arXiv subjects

Yoel Shkolnisky

Publications and source records attributed to Yoel Shkolnisky.

32 records · Page 2Linked to original sources

arXiv2019

Rank-one Multi-Reference Factor Analysis

In recent years, there is a growing need for processing methods aimed at extracting useful information from large datasets. In many cases the challenge is to discover a low-dimensional structure in the data, often concealed by the existence of nuisance parameters and noise. Motivated by such challenges, we consider the problem of estimating a signal from its scaled, cyclically-shifted and noisy observations. We focus on the particularly challenging regime of low signal-to-noise ratio (SNR), where different observations cannot be shift-aligned. We show that an accurate estimation of the signal from its noisy observations is possible, and derive a procedure which is proved to consistently estimate the signal. The asymptotic sample complexity (the number of observations required to recover the signal) of the procedure is $1/\operatorname{SNR}^4$. Additionally, we propose a procedure which is experimentally shown to improve the sample complexity by a factor equal to the signal's length. Finally, we present numerical experiments which demonstrate the performance of our algorithms, and corroborate our theoretical findings.

math.ST↗

arXiv2019

Common lines ab-initio reconstruction of $D_2$-symmetric molecules

Cryo-electron microscopy is a state-of-the-art method for determining high-resolution three-dimensional models of molecules, from their two-dimensional projection images taken by an electron microscope. A crucial step in this method is to determine a low-resolution model of the molecule using only the given projection images, without using any three-dimensional information, such as an assumed reference model. For molecules without symmetry, this is often done by exploiting common lines between pairs of images. Common lines algorithms have been recently devised for molecules with cyclic symmetry, but no such algorithms exist for molecules with dihedral symmetry. In this work, we present a common lines algorithm for determining the structure of molecules with $D_{2}$ symmetry. The algorithm exploits the common lines between all pairs of images simultaneously, as well as common lines within each image. We demonstrate the applicability of our algorithm using experimental cryo-electron microscopy data.

eess.IV↗

arXiv2019

Multi-View Kernel Consensus For Data Analysis

The input data features set for many data driven tasks is high-dimensional while the intrinsic dimension of the data is low. Data analysis methods aim to uncover the underlying low dimensional structure imposed by the low dimensional hidden parameters by utilizing distance metrics that consider the set of attributes as a single monolithic set. However, the transformation of the low dimensional phenomena into the measured high dimensional observations might distort the distance metric, This distortion can effect the desired estimated low dimensional geometric structure. In this paper, we suggest to utilize the redundancy in the attribute domain by partitioning the attributes into multiple subsets we call views. The proposed methods utilize the agreement also called consensus between different views to extract valuable geometric information that unifies multiple views about the intrinsic relationships among several different observations. This unification enhances the information that a single view or a simple concatenations of views provides.

cs.LG↗

arXiv2018

Evaluating Non-Analytic Functions of Matrices

The paper revisits the classical problem of evaluating $f(A)$ for a real function $f$ and a matrix $A$ with real spectrum. The evaluation is based on expanding $f$ in Chebyshev polynomials, and the focus of the paper is to study the convergence rates of these expansions. In particular, we derive bounds on the convergence rates which reveal the relation between the smoothness of $f$ and the diagonalizability of the matrix A. We present several numerical examples to illustrate our analysis.

math.NA↗

arXiv2018

Sampling and Approximation of Bandlimited Volumetric Data

We present an approximation scheme for functions in three dimensions, that requires only their samples on the Cartesian grid, under the assumption that the functions are sufficiently concentrated in both space and frequency. The scheme is based on expanding the given function in the basis of generalized prolate spheroidal wavefunctions, with the expansion coefficients given by weighted dot products between the samples of the function and the samples of the basis functions. As numerical implementations require all expansions to be finite, we present a truncation rule for the expansions. Finally, we derive a bound on the overall approximation error in terms of the assumed space/frequency concentration.

math.NA↗

arXiv2018

Common lines modeling for reference free ab-initio reconstruction in cryo-EM

We consider the problem of estimating an unbiased and reference-free ab-inito model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines' detection errors. The key property of the proposed algorithm is that it finds the global optimum for the orientations given the common lines. In particular, any local optima in the common lines energy landscape do not affect the proposed algorithm. As a result, it is applicable to thousands of images at once, very robust to noise, completely reference free, and not biased towards any initial model. A byproduct of the algorithm is a set of measures that allow to asses the reliability of the obtained ab-initio model. We demonstrate the algorithm using class averages from two experimental data sets, resulting in ab-initio models with resolutions of 20A or better, even from class averages consisting of as few as three raw images per class.

q-bio.QM↗

arXiv2018

Steerable Principal Components for Space-Frequency Localized Images

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.

cs.CV↗

arXiv2018

The steerable graph Laplacian and its application to filtering image data-sets

In recent years, improvements in various image acquisition techniques gave rise to the need for adaptive processing methods, aimed particularly for large datasets corrupted by noise and deformations. In this work, we consider datasets of images sampled from a low-dimensional manifold (i.e. an image-valued manifold), where the images can assume arbitrary planar rotations. To derive an adaptive and rotation-invariant framework for processing such datasets, we introduce a graph Laplacian (GL)-like operator over the dataset, termed ${\textit{steerable graph Laplacian}}$. Essentially, the steerable GL extends the standard GL by accounting for all (infinitely-many) planar rotations of all images. As it turns out, similarly to the standard GL, a properly normalized steerable GL converges to the Laplace-Beltrami operator on the low-dimensional manifold. However, the steerable GL admits an improved convergence rate compared to the GL, where the improved convergence behaves as if the intrinsic dimension of the underlying manifold is lower by one. Moreover, it is shown that the steerable GL admits eigenfunctions of the form of Fourier modes (along the orbits of the images' rotations) multiplied by eigenvectors of certain matrices, which can be computed efficiently by the FFT. For image datasets corrupted by noise, we employ a subset of these eigenfunctions to "filter" the dataset via a Fourier-like filtering scheme, essentially using all images and their rotations simultaneously. We demonstrate our filtering framework by de-noising simulated single-particle cryo-EM image datasets.

cs.CV↗

arXiv2016

Machine olfaction using time scattering of sensor multiresolution graphs

In this paper we construct a learning architecture for high dimensional time series sampled by sensor arrangements. Using a redundant wavelet decomposition on a graph constructed over the sensor locations, our algorithm is able to construct discriminative features that exploit the mutual information between the sensors. The algorithm then applies scattering networks to the time series graphs to create the feature space. We demonstrate our method on a machine olfaction problem, where one needs to classify the gas type and the location where it originates from data sampled by an array of sensors. Our experimental results clearly demonstrate that our method outperforms classical machine learning techniques used in previous studies.

cs.AI↗

arXiv2016

Direct Inversion of the 3D Pseudo-polar Fourier Transform

The pseudo-polar Fourier transform is a specialized non-equally spaced Fourier transform, which evaluates the Fourier transform on a near-polar grid, known as the pseudo-polar grid. The advantage of the pseudo-polar grid over other non-uniform sampling geometries is that the transformation, which samples the Fourier transform on the pseudo-polar grid, can be inverted using a fast and stable algorithm. For other sampling geometries, even if the non-equally spaced Fourier transform can be inverted, the only known algorithms are iterative. The convergence speed of these algorithms as well as their accuracy are difficult to control, as they depend both on the sampling geometry as well as on the unknown reconstructed object. In this paper, we present a direct inversion algorithm for the three-dimensional pseudo-polar Fourier transform. The algorithm is based only on one-dimensional resampling operations, and is shown to be significantly faster than existing iterative inversion algorithms.

math.NA↗

arXiv2015

Fast Steerable Principal Component Analysis

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.

cs.CV↗

arXiv2014

An algorithm for improving Non-Local Means operators via low-rank approximation

We present a method for improving a Non Local Means operator by computing its low-rank approximation. The low-rank operator is constructed by applying a filter to the spectrum of the original Non Local Means operator. This results in an operator which is less sensitive to noise while preserving important properties of the original operator. The method is efficiently implemented based on Chebyshev polynomials and is demonstrated on the application of natural images denoising. For this application, we provide a comprehensive comparison of our method with leading denoising methods.

cs.CV↗

arXiv2013

A Fourier-based Approach for Iterative 3D Reconstruction from Cryo-EM Images

A major challenge in single particle reconstruction methods using cryo-electron microscopy is to attain a resolution sufficient to interpret fine details in three-dimensional (3D) macromolecular structures. Obtaining high resolution 3D reconstructions is difficult due to unknown orientations and positions of the imaged particles, possible incomplete coverage of the viewing directions, high level of noise in the projection images, and limiting effects of the contrast transfer function of the electron microscope. In this paper, we focus on the 3D reconstruction problem from projection images assuming an existing estimate for their orientations and positions. We propose a fast and accurate Fourier-based Iterative Reconstruction Method (FIRM) that exploits the Toeplitz structure of the operator ${\bf A}^{*}{\bf A}$, where $\bf A$ is the forward projector and ${\bf A}^{*}$ is the back projector. The operator ${\bf A}^{*}{\bf A}$ is equivalent to a convolution with a kernel. The kernel is pre-computed using the non-uniform Fast Fourier Transform and is efficiently applied in each iteration step. The iterations by FIRM are therefore considerably faster than those of traditional iterative algebraic approaches, while maintaining the same accuracy even when the viewing directions are unevenly distributed. The time complexity of FIRM is comparable to the direct Fourier inversion method. Moreover, FIRM combines images from different defocus groups simultaneously and can handle a wide range of regularization terms. We provide experimental results on simulated data that demonstrate the speed and accuracy of FIRM in comparison with current methods.

math.NA↗

arXiv2011

An algorithm for the principal component analysis of large data sets

Recently popularized randomized methods for principal component analysis (PCA) efficiently and reliably produce nearly optimal accuracy --- even on parallel processors --- unlike the classical (deterministic) alternatives. We adapt one of these randomized methods for use with data sets that are too large to be stored in random-access memory (RAM). (The traditional terminology is that our procedure works efficiently "out-of-core.") We illustrate the performance of the algorithm via several numerical examples. For example, we report on the PCA of a data set stored on disk that is so large that less than a hundredth of it can fit in our computer's RAM.

stat.CO↗