We consider the class of convex minimization problems, composed of a self-concordant function, such as the $\log\det$ metric, a convex data fidelity term $h(\cdot)$ and, a regularizing -- possibly non-smooth -- function $g(\cdot)$. This type of problems have recently attracted a great deal of interest, mainly due to their omnipresence in top-notch applications. Under this \emph{locally} Lipschitz continuous gradient setting, we analyze the convergence behavior of proximal Newton schemes with the added twist of a probable presence of inexact evaluations. We prove attractive convergence rate guarantees and enhance state-of-the-art optimization schemes to accommodate such developments. Experimental results on sparse covariance estimation show the merits of our algorithm, both in terms of recovery efficiency and complexity.
In many real-world problems, complex dependencies are present both among samples and among features. The Kronecker sum or the Cartesian product of two graphs, each modeling dependencies across features and across samples, has been used as an inverse covariance matrix for a matrix-variate Gaussian distribution, as an alternative to a Kronecker-product inverse covariance matrix, due to its more intuitive sparse structure. However, the existing methods for sparse Kronecker-sum inverse covariance estimation are limited in that they do not scale to more than a few hundred features and samples and t…
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…
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…
We study the problem of estimating from data, a sparse approximation to the inverse covariance matrix. Estimating a sparsity constrained inverse covariance matrix is a key component in Gaussian graphical model learning, but one that is numerically very challenging. We address this challenge by developing a new adaptive gradient-based method that carefully combines gradient information with an adaptive step-scaling strategy, which results in a scalable, highly competitive method. Our algorithm, like its predecessors, maximizes an $\ell_1$-norm penalized log-likelihood and has the same per itera…
UC Berkeley（加州大学伯克利分校）；Carnegie Mellon University（卡内基梅隆大学）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；Berkeley Institute for Data Science, UC Berkeley（加州大学伯克利分校伯克利数据科学研究所）；UC Santa Barbara（加州大学圣塔芭芭拉分校）；Google Brain（谷歌大脑）
Across a variety of scientific disciplines, sparse inverse covariance estimation is a popular tool for capturing the underlying dependency relationships in multivariate data. Unfortunately, most estimators are not scalable enough to handle the sizes of modern high-dimensional data sets (often on the order of terabytes), and assume Gaussian samples. To address these deficiencies, we introduce HP-CONCORD, a highly scalable optimization method for estimating a sparse inverse covariance matrix based on a regularized pseudolikelihood framework, without assuming Gaussianity. Our parallel proximal gr…
This paper presents a new method for estimating high dimensional covariance matrices. The method, permuted rank-penalized least-squares (PRLS), is based on a Kronecker product series expansion of the true covariance matrix. Assuming an i.i.d. Gaussian random sample, we establish high dimensional rates of convergence to the true covariance as both the number of samples and the number of variables go to infinity. For covariance matrices of low separation rank, our results establish that PRLS has significantly faster convergence than the standard sample covariance matrix (SCM) estimator. The conv…
We develop a method for estimating well-conditioned and sparse covariance and inverse covariance matrices from a sample of vectors drawn from a sub-gaussian distribution in high dimensional setting. The proposed estimators are obtained by minimizing the quadratic loss function and joint penalty of `1 norm and variance of its eigenvalues. In contrast to some of the existing methods of covariance and inverse covariance matrix estimation, where often the interest is to estimate a sparse matrix, the proposed method is flexible in estimating both a sparse and well-conditioned covariance matrix simu…
Linear regression models depend directly on the design matrix and its properties. Techniques that efficiently estimate model coefficients by partitioning rows of the design matrix are increasingly popular for large-scale problems because they fit well with modern parallel computing architectures. We propose a simple measure of {\em concordance} between a design matrix and a subset of its rows that estimates how well a subset captures the variance-covariance structure of a larger data set. We illustrate the use of this measure in a heuristic method for selecting row partition sizes that balance…
In spatial statistics, it is often assumed that the spatial field of interest is stationary and its covariance has a simple parametric form, but these assumptions are not appropriate in many applications. Given replicate observations of a Gaussian spatial field, we propose nonstationary and nonparametric Bayesian inference on the spatial dependence. Instead of estimating the quadratic (in the number of spatial locations) entries of the covariance matrix, the idea is to infer a near-linear number of nonzero entries in a sparse Cholesky factor of the precision matrix. Our prior assumptions are m…
High-dimensional compositional data arise naturally in many applications such as metagenomic data analysis. The observed data lie in a high-dimensional simplex, and conventional statistical methods often fail to produce sensible results due to the unit-sum constraint. In this article, we address the problem of covariance estimation for high-dimensional compositional data, and introduce a composition-adjusted thresholding (COAT) method under the assumption that the basis covariance matrix is sparse. Our method is based on a decomposition relating the compositional covariance to the basis covari…
Sparse PCA: A New Scalable Estimator Based On Integer Programming
Operations Research Center, Massachusetts Institute of Technology（麻省理工学院运筹学中心）；Sloan School of Management, Massachusetts Institute of Technology（麻省理工学院斯隆管理学院）
We propose a scalable, efficient and statistically motivated computational framework for Graphical Lasso (Friedman et al., 2007b) - a covariance regularization framework that has received significant attention in the statistics community over the past few years. Existing algorithms have trouble in scaling to dimensions larger than a thousand. Our proposal significantly enhances the state-of-the-art for such moderate sized problems and gracefully scales to larger problems where other algorithms become practically infeasible. This requires a few key new ideas. We operate on the primal problem an…
For smoothing covariance functions, we propose two fast algorithms that scale linearly with the number of observations per function. Most available methods and software cannot smooth covariance matrices of dimension $J \times J$ with $J>500$; the recently introduced sandwich smoother is an exception, but it is not adapted to smooth covariance matrices of large dimensions such as $J \ge 10,000$. Covariance matrices of order $J=10,000$, and even $J=100,000$, are becoming increasingly common, e.g., in 2- and 3-dimensional medical imaging and high-density wearable sensor data. We introduce two new…
It is of great interest to quantify the contributions of genetic variation to brain structure and function, which are usually measured by high-dimensional imaging data (e.g., magnetic resonance imaging). In addition to the variance, the covariance patterns in the genetic effects of a functional phenotype are of biological importance, and covariance patterns have been linked to psychiatric disorders. The aim of this paper is to develop a scalable method to estimate heritability and the non-stationary covariance components in high-dimensional imaging data from twin studies. Our motivating exampl…
In this work we consider the problem of estimating a high-dimensional $p \times p$ covariance matrix $Σ$, given $n$ observations of confounded data with covariance $Σ+ ΓΓ^T$, where $Γ$ is an unknown $p \times q$ matrix of latent factor loadings. We propose a simple and scalable estimator based on the projection on to the right singular vectors of the observed data matrix, which we call RSVP. Our theoretical analysis of this method reveals that in contrast to PCA-based approaches, RSVP is able to cope well with settings where the smallest eigenvalue of $Γ^T Γ$ is close to the largest eigenvalue…
This paper revisits a fundamental problem in statistical inference from a non-asymptotic theoretical viewpoint $\unicode{x2013}$ the construction of confidence sets. We establish a finite-sample bound for the estimator, characterizing its asymptotic behavior in a non-asymptotic fashion. An important feature of our bound is that its dimension dependency is captured by the effective dimension $\unicode{x2013}$ the trace of the limiting sandwich covariance $\unicode{x2013}$ which can be much smaller than the parameter dimension in some regimes. We then illustrate how the bound can be used to obta…
We implement gradient-based variational inference routines for Wishart and inverse Wishart processes, which we apply as Bayesian models for the dynamic, heteroskedastic covariance matrix of a multivariate time series. The Wishart and inverse Wishart processes are constructed from i.i.d. Gaussian processes, existing variational inference algorithms for which form the basis of our approach. These methods are easy to implement as a black-box and scale favorably with the length of the time series, however, they fail in the case of the Wishart process, an issue we resolve with a simple modification…
In applications of Gaussian processes where quantification of uncertainty is of primary interest, it is necessary to accurately characterize the posterior distribution over covariance parameters. This paper proposes an adaptation of the Stochastic Gradient Langevin Dynamics algorithm to draw samples from the posterior distribution over covariance parameters with negligible bias and without the need to compute the marginal likelihood. In Gaussian process regression, this has the enormous advantage that stochastic gradients can be computed by solving linear systems only. A novel unbiased linear …
In this paper we introduce a novel online time series forecasting model we refer to as the pM-GP filter. We show that our model is equivalent to Gaussian process regression, with the advantage that both online forecasting and online learning of the hyper-parameters have a constant (rather than cubic) time complexity and a constant (rather than squared) memory requirement in the number of observations, without resorting to approximations. Moreover, the proposed model is expressive in that the family of covariance functions of the implied latent process, namely the spectral Matern kernels, have …
Scalable Frank-Wolfe on Generalized Self-concordant Functions via Simple Steps
Georgia Institute of Technology（佐治亚理工学院）；Zuse Institute Berlin（柏林祖斯研究所）；Univ. Grenoble Alpes（格勒诺布尔大学）；Inria（法国国家信息与自动化研究所）；Technische Universität Berlin（柏林工业大学）
The accurate prediction of time-changing covariances is an important problem in the modeling of multivariate financial data. However, some of the most popular models suffer from a) overfitting problems and multiple local optima, b) failure to capture shifts in market conditions and c) large computational costs. To address these problems we introduce a novel dynamic model for time-changing covariances. Over-fitting and local optima are avoided by following a Bayesian approach instead of computing point estimates. Changes in market conditions are captured by assuming a diffusion process in param…
Gaussian processes (GPs) are non-linear probabilistic models popular in many applications. However, naïve GP realizations require quadratic memory to store the covariance matrix and cubic computation to perform inference or evaluate the likelihood function. These bottlenecks have driven much investment in the development of approximate GP alternatives that scale to the large data sizes common in modern data-driven applications. We present in this manuscript MuyGPs, a novel efficient GP hyperparameter estimation method. MuyGPs builds upon prior methods that take advantage of the nearest neighbo…
Gaussian processes are rich distributions over functions, with generalization properties determined by a kernel function. When used for long-range extrapolation, predictions are particularly sensitive to the choice of kernel parameters. It is therefore critical to account for kernel uncertainty in our predictive distributions. We propose a distribution over kernels formed by modelling a spectral mixture density with a Lévy process. The resulting distribution has support for all stationary covariances--including the popular RBF, periodic, and Matérn kernels--combined with inductive biases which…
We develop an exact and scalable algorithm for one-dimensional Gaussian process regression with Matérn correlations whose smoothness parameter $ν$ is a half-integer. The proposed algorithm only requires $\mathcal{O}(ν^3 n)$ operations and $\mathcal{O}(νn)$ storage. This leads to a linear-cost solver since $ν$ is chosen to be fixed and usually very small in most applications. The proposed method can be applied to multi-dimensional problems if a full grid or a sparse grid design is used. The proposed method is based on a novel theory for Matérn correlation functions. We find that a suitable rear…
The University of New South Wales（新南威尔士大学）；CSIRO’s Data61（澳大利亚联邦科学与工业研究组织Data61）
We consider multi-task regression models where observations are assumed to be a linear combination of several latent node and weight functions, all drawn from Gaussian process (GP) priors that allow nonzero covariance between grouped latent functions. We show that when these grouped functions are conditionally independent given a group-dependent pivot, it is possible to parameterize the prior through sparse Cholesky factors directly, hence avoiding their computation during inference. Furthermore, we establish that kernels that are multiplicatively separable over input points give rise to such …
In this work, we propose a new variant of natural evolution strategies (NES) for high-dimensional black-box optimization problems. The proposed method, CR-FM-NES, extends a recently proposed state-of-the-art NES, Fast Moving Natural Evolution Strategy (FM-NES), in order to be applicable in high-dimensional problems. CR-FM-NES builds on an idea using a restricted representation of a covariance matrix instead of using a full covariance matrix, while inheriting an efficiency of FM-NES. The restricted representation of the covariance matrix enables CR-FM-NES to update parameters of a multivariate …
Gaussian processes (GPs) are frequently used in machine learning and statistics to construct powerful models. However, when employing GPs in practice, important considerations must be made, regarding the high computational burden, approximation of the posterior, choice of the covariance function and inference of its hyperparmeters. To address these issues, Hensman et al. (2015) combine variationally sparse GPs with Markov chain Monte Carlo (MCMC) to derive a scalable, flexible and general framework for GP models. Nevertheless, the resulting approach requires intractable likelihood evaluations …
Statistical learning additions to physically derived mathematical models are gaining traction in the literature. A recent approach has been to augment the underlying physics of the governing equations with data driven Bayesian statistical methodology. Coined statFEM, the method acknowledges a priori model misspecification, by embedding stochastic forcing within the governing equations. Upon receipt of additional data, the posterior distribution of the discretised finite element solution is updated using classical Bayesian filtering techniques. The resultant posterior jointly quantifies uncerta…
