Incorporating covariates into functional principal component analysis (PCA) can substantially improve the representation efficiency of the principal components and predictive performance. However, many existing functional PCA methods do not make use of covariates, and those that do often have high computational cost or make overly simplistic assumptions that are violated in practice. In this article, we propose a new framework, called Covariate Dependent Functional Principal Component Analysis (CD-FPCA), in which both the mean and covariance structure depend on covariates. We propose a corresponding estimation algorithm, which makes use of spline basis representations and roughness penalties, and is substantially more computationally efficient than competing approaches of adequate estimation and prediction accuracy. A key aspect of our work is our novel approach for modeling the covariance function and ensuring that it is symmetric positive semi-definite. We demonstrate the advantages of our methodology through a simulation study and an astronomical data analysis.
Mahalanobis distance between treatment group and control group covariate means is often adopted as a balance criterion when implementing a rerandomization strategy. However, this criterion may not work well for high-dimensional cases because it balances all orthogonalized covariates equally. Here, we propose leveraging principal component analysis (PCA) to identify proper subspaces in which Mahalanobis distance should be calculated. Not only can PCA effectively reduce the dimensionality for high-dimensional cases while capturing most of the information in the covariates, but it also provides c…
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…
We consider the problem of decomposing a large covariance matrix into the sum of a low-rank matrix and a diagonally dominant matrix, and we call this problem the "Diagonally-Dominant Principal Component Analysis (DD-PCA)". DD-PCA is an effective tool for designing statistical methods for strongly correlated data. We showcase the use of DD-PCA in two statistical problems: covariance matrix estimation, and global detection in multiple testing. Using the output of DD-PCA, we propose a new estimator for estimating a large covariance matrix with factor structure. Thanks to a nice property of diagon…
We consider the properties of the bootstrap as a tool for inference concerning the eigenvalues of a sample covariance matrix computed from an $n\times p$ data matrix $X$. We focus on the modern framework where $p/n$ is not close to 0 but remains bounded as $n$ and $p$ tend to infinity. Through a mix of numerical and theoretical considerations, we show that the bootstrap is not in general a reliable inferential tool in the setting we consider. However, in the case where the population covariance matrix is well-approximated by a finite rank matrix, the bootstrap performs as it does in finite dim…
Principal component analysis (PCA) is the most commonly used statistical procedure for dimension reduction. An important issue for applying PCA is to determine the rank, which is the number of dominant eigenvalues of the covariance matrix. The Akaike information criterion (AIC) and Bayesian information criterion (BIC) are among the most widely used rank selection methods. Both use the number of free parameters for assessing model complexity. In this work, we adopt the generalized information criterion (GIC) to propose a new method for PCA rank selection under the high-dimensional framework. Th…
We consider the problem of comparing several samples of stochastic processes with respect to their second-order structure, and describing the main modes of variation in this second order structure, if present. These tasks can be seen as an Analysis of Variance (ANOVA) and a Principal Component Analysis (PCA) of covariance operators, respectively. They arise naturally in functional data analysis, where several populations are to be contrasted relative to the nature of their dispersion around their means, rather than relative to their means themselves. We contribute a novel approach based on opt…
Many applications, such as photon-limited imaging and genomics, involve large datasets with noisy entries from exponential family distributions. It is of interest to estimate the covariance structure and principal components of the noiseless distribution. Principal Component Analysis (PCA), the standard method for this setting, can be inefficient when the noise is non-Gaussian. We develop $e$PCA (exponential family PCA), a new methodology for PCA on exponential family distributions. $e$PCA can be used for dimensionality reduction and denoising of large data matrices. $e$PCA involves the eigend…
A general framework for principal component analysis (PCA) in the presence of heteroskedastic noise is introduced. We propose an algorithm called HeteroPCA, which involves iteratively imputing the diagonal entries of the sample covariance matrix to remove estimation bias due to heteroskedasticity. This procedure is computationally efficient and provably optimal under the generalized spiked covariance model. A key technical step is a deterministic robust perturbation analysis on singular subspaces, which can be of independent interest. The effectiveness of the proposed algorithm is demonstrated…
Covariance matrix estimation and principal component analysis (PCA) are two cornerstones of multivariate analysis. Classic textbook solutions perform poorly when the dimension of the data is of a magnitude similar to the sample size, or even larger. In such settings, there is a common remedy for both statistical problems: nonlinear shrinkage of the eigenvalues of the sample covariance matrix. The optimal nonlinear shrinkage formula depends on unknown population quantities and is thus not available. It is, however, possible to consistently estimate an oracle nonlinear shrinkage, which is motiva…
In statistical learning, high covariate dimensionality poses challenges for robust prediction and inference. To address this challenge, supervised dimension reduction is often performed, where dependence on the outcome is maximized for a selected covariate subspace with smaller dimensionality. Prevalent dimension reduction techniques assume data are $i.i.d.$, which is not appropriate for longitudinal data comprising multiple subjects with repeated measurements over time. In this paper, we derive a decomposition of the Hilbert-Schmidt Independence Criterion as a supervised loss function for lon…
University of Pennsylvania（宾夕法尼亚大学）；University of Rochester（罗切斯特大学）
Graph neural networks (GNN) are an effective framework that exploit inter-relationships within graph-structured data for learning. Principal component analysis (PCA) involves the projection of data on the eigenspace of the covariance matrix and draws similarities with the graph convolutional filters in GNNs. Motivated by this observation, we study a GNN architecture, called coVariance neural network (VNN), that operates on sample covariance matrices as graphs. We theoretically establish the stability of VNNs to perturbations in the covariance matrix, thus, implying an advantage over standard P…
Instituto de Física Teórica, UAM/CSIC（UAM/CSIC理论物理研究所）；Universidad Autónoma de Madrid（马德里自治大学）；Los Alamos National Laboratory（洛斯阿拉莫斯国家实验室）；Quantum Science Center（量子科学中心）
Principal component analysis (PCA) is a dimensionality reduction method in data analysis that involves diagonalizing the covariance matrix of the dataset. Recently, quantum algorithms have been formulated for PCA based on diagonalizing a density matrix. These algorithms assume that the covariance matrix can be encoded in a density matrix, but a concrete protocol for this encoding has been lacking. Our work aims to address this gap. Assuming amplitude encoding of the data, with the data given by the ensemble $\{p_i,| ψ_i \rangle\}$, then one can easily prepare the ensemble average density matri…
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…
In this work the detection of moving targets in multiantenna SAR is considered. As a high resolution radar imaging modality, SAR detects and identifies stationary targets very well, giving it an advantage over classical GMTI radars. Moving target detection is more challenging due to the "burying" of moving targets in the clutter and is often achieved using space-time adaptive processing (STAP) (based on learning filters from the spatio-temporal clutter covariance) to remove the stationary clutter and enhance the moving targets. In this work, it is noted that in addition to the oft noted low ra…
Hong Kong University of Science and Technology（香港科技大学）
The problem of estimating sparse eigenvectors of a symmetric matrix attracts a lot of attention in many applications, especially those with high dimensional data set. While classical eigenvectors can be obtained as the solution of a maximization problem, existing approaches formulate this problem by adding a penalty term into the objective function that encourages a sparse solution. However, the resulting methods achieve sparsity at the expense of sacrificing the orthogonality property. In this paper, we develop a new method to estimate dominant sparse eigenvectors without trading off their or…
Highly robust factored principal component analysis for matrix-valued outlier accommodation and explainable detection via matrix minimum covariance determinant
In this paper, we propose a novel robust Principal Component Analysis (PCA) for high-dimensional data in the presence of various heterogeneities, especially the heavy-tailedness and outliers. A transformation motivated by the characteristic function is constructed to improve the robustness of the classical PCA. Besides the typical outliers, the proposed method has the unique advantage of dealing with heavy-tail-distributed data, whose covariances could be nonexistent (positively infinite, for instance). The proposed approach is also a case of kernel principal component analysis (KPCA) method a…
We discuss a clustering method for Gaussian mixture model based on the sparse principal component analysis (SPCA) method and compare it with the IF-PCA method. We also discuss the dependent case where the covariance matrix $Σ$ is not necessarily diagonal.
We derive high-probability bounds for the reconstruction error of PCA in infinite dimensions. We apply our bounds in the case that the eigenvalues of the covariance operator satisfy polynomial or exponential upper bounds.
Consider a linear model $y = X β+ z$, $z \sim N(0, σ^2 I_n)$. The Gram matrix $Θ= \frac{1}{n} X'X$ is non-sparse, but it is approximately the sum of two components, a low-rank matrix and a sparse matrix, where neither component is known to us. We are interested in the Rare/Weak signal setting where all but a small fraction of the entries of $β$ are nonzero, and the nonzero entries are relatively small individually. The goal is to rank the variables in a way so as to maximize the area under the ROC curve. We propose Factor-adjusted Covariate Assisted Ranking (FA-CAR) as a two-step approach to v…
This paper introduces a Projected Principal Component Analysis (Projected-PCA), which employs principal component analysis to the projected (smoothed) data matrix onto a given linear space spanned by covariates. When it applies to high-dimensional factor analysis, the projection removes noise components. We show that the unobserved latent factors can be more accurately estimated than the conventional PCA if the projection is genuine, or more precisely, when the factor loading matrices are related to the projected linear space. When the dimensionality is large, the factors can be estimated accu…
Phylogenetic PCA (p-PCA) is a version of PCA for observations that are leaf nodes of a phylogenetic tree. P-PCA accounts for the fact that such observations are not independent, due to shared evolutionary history. The method works on Euclidean data, but in evolutionary biology there is a need for applying it to data on manifolds, particularly shapes. We provide a generalization of p-PCA to data lying on Riemannian manifolds, called Tangent p-PCA. Tangent p-PCA thus makes it possible to perform dimension reduction on a data set of shapes, taking into account both the non-linear structure of the…
Generalized principal component analysis (GLM-PCA) facilitates dimension reduction of non-normally distributed data. We provide a detailed derivation of GLM-PCA with a focus on optimization. We also demonstrate how to incorporate covariates, and suggest post-processing transformations to improve interpretability of latent factors.
Principal component analysis (PCA) is fundamental to statistical machine learning. It extracts latent principal factors that contribute to the most variation of the data. When data are stored across multiple machines, however, communication cost can prohibit the computation of PCA in a central location and distributed algorithms for PCA are thus needed. This paper proposes and studies a distributed PCA algorithm: each node machine computes the top $K$ eigenvectors and transmits them to the central server; the central server then aggregates the information from all the node machines and conduct…
In the context of principal components analysis (PCA), the bootstrap is commonly applied to solve a variety of inference problems, such as constructing confidence intervals for the eigenvalues of the population covariance matrix $Σ$. However, when the data are high-dimensional, there are relatively few theoretical guarantees that quantify the performance of the bootstrap. Our aim in this paper is to analyze how well the bootstrap can approximate the joint distribution of the leading eigenvalues of the sample covariance matrix $\hatΣ$, and we establish non-asymptotic rates of approximation with…
Random projection is widely used as a method of dimension reduction. In recent years, its combination with standard techniques of regression and classification has been explored. Here we examine its use with principal component analysis (PCA) and subspace detection methods. Specifically, we show that, under appropriate conditions, with high probability the magnitude of the residuals of a PCA analysis of randomly projected data behaves comparably to that of the residuals of a similar PCA analysis of the original data. Our results indicate the feasibility of applying subspace-based anomaly detec…
The mixture of Dirichlet process (MDP) defines a flexible prior distribution on the space of probability measures. This study shows that ordinary least-squares (OLS) estimator, as a functional of the MDP posterior distribution, has posterior mean given by weighted least-squares (WLS), and has posterior covariance matrix given by the (weighted) heteroscedastic-consistent sandwich estimator. This is according to a pairs bootstrap distribution approximation of the posterior, using a Pólya urn scheme. Also, when the MDP prior baseline distribution is specified as a product of independent probabili…
In this paper we show that the negative sample distance covariance function is a quasi-concave set function of samples of random variables that are not statistically independent. We use these properties to propose greedy algorithms to combinatorially optimize some diversity (low statistical dependence) promoting functions of distance covariance. Our greedy algorithm obtains all the inclusion-minimal maximizers of this diversity promoting objective. Inclusion-minimal maximizers are multiple solution sets of globally optimal maximizers that are not a proper subset of any other maximizing set in …
We study the basic problem of robust subspace recovery. That is, we assume a data set that some of its points are sampled around a fixed subspace and the rest of them are spread in the whole ambient space, and we aim to recover the fixed underlying subspace. We first estimate "robust inverse sample covariance" by solving a convex minimization procedure; we then recover the subspace by the bottom eigenvectors of this matrix (their number correspond to the number of eigenvalues close to 0). We guarantee exact subspace recovery under some conditions on the underlying data. Furthermore, we propose…
In sparse principal component analysis we are given noisy observations of a low-rank matrix of dimension $n\times p$ and seek to reconstruct it under additional sparsity assumptions. In particular, we assume here each of the principal components $\mathbf{v}_1,\dots,\mathbf{v}_r$ has at most $s_0$ non-zero entries. We are particularly interested in the high dimensional regime wherein $p$ is comparable to, or even much larger than $n$. In an influential paper, \cite{johnstone2004sparse} introduced a simple algorithm that estimates the support of the principal vectors $\mathbf{v}_1,\dots,\mathbf{…
Functional Principal Component Analysis (FPCA) has become a widely-used dimension reduction tool for functional data analysis. When additional covariates are available, existing FPCA models integrate them either in the mean function or in both the mean function and the covariance function. However, methods of the first kind are not suitable for data that display second-order variation, while those of the second kind are time-consuming and make it difficult to perform subsequent statistical analyses on the dimension-reduced representations. To tackle these issues, we introduce an eigen-adjusted…
We study the estimation of a high dimensional approximate factor model in the presence of both cross sectional dependence and heteroskedasticity. The classical method of principal components analysis (PCA) does not efficiently estimate the factor loadings or common factors because it essentially treats the idiosyncratic error to be homoskedastic and cross sectionally uncorrelated. For efficient estimation it is essential to estimate a large error covariance matrix. We assume the model to be conditionally sparse, and propose two approaches to estimating the common factors and factor loadings; b…
The University of Texas at Austin（得克萨斯大学奥斯汀分校）；Microsoft Research India（微软研究院印度分院）
We consider streaming, one-pass principal component analysis (PCA), in the high-dimensional regime, with limited memory. Here, $p$-dimensional samples are presented sequentially, and the goal is to produce the $k$-dimensional subspace that best approximates these points. Standard algorithms require $O(p^2)$ memory; meanwhile no algorithm can do better than $O(kp)$ memory, since this is what the output itself requires. Memory (or storage) complexity is most meaningful when understood in the context of computational and sample complexity. Sample complexity for high-dimensional PCA is typically s…
The problem of estimating a spiked covariance matrix in high dimensions under Frobenius loss, and the parallel problem of estimating the noise in spiked PCA is investigated. We propose an estimator of the noise parameter by minimizing an unbiased estimator of the invariant Frobenius risk using calculus of variations. The resulting estimator is shown, using random matrix theory, to be strongly consistent and essentially asymptotically normal and minimax for the noise estimation problem. We apply the construction to construct a robust spiked covariance matrix estimator with consistent eigenvalue…
Sparse PCA (SPCA) is a fundamental model in machine learning and data analytics, which has witnessed a variety of application areas such as finance, manufacturing, biology, healthcare. To select a prespecified-size principal submatrix from a covariance matrix to maximize its largest eigenvalue for the better interpretability purpose, SPCA advances the conventional PCA with both feature selection and dimensionality reduction. This paper proposes two exact mixed-integer SDPs (MISDPs) by exploiting the spectral decomposition of the covariance matrix and the properties of the largest eigenvalues. …
We analyse the reconstruction error of principal component analysis (PCA) and prove non-asymptotic upper bounds for the corresponding excess risk. These bounds unify and improve existing upper bounds from the literature. In particular, they give oracle inequalities under mild eigenvalue conditions. The bounds reveal that the excess risk differs significantly from usually considered subspace distances based on canonical angles. Our approach relies on the analysis of empirical spectral projectors combined with concentration inequalities for weighted empirical covariance operators and empirical e…
In this paper, we propose an acceleration scheme for online memory-limited PCA methods. Our scheme converges to the first $k>1$ eigenvectors in a single data pass. We provide empirical convergence results of our scheme based on the spiked covariance model. Our scheme does not require any predefined parameters such as the eigengap and hence is well facilitated for streaming data scenarios. Furthermore, we apply our scheme to challenging time-varying systems where online PCA methods fail to converge. Specifically, we discuss a family of time-varying systems that are based on Molecular Dynamics s…
