Covariance matrix estimation is a fundamental statistical task in many applications, but the sample covariance matrix is sub-optimal when the sample size is comparable to or less than the number of features. Such high-dimensional settings are common in modern genomics, where covariance matrix estimation is frequently employed as a method for inferring gene networks. To achieve estimation accuracy in these settings, existing methods typically either assume that the population covariance matrix has some particular structure, for example sparsity, or apply shrinkage to better estimate the population eigenvalues. In this paper, we study a new approach to estimating high-dimensional covariance matrices. We first frame covariance matrix estimation as a compound decision problem. This motivates defining a class of decision rules and using a nonparametric empirical Bayes g-modeling approach to estimate the optimal rule in the class. Simulation results and gene network inference in an RNA-seq experiment in mouse show that our approach is comparable to or can outperform a number of state-of-the-art proposals.
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We propose a data-driven way to reduce the noise of covariance matrices of nonstationary systems. In the case of stationary systems, asymptotic approaches were proved to converge to the optimal solutions. Such methods produce eigenvalues that are highly dependent on the inputs, as common sense would suggest. Our approach proposes instead to use a set of eigenvalues totally independent from the inputs and that encode the long-term averaging of the influence of the future on present eigenvalues. Such an influence can be the predominant factor in nonstationary systems. Using real and synthetic data, we show that our data-driven method outperforms optimal methods designed for stationary systems for the filtering of both covariance matrix and its inverse, as illustrated by financial portfolio variance minimization, which makes out method generically relevant to many problems of multivariate inference.
Spatial data can exhibit dependence structures more complicated than can be represented using models that rely on the traditional assumptions of stationarity and isotropy. Several statistical methods have been developed to relax these assumptions. One in particular, the "spatial deformation approach" defines a transformation from the geographic space in which data are observed, to a latent space in which stationarity and isotropy are assumed to hold. Taking inspiration from this class of models, we develop a new model for spatially dependent data observed on graphs. Our method implies an embedding of the graph into Euclidean space wherein the covariance can be modeled using traditional covariance functions such as those from the Mat\'{e}rn family. This is done via a class of graph metrics compatible with such covariance functions. By estimating the edge weights which underlie these metrics, we can recover the "intrinsic distance" between nodes of a graph. We compare our model to existing methods for spatially dependent graph data, primarily conditional autoregressive (CAR) models and their variants and illustrate the advantages our approach has over traditional methods. We fit our model and competitors to bird abundance data for several species in North Carolina. We find that our model fits the data best, and provides insight into the interaction between species-specific spatial distributions and geography.
Consider the sum $Y=B+B(H)$ of a Brownian motion $B$ and an independent fractional Brownian motion $B(H)$ with Hurst parameter $H\in(0,1)$. Surprisingly, even though $B(H)$ is not a semimartingale, Cheridito proved in [Bernoulli 7 (2001) 913--934] that $Y$ is a semimartingale if $H>3/4$. Moreover, $Y$ is locally equivalent to $B$ in this case, so $H$ cannot be consistently estimated from local observations of $Y$. This paper pivots on a second surprise in this model: if $B$ and $B(H)$ become correlated, then $Y$ will never be a semimartingale, and $H$ can be identified, regardless of its value. This and other results will follow from a detailed statistical analysis of a more general class of processes called mixed semimartingales, which are semiparametric extensions of $Y$ with stochastic volatility in both the martingale and the fractional component. In particular, we derive consistent estimators and feasible central limit theorems for all parameters and processes that can be identified from high-frequency observations. We further show that our estimators achieve optimal rates in a minimax sense. The estimation of mixed semimartingales with correlation is motivated by applications to high-frequency financial data contaminated by rough noise.
We study the convergence properties, in Hellinger and related distances, of nonparametric density estimators based on measure transport. These estimators represent the measure of interest as the pushforward of a chosen reference distribution under a transport map, where the map is chosen via a maximum likelihood objective (equivalently, minimizing an empirical Kullback-Leibler loss) or a penalized version thereof. We establish concentration inequalities for a general class of penalized measure transport estimators, by combining techniques from M-estimation with analytical properties of the transport-based density representation. We then demonstrate the implications of our theory for the case of triangular Knothe-Rosenblatt (KR) transports on the $d$-dimensional unit cube, and show that both penalized and unpenalized versions of such estimators achieve minimax optimal convergence rates over H\"older classes of densities. Specifically, we establish optimal rates for unpenalized nonparametric maximum likelihood estimation over bounded H\"older-type balls, and then for certain Sobolev-penalized estimators and sieved wavelet estimators.
Mark-point dependence plays a critical role in research problems that can be fitted into the general framework of marked point processes. In this work, we focus on adjusting for mark-point dependence when estimating the mean and covariance functions of the mark process, given independent replicates of the marked point process. We assume that the mark process is a Gaussian process and the point process is a log-Gaussian Cox process, where the mark-point dependence is generated through the dependence between two latent Gaussian processes. Under this framework, naive local linear estimators ignoring the mark-point dependence can be severely biased. We show that this bias can be corrected using a local linear estimator of the cross-covariance function and establish uniform convergence rates of the bias-corrected estimators. Furthermore, we propose a test statistic based on local linear estimators for mark-point independence, which is shown to converge to an asymptotic normal distribution in a parametric $\sqrt{n}$-convergence rate. Model diagnostics tools are developed for key model assumptions and a robust functional permutation test is proposed for a more general class of mark-point processes. The effectiveness of the proposed methods is demonstrated using extensive simulations and applications to two real data examples.
Real world-datasets characterized by discrete features are ubiquitous: from categorical surveys to clinical questionnaires, from unweighted networks to DNA sequences. Nevertheless, the most common unsupervised dimensional reduction methods are designed for continuous spaces, and their use for discrete spaces can lead to errors and biases. In this letter we introduce an algorithm to infer the intrinsic dimension (ID) of datasets embedded in discrete spaces. We demonstrate its accuracy on benchmark datasets, and we apply it to analyze a metagenomic dataset for species fingerprinting, finding a surprisingly small ID, of order 2. This suggests that evolutive pressure acts on a low-dimensional manifold despite the high-dimensionality of sequences' space.
Many mobile manufacturers recently have adopted Dual-Pixel (DP) sensors in their flagship models for faster auto-focus and aesthetic image captures. Despite their advantages, research on their usage for 3D facial understanding has been limited due to the lack of datasets and algorithmic designs that exploit parallax in DP images. This is because the baseline of sub-aperture images is extremely narrow and parallax exists in the defocus blur region. In this paper, we introduce a DP-oriented Depth/Normal network that reconstructs the 3D facial geometry. For this purpose, we collect a DP facial data with more than 135K images for 101 persons captured with our multi-camera structured light systems. It contains the corresponding ground-truth 3D models including depth map and surface normal in metric scale. Our dataset allows the proposed matching network to be generalized for 3D facial depth/normal estimation. The proposed network consists of two novel modules: Adaptive Sampling Module and Adaptive Normal Module, which are specialized in handling the defocus blur in DP images. Finally, the proposed method achieves state-of-the-art performances over recent DP-based depth/normal estimation methods. We also demonstrate the applicability of the estimated depth/normal to face spoofing and relighting.
Propensity score weighting is widely used to improve the representativeness and correct the selection bias in the voluntary sample. The propensity score is often developed using a model for the sampling probability, which can be subject to model misspecification. In this paper, we consider an alternative approach of estimating the inverse of the propensity scores using the density ratio function satisfying the self-efficiency condition. The smoothed density ratio function is obtained by the solution to the information projection onto the space satisfying the moment conditions on the balancing scores. By including the covariates for the outcome regression models only in the density ratio model, we can achieve efficient propensity score estimation. Penalized regression is used to identify important covariates. We further extend the proposed approach to the multivariate missing case. Some limited simulation studies are presented to compare with the existing methods.
Asymmetry along with heteroscedasticity or contamination often occurs with the growth of data dimensionality. In ultra-high dimensional data analysis, such irregular settings are usually overlooked for both theoretical and computational convenience. In this paper, we establish a framework for estimation in high-dimensional regression models using Penalized Robust Approximated quadratic M-estimators (PRAM). This framework allows general settings such as random errors lack of symmetry and homogeneity, or the covariates are not sub-Gaussian. To reduce the possible bias caused by the data's irregularity in mean regression, PRAM adopts a loss function with a flexible robustness parameter growing with the sample size. Theoretically, we first show that, in the ultra-high dimension setting, PRAM estimators have local estimation consistency at the minimax rate enjoyed by the LS-Lasso. Then we show that PRAM with an appropriate non-convex penalty in fact agrees with the local oracle solution, and thus obtain its oracle property. Computationally, we demonstrate the performances of six PRAM estimators using three types of loss functions for approximation (Huber, Tukey's biweight and Cauchy loss) combined with two types of penalty functions (Lasso and MCP). Our simulation studies and real data analysis demonstrate satisfactory finite sample performances of the PRAM estimator under general irregular settings.
In 1954, Alston S. Householder published Principles of Numerical Analysis, one of the first modern treatments on matrix decomposition that favored a (block) LU decomposition-the factorization of a matrix into the product of lower and upper triangular matrices. And now, matrix decomposition has become a core technology in machine learning, largely due to the development of the back propagation algorithm in fitting a neural network. The sole aim of this survey is to give a self-contained introduction to concepts and mathematical tools in numerical linear algebra and matrix analysis in order to seamlessly introduce matrix decomposition techniques and their applications in subsequent sections. However, we clearly realize our inability to cover all the useful and interesting results concerning matrix decomposition and given the paucity of scope to present this discussion, e.g., the separated analysis of the Euclidean space, Hermitian space, Hilbert space, and things in the complex domain. We refer the reader to literature in the field of linear algebra for a more detailed introduction to the related fields.
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