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Register a new userClustering and Feature Selection using Sparse Principal Component Analysis
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Added by
Alexandre d'Aspremont
Publication date
2008
fields
Informatics Engineering
and research's language is
English
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In this paper, we study the application of sparse principal component analysis (PCA) to clustering and feature selection problems. Sparse PCA seeks sparse factors, or linear combinations of the data variables, explaining a maximum amount of variance in the data while having only a limited number of nonzero coefficients. PCA is often used as a simple clustering technique and sparse factors allow us here to interpret the clusters in terms of a reduced set of variables. We begin with a brief introduction and motivation on sparse PCA and detail our implementation of the algorithm in dAspremont et al. (2005). We then apply these results to some classic clustering and feature selection problems arising in biology.
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Sparse Principal Component Analysis (SPCA) is widely used in data processing and dimension reduction; it uses the lasso to produce modified principal components with sparse loadings for better interpretability. However, sparse PCA never considers an additional grouping structure where the loadings share similar coefficients (i.e., feature grouping), besides a special group with all coefficients being zero (i.e., feature selection). In this paper, we propose a novel method called Feature Grouping and Sparse Principal Component Analysis (FGSPCA) which allows the loadings to belong to disjoint homogeneous groups, with sparsity as a special case. The proposed FGSPCA is a subspace learning method designed to simultaneously perform grouping pursuit and feature selection, by imposing a non-convex regularization with naturally adjustable sparsity and grouping effect. To solve the resulting non-convex optimization problem, we propose an alternating algorithm that incorporates the difference-of-convex programming, augmented Lagrange and coordinate descent methods. Additionally, the experimental results on real data sets show that the proposed FGSPCA benefits from the grouping effect compared with methods without grouping effect.
Principal component analysis (PCA) is a statistical technique commonly used in multivariate data analysis. However, PCA can be difficult to interpret and explain since the principal components (PCs) are linear combinations of the original variables. Sparse PCA (SPCA) aims to balance statistical fidelity and interpretability by approximating sparse PCs whose projections capture the maximal variance of original data. In this paper we present an efficient and paralleled method of SPCA using graphics processing units (GPUs), which can process large blocks of data in parallel. Specifically, we construct parallel implementations of the four optimization formulations of the generalized power method of SPCA (GP-SPCA), one of the most efficient and effective SPCA approaches, on a GPU. The parallel GPU implementation of GP-SPCA (using CUBLAS) is up to eleven times faster than the corresponding CPU implementation (using CBLAS), and up to 107 times faster than a MatLab implementation. Extensive comparative experiments in several real-world datasets confirm that SPCA offers a practical advantage.
Principal Component Analysis (PCA) finds a linear mapping and maximizes the variance of the data which makes PCA sensitive to outliers and may cause wrong eigendirection. In this paper, we propose techniques to solve this problem; we use the data-centering method and reestimate the covariance matrix using robust statistic techniques such as median, robust scaling which is a booster to data-centering and Huber M-estimator which measures the presentation of outliers and reweight them with small values. The results on several real world data sets show that our proposed method handles outliers and gains better results than the original PCA and provides the same accuracy with lower computation cost than the Kernel PCA using the polynomial kernel in classification tasks.
We show how to efficiently project a vector onto the top principal components of a matrix, without explicitly computing these components. Specifically, we introduce an iterative algorithm that provably computes the projection using few calls to any black-box routine for ridge regression. By avoiding explicit principal component analysis (PCA), our algorithm is the first with no runtime dependence on the number of top principal components. We show that it can be used to give a fast iterative method for the popular principal component regression problem, giving the first major runtime improvement over the naive method of combining PCA with regression. To achieve our results, we first observe that ridge regression can be used to obtain a smooth projection onto the top principal components. We then sharpen this approximation to true projection using a low-degree polynomial approximation to the matrix step function. Step function approximation is a topic of long-term interest in scientific computing. We extend prior theory by constructing polynomials with simple iterative structure and rigorously analyzing their behavior under limited precision.
Sparse principal component analysis (PCA) is a popular tool for dimensional reduction of high-dimensional data. Despite its massive popularity, there is still a lack of theoretically justifiable Bayesian sparse PCA that is computationally scalable. A major challenge is choosing a suitable prior for the loadings matrix, as principal components are mutually orthogonal. We propose a spike and slab prior that meets this orthogonality constraint and show that the posterior enjoys both theoretical and computational advantages. Two computational algorithms, the PX-CAVI and the PX-EM algorithms, are developed. Both algorithms use parameter expansion to deal with the orthogonality constraint and to accelerate their convergence speeds. We found that the PX-CAVI algorithm has superior empirical performance than the PX-EM algorithm and two other penalty methods for sparse PCA. The PX-CAVI algorithm is then applied to study a lung cancer gene expression dataset. $mathsf{R}$ package $mathsf{VBsparsePCA}$ with an implementation of the algorithm is available on The Comprehensive R Archive Network.
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