The heteroscedastic probabilistic principal component analysis (PCA) technique, a variant of the classic PCA that considers data heterogeneity, is receiving more and more attention in the data science and signal processing communities. In this paper, to estimate the underlying low-dimensional linear subspace (simply called \emph{ground truth}) from available heterogeneous data samples, we consider the associated non-convex maximum-likelihood estimation problem, which involves maximizing a sum of heterogeneous quadratic forms over an orthogonality constraint (HQPOC). We propose a first-order method -- generalized power method (GPM) -- to tackle the problem and establish its \emph{estimation performance} guarantee. Specifically, we show that, given a suitable initialization, the distances between the iterates generated by GPM and the ground truth decrease at least geometrically to some threshold associated with the residual part of certain "population-residual decomposition". In establishing the estimation performance result, we prove a novel local error bound property of another closely related optimization problem, namely quadratic optimization with orthogonality constraint (QPOC), which is new and can be of independent interest. Numerical experiments are conducted to demonstrate the superior performance of GPM in both Gaussian noise and sub-Gaussian noise settings.
Principal Component Analysis (PCA) is a method for estimating a subspace given noisy samples. It is useful in a variety of problems ranging from dimensionality reduction to anomaly detection and the visualization of high dimensional data. PCA performs well in the presence of moderate noise and even with missing data, but is also sensitive to outliers. PCA is also known to have a phase transition when noise is independent and identically distributed; recovery of the subspace sharply declines at a threshold noise variance. Effective use of PCA requires a rigorous understanding of these behaviors…
Mixtures of probabilistic principal component analysis (MPPCA) is a well-known mixture model extension of principal component analysis (PCA). Similar to PCA, MPPCA assumes the data samples in each mixture contain homoscedastic noise. However, datasets with heterogeneous noise across samples are becoming increasingly common, as larger datasets are generated by collecting samples from several sources with varying noise profiles. The performance of MPPCA is suboptimal for data with heteroscedastic noise across samples. This paper proposes a heteroscedastic mixtures of probabilistic PCA technique …
Principal component analysis (PCA) is a classical and ubiquitous method for reducing data dimensionality, but it is suboptimal for heterogeneous data that are increasingly common in modern applications. PCA treats all samples uniformly so degrades when the noise is heteroscedastic across samples, as occurs, e.g., when samples come from sources of heterogeneous quality. This paper develops a probabilistic PCA variant that estimates and accounts for this heterogeneity by incorporating it in the statistical model. Unlike in the homoscedastic setting, the resulting nonconvex optimization problem i…
Principal Component Analysis (PCA) is a classical method for reducing the dimensionality of data by projecting them onto a subspace that captures most of their variation. Effective use of PCA in modern applications requires understanding its performance for data that are both high-dimensional and heteroscedastic. This paper analyzes the statistical performance of PCA in this setting, i.e., for high-dimensional data drawn from a low-dimensional subspace and degraded by heteroscedastic noise. We provide simplified expressions for the asymptotic PCA recovery of the underlying subspace, subspace a…
Modern data are increasingly both high-dimensional and heteroscedastic. This paper considers the challenge of estimating underlying principal components from high-dimensional data with noise that is heteroscedastic across samples, i.e., some samples are noisier than others. Such heteroscedasticity naturally arises, e.g., when combining data from diverse sources or sensors. A natural way to account for this heteroscedasticity is to give noisier blocks of samples less weight in PCA by using the leading eigenvectors of a weighted sample covariance matrix. We consider the problem of choosing weigh…
This paper studies the related problems of prediction, covariance estimation, and principal component analysis for the spiked covariance model with heteroscedastic noise. We consider an estimator of the principal components based on whitening the noise, and we derive optimal singular value and eigenvalue shrinkers for use with these estimated principal components. Underlying these methods are new asymptotic results for the high-dimensional spiked model with heteroscedastic noise, and consistent estimators for the relevant population parameters. We extend previous analysis on out-of-sample pred…
Auto-Associative models cover a large class of methods used in data analysis. In this paper, we describe the generals properties of these models when the projection component is linear and we propose and test an easy to implement Probabilistic Semi-Linear Auto- Associative model in a Gaussian setting. We show it is a generalization of the PCA model to the semi-linear case. Numerical experiments on simulated datasets and a real astronomical application highlight the interest of this approach
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 …
Locally Linear Embedding (LLE) is a nonlinear spectral dimensionality reduction and manifold learning method. It has two main steps which are linear reconstruction and linear embedding of points in the input space and embedding space, respectively. In this work, we look at the linear reconstruction step from a stochastic perspective where it is assumed that every data point is conditioned on its linear reconstruction weights as latent factors. The stochastic linear reconstruction of LLE is solved using expectation maximization. We show that there is a theoretical connection between three funda…
Principal Component Analysis (PCA) is a popular tool for dimensionality reduction and feature extraction in data analysis. There is a probabilistic version of PCA, known as Probabilistic PCA (PPCA). However, standard PCA and PPCA are not robust, as they are sensitive to outliers. To alleviate this problem, this paper introduces the Self-Paced Learning mechanism into PPCA, and proposes a novel method called Self-Paced Probabilistic Principal Component Analysis (SP-PPCA). Furthermore, we design the corresponding optimization algorithm based on the alternative search strategy and the expectation-…
Network anomaly detection is a very relevant research area nowadays, especially due to its multiple applications in the field of network security. The boost of new models based on variational autoencoders and generative adversarial networks has motivated a reevaluation of traditional techniques for anomaly detection. It is, however, essential to be able to understand these new models from the perspective of the experience attained from years of evaluating network security data for anomaly detection. In this paper, we revisit anomaly detection techniques based on PCA from a probabilistic genera…
Principal Component Analysis (PCA) is a powerful tool in statistics and machine learning. While existing study of PCA focuses on the recovery of principal components and their associated eigenvalues, there are few precise characterizations of individual principal component scores that yield low-dimensional embedding of samples. That hinders the analysis of various spectral methods. In this paper, we first develop an $\ell_p$ perturbation theory for a hollowed version of PCA in Hilbert spaces which provably improves upon the vanilla PCA in the presence of heteroscedastic noises. Through a novel…
Berkeley Center for Cosmological Physics（伯克利宇宙物理中心）；University of California（加利福尼亚大学）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）
Principal Component Analysis (PCA) minimizes the reconstruction error given a class of linear models of fixed component dimensionality. Probabilistic PCA adds a probabilistic structure by learning the probability distribution of the PCA latent space weights, thus creating a generative model. Autoencoders (AE) minimize the reconstruction error in a class of nonlinear models of fixed latent space dimensionality and outperform PCA at fixed dimensionality. Here, we introduce the Probabilistic Autoencoder (PAE) that learns the probability distribution of the AE latent space weights using a normaliz…
CNRS（法国国家科学研究中心）；Telecom Paristech（巴黎高等电信学院）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；Université Bordeaux 1（波尔多第一大学）；Duke University（杜克大学）
Photon-limited imaging arises when the number of photons collected by a sensor array is small relative to the number of detector elements. Photon limitations are an important concern for many applications such as spectral imaging, night vision, nuclear medicine, and astronomy. Typically a Poisson distribution is used to model these observations, and the inherent heteroscedasticity of the data combined with standard noise removal methods yields significant artifacts. This paper introduces a novel denoising algorithm for photon-limited images which combines elements of dictionary learning and sp…
Quanzhou Institute of Equipment Manufacturing, Haixi Institutes, Chinese Academy of Sciences（中国科学院海西研究院泉州装备制造研究所）；University of Reading（雷丁大学）
An improved mixture of probabilistic principal component analysis (PPCA) has been introduced for nonlinear data-driven process monitoring in this paper. To realize this purpose, the technique of a mixture of probabilistic principal component analysers is utilized to establish the model of the underlying nonlinear process with local PPCA models, where a novel composite monitoring statistic is proposed based on the integration of two monitoring statistics in modified PPCA-based fault detection approach. Besides, the weighted mean of the monitoring statistics aforementioned is utilised as a metri…
We provide a probabilistic and infinitesimal view of how the principal component analysis procedure (PCA) can be generalized to analysis of nonlinear manifold valued data. Starting with the probabilistic PCA interpretation of the Euclidean PCA procedure, we show how PCA can be generalized to manifolds in an intrinsic way that does not resort to linearization of the data space. The underlying probability model is constructed by mapping a Euclidean stochastic process to the manifold using stochastic development of Euclidean semimartingales. The construction uses a connection and bundles of covar…
Academy of Mathematics and Systems Science, Chinese Academy of Sciences（中国科学院数学与系统科学研究院）；University of Chinese Academy of Sciences（中国科学院大学）
Principal component analysis (PCA) is one of the most widely used dimension reduction and multivariate statistical techniques. From a probabilistic perspective, PCA seeks a low-dimensional representation of data in the presence of independent identical Gaussian noise. Probabilistic PCA (PPCA) and its variants have been extensively studied for decades. Most of them assume the underlying noise follows a certain independent identical distribution. However, the noise in the real world is usually complicated and structured. To address this challenge, some variants of PCA for data with non-IID noise…
University of California, Santa Cruz（加利福尼亚大学圣克鲁兹分校）；Google Brain（谷歌大脑）
We shed new insights on the two commonly used updates for the online $k$-PCA problem, namely, Krasulina's and Oja's updates. We show that Krasulina's update corresponds to a projected gradient descent step on the Stiefel manifold of the orthonormal $k$-frames, while Oja's update amounts to a gradient descent step using the unprojected gradient. Following these observations, we derive a more \emph{implicit} form of Krasulina's $k$-PCA update, i.e. a version that uses the information of the future gradient as much as possible. Most interestingly, our implicit Krasulina update avoids the costly Q…
Center for Advanced Intelligence Project RIKEN（理化学研究所先进智能项目中心）
We present a method to compute the Shapley values of reconstruction errors of principal component analysis (PCA), which is particularly useful in explaining the results of anomaly detection based on PCA. Because features are usually correlated when PCA-based anomaly detection is applied, care must be taken in computing a value function for the Shapley values. We utilize the probabilistic view of PCA, particularly its conditional distribution, to exactly compute a value function for the Shapely values. We also present numerical examples, which imply that the Shapley values are advantageous for …
Accurate predictions of pollutant concentrations at new locations are often of interest in air pollution studies on fine particulate matters (PM$_{2.5}$), in which data is usually not measured at all study locations. PM$_{2.5}$ is also a mixture of many different chemical components. Principal component analysis (PCA) can be incorporated to obtain lower-dimensional representative scores of such multi-pollutant data. Spatial prediction can then be used to estimate these scores at new locations. Recently developed predictive PCA modifies the traditional PCA algorithm to obtain scores with spatia…
Principal component analysis (PCA) is a well-established tool in machine learning and data processing. The principal axes in PCA were shown to be equivalent to the maximum marginal likelihood estimator of the factor loading matrix in a latent factor model for the observed data, assuming that the latent factors are independently distributed as standard normal distributions. However, the independence assumption may be unrealistic for many scenarios such as modeling multiple time series, spatial processes, and functional data, where the outcomes are correlated. In this paper, we introduce the gen…
Sparse Principal Component Analysis (PCA) is a dimensionality reduction technique wherein one seeks a low-rank representation of a data matrix with additional sparsity constraints on the obtained representation. We consider two probabilistic formulations of sparse PCA: a spiked Wigner and spiked Wishart (or spiked covariance) model. We analyze an Approximate Message Passing (AMP) algorithm to estimate the underlying signal and show, in the high dimensional limit, that the AMP estimates are information-theoretically optimal. As an immediate corollary, our results demonstrate that the posterior …
Helsinki Institute for Information Technology（赫尔辛基信息技术研究所）；University of Ljubljana（卢布尔雅那大学）
Methods for analysis of principal components in discrete data have existed for some time under various names such as grade of membership modelling, probabilistic latent semantic analysis, and genotype inference with admixture. In this paper we explore a number of extensions to the common theory, and present some application of these methods to some common statistical tasks. We show that these methods can be interpreted as a discrete version of ICA. We develop a hierarchical version yielding components at different levels of detail, and additional techniques for Gibbs sampling. We compare the a…
High dimensional data has introduced challenges that are difficult to address when attempting to implement classical approaches of statistical process control. This has made it a topic of interest for research due in recent years. However, in many cases, data sets have underlying structures, such as in advanced manufacturing systems. If extracted correctly, efficient methods for process control can be developed. This paper proposes a robust sparse dimensionality reduction approach for correlated high-dimensional process monitoring to address the aforementioned issues. The developed monitoring …
University of Twente（特文特大学）；Imperial College London（帝国理工学院）
We present a unifying framework which reduces the construction of probabilistic component analysis techniques to a mere selection of the latent neighbourhood, thus providing an elegant and principled framework for creating novel component analysis models as well as constructing probabilistic equivalents of deterministic component analysis methods. Under our framework, we unify many very popular and well-studied component analysis algorithms, such as Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA), Locality Preserving Projections (LPP) and Slow Feature Analysis (SFA), som…
Lawrence Livermore National Laboratory（劳伦斯利弗莫尔国家实验室）；Sandia National Laboratories（桑迪亚国家实验室）
Principal component analysis (PCA) is arguably the most popular tool in multivariate exploratory data analysis. In this paper, we consider the question of how to handle heterogeneous variables that include continuous, binary, and ordinal. In the probabilistic interpretation of low-rank PCA, the data has a normal multivariate distribution and, therefore, normal marginal distributions for each column. If some marginals are continuous but not normal, the semiparametric copula-based principal component analysis (COCA) method is an alternative to PCA that combines a Gaussian copula with nonparametr…
University of Tsukuba（筑波大学）；The Institute of Statistical Mathematics（统计数理研究所）
Principal component analysis (PCA) is a widely used method for data processing, such as for dimension reduction and visualization. Standard PCA is known to be sensitive to outliers, and thus, various robust PCA methods have been proposed. It has been shown that the robustness of many statistical methods can be improved using mode estimation instead of mean estimation, because mode estimation is not significantly affected by the presence of outliers. Thus, this study proposes a modal principal component analysis (MPCA), which is a robust PCA method based on mode estimation. The proposed method …
How does missing data affect our ability to learn signal structures? It has been shown that learning signal structure in terms of principal components is dependent on the ratio of sample size and dimensionality and that a critical number of observations is needed before learning starts (Biehl and Mietzner, 1993). Here we generalize this analysis to include missing data. Probabilistic principal component analysis is regularly used for estimating signal structures in datasets with missing data. Our analytic result suggests that the effect of missing data is to effectively reduce signal-to-noise …
University of Sheffield（谢菲尔德大学）；Sheffield Institute for Translational Neuroscience（谢菲尔德转化神经科学研究所）
Probabilistic principal component analysis (PPCA) seeks a low dimensional representation of a data set in the presence of independent spherical Gaussian noise. The maximum likelihood solution for the model is an eigenvalue problem on the sample covariance matrix. In this paper we consider the situation where the data variance is already partially explained by other actors, for example sparse conditional dependencies between the covariates, or temporal correlations leaving some residual variance. We decompose the residual variance into its components through a generalised eigenvalue problem, wh…
It was recently shown how graphs can be used to provide descriptions of psychopathologies, where symptoms of, say, depression, affect each other and certain configurations determine whether someone could fall into a sudden depression. To analyse changes over time and characterise possible future behaviour is rather difficult for large graphs. We describe the dynamics of networks using one-dimensional discrete time dynamical systems theory obtained from a mean field approach to (elementary) probabilistic cellular automata (PCA). Often the mean field approach is used on a regular graph (a grid o…
Aston University（阿斯顿大学）；Radboud University（拉德堡德大学）；Massachussetts Institute of Technology（麻省理工学院）
Using the linear Gaussian latent variable model as a starting point we relax some of the constraints it imposes by deriving a nonparametric latent feature Gaussian variable model. This model introduces additional discrete latent variables to the original structure. The Bayesian nonparametric nature of this new model allows it to adapt complexity as more data is observed and project each data point onto a varying number of subspaces. The linear relationship between the continuous latent and observed variables make the proposed model straightforward to interpret, resembling a locally adaptive pr…
Stanford University（斯坦福大学）；Broad Institute of MIT and Harvard（麻省理工学院与哈佛大学布罗德研究所）
Autoencoders are a deep learning model for representation learning. When trained to minimize the distance between the data and its reconstruction, linear autoencoders (LAEs) learn the subspace spanned by the top principal directions but cannot learn the principal directions themselves. In this paper, we prove that $L_2$-regularized LAEs are symmetric at all critical points and learn the principal directions as the left singular vectors of the decoder. We smoothly parameterize the critical manifold and relate the minima to the MAP estimate of probabilistic PCA. We illustrate these results empir…
Efficient and high-fidelity prior sampling and inversion for complex geological media is still a largely unsolved challenge. Here, we use a deep neural network of the variational autoencoder type to construct a parametric low-dimensional base model parameterization of complex binary geological media. For inversion purposes, it has the attractive feature that random draws from an uncorrelated standard normal distribution yield model realizations with spatial characteristics that are in agreement with the training set. In comparison with the most commonly used parametric representations in proba…
Principal component analysis (PCA) is by far the most widespread tool for unsupervised learning with high-dimensional data sets. Its application is popularly studied for the purpose of exploratory data analysis and online process monitoring. Unfortunately, fine-tuning PCA models and particularly the number of components remains a challenging task. Today, this selection is often based on a combination of guiding principles, experience, and process understanding. Unlike the case of regression, where cross-validation of the prediction error is a widespread and trusted approach for model selection…
In the era of big data, reducing data dimensionality is critical in many areas of science. Widely used Principal Component Analysis (PCA) addresses this problem by computing a low dimensional data embedding that maximally explain variance of the data. However, PCA has two major weaknesses. Firstly, it only considers linear correlations among variables (features), and secondly it is not suitable for categorical data. We resolve these issues by proposing Maximally Correlated Principal Component Analysis (MCPCA). MCPCA computes transformations of variables whose covariance matrix has the largest …
Count data is becoming more and more ubiquitous in a wide range of applications, with datasets growing both in size and in dimension. In this context, an increasing amount of work is dedicated to the construction of statistical models directly accounting for the discrete nature of the data. Moreover, it has been shown that integrating dimension reduction to clustering can drastically improve performance and stability. In this paper, we rely on the mixture of multinomial PCA, a mixture model for the clustering of count data, also known as the probabilistic clustering-projection model in the lit…
Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that allow for complex population structure. We formulate two general probabilistic models, and we propose computationally efficient algorithms to estimate them. First, we show how principal component analysis (PCA) can be utilized to estimate a general model that includes the well-known Pritchard-Stephens-Donnelly mixed-membership model as a special case. Notin…
In this paper, we develop new statistical theory for probabilistic principal component analysis models in high dimensions. The focus is the estimation of the noise variance, which is an important and unresolved issue when the number of variables is large in comparison with the sample size. We first unveil the reasons of a widely observed downward bias of the maximum likelihood estimator of the variance when the data dimension is high. We then propose a bias-corrected estimator using random matrix theory and establish its asymptotic normality. The superiority of the new (bias-corrected) estimat…
Highly robust factored principal component analysis for matrix-valued outlier accommodation and explainable detection via matrix minimum covariance determinant
