Dimensionality reduction is an important operation in information visualization, feature extraction, clustering, regression, and classification, especially for processing noisy high dimensional data. However, most existing approaches preserve either the global or the local structure of the data, but not both. Approaches that preserve only the global data structure, such as principal component analysis (PCA), are usually sensitive to outliers. Approaches that preserve only the local data structure, such as locality preserving projections, are usually unsupervised (and hence cannot use label information) and uses a fixed similarity graph. We propose a novel linear dimensionality reduction approach, supervised discriminative sparse PCA with adaptive neighbors (SDSPCAAN), to integrate neighborhood-free supervised discriminative sparse PCA and projected clustering with adaptive neighbors. As a result, both global and local data structures, as well as the label information, are used for better dimensionality reduction. Classification experiments on nine high-dimensional datasets validated the effectiveness and robustness of our proposed SDSPCAAN.
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 …
Dimensionality reduction methods are very common in the field of high dimensional data analysis. Typically, algorithms for dimensionality reduction are computationally expensive. Therefore, their applications for the analysis of massive amounts of data are impractical. For example, repeated computations due to accumulated data are computationally prohibitive. In this paper, an out-of-sample extension scheme, which is used as a complementary method for dimensionality reduction, is presented. We describe an algorithm which performs an out-of-sample extension to newly-arrived data points. Unlike …
We investigate whether the standard dimensionality reduction technique of PCA inadvertently produces data representations with different fidelity for two different populations. We show on several real-world data sets, PCA has higher reconstruction error on population A than on B (for example, women versus men or lower- versus higher-educated individuals). This can happen even when the data set has a similar number of samples from A and B. This motivates our study of dimensionality reduction techniques which maintain similar fidelity for A and B. We define the notion of Fair PCA and give a poly…
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…
Ultralow-dimensionality reduction for identifying critical transitions by spatial-temporal PCA
School of Mathematics, South China University of Technology（华南理工大学数学学院）；Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences（中国科学院分子细胞科学卓越创新中心）
RIKEN Center for Brain Science（理化学研究所脑科学中心）；The University of Tokyo（东京大学）
For many years, a combination of principal component analysis (PCA) and independent component analysis (ICA) has been used for blind source separation (BSS). However, it remains unclear why these linear methods work well with real-world data that involve nonlinear source mixtures. This work theoretically validates that a cascade of linear PCA and ICA can solve a nonlinear BSS problem accurately -- when the sensory inputs are generated from hidden sources via nonlinear mappings with sufficient dimensionality. Our proposed theorem, termed the asymptotic linearization theorem, theoretically guara…
Principal component analysis (PCA) is widely used for feature extraction and dimensionality reduction, with documented merits in diverse tasks involving high-dimensional data. Standard PCA copes with one dataset at a time, but it is challenged when it comes to analyzing multiple datasets jointly. In certain data science settings however, one is often interested in extracting the most discriminative information from one dataset of particular interest (a.k.a. target data) relative to the other(s) (a.k.a. background data). To this end, this paper puts forth a novel approach, termed discriminative…
National Research Council of Canada（加拿大国家研究委员会）；Université Paris-Saclay（巴黎萨克雷大学）；CNRS（法国国家科学研究中心）
Autoencoders (AE) provide a useful method for nonlinear dimensionality reduction but are ill-suited for low data regimes. Conversely, Principal Component Analysis (PCA) is data-efficient but is limited to linear dimensionality reduction, posing a problem when data exhibits inherent nonlinearity. This presents a challenge in various scientific and engineering domains such as the nanophotonic component design, where data exhibits nonlinear features while being expensive to obtain due to costly real measurements or resource-consuming solutions of partial differential equations. To address this di…
Principal component analysis (PCA) for binary data, known as logistic PCA, has become a popular alternative to dimensionality reduction of binary data. It is motivated as an extension of ordinary PCA by means of a matrix factorization, akin to the singular value decomposition, that maximizes the Bernoulli log-likelihood. We propose a new formulation of logistic PCA which extends Pearson's formulation of a low dimensional data representation with minimum error to binary data. Our formulation does not require a matrix factorization, as previous methods do, but instead looks for projections of th…
Graph Neural Networks (GNNs) have become a popular approach for various applications, ranging from social network analysis to modeling chemical properties of molecules. While GNNs often show remarkable performance on public datasets, they can struggle to learn long-range dependencies in the data due to over-smoothing and over-squashing tendencies. To alleviate this challenge, we propose PCAPass, a method which combines Principal Component Analysis (PCA) and message passing for generating node embeddings in an unsupervised manner and leverages gradient boosted decision trees for classification …
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…
Johns Hopkins University（约翰斯·霍普金斯大学）；Flatiron Institute（熨斗研究所）；New York University（纽约大学）
Overparameterization in deep learning is powerful: Very large models fit the training data perfectly and yet often generalize well. This realization brought back the study of linear models for regression, including ordinary least squares (OLS), which, like deep learning, shows a "double-descent" behavior: (1) The risk (expected out-of-sample prediction error) can grow arbitrarily when the number of parameters $p$ approaches the number of samples $n$, and (2) the risk decreases with $p$ for $p>n$, sometimes achieving a lower value than the lowest risk for $p<n$. The divergence of the risk for O…
We consider principal component analysis for contaminated data-set in the high dimensional regime, where the dimensionality of each observation is comparable or even more than the number of observations. We propose a deterministic high-dimensional robust PCA algorithm which inherits all theoretical properties of its randomized counterpart, i.e., it is tractable, robust to contaminated points, easily kernelizable, asymptotic consistent and achieves maximal robustness -- a breakdown point of 50%. More importantly, the proposed method exhibits significantly better computational efficiency, which …
This paper studies Principal Component Analysis (PCA) for data lying in hyperbolic spaces. Given directions, PCA relies on: (1) a parameterization of subspaces spanned by these directions, (2) a method of projection onto subspaces that preserves information in these directions, and (3) an objective to optimize, namely the variance explained by projections. We generalize each of these concepts to the hyperbolic space and propose HoroPCA, a method for hyperbolic dimensionality reduction. By focusing on the core problem of extracting principal directions, HoroPCA theoretically better preserves in…
Principal Component Analysis (PCA) is a very successful dimensionality reduction technique, widely used in predictive modeling. A key factor in its widespread use in this domain is the fact that the projection of a dataset onto its first $K$ principal components minimizes the sum of squared errors between the original data and the projected data over all possible rank $K$ projections. Thus, PCA provides optimal low-rank representations of data for least-squares linear regression under standard modeling assumptions. On the other hand, when the loss function for a prediction problem is not the l…
High-content screening uses large collections of unlabeled cell image data to reason about genetics or cell biology. Two important tasks are to identify those cells which bear interesting phenotypes, and to identify sub-populations enriched for these phenotypes. This exploratory data analysis usually involves dimensionality reduction followed by clustering, in the hope that clusters represent a phenotype. We propose the use of stacked de-noising auto-encoders to perform dimensionality reduction for high-content screening. We demonstrate the superior performance of our approach over PCA, Local …
PCA-Guided Autoencoding for Structured Dimensionality Reduction in Active Infrared Thermography
Khalifa University of Science and Technology（卡利法科技科学大学）；Advanced Research and Innovation Center（先进研究与创新中心）；Department of Aerospace Engineering（航空航天工程系）；BioMedIA Lab（BioMedIA实验室）；Mohamed Bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）；Department of Electrical Engineering and Computer Science（电气工程与计算机科学系）；Department of Information Systems and Operations Research（信息系统与运营管理系）；Vienna University of Economics and Business（维也纳经济与商业大学）；Department of Industrial and Information Engineering and Economics (DIIIE)（工业与信息工程与经济学系）；University of L’Aquila（拉奎拉大学）；Department of Industrial and Systems Engineering（工业与系统工程系）
University of Gothenburg（哥德堡大学）；Chalmers University of Technology（查尔姆斯理工大学）
High-dimensional data sets are often analyzed and explored via the construction of a latent low-dimensional space which enables convenient visualization and efficient predictive modeling or clustering. For complex data structures, linear dimensionality reduction techniques like PCA may not be sufficiently flexible to enable low-dimensional representation. Non-linear dimension reduction techniques, like kernel PCA and autoencoders, suffer from loss of interpretability since each latent variable is dependent of all input dimensions. To address this limitation, we here present path lasso penalize…
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…
ECE Dept. and Digital Tech. Center, U. of Minnesota（明尼苏达大学电子与计算机工程系及数字技术中心）
Principal component analysis (PCA) has well-documented merits for data extraction and dimensionality reduction. PCA deals with a single dataset at a time, and it is challenged when it comes to analyzing multiple datasets. Yet in certain setups, one wishes to extract the most significant information of one dataset relative to other datasets. Specifically, the interest may be on identifying, namely extracting features that are specific to a single target dataset but not the others. This paper develops a novel approach for such so-termed discriminative data analysis, and establishes its optimalit…
In this research, we have two serum SELDI (surface-enhanced laser desorption and ionization) mass spectra (MS) datasets to be used to select features amongst them to identify proteomic cancerous serums from normal serums. Features selection techniques have been applied and classification techniques have been applied as well. Amongst the features selection techniques we have chosen to evaluate the performance of PCA (Principal Component Analysis ) and GA (Genetic algorithm), and amongst the classification techniques we have chosen the LDA (Linear Discriminant Analysis) and Neural networks so as…
Mitsubishi Electric Research Laboratories（三菱电机研究实验室）
We propose a new concept of rateless auto-encoders (RL-AEs) that enable a flexible latent dimensionality, which can be seamlessly adjusted for varying distortion and dimensionality requirements. In the proposed RL-AEs, instead of a deterministic bottleneck architecture, we use an over-complete representation that is stochastically regularized with weighted dropouts, in a manner analogous to sparse AE (SAE). Unlike SAEs, our RL-AEs employ monotonically increasing dropout rates across the latent representation nodes such that the latent variables become sorted by importance like in principal com…
Principal Component Analysis (PCA) is the workhorse tool for dimensionality reduction in this era of big data. While often overlooked, the purpose of PCA is not only to reduce data dimensionality, but also to yield features that are uncorrelated. Furthermore, the ever-increasing volume of data in the modern world often requires storage of data samples across multiple machines, which precludes the use of centralized PCA algorithms. This paper focuses on the dual objective of PCA, namely, dimensionality reduction and decorrelation of features, but in a distributed setting. This requires estimati…
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-…
TU Berlin（柏林工业大学）；Univ. Bordeaux（波尔多大学）；Bordeaux INP（波尔多国立理工学院）；CNRS（法国国家科学研究中心）
Despite the rapid development of computational hardware, the treatment of large and high dimensional data sets is still a challenging problem. This paper provides a twofold contribution to the topic. First, we propose a Gaussian Mixture Model in conjunction with a reduction of the dimensionality of the data in each component of the model by principal component analysis, called PCA-GMM. To learn the (low dimensional) parameters of the mixture model we propose an EM algorithm whose M-step requires the solution of constrained optimization problems. Fortunately, these constrained problems do not d…
Revisiting PCA for time series reduction in temporal dimension
Shanghai Jiao Tong University（上海交通大学）；Ningbo Institute of Digital Twin（宁波数字孪生研究院）；Eastern Institute of Technology（东方理工学院）；Hefei University of Technology（合肥工业大学）
This is a tutorial and survey paper on unification of spectral dimensionality reduction methods, kernel learning by Semidefinite Programming (SDP), Maximum Variance Unfolding (MVU) or Semidefinite Embedding (SDE), and its variants. We first explain how the spectral dimensionality reduction methods can be unified as kernel Principal Component Analysis (PCA) with different kernels. This unification can be interpreted as eigenfunction learning or representation of kernel in terms of distance matrix. Then, since the spectral methods are unified as kernel PCA, we say let us learn the best kernel fo…
Though there is a growing body of literature on fairness for supervised learning, the problem of incorporating fairness into unsupervised learning has been less well-studied. This paper studies fairness in the context of principal component analysis (PCA). We first present a definition of fairness for dimensionality reduction, and our definition can be interpreted as saying that a reduction is fair if information about a protected class (e.g., race or gender) cannot be inferred from the dimensionality-reduced data points. Next, we develop convex optimization formulations that can improve the f…
This paper introduces a new unsupervised method for dimensionality reduction via regression (DRR). The algorithm belongs to the family of invertible transforms that generalize Principal Component Analysis (PCA) by using curvilinear instead of linear features. DRR identifies the nonlinear features through multivariate regression to ensure the reduction in redundancy between he PCA coefficients, the reduction of the variance of the scores, and the reduction in the reconstruction error. More importantly, unlike other nonlinear dimensionality reduction methods, the invertibility, volume-preservati…
University of Konstanz（康斯坦茨大学）；University of Stuttgart（斯图加特大学）
We present a technique to perform dimensionality reduction on data that is subject to uncertainty. Our method is a generalization of traditional principal component analysis (PCA) to multivariate probability distributions. In comparison to non-linear methods, linear dimensionality reduction techniques have the advantage that the characteristics of such probability distributions remain intact after projection. We derive a representation of the PCA sample covariance matrix that respects potential uncertainty in each of the inputs, building the mathematical foundation of our new method: uncertain…
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 Washington（华盛顿大学）；Georgia Institute of Technology（佐治亚理工学院）
Dimensionality reduction is a classical technique widely used for data analysis. One foundational instantiation is Principal Component Analysis (PCA), which minimizes the average reconstruction error. In this paper, we introduce the "multi-criteria dimensionality reduction" problem where we are given multiple objectives that need to be optimized simultaneously. As an application, our model captures several fairness criteria for dimensionality reduction such as our novel Fair-PCA problem and the Nash Social Welfare (NSW) problem. In Fair-PCA, the input data is divided into $k$ groups, and the g…
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 …
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…
Implementation of the Principal Component Analysis onto High-Performance Computer Facilities for Hyperspectral Dimensionality Reduction: Results and Comparisons
Institute for Applied Microelectronics (IUMA), University of Las Palmas de Gran Canaria (ULPGC)（拉斯帕尔马斯大学应用微电子研究所）；Universidad Politecnica de Madrid（马德里理工大学）
KAIST（韩国科学技术院）；UC Berkeley IEOR（加州大学伯克利分校工业工程与运筹学系）；Citadel（城堡投资）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
This paper defines fair principal component analysis (PCA) as minimizing the maximum mean discrepancy (MMD) between dimensionality-reduced conditional distributions of different protected classes. The incorporation of MMD naturally leads to an exact and tractable mathematical formulation of fairness with good statistical properties. We formulate the problem of fair PCA subject to MMD constraints as a non-convex optimization over the Stiefel manifold and solve it using the Riemannian Exact Penalty Method with Smoothing (REPMS; Liu and Boumal, 2019). Importantly, we provide local optimality guar…
A particularly challenging context for dimensionality reduction is multivariate circular data, i.e., data supported on a torus. Such kind of data appears, e.g., in the analysis of various phenomena in ecology and astronomy, as well as in molecular structures. This paper introduces Scaled Torus Principal Component Analysis (ST-PCA), a novel approach to perform dimensionality reduction with toroidal data. ST-PCA finds a data-driven map from a torus to a sphere of the same dimension and a certain radius. The map is constructed with multidimensional scaling to minimize the discrepancy between pair…
Oregon State University（俄勒冈州立大学）；Vrije Universiteit Brussel（布鲁塞尔自由大学）；Washington State University（华盛顿州立大学）
Reinforcement learning algorithms need to deal with the exponential growth of states and actions when exploring optimal control in high-dimensional spaces. This is known as the curse of dimensionality. By projecting the agent's state onto a low-dimensional manifold, we can represent the state space in a smaller and more efficient representation. By using this representation during learning, the agent can converge to a good policy much faster. We test this approach in the Mario Benchmarking Domain. When using dimensionality reduction in Mario, learning converges much faster to a good policy. Bu…
