest. Among various matrix estimation methods, the modified Cholesky decomposition is a commonly used technique. It has the advantage of transforming the matrix estimation task into solving a sequence of regression models. Moreover, the sparsity on the regression coefficients implies certain sparse structure on the covariance and precision matrices. In this chapter, we first overview the Cholesky-based covariance and precision matrices estimation. It is known that the Cholesky-based matrix estimation depends on a prespecified ordering of variables, which is often not available in practice. To address this issue, we then introduce several techniques to enhance the Cholesky-based estimation of covariance and precision matrices. These approaches are able to ensure the positive definiteness of the matrix estimate and applicable in general situations without specifying the ordering of variables. The advantage of Cholesky-based estimation is illustrated by numerical studies and several real-case applications.

In this article, we consider the problem of estimating the precision matrix when the sample data contains cellwise contamination. For the widely employed methodologies (e.g. Graphical Lasso), using the sample covariance matrix as an input matrix potentially deteriorates the precision matrix estimation performance in the presence of outliers. We propose several robust alternatives for the covariance matrix, which are constructed by combining robust correlation estimators with robust variation measures. Through extensive numerical studies we demonstrate the robust performance of our proposed approaches compared to the standard methods based on the sample covariance matrix. Further, we apply our proposals to a real data application, aimed at studying the optimal portfolio allocations in Shanghai Stock Exchange Composite index. The results show that the proposed alternatives provide desirable out-of-sample performance.

Estimating large covariance and precision (inverse covariance) matrices has become increasingly important in high dimensional statistics because of its wide applications. The estimation problem is challenging not only theoretically due to the constraint of its positive definiteness, but also computationally because of the curse of dimensionality. Many types of estimators have been proposed such as thresholding under the sparsity assumption of the target matrix, banding and tapering the sample covariance matrix. However, these estimators are not always guaranteed to be positive-definite, especially, for finite samples, and the sparsity assumption is rather restrictive. We propose a novel two-stage adaptive method based on the Cholesky decomposition of a general covariance matrix. By banding the precision matrix in the first stage and adapting the estimates to the second stage estimation, we develop a computationally efficient and statistically accurate method for estimating high dimensional precision matrices. We demonstrate the finite-sample performance of the proposed method by simulations from autoregressive, moving average, and long-range dependent processes. We illustrate its wide applicability by analyzing financial data such S&amp;P 500 index and IBM stock returns, and electric power consumption of individual households. The theoretical properties of the proposed method are also investigated within a large class of covariance matrices.

A sparse precision matrix can be directly translated into a sparse Gaussian graphical model under the assumption that the data follow a joint normal distribution. This neat property makes high-dimensional precision matrix estimation very appealing in many applications. However, in practice we often face nonnormal data, and variable transformation is often used to achieve normality. In this paper we consider the nonparanormal model that assumes that the variables follow a joint normal distribution after a set of unknown monotone transformations. The nonparanormal model is much more flexible than the normal model while retaining the good interpretability of the latter in that each zero entry in the sparse precision matrix of the nonparanormal model corresponds to a pair of conditionally independent variables. In this paper we show that the nonparanormal graphical model can be efficiently estimated by using a rank-based estimation scheme which does not require estimating these unknown transformation functions. In particular, we study the rank-based graphical lasso, the rank-based neighborhood Dantzig selector and the rank-based CLIME. We establish their theoretical properties in the setting where the dimension is nearly exponentially large relative to the sample size. It is shown that the proposed rank-based estimators work as well as their oracle counterparts defined with the oracle data. Furthermore, the theory motivates us to consider the adaptive version of the rank-based neighborhood Dantzig selector and the rank-based CLIME that are shown to enjoy graphical model selection consistency without assuming the irrepresentable condition for the oracle and rank-based graphical lasso. Simulated and real data are used to demonstrate the finite performance of the rank-based estimators.

The determination of the covariance matrix and its inverse, the precision matrix, is critical in the statistical analysis of cosmological measurements. The covariance matrix is typically estimated with a limited number of simulations at great computational cost before inversion into the precision matrix; therefore, it can be ill-conditioned and overly noisy when the sample size n used for estimation is not much larger than the data vector dimension. In this work, we consider a class of methods known as shrinkage estimation for the precision matrix, which combines an empirical estimate with a target that is either analytical or stochastic. These methods include linear and non-linear shrinkage applied to the covariance matrix (the latter represented by the so-called NERCOME estimator), and the direct linear shrinkage estimation of the precision matrix which we introduce in a cosmological setting. By performing Bayesian parameter inference and using metrics like matrix loss functions, the Kullback–Leibler divergence and the eigenvalue spectrum, we compare their performance against the standard sample estimator with varying sample size n. We have found the shrinkage estimators to significantly improve the posterior distribution at low n, especially for the linear shrinkage estimators either inverted from the covariance matrix or applied directly to the precision matrix, with an empirical target constructed from the sample estimate. Our results are particularly relevant to the analyses of Stage-IV spectroscopic galaxy surveys such as the Dark Energy Spectroscopic Instrument and Euclid, whose statistical power can be limited by the computational cost of obtaining an accurate precision matrix estimate.

Estimation of sparse covariance matrices and their inverse subject to positive definiteness constraints has drawn a lot of attention in recent years. The abundance of high-dimensional data, where the sample size (n) is less than the dimension (d), requires shrinkage estimation methods since the maximum likelihood estimator is not positive definite in this case. Furthermore, when n is larger than d but not sufficiently larger, shrinkage estimation is more stable than maximum likelihood as it reduces the condition number of the precision matrix. Frequentist methods have utilized penalized likelihood methods, whereas Bayesian approaches rely on matrix decompositions or Wishart priors for shrinkage. In this paper we propose a new method, called the Bayesian Covariance Lasso (BCLASSO), for the shrinkage estimation of a precision (covariance) matrix. We consider a class of priors for the precision matrix that leads to the popular frequentist penalties as special cases, develop a Bayes estimator for the precision matrix, and propose an efficient sampling scheme that does not precalculate boundaries for positive definiteness. The proposed method is permutation invariant and performs shrinkage and estimation simultaneously for non-full rank data. Simulations show that the proposed BCLASSO performs similarly as frequentist methods for non-full rank data.

We consider the problem of Bayesian discriminant analysis using a high dimensional predictor. In this setting, the underlying precision matrices can be estimated with reasonable accuracy only if some appropriate additional structure like sparsity is assumed. We induce a prior on the precision matrix through a sparse prior on its Cholesky decomposition. For computational ease, we use shrinkage priors to induce sparsity on the off-diagonal entries of the Cholesky decomposition matrix and exploit certain conditional conjugacy structure. We obtain the contraction rate of the posterior distribution for the mean and the precision matrix respectively using the Euclidean and the Frobenius distance, and show that under some milder restriction on the growth of the dimension, the misclassification probability of the Bayesian classification procedure converges to that of the oracle classifier for both linear and quadratic discriminant analysis. Extensive simulations show that the proposed Bayesian methods perform very well. An application to identify cancerous breast tumorbased on image data obtained using find needle aspirate is considered.

Estimation of the high-dimensional banded covariance matrix is widely used in multivariate statistical analysis. To ensure the validity of estimation, we aim to test the hypothesis that the covariance matrix is banded with a certain bandwidth under the high-dimensional framework. Though several testing methods have been proposed in the literature, the existing tests are only powerful for some alternatives with certain sparsity levels, whereas they may not be powerful for alternatives with other sparsity structures. The goal of this paper is to propose a new test for the bandedness of high-dimensional covariance matrix, which is powerful for alternatives with various sparsity levels. The proposed new test also be used for testing the banded structure of covariance matrices of error vectors in high-dimensional factor models. Based on these statistics, a consistent bandwidth estimator is also introduced for a banded high dimensional covariance matrix. Extensive simulation studies and an application to a prostate cancer dataset from protein mass spectroscopy are conducted for evaluating the effectiveness of the proposed adaptive tests blue and bandwidth estimator for the banded covariance matrix.

Motivated by establishing theoretical foundations for various manifold learning algorithms, we study the problem of Mahalanobis distance (MD) and the associated precision matrix estimation from high-dimensional noisy data. By relying on recent transformative results in covariance matrix estimation, we demonstrate the sensitivity of MD and the associated precision matrix to measurement noise, determining the exact asymptotic signal-to-noise ratio at which MD fails, and quantifying its performance otherwise. In addition, for an appropriate loss function, we propose an asymptotically optimal shrinker, which is shown to be beneficial over the classical implementation of the MD, both analytically and in simulations. The result is extended to the manifold setup, where the nonlinear interaction between curvature and high-dimensional noise is taken care of. The developed solution is applied to study a multi-scale reduction problem in the dynamical system analysis.

High-dimensional compositional data are prevalent in many applications. The simplex constraint poses intrinsic challenges to inferring the conditional dependence relationships among the components forming a composition, as encoded by a large precision matrix. We introduce a precise specification of the compositional precision matrix and relate it to its basis counterpart, which is shown to be asymptotically identifiable under suitable sparsity assumptions. By exploiting this connection, we propose a composition adaptive regularized estimation (CARE) method for estimating the sparse basis precision matrix. We derive rates of convergence for the estimator and provide theoretical guarantees on support recovery and data-driven parameter tuning. Our theory reveals an intriguing tradeoff between identification and estimation, thereby highlighting the blessing of dimensionality in compositional data analysis. In particular, in sufficiently high dimensions, the CARE estimator achieves minimax optimality and performs as well as if the basis were observed. We further discuss how our framework can be extended to handle data containing zeros, including sampling zeros and structural zeros. The advantages of CARE over existing methods are illustrated by simulation studies and an application to inferring microbial ecological networks in the human gut. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.