Sparse principal component analysis via regularized low rank matrix approximation

Principal component analysis (PCA) is a widely used tool for data analysis and dimension reduction in applications throughout science and engineering. However, the principal components (PCs) can sometimes be difficult to interpret, because they are linear combinations of all the original variables. To facilitate interpretation, sparse PCA produces modified PCs with sparse loadings, i.e. loadings with very few non-zero elements. In this paper, we propose a new sparse PCA method, namely sparse PCA via regularized SVD (sPCA-rSVD). We use the connection of PCA with singular value decomposition (SVD) of the data matrix and extract the PCs through solving a low rank matrix approximation problem. Regularization penalties are introduced to the corresponding minimization problem to promote sparsity in PC loadings. An efficient iterative algorithm is proposed for computation. Two tuning parameter selection methods are discussed. Some theoretical results are established to justify the use of sPCA-rSVD when only the data covariance matrix is available. In addition, we give a modified definition of variance explained by the sparse PCs. The sPCA-rSVD provides a uniform treatment of both classical multivariate data and high-dimension-low-sample-size (HDLSS) data. Further understanding of sPCA-rSVD and some existing alternatives is gained through simulation studies and real data examples, which suggests that sPCA-rSVD provides competitive results.     

Sparsest factor analysis for clustering variables: a matrix decomposition approach

We propose a new procedure for sparse factor analysis (FA) such that each variable loads only one common factor. Thus, the loading matrix has a single nonzero element in each row and zeros elsewhere. Such a loading matrix is the sparsest possible for certain number of variables and common factors. For this reason, the proposed method is named sparsest FA (SSFA). It may also be called FA-based variable clustering, since the variables loading the same common factor can be classified into a cluster. In SSFA, all model parts of FA (common factors, their correlations, loadings, unique factors, and unique variances) are treated as fixed unknown parameter matrices and their least squares function is minimized through specific data matrix decomposition. A useful feature of the algorithm is that the matrix of common factor scores is re-parameterized using QR decomposition in order to efficiently estimate factor correlations. A simulation study shows that the proposed procedure can exactly identify the true sparsest models. Real data examples demonstrate the usefulness of the variable clustering performed by SSFA.     

Strong formulations for quadratic optimization with M-matrices and indicator variables

We propose a DC (Difference of two Convex functions) formulation approach for sparse optimization problems having a cardinality or rank constraint. With the largest-k norm, an exact DC representation of the cardinality constraint is provided. We then transform the cardinality-constrained problem into a penalty function form and derive exact penalty parameter values for some optimization problems, especially for quadratic minimization problems which often appear in practice. A DC Algorithm (DCA) is presented, where the dual step at each iteration can be efficiently carried out due to the accessible subgradient of the largest-k norm. Furthermore, we can solve each DCA subproblem in linear time via a soft thresholding operation if there are no additional constraints. The framework is extended to the rank-constrained problem as well as the cardinality- and the rank-minimization problems. Numerical experiments demonstrate the efficiency of the proposed DCA in comparison with existing methods which have other penalty terms.     

Sparse Steinian Covariance Estimation

We consider a new method for sparse covariance matrix estimation which is motivated by previous results for the so-called Stein-type estimators. Stein proposed a method for regularizing the sample covariance matrix by shrinking together the eigenvalues; the amount of shrinkage is chosen to minimize an unbiased estimate of the risk (UBEOR) under the entropy loss function. The resulting estimator has been shown in simulations to yield significant risk reductions over the maximum likelihood estimator. Our method extends the UBEOR minimization problem by adding an ?₁ penalty on the entries of the estimated covariance matrix, which encourages a sparse estimate. For a multivariate Gaussian distribution, zeros in the covariance matrix correspond to marginal independences between variables. Unlike the ?₁-penalized Gaussian likelihood function, our penalized UBEOR objective is convex and can be minimized via a simple block coordinate descent procedure. We demonstrate via numerical simulations and an analysis of microarray data from breast cancer patients that our proposed method generally outperforms other methods for sparse covariance matrix estimation and can be computed efficiently even in high dimensions.     

Low-rank and sparse matrix recovery from noisy observations via 3-block ADMM algorithm

Recovering low-rank and sparse matrix from a given matrix arises in many applications, such as image processing, video background substraction, and so on. The 3-block alternating direction method of multipliers (ADMM) has been applied successfully to solve convex problems with 3-block variables. However, the existing sufficient conditions to guarantee the convergence of the 3-block ADMM usually require the penalty parameter $\gamma$ to satisfy a certain bound, which may affect the performance of solving the large scale problem in practice. In this paper, we propose the 3-block ADMM to recover low-rank and sparse matrix from noisy observations. In theory, we prove that the 3-block ADMM is convergent when the penalty parameters satisfy a certain condition and the objective function value sequences generated by 3-block ADMM converge to the optimal value. Numerical experiments verify that proposed method can achieve higher performance than existing methods in terms of both efficiency and accuracy.     

Penalized Orthogonal Iteration for Sparse Estimation of Generalized Eigenvalue Problem

We propose a new algorithm for sparse estimation of eigenvectors in generalized eigenvalue problems (GEPs). The GEP arises in a number of modern data-analytic situations and statistical methods, including principal component analysis (PCA), multiclass linear discriminant analysis (LDA), canonical correlation analysis (CCA), sufficient dimension reduction (SDR), and invariant co-ordinate selection. We propose to modify the standard generalized orthogonal iteration with a sparsity-inducing penalty for the eigenvectors. To achieve this goal, we generalize the equation-solving step of orthogonal iteration to a penalized convex optimization problem. The resulting algorithm, called penalized orthogonal iteration, provides accurate estimation of the true eigenspace, when it is sparse. Also proposed is a computationally more efficient alternative, which works well for PCA and LDA problems. Numerical studies reveal that the proposed algorithms are competitive, and that our tuning procedure works well. We demonstrate applications of the proposed algorithm to obtain sparse estimates for PCA, multiclass LDA, CCA, and SDR. Supplementary materials for this article are available online.     

Group-Wise Principal Component Analysis for Exploratory Data Analysis

In this article, we propose a new framework for matrix factorization based on principal component analysis (PCA) where sparsity is imposed. The structure to impose sparsity is defined in terms of groups of correlated variables found in correlation matrices or maps. The framework is based on three new contributions: an algorithm to identify the groups of variables in correlation maps, a visualization for the resulting groups, and a matrix factorization. Together with a method to compute correlation maps with minimum noise level, referred to as missing-data for exploratory data analysis (MEDA), these three contributions constitute a complete matrix factorization framework. Two real examples are used to illustrate the approach and compare it with PCA, sparse PCA, and structured sparse PCA. Supplementary materials for this article are available online.     

Supervised Sparse and Functional Principal Component Analysis

Principal component analysis (PCA) is an important tool for dimension reduction in multivariate analysis. Regularized PCA methods, such as sparse PCA and functional PCA, have been developed to incorporate special features in many real applications. Sometimes additional variables (referred to as supervision) are measured on the same set of samples, which can potentially drive low-rank structures of the primary data of interest. Classical PCA methods cannot make use of such supervision data. In this article, we propose a supervised sparse and functional principal component (SupSFPC) framework that can incorporate supervision information to recover underlying structures that are more interpretable. The framework unifies and generalizes several existing methods and flexibly adapts to the practical scenarios at hand. The SupSFPC model is formulated in a hierarchical fashion using latent variables. We develop an efficient modified expectation-maximization (EM) algorithm for parameter estimation. We also implement fast data-driven procedures for tuning parameter selection. Our comprehensive simulation and real data examples demonstrate the advantages of SupSFPC. Supplementary materials for this article are available online.     

Optimization of unconstrained functions with sparse hessian matrices-newton-type methods

Newton-type methods for unconstrained optimization problems have been very successful when coupled with a modified Cholesky factorization to take into account the possible lack of positive-definiteness in the Hessian matrix. In this paper we discuss the application of these method to large problems that have a sparse Hessian matrix whose sparsity is known a priori. Quite often it is difficult, if not impossible, to obtain an analytic representation of the Hessian matrix. Determining the Hessian matrix by the standard method of finite-differences is costly in terms of gradient evaluations for large problems. Automatic procedures that reduce the number of gradient evaluations by exploiting sparsity are examined and a new procedure is suggested. Once a sparse approximation to the Hessian matrix has been obtained, there still remains the problem of solving a sparse linear system of equations at each iteration. A modified Cholesky factorization can be used. However, many additional nonzeros (fill-in) may be created in the factors, and storage problems may arise. One way of approaching this problem is to ignore fill-in in a systematic manner. Such technique are calledpartial factorization schemes. Various existing partial factorization are analyzed and three new ones are developed. The above algorithms were tested on a set of problems. The overall conclusions were that these methods perfom well in practice.     

Transient response of a transversely isotropic multilayered half-space due to a vertical loading

This paper investigates the transient response of a transversely isotropic multilayered half-space under vertical loadings. With the aid of a Laplace–Hankel transform, the global stiffness matrix for a multilayered half-space is acquired by assembling the analytical layer-element of each layer medium. The solutions for the displacements in the time domain are obtained by using the global stiffness matrix equations and a numerical inversion procedure. The accuracy of the proposed method is verified through comparisons with existing solutions for displacements induced by a step and rectangular pulse loading. In addition, selected numerical results for displacements induced by the buried loading are presented to illustrate the effect of transient loading type and material anisotropy on the transient response.     

半监督距离度量学习内蕴加速投影梯度算法

考虑求解一类半监督距离度量学习问题. 由于样本集(数据库)的规模与复杂性的激增, 在考虑距离度量学习问题时, 必须考虑学习来的距离度量矩阵具有稀疏性的特点. 因此, 在现有的距离度量学习模型中, 增加了学习矩阵的稀疏约束. 为了便于模型求解, 稀疏约束应用了Frobenius 范数约束. 进一步, 通过罚函数方法将Frobenius范数约束罚到目标函数, 使得具有稀疏约束的模型转化成无约束优化问题. 为了求解问题, 提出了正定矩阵群上加速投影梯度算法, 克服了矩阵群上不能直接进行线性组合的困难, 并分析了算法的收敛性. 最后通过UCI数据库的分类问题的例子, 进行了数值实验, 数值实验的结果说明了学习矩阵的稀疏性以及加速投影梯度算法的有效性.     

稳健稀疏主成分分析法及其实证研究

主成分分析是多元统计分析中一种非常经典的降维技术。然而,经典主成分分析却是对离群值非常敏感的,常因离群值的存在导致结果与实际不相符。另一方面,当主成分分析用于综合评价时,主成分的含义常因载荷间绝对值大小不分明而含糊不清,从而导致综合评价难以展开。本文通过使用稳健稀疏主成分分析法进行模拟实验和实证分析,结果表明:该方法不仅能很好地抵抗离群值的影响,而且还能准确地识别出离群样本。通过该方法得出的主成分的含义也较经典主成分分析和稳健主成分分析更加地明确和贴近实际。     

An exact approach to sparse principal component analysis

We show a branch and bound approach to exactly find the best sparse dimension reduction of a matrix. We can choose between enforcing orthogonality of the coefficients and uncorrelation of the components, and can explicitly set the degree of sparsity. We suggest methods to choose the number of non-zero loadings for each component; illustrate and compare our approach with existing methods through a benchmark data set.     

Computation of sparse low degree interpolating polynomials and their application to derivative-free optimization

Interpolation-based trust-region methods are an important class of algorithms for Derivative-Free Optimization which rely on locally approximating an objective function by quadratic polynomial interpolation models, frequently built from less points than there are basis components. Often, in practical applications, the contribution of the problem variables to the objective function is such that many pairwise correlations between variables are negligible, implying, in the smooth case, a sparse structure in the Hessian matrix. To be able to exploit Hessian sparsity, existing optimization approaches require the knowledge of the sparsity structure. The goal of this paper is to develop and analyze a method where the sparse models are constructed automatically. The sparse recovery theory developed recently in the field of compressed sensing characterizes conditions under which a sparse vector can be accurately recovered from few random measurements. Such a recovery is achieved by minimizing the ℓ ₁-norm of a vector subject to the measurements constraints. We suggest an approach for building sparse quadratic polynomial interpolation models by minimizing the ℓ ₁-norm of the entries of the model Hessian subject to the interpolation conditions. We show that this procedure recovers accurate models when the function Hessian is sparse, using relatively few randomly selected sample points. Motivated by this result, we developed a practical interpolation-based trust-region method using deterministic sample sets and minimum ℓ ₁-norm quadratic models. Our computational results show that the new approach exhibits a promising numerical performance both in the general case and in the sparse one.     

A Frisch-Newton Algorithm for Sparse Quantile Regression

Recent experience has shown that interior-point methods using a log barrier approach are far superior to classical simplex methods for computing solutions to large parametric quantile regression problems. In many large empirical applications, the design matrix has a very sparse structure. A typical example is the classical fixed-effect model for panel data where the parametric dimension of the model can be quite large, but the number of non-zero elements is quite small. Adopting recent developments in sparse linear algebra we introduce a modified version of the Prisch-Newton algorithm for quantile regression described in Portnoy and Koenker~([28]). The new algorithm substantially reduces the storage (memory) requirements and increases computational speed. The modified algorithm also facilitates the development of nonparametric quantile regression methods. The pseudo design matrices employed in nonparametric quantile regression smoothing are inherently sparse in both the fidelity and roughness penalty components. Exploiting the sparse structure of these problems opens up a whole range of new possibilities for multivariate smoothing on large data sets via ANOVA-type decomposition and partial linear models.     

Variable Selection in General Frailty Models Using Penalized H-Likelihood

Variable selection methods using a penalized likelihood have been widely studied in various statistical models. However, in semiparametric frailty models, these methods have been relatively less studied because the marginal likelihood function involves analytically intractable integrals, particularly when modeling multicomponent or correlated frailties. In this article, we propose a simple but unified procedure via a penalized h-likelihood (HL) for variable selection of fixed effects in a general class of semiparametric frailty models, in which random effects may be shared, nested, or correlated. We consider three penalty functions (least absolute shrinkage and selection operator [LASSO], smoothly clipped absolute deviation [SCAD], and HL) in our variable selection procedure. We show that the proposed method can be easily implemented via a slight modification to existing HL estimation approaches. Simulation studies also show that the procedure using the SCAD or HL penalty performs well. The usefulness of the new method is illustrated using three practical datasets too. Supplementary materials for the article are available online.     

From simple structure to sparse components: a review

The article begins with a review of the main approaches for interpretation the results from principal component analysis (PCA) during the last 50–60 years. The simple structure approach is compared to the modern approach of sparse PCA where interpretable solutions are directly obtained. It is shown that their goals are identical but they differ by the way they are realized. Next, the most popular and influential methods for sparse PCA are briefly reviewed. In the remaining part of the paper, a new approach to define sparse PCA is introduced. Several alternative definitions are considered and illustrated on a well-known data set. Finally, it is demonstrated, how one of these possible versions of sparse PCA can be used as a sparse alternative to the classical rotation methods.     

An augmented Lagrangian approach for sparse principal component analysis

Principal component analysis (PCA) is a widely used technique for data analysis and dimension reduction with numerous applications in science and engineering. However, the standard PCA suffers from the fact that the principal components (PCs) are usually linear combinations of all the original variables, and it is thus often difficult to interpret the PCs. To alleviate this drawback, various sparse PCA approaches were proposed in the literature (Cadima and Jolliffe in J Appl Stat 22:203–214, 1995; d’Aspremont et?al. in J Mach Learn Res 9:1269–1294, 2008; d’Aspremont et?al. SIAM Rev 49:434–448, 2007; Jolliffe in J Appl Stat 22:29–35, 1995; Journée et?al. in J Mach Learn Res 11:517–553, 2010; Jolliffe et?al. in J Comput Graph Stat 12:531–547, 2003; Moghaddam et?al. in Advances in neural information processing systems 18:915–922, MIT Press, Cambridge, 2006; Shen and Huang in J Multivar Anal 99(6):1015–1034, 2008; Zou et?al. in J Comput Graph Stat 15(2):265–286, 2006). Despite success in achieving sparsity, some important properties enjoyed by the standard PCA are lost in these methods such as uncorrelation of PCs and orthogonality of loading vectors. Also, the total explained variance that they attempt to maximize can be too optimistic. In this paper we propose a new formulation for sparse PCA, aiming at finding sparse and nearly uncorrelated PCs with orthogonal loading vectors while explaining as much of the total variance as possible. We also develop a novel augmented Lagrangian method for solving a class of nonsmooth constrained optimization problems, which is well suited for our formulation of sparse PCA. We show that it converges to a feasible point, and moreover under some regularity assumptions, it converges to a stationary point. Additionally, we propose two nonmonotone gradient methods for solving the augmented Lagrangian subproblems, and establish their global and local convergence. Finally, we compare our sparse PCA approach with several existing methods on synthetic (Zou et?al. in J Comput Graph Stat 15(2):265–286, 2006), Pitprops (Jeffers in Appl Stat 16:225–236, 1967), and gene expression data (Chin et?al in Cancer Cell 10:529C–541C, 2006), respectively. The computational results demonstrate that the sparse PCs produced by our approach substantially outperform those by other methods in terms of total explained variance, correlation of PCs, and orthogonality of loading vectors. Moreover, the experiments on random data show that our method is capable of solving large-scale problems within a reasonable amount of time.     

1-Bit compressive sensing: Reformulation and RRSP-based sign recovery theory

Recently, the 1-bit compressive sensing(1-bit CS) has been studied in the field of sparse signal recovery. Since the amplitude information of sparse signals in 1-bit CS is not available, it is often the support or the sign of a signal that can be exactly recovered with a decoding method. We first show that a necessary assumption(that has been overlooked in the literature) should be made for some existing theories and discussions for 1-bit CS. Without such an assumption, the found solution by some existing decoding algorithms might be inconsistent with 1-bit measurements. This motivates us to pursue a new direction to develop uniform and nonuniform recovery theories for 1-bit CS with a new decoding method which always generates a solution consistent with 1-bit measurements. We focus on an extreme case of 1-bit CS, in which the measurements capture only the sign of the product of a sensing matrix and a signal. We show that the 1-bit CS model can be reformulated equivalently as an ?_0-minimization problem with linear constraints. This reformulation naturally leads to a new linear-program-based decoding method, referred to as the 1-bit basis pursuit, which is remarkably different from existing formulations. It turns out that the uniqueness condition for the solution of the 1-bit basis pursuit yields the so-called restricted range space property(RRSP) of the transposed sensing matrix. This concept provides a basis to develop sign recovery conditions for sparse signals through 1-bit measurements. We prove that if the sign of a sparse signal can be exactly recovered from 1-bit measurements with 1-bit basis pursuit, then the sensing matrix must admit a certain RRSP, and that if the sensing matrix admits a slightly enhanced RRSP, then the sign of a k-sparse signal can be exactly recovered with 1-bit basis pursuit.     

An alternating direction and projection algorithm for structure-enforced matrix factorization

Structure-enforced matrix factorization (SeMF) represents a large class of mathematical models appearing in various forms of principal component analysis, sparse coding, dictionary learning and other machine learning techniques useful in many applications including neuroscience and signal processing. In this paper, we present a unified algorithm framework, based on the classic alternating direction method of multipliers (ADMM), for solving a wide range of SeMF problems whose constraint sets permit low-complexity projections. We propose a strategy to adaptively adjust the penalty parameters which is the key to achieving good performance for ADMM. We conduct extensive numerical experiments to compare the proposed algorithm with a number of state-of-the-art special-purpose algorithms on test problems including dictionary learning for sparse representation and sparse nonnegative matrix factorization. Results show that our unified SeMF algorithm can solve different types of factorization problems as reliably and as efficiently as special-purpose algorithms. In particular, our SeMF algorithm provides the ability to explicitly enforce various combinatorial sparsity patterns that, to our knowledge, has not been considered in existing approaches.