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Register a new userFast Steerable Principal Component Analysis
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Added by
Zhizhen Zhao
Publication date
2014
fields
Informatics Engineering
and research's language is
English
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Cryo-electron microscopy nowadays often requires the analysis of hundreds of thousands of 2D images as large as a few hundred pixels in each direction. Here we introduce an algorithm that efficiently and accurately performs principal component analysis (PCA) for a large set of two-dimensional images, and, for each image, the set of its uniform rotations in the plane and their reflections. For a dataset consisting of $n$ images of size $L times L$ pixels, the computational complexity of our algorithm is $O(nL^3 + L^4)$, while existing algorithms take $O(nL^4)$. The new algorithm computes the expansion coefficients of the images in a Fourier-Bessel basis efficiently using the non-uniform fast Fourier transform. We compare the accuracy and efficiency of the new algorithm with traditional PCA and existing algorithms for steerable PCA.
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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.
This paper describes a fast and accurate method for obtaining steerable principal components from a large dataset of images, assuming the images are well localized in space and frequency. The obtained steerable principal components are optimal for expanding the images in the dataset and all of their rotations. The method relies upon first expanding the images using a series of two-dimensional Prolate Spheroidal Wave Functions (PSWFs), where the expansion coefficients are evaluated using a specially designed numerical integration scheme. Then, the expansion coefficients are used to construct a rotationally-invariant covariance matrix which admits a block-diagonal structure, and the eigen-decomposition of its blocks provides us with the desired steerable principal components. The proposed method is shown to be faster then existing methods, while providing appropriate error bounds which guarantee its accuracy.
Principal component analysis (PCA) is an important tool in exploring data. The conventional approach to PCA leads to a solution which favours the structures with large variances. This is sensitive to outliers and could obfuscate interesting underlying structures. One of the equivalent definitions of PCA is that it seeks the subspaces that maximize the sum of squared pairwise distances between data projections. This definition opens up more flexibility in the analysis of principal components which is useful in enhancing PCA. In this paper we introduce scales into PCA by maximizing only the sum of pairwise distances between projections for pairs of datapoints with distances within a chosen interval of values [l,u]. The resulting principal component decompositions in Multiscale PCA depend on point (l,u) on the plane and for each point we define projectors onto principal components. Cluster analysis of these projectors reveals the structures in the data at various scales. Each structure is described by the eigenvectors at the medoid point of the cluster which represent the structure. We also use the distortion of projections as a criterion for choosing an appropriate scale especially for data with outliers. This method was tested on both artificial distribution of data and real data. For data with multiscale structures, the method was able to reveal the different structures of the data and also to reduce the effect of outliers in the principal component analysis.
Principal Component Analysis (PCA) is one of the most important methods to handle high dimensional data. However, most of the studies on PCA aim to minimize the loss after projection, which usually measures the Euclidean distance, though in some fields, angle distance is known to be more important and critical for analysis. In this paper, we propose a method by adding constraints on factors to unify the Euclidean distance and angle distance. However, due to the nonconvexity of the objective and constraints, the optimized solution is not easy to obtain. We propose an alternating linearized minimization method to solve it with provable convergence rate and guarantee. Experiments on synthetic data and real-world datasets have validated the effectiveness of our method and demonstrated its advantages over state-of-art clustering methods.
We consider the problem of principal component analysis from a data matrix where the entries of each column have undergone some unknown permutation, termed Unlabeled Principal Component Analysis (UPCA). Using algebraic geometry, we establish that for generic enough data, and up to a permutation of the coordinates of the ambient space, there is a unique subspace of minimal dimension that explains the data. We show that a permutation-invariant system of polynomial equations has finitely many solutions, with each solution corresponding to a row permutation of the ground-truth data matrix. Allowing for missing entries on top of permutations leads to the problem of unlabeled matrix completion, for which we give theoretical results of similar flavor. We also propose a two-stage algorithmic pipeline for UPCA suitable for the practically relevant case where only a fraction of the data has been permuted. Stage-I of this pipeline employs robust-PCA methods to estimate the ground-truth column-space. Equipped with the column-space, stage-II applies methods for linear regression without correspondences to restore the permuted data. A computational study reveals encouraging findings, including the ability of UPCA to handle face images from the Extended Yale-B database with arbitrarily permuted patches of arbitrary size in $0.3$ seconds on a standard desktop computer.
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