When the dimension of data is comparable to or larger than the number of data samples, Principal Components Analysis (PCA) may exhibit problematic high-dimensional noise. In this work, we propose an Empirical Bayes PCA method that reduces this noise by estimating a joint prior distribution for the principal components. EB-PCA is based on the classical Kiefer-Wolfowitz nonparametric MLE for empirical Bayes estimation, distributional results derived from random matrix theory for the sample PCs, and iterative refinement using an Approximate Message Passing (AMP) algorithm. In theoretical "spiked" models, EB-PCA achieves Bayes-optimal estimation accuracy in the same settings as an oracle Bayes AMP procedure that knows the true priors. Empirically, EB-PCA significantly improves over PCA when there is strong prior structure, both in simulation and on quantitative benchmarks constructed from the 1000 Genomes Project and the International HapMap Project. An illustration is presented for analysis of gene expression data obtained by single-cell RNA-seq.
Sparse versions of principal component analysis (PCA) have imposed themselves as simple, yet powerful ways of selecting relevant features of high-dimensional data in an unsupervised manner. However, when several sparse principal components are computed, the interpretation of the selected variables is difficult since each axis has its own sparsity pattern and has to be interpreted separately. To overcome this drawback, we propose a Bayesian procedure called globally sparse probabilistic PCA (GSPPCA) that allows to obtain several sparse components with the same sparsity pattern. This allows the …
Commonly used in computer vision and other applications, robust PCA represents an algorithmic attempt to reduce the sensitivity of classical PCA to outliers. The basic idea is to learn a decomposition of some data matrix of interest into low rank and sparse components, the latter representing unwanted outliers. Although the resulting optimization problem is typically NP-hard, convex relaxations provide a computationally-expedient alternative with theoretical support. However, in practical regimes performance guarantees break down and a variety of non-convex alternatives, including Bayesian-ins…
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…
Bayes-optimal limits in structured PCA, and how to reach them
Abdus Salam International Center for Theoretical Physics（阿卜杜勒·萨拉姆国际理论物理中心）；Institute of Science and Technology, Austria（奥地利科学技术研究所）；Universidad de La República（共和国大学）
本文研究结构化噪声下尖峰 PCA 的贝叶斯最优极限，利用复本方法刻画信息论阈值，并提出由自适应 TAP 方程启发的新型 AMP 达到该极限。
Based on some new robust estimators of the covariance matrix, we propose stable versions of Principal Component Analysis (PCA) and we qualify it independently of the dimension of the ambient space. We first provide a robust estimator of the orthogonal projector on the largest eigenvectors of the covariance matrix. The behavior of such an estimator is related to the size of the gap in the spectrum of the covariance matrix and in particular a large gap is needed in order to get a good approximation. To avoid the assumption of a large eigengap in the spectrum of the covariance matrix we propose a…
The Nyström method is one of the most popular techniques for improving the scalability of kernel methods. However, it has not yet been derived for kernel PCA in line with classical PCA. In this paper we derive kernel PCA with the Nyström method, thereby providing one of the few available options to make kernel PCA scalable. We further study its statistical accuracy through a finite-sample confidence bound on the empirical reconstruction error compared to the full method. The behaviours of the method and bound are illustrated through computer experiments on multiple real-world datasets. As an a…
We performed an empirical comparison of ICA and PCA algorithms by applying them on two simulated noisy time series with varying distribution parameters and level of noise. In general, ICA shows better results than PCA because it takes into account higher moments of data distribution. On the other hand, PCA remains quite sensitive to the level of correlations among signals.
Toyota Technological Institute at Chicago（芝加哥丰田理工学院）
We study PCA as a stochastic optimization problem and propose a novel stochastic approximation algorithm which we refer to as "Matrix Stochastic Gradient" (MSG), as well as a practical variant, Capped MSG. We study the method both theoretically and empirically.
Another Look at Log-PCA for Probability Measures: A Dynamical Formulation and Statistical Convergence
Department of Statistics University of Illinois Urbana-Champaign（统计学系伊利诺伊大学厄巴纳-香槟分校）；Department of ACMS University of Notre Dame（ACMS系诺丁汉大学）；Department of Mathematics University of British Columbia（数学系不列颠哥伦比亚大学）；Department of Mathematics Thomas Lord Department of Computer Science University of Southern California（数学系托马斯·劳德计算机科学系南加州大学）
Inria（法国国家信息与自动化研究所）；University College London（伦敦大学学院）
Principal Component Analysis (PCA) is a popular method for dimension reduction and has attracted an unfailing interest for decades. More recently, kernel PCA (KPCA) has emerged as an extension of PCA but, despite its use in practice, a sound theoretical understanding of KPCA is missing. We contribute several lower and upper bounds on the efficiency of KPCA, involving the empirical eigenvalues of the kernel Gram matrix and new quantities involving a notion of variance. These bounds show how much information is captured by KPCA on average and contribute a better theoretical understanding of its …
Kernel methods provide an elegant framework for developing nonlinear learning algorithms from simple linear methods. Though these methods have superior empirical performance in several real data applications, their usefulness is inhibited by the significant computational burden incurred in large sample situations. Various approximation schemes have been proposed in the literature to alleviate these computational issues, and the approximate kernel machines are shown to retain the empirical performance. However, the theoretical properties of these approximate kernel machines are less well unders…
Principal component analysis (PCA) is a well-established method commonly used to explore and visualise data. A classical PCA model is the fixed effect model where data are generated as a fixed structure of low rank corrupted by noise. Under this model, PCA does not provide the best recovery of the underlying signal in terms of mean squared error. Following the same principle as in ridge regression, we propose a regularised version of PCA that boils down to threshold the singular values. Each singular value is multiplied by a term which can be seen as the ratio of the signal variance over the t…
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…
Matrix factorization methods - including Factor analysis (FA), and Principal Components Analysis (PCA) - are widely used for inferring and summarizing structure in multivariate data. Many matrix factorization methods exist, corresponding to different assumptions on the elements of the underlying matrix factors. For example, many recent methods use a penalty or prior distribution to achieve sparse representations ("Sparse FA/PCA"). Here we introduce a general Empirical Bayes approach to matrix factorization (EBMF), whose key feature is that it uses the observed data to estimate prior distributi…
We propose a multiple imputation method based on principal component analysis (PCA) to deal with incomplete continuous data. To reflect the uncertainty of the parameters from one imputation to the next, we use a Bayesian treatment of the PCA model. Using a simulation study and real data sets, the method is compared to two classical approaches: multiple imputation based on joint modelling and on fully conditional modelling. Contrary to the others, the proposed method can be easily used on data sets where the number of individuals is less than the number of variables and when the variables are h…
We consider a clustering problem where we observe feature vectors $X_i \in R^p$, $i = 1, 2, \ldots, n$, from $K$ possible classes. The class labels are unknown and the main interest is to estimate them. We are primarily interested in the modern regime of $p \gg n$, where classical clustering methods face challenges. We propose Influential Features PCA (IF-PCA) as a new clustering procedure. In IF-PCA, we select a small fraction of features with the largest Kolmogorov-Smirnov (KS) scores, where the threshold is chosen by adapting the recent notion of Higher Criticism, obtain the first $(K-1)$ l…
We introduce the method of Geodesic Principal Component Analysis (GPCA) on the space of probability measures on the line, with finite second moment, endowed with the Wasserstein metric. We discuss the advantages of this approach, over a standard functional PCA of probability densities in the Hilbert space of square-integrable functions. We establish the consistency of the method by showing that the empirical GPCA converges to its population counterpart, as the sample size tends to infinity. A key property in the study of GPCA is the isometry between the Wasserstein space and a closed convex su…
We study the problem of estimating a rank-$1$ signal in the presence of rotationally invariant noise-a class of perturbations more general than Gaussian noise. Principal Component Analysis (PCA) provides a natural estimator, and sharp results on its performance have been obtained in the high-dimensional regime. Recently, an Approximate Message Passing (AMP) algorithm has been proposed as an alternative estimator with the potential to improve the accuracy of PCA. However, the existing analysis of AMP requires an initialization that is both correlated with the signal and independent of the noise…
We present Matrix Krasulina, an algorithm for online k-PCA, by generalizing the classic Krasulina's method (Krasulina, 1969) from vector to matrix case. We show, both theoretically and empirically, that the algorithm naturally adapts to data low-rankness and converges exponentially fast to the ground-truth principal subspace. Notably, our result suggests that despite various recent efforts to accelerate the convergence of stochastic-gradient based methods by adding a O(n)-time variance reduction step, for the k-PCA problem, a truly online SGD variant suffices to achieve exponential convergence…
ITMO University（圣彼得堡国立信息技术机械与光学大学）；Leiden University（莱顿大学）；Technical University of Munich（慕尼黑工业大学）；Sorbonne Université（索邦大学）；CNRS（法国国家科学研究中心）
Bayesian Optimization (BO) is a surrogate-based global optimization strategy that relies on a Gaussian Process regression (GPR) model to approximate the objective function and an acquisition function to suggest candidate points. It is well-known that BO does not scale well for high-dimensional problems because the GPR model requires substantially more data points to achieve sufficient accuracy and acquisition optimization becomes computationally expensive in high dimensions. Several recent works aim at addressing these issues, e.g., methods that implement online variable selection or conduct t…
Researchers often have datasets measuring features $x_{ij}$ of samples, such as test scores of students. In factor analysis and PCA, these features are thought to be influenced by unobserved factors, such as skills. Can we determine how many components affect the data? This is an important problem, because it has a large impact on all downstream data analysis. Consequently, many approaches have been developed to address it. Parallel Analysis is a popular permutation method. It works by randomly scrambling each feature of the data. It selects components if their singular values are larger than …
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…
We present a Bayesian model selection approach to estimate the intrinsic dimensionality of a high-dimensional dataset. To this end, we introduce a novel formulation of the probabilisitic principal component analysis model based on a normal-gamma prior distribution. In this context, we exhibit a closed-form expression of the marginal likelihood which allows to infer an optimal number of components. We also propose a heuristic based on the expected shape of the marginal likelihood curve in order to choose the hyperparameters. In non-asymptotic frameworks, we show on simulated data that this exac…
Incremental versions of batch algorithms are often desired, for increased time efficiency in the streaming data setting, or increased memory efficiency in general. In this paper we present a novel algorithm for incremental kernel PCA, based on rank one updates to the eigendecomposition of the kernel matrix, which is more computationally efficient than comparable existing algorithms. We extend our algorithm to incremental calculation of the Nyström approximation to the kernel matrix, the first such algorithm proposed. Incremental calculation of the Nyström approximation leads to further gains i…
This paper studies the multiplicity-correction effect of standard Bayesian variable-selection priors in linear regression. Our first goal is to clarify when, and how, multiplicity correction happens automatically in Bayesian analysis, and to distinguish this correction from the Bayesian Ockham's-razor effect. Our second goal is to contrast empirical-Bayes and fully Bayesian approaches to variable selection through examples, theoretical results and simulations. Considerable differences between the two approaches are found. In particular, we prove a theorem that characterizes a surprising aympto…
Following widely used in visual recognition concept of relative attributes, the article establishes definition of the relative PCA attributes for a class of objects defined by vectors of their parameters. A new rating model (RELARM) is built using relative PCA attribute ranking functions for rating object description and k-means clustering algorithm. Rating assignment of each rating object to a rating category is derived as a result of cluster centers projection on the specially selected rating vector. Empirical study has shown a high level of approximation to the existing S & P, Moody's and F…
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…
Methods for supervised principal component analysis (SPCA) aim to incorporate label information into principal component analysis (PCA), so that the extracted features are more useful for a prediction task of interest. Prior work on SPCA has focused primarily on optimizing prediction error, and has neglected the value of maximizing variance explained by the extracted features. We propose a new method for SPCA that addresses both of these objectives jointly, and demonstrate empirically that our approach dominates existing approaches, i.e., outperforms them with respect to both prediction error …
We introduce a variant of (sparse) PCA in which the set of feasible support sets is determined by a graph. In particular, we consider the following setting: given a directed acyclic graph $G$ on $p$ vertices corresponding to variables, the non-zero entries of the extracted principal component must coincide with vertices lying along a path in $G$. From a statistical perspective, information on the underlying network may potentially reduce the number of observations required to recover the population principal component. We consider the canonical estimator which optimally exploits the prior know…
Microwave-based breast cancer detection has been proposed as a complementary approach to compensate for some drawbacks of existing breast cancer detection techniques. Among the existing microwave breast cancer detection methods, machine learning-type algorithms have recently become more popular. These focus on detecting the existence of breast tumours rather than performing imaging to identify the exact tumour position. A key step of the machine learning approaches is feature extraction. One of the most widely used feature extraction method is principle component analysis (PCA). However, it ca…
University of Passau（帕绍大学）；Freie Universität Berlin（柏林自由大学）
We describe how cross-kernel matrices, that is, kernel matrices between the data and a custom chosen set of `feature spanning points' can be used for learning. The main potential of cross-kernels lies in the fact that (a) only one side of the matrix scales with the number of data points, and (b) cross-kernels, as opposed to the usual kernel matrices, can be used to certify for the data manifold. Our theoretical framework, which is based on a duality involving the feature space and vanishing ideals, indicates that cross-kernels have the potential to be used for any kind of kernel learning. We p…
In 2018, at the World Economic Forum in Davos it was presented a new countries' economic performance metric named the Inclusive Development Index (IDI) composed of 12 indicators. The new metric implies that countries might need to realize structural reforms for improving both economic expansion and social inclusion performance. That is why, it is vital for the IDI calculation method to have strong statistical and mathematical basis, so that results are accurate and transparent for public purposes. In the current work, we propose a novel approach for the IDI estimation - the Ranking Relative Pr…
We analyze a practical algorithm for sparse PCA on incomplete and noisy data under a general non-random sampling scheme. The algorithm is based on a semidefinite relaxation of the $\ell_1$-regularized PCA problem. We provide theoretical justification that under certain conditions, we can recover the support of the sparse leading eigenvector with high probability by obtaining a unique solution. The conditions involve the spectral gap between the largest and second-largest eigenvalues of the true data matrix, the magnitude of the noise, and the structural properties of the observed entries. The …
One of the major problems in natural language processing (NLP) is the word sense disambiguation (WSD) problem. It is the task of computationally identifying the right sense of a polysemous word based on its context. Resolving the WSD problem boosts the accuracy of many NLP focused algorithms such as text classification and machine translation. In this paper, we introduce a new supervised algorithm for WSD, that is based on Kernel PCA and Semantic Diffusion Kernel, which is called Diffusion Kernel PCA (DKPCA). DKPCA grasps the semantic similarities within terms, and it is based on PCA. These pr…
Harbin Institute of Technology（哈尔滨工业大学）；Qufu Normal University（曲阜师范大学）；Anhui University（安徽大学）
Principal Component Analysis (PCA) has been used to study the pathogenesis of diseases. To enhance the interpretability of classical PCA, various improved PCA methods have been proposed to date. Among these, a typical method is the so-called sparse PCA, which focuses on seeking sparse loadings. However, the performance of these methods is still far from satisfactory due to their limitation of using unsupervised learning methods; moreover, the class ambiguity within the sample is high. To overcome this problem, this study developed a new PCA method, which is named the Supervised Discriminative …
Carnegie Mellon University（卡内基梅隆大学）；Air Force Research Laboratory（空军研究实验室）
Tensor robust principal component analysis (RPCA), which seeks to separate a low-rank tensor from its sparse corruptions, has been crucial in data science and machine learning where tensor structures are becoming more prevalent. While powerful, existing tensor RPCA algorithms can be difficult to use in practice, as their performance can be sensitive to the choice of additional hyperparameters, which are not straightforward to tune. In this paper, we describe a fast and simple self-supervised model for tensor RPCA using deep unfolding by only learning four hyperparameters. Despite its simplicit…
Sapienza Università di Roma（罗马大学）；INFN – Sezione di Roma1（意大利国家核物理研究所罗马第一分部）；CNR-Nanotec（意大利国家研究委员会纳米技术研究所）
In many high-dimensional estimation problems the main task consists in minimizing a cost function, which is often strongly non-convex when scanned in the space of parameters to be estimated. A standard solution to flatten the corresponding rough landscape consists in summing the losses associated to different data points and obtain a smoother empirical risk. Here we propose a complementary method that works for a single data point. The main idea is that a large amount of the roughness is uncorrelated in different parts of the landscape. One can then substantially reduce the noise by evaluating…
Chicago Booth School of Business（芝加哥大学布斯商学院）；University of Chicago（芝加哥大学）；George Mason University（乔治梅森大学）
Deep learning is a form of machine learning for nonlinear high dimensional pattern matching and prediction. By taking a Bayesian probabilistic perspective, we provide a number of insights into more efficient algorithms for optimisation and hyper-parameter tuning. Traditional high-dimensional data reduction techniques, such as principal component analysis (PCA), partial least squares (PLS), reduced rank regression (RRR), projection pursuit regression (PPR) are all shown to be shallow learners. Their deep learning counterparts exploit multiple deep layers of data reduction which provide predicti…
We analyze the decomposition of a data matrix, assumed to be a superposition of a low-rank component and a component which is sparse in a known dictionary, using a convex demixing method. We provide a unified analysis, encompassing both undercomplete and overcomplete dictionary cases, and show that the constituent components can be successfully recovered under some relatively mild assumptions up to a certain $\textit{global}$ sparsity level. Further, we corroborate our theoretical results by presenting empirical evaluations in terms of phase transitions in rank and sparsity for various diction…
In 2019, Yoshida et al. introduced a notion of tropical principal component analysis (PCA). The output is a tropical polytope with a fixed number of vertices that best fits the data. We here apply tropical PCA to dimension reduction and visualization of data sampled from the space of phylogenetic trees. Our main results are twofold: the existence of a tropical cell decomposition into regions of fixed tree topology and the development of a stochastic optimization method to estimate the tropical PCA using a Markov Chain Monte Carlo (MCMC) approach. This method performs well with simulation studi…
University of California, Irvine（加利福尼亚大学欧文分校）；Duke University（杜克大学）；Google Research（谷歌研究院）
Developing efficient and guaranteed nonconvex algorithms has been an important challenge in modern machine learning. Algorithms with good empirical performance such as stochastic gradient descent often lack theoretical guarantees. In this paper, we analyze the class of homotopy or continuation methods for global optimization of nonconvex functions. These methods start from an objective function that is efficient to optimize (e.g. convex), and progressively modify it to obtain the required objective, and the solutions are passed along the homotopy path. For the challenging problem of tensor PCA…
In this on-going work, I explore certain theoretical and empirical implications of data transformations under the PCA. In particular, I state and prove three theorems about PCA, which I paraphrase as follows: 1). PCA without discarding eigenvector rows is injective, but looses this injectivity when eigenvector rows are discarded 2). PCA without discarding eigen- vector rows preserves pair-wise distances, but tends to cause pair-wise distances to shrink when eigenvector rows are discarded. 3). For any pair of points, the shrinkage in pair-wise distance is bounded above by an L1 norm reconstruct…
In many reacting flow systems, the thermo-chemical state-space is known or assumed to evolve close to a low-dimensional manifold (LDM). Various approaches are available to obtain those manifolds and subsequently express the original high-dimensional space with fewer parameterizing variables. Principal component analysis (PCA) is one of the dimensionality reduction methods that can be used to obtain LDMs. PCA does not make prior assumptions about the parameterizing variables and retrieves them empirically from the training data. In this paper, we show that PCA applied in local clusters of data …
