Random Projection (RP) technique has been widely applied in many scenarios because it can reduce high-dimensional features into low-dimensional space within short time and meet the need of real-time analysis of massive data. There is an urgent need of dimensionality reduction with fast increase of big genomics data. However, the performance of RP is usually lower. We attempt to improve classification accuracy of RP through combining other reduction dimension methods such as Principle Component Analysis (PCA), Linear Discriminant Analysis (LDA), and Feature Selection (FS). We compared classification accuracy and running time of different combination methods on three microarray datasets and a simulation dataset. Experimental results show a remarkable improvement of 14.77 in classification accuracy of FS followed by RP compared to RP on BC-TCGA dataset. LDA followed by RP also helps RP to yield a more discriminative subspace with an increase of 13.65 on classification accuracy on the same dataset. FS followed by RP outperforms other combination methods in classification accuracy on most of the datasets.
PCA finds dimensions with maximum covariance in an unsupervised way @cite_17 . It's mathematically defined as an orthogonal linear transformation to convert possibly correlated variables into values of linearly uncorrelated variables. The optimization problem for PCA can be summarized as follows:
@cite_17
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We study the problem of multimodal dimensionality reduction assuming that data samples can be missing at training time, and not all data modalities may be present at application time. Maximum covariance analysis, as a generalization of PCA, has many desirable properties, but its application to practical problems is limited by its need for perfectly paired data. We overcome this limitation by a latent variable approach that allows working with weakly paired data and is still able to efficiently process large datasets using standard numerical routines. The resulting weakly paired maximum covariance analysis often finds better representations than alternative methods, as we show in two exemplary tasks: texture discrimination and transfer learning. Given a covariance matrix, we consider the problem of maximizing the variance explained by a particular linear combination of the input variables while constraining the number of nonzero coefficients in this combination. This problem arises in the decomposition of a covariance matrix into sparse factors or sparse principal component analysis (PCA), and has wide applications ranging from biology to finance. We use a modification of the classical variational representation of the largest eigenvalue of a symmetric matrix, where cardinality is constrained, and derive a semidefinite programming-based relaxation for our problem. We also discuss Nesterov's smooth minimization technique applied to the semidefinite program arising in the semidefinite relaxation of the sparse PCA problem. The method has complexity @math , where @math is the size of the underlying covariance matrix and @math is the desired absolute accuracy on the optimal value of the problem. When faced with high-dimensional data, one often uses principal component analysis (PCA) for dimension reduction. Classical PCA constructs a set of uncorrelated variables, which correspond to eigenvectors of the sample covariance matrix. However, it is well-known that this covariance matrix is strongly affected by anomalous observations. It is therefore necessary to apply robust methods that are resistant to possible outliers. Li and Chen [J. Am. Stat. Assoc. 80 (1985) 759] proposed a solution based on projection pursuit (PP). The idea is to search for the direction in which the projected observations have the largest robust scale. In subsequent steps, each new direction is constrained to be orthogonal to all previous directions. This method is very well suited for high-dimensional data, even when the number of variables p is higher than the number of observations n. However, the algorithm of Li and Chen has a high computational cost. In the references [C. Croux, A. Ruiz-Gazen, in COMPSTAT: Proceedings in Computational Statistics 1996, Physica-Verlag, Heidelberg, 1996, pp. 211–217; C. Croux and A. Ruiz-Gazen, High Breakdown Estimators for Principal Components: the Projection-Pursuit Approach Revisited, 2000, submitted for publication.], a computationally much more attractive method is presented, but in high dimensions (large p) it has a numerical accuracy problem and still consumes much computation time. In this paper, we construct a faster two-step algorithm that is more stable numerically. The new algorithm is illustrated on a data set with four dimensions and on two chemometrical data sets with 1200 and 600 dimensions. Minimum variance (MV) beamforming has been studied for improving the performance of a diagnostic ultrasound imaging system. However, it is not easy for the MV beamforming to be implemented in a real-time ultrasound imaging system because of the enormous amount of computation time associated with the covariance matrix inversion. In this paper, to address this problem, we propose a new fast MV beamforming method that almost optimally approximates the MV beamforming while reducing the computational complexity greatly through dimensionality reduction using principal component analysis (PCA). The principal components are estimated offline from pre-calculated conventional MV weights. Thus, the proposed method does not directly calculate the MV weights but approximates them by a linear combination of a few selected dominant principal components. The combinational weights are calculated in almost the same way as in MV beamforming, but in the transformed domain of beamformer input signal by the PCA, where the dimension of the transformed covariance matrix is identical to the number of some selected principal component vectors. Both computer simulation and experiment were carried out to verify the effectiveness of the proposed method with echo signals from simulation as well as phantom and in vivo experiments. It is confirmed that our method can reduce the dimension of the covariance matrix down to as low as 2 × 2 while maintaining the good image quality of MV beamforming. In this paper we introduce a new underlying probabilistic model for principal component analysis (PCA). Our formulation interprets PCA as a particular Gaussian process prior on a mapping from a latent space to the observed data-space. We show that if the prior's covariance function constrains the mappings to be linear the model is equivalent to PCA, we then extend the model by considering less restrictive covariance functions which allow non-linear mappings. This more general Gaussian process latent variable model (GPLVM) is then evaluated as an approach to the visualisation of high dimensional data for three different data-sets. Additionally our non-linear algorithm can be further kernelised leading to 'twin kernel PCA' in which a mapping between feature spaces occurs. Principal component analysis (PCA) is a powerful tool for dimensionality reduction. Unfortunately, it is sensitive to outliers, so that various robust PCA variants were proposed in the literature. Among them the so-called rotational invariant @math -norm PCA is rather popular. In this paper, we reinterpret this robust method as conditional gradient algorithm and show moreover that it coincides with a gradient descent algorithm on Grassmannian manifolds. Based on this point of view, we prove for the first time convergence of the whole series of iterates to a critical point using the Kurdyka- ojasiewicz property of the energy functional. In this study, we propose the application of principal components analysis (PCA) to scale-spaces. PCA is a standard method used in computer vision. The translation of an input image into scale-space is a continuous operation, which requires the extension of conventional finite matrix- based PCA to an infinite number of dimensions. In this study, we use spectral decomposition to resolve this infinite eigenproblem by integration and we propose an approximate solution based on polynomial equations. To clarify its eigensolutions, we apply spectral decomposition to the Gaussian scale-space and scale-normalized Laplacian of Gaussian (LoG) space. As an application of this proposed method, we introduce a method for generating Gaussian blur images and scale-normalized LoG images, where we demonstrate that the accuracy of these images can be very high when calculating an arbitrary scale using a simple linear combination. We also propose a new Scale Invariant Feature Transform (SIFT) detector as a more practical example. Sparse Principal Component Analysis (PCA) is a dimensionality reduction technique wherein one seeks a lowrank 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 expectation of the underlying signal, which is often intractable to compute, can be obtained using a polynomial-time scheme. Our results also effectively provide a single-letter characterization of the sparse PCA problem. In this paper we present a practical solution with performance guarantees to the problem of dimensionality reduction for very large scale sparse matrices. We show applications of our approach to computing the Principle Component Analysis (PCA) of any @math matrix, using one pass over the stream of its rows. Our solution uses coresets: a scaled subset of the @math rows that approximates their sum of squared distances to @math -dimensional subspace. An open theoretical problem has been to compute such a coreset that is independent of both @math and @math . An open practical problem has been to compute a non-trivial approximation to the PCA of very large but sparse databases such as the Wikipedia document-term matrix in a reasonable time. We answer both of these questions affirmatively. Our main technical result is a new framework for deterministic coreset constructions based on a reduction to the problem of counting items in a stream. 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. We propose a new method for robust PCA -- the task of recovering a low-rank matrix from sparse corruptions that are of unknown value and support. Our method involves alternating between projecting appropriate residuals onto the set of low-rank matrices, and the set of sparse matrices; each projection is non-convex but easy to compute. In spite of this non-convexity, we establish exact recovery of the low-rank matrix, under the same conditions that are required by existing methods (which are based on convex optimization). For an @math input matrix ( @math , our method has a running time of @math per iteration, and needs @math iterations to reach an accuracy of @math . This is close to the running time of simple PCA via the power method, which requires @math per iteration, and @math iterations. In contrast, existing methods for robust PCA, which are based on convex optimization, have @math complexity per iteration, and take @math iterations, i.e., exponentially more iterations for the same accuracy. Experiments on both synthetic and real data establishes the improved speed and accuracy of our method over existing convex implementations. Principal Component Analysis (PCA) is the most widely used tool for linear dimensionality reduction and clustering. Still it is highly sensitive to outliers and does not scale well with respect to the number of data samples. Robust PCA solves the first issue with a sparse penalty term. The second issue can be handled with the matrix factorization model, which is however non-convex. Besides, PCA based clustering can also be enhanced by using a graph of data similarity. In this article, we introduce a new model called 'Robust PCA on Graphs' which incorporates spectral graph regularization into the Robust PCA framework. Our proposed model benefits from 1) the robustness of principal components to occlusions and missing values, 2) enhanced low-rank recovery, 3) improved clustering property due to the graph smoothness assumption on the low-rank matrix, and 4) convexity of the resulting optimization problem. Extensive experiments on 8 benchmark, 3 video and 2 artificial datasets with corruptions clearly reveal that our model outperforms 10 other state-of-the-art models in its clustering and low-rank recovery tasks. Principal Component Analysis (PCA) is the most widely used tool for linear dimensionality reduction and clustering. Still it is highly sensitive to outliers and does not scale well with respect to the number of data samples. Robust PCA solves the first issue with a sparse penalty term. The second issue can be handled with the matrix factorization model, which is however non-convex. Besides, PCA based clustering can also be enhanced by using a graph of data similarity. In this article, we introduce a new model called "Robust PCA on Graphs" which incorporates spectral graph regularization into the Robust PCA framework. Our proposed model benefits from 1) the robustness of principal components to occlusions and missing values, 2) enhanced low-rank recovery, 3) improved clustering property due to the graph smoothness assumption on the low-rank matrix, and 4) convexity of the resulting optimization problem. Extensive experiments on 8 benchmark, 3 video and 2 artificial datasets with corruptions clearly reveal that our model outperforms 10 other state-of-the-art models in its clustering and low-rank recovery tasks. We study the basic problem of robust subspace recovery. That is, we assume a data set that some of its points are sampled around a fixed subspace and the rest of them are spread in the whole ambient space, and we aim to recover the fixed underlying subspace. We first estimate "robust inverse sample covariance" by solving a convex minimization procedure; we then recover the subspace by the bottom eigenvectors of this matrix (their number correspond to the number of eigenvalues close to 0). We guarantee exact subspace recovery under some conditions on the underlying data. Furthermore, we propose a fast iterative algorithm, which linearly converges to the matrix minimizing the convex problem. We also quantify the effect of noise and regularization and discuss many other practical and theoretical issues for improving the subspace recovery in various settings. When replacing the sum of terms in the convex energy function (that we minimize) with the sum of squares of terms, we obtain that the new minimizer is a scaled version of the inverse sample covariance (when exists). We thus interpret our minimizer and its subspace (spanned by its bottom eigenvectors) as robust versions of the empirical inverse covariance and the PCA subspace respectively. We compare our method with many other algorithms for robust PCA on synthetic and real data sets and demonstrate state-of-the-art speed and accuracy. We describe and analyze a simple algorithm for principal component analysis and singular value decomposition, VR-PCA, which uses computationally cheap stochastic iterations, yet converges exponentially fast to the optimal solution. In contrast, existing algorithms suffer either from slow convergence, or computationally intensive iterations whose runtime scales with the data size. The algorithm builds on a recent variance-reduced stochastic gradient technique, which was previously analyzed for strongly convex optimization, whereas here we apply it to an inherently non-convex problem, using a very different analysis. Principal component analysis (PCA) is a commonly applied technique for dimensionality reduction. PCA implicitly minimizes a squared loss function, which may be inappropriate for data that is not real-valued, such as binary-valued data. This paper draws on ideas from the Exponential family, Generalized linear models, and Bregman distances, to give a generalization of PCA to loss functions that we argue are better suited to other data types. We describe algorithms for minimizing the loss functions, and give examples on simulated data. The paper addresses large scale image retrieval with short vector representations. We study dimensionality reduction by Principal Component Analysis (PCA) and propose improvements to its different phases. We show and explicitly exploit relations between i) mean subtraction and the negative evidence, i.e., a visual word that is mutually missing in two descriptions being compared, and ii) the axis de-correlation and the co-occurrences phenomenon. Finally, we propose an effective way to alleviate the quantization artifacts through a joint dimensionality reduction of multiple vocabularies. The proposed techniques are simple, yet significantly and consistently improve over the state of the art on compact image representations. Complementary experiments in image classification show that the methods are generally applicable. Fourier PCA is Principal Component Analysis of a matrix obtained from higher order derivatives of the logarithm of the Fourier transform of a distribution.We make this method algorithmic by developing a tensor decomposition method for a pair of tensors sharing the same vectors in rank- @math decompositions. Our main application is the first provably polynomial-time algorithm for underdetermined ICA, i.e., learning an @math matrix @math from observations @math where @math is drawn from an unknown product distribution with arbitrary non-Gaussian components. The number of component distributions @math can be arbitrarily higher than the dimension @math and the columns of @math only need to satisfy a natural and efficiently verifiable nondegeneracy condition. As a second application, we give an alternative algorithm for learning mixtures of spherical Gaussians with linearly independent means. These results also hold in the presence of Gaussian noise. Principal component analysis (PCA) is a ubiquitous technique for data analysis and processing, but one which is not based upon a probability model. In this paper we demonstrate how the principal axes of a set of observed data vectors may be determined through maximum-likelihood estimation of parameters in a latent variable model closely related to factor analysis. We consider the properties of the associated likelihood function, giving an EM algorithm for estimating the principal subspace iteratively, and discuss the advantages conveyed by the definition of a probability density function for PCA. In this paper, we consider principal component analysis (PCA) in decomposable Gaussian graphical models. We exploit the prior information in these models in order to distribute PCA computation. For this purpose, we reformulate the PCA problem in the sparse inverse covariance (concentration) domain and address the global eigenvalue problem by solving a sequence of local eigenvalue problems in each of the cliques of the decomposable graph. We illustrate our methodology in the context of decentralized anomaly detection in the Abilene backbone network. Based on the topology of the network, we propose an approximate statistical graphical model and distribute the computation of PCA.