30 citations · 101 across the 28 of their papers we have counts for
32 papers
nvPAX: Constrained Optimization for Dynamic Power Allocation in Hierarchical and Multi-Tenant Systems
Hadar Sivan, Gil Shabat, Yoel Shkolnisky
Power oversubscription is increasingly central to datacenter operation as power density grows, making it necessary to dynamically allocate limited power budgets across devices base…
SHREC: A Spectral Embedding-Based Approach for Ab-Initio Reconstruction of Helical Molecules
Guy Shapira, Yoel Shkolnisky
Cryo-electron microscopy (cryo-EM) has emerged as a powerful technique for determining the three-dimensional structures of biological molecules at near-atomic resolution. However,…
SOLVAR: Fast covariance-based heterogeneity analysis with pose refinement for cryo-EM
Roey Yadgar, Roy R. Lederman, Yoel Shkolnisky
Cryo-electron microscopy (cryo-EM) has emerged as a powerful technique for resolving the three-dimensional structures of macromolecules. A key challenge in cryo-EM is characterizin…
Object detection under the linear subspace model with application to cryo-EM images
Amitay Eldar, Keren Mor Waknin, Samuel Davenport +3
Detecting multiple unknown objects in noisy data is a key problem in many scientific fields, such as electron microscopy imaging. A common model for the unknown objects is the line…
G-invariant diffusion maps
Eitan Rosen, Xiuyuan Cheng, Yoel Shkolnisky
The diffusion maps embedding of data lying on a manifold has shown success in tasks such as dimensionality reduction, clustering, and data visualization. In this work, we consider…
The G-invariant graph Laplacian
Eitan Rosen, Paulina Hoyos, Xiuyuan Cheng +2
Graph Laplacian based algorithms for data lying on a manifold have been proven effective for tasks such as dimensionality reduction, clustering, and denoising. In this work, we con…
Signal enhancement for two-dimensional cryo-EM data processing
Guy Sharon, Yoel Shkolnisky, Tamir Bendory
Different tasks in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM) require enhancing the quality of the highly noisy raw images. To this end, we de…
A common lines approach for ab-initio modeling of molecules with tetrahedral and octahedral symmetry
Adi Shasha Geva, Yoel Shkolnisky
A main task in cryo-electron microscopy single particle reconstruction is to find a three-dimensional model of a molecule given a set of its randomly oriented and positioned noisy…
Three-Dimensional Alignment of Density Maps in Cryo-Electron Microscopy
Yael Harpaz, Yoel Shkolnisky
A common task in cryo-electron microscopy (cryo-EM) data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for align…
ASOCEM: Automatic Segmentation Of Contaminations in cryo-EM
Amitay Eldar, Ido Amos, Yoel Shkolnisky
Particle picking is currently a critical step in the cryo-electron microscopy single particle reconstruction pipeline. Contaminations in the acquired micrographs severely degrade t…
A Perturbation-Based Kernel Approximation Framework
Roy Mitz, Yoel Shkolnisky
Kernel methods are powerful tools in various data analysis tasks. Yet, in many cases, their time and space complexity render them impractical for large datasets. Various kernel app…
Super-resolution SAXS based on PSF engineering and sub-pixel detector translations
Benjamin Gutman, Michael Mrejen, Gil Shabat +3
Small-angle X-ray scattering (SAXS) technique enables convenient nanoscopic characterization for various systems and conditions. Nonetheless, lab-based SAXS systems intrinsically s…
KLT Picker: Particle Picking Using Data-Driven Optimal Templates
Amitay Eldar, Boris Landa, Yoel Shkolnisky
Particle picking is currently a critical step in the cryo-EM single particle reconstruction pipeline. Despite extensive work on this problem, for many data sets it is still challen…
ROIPCA: An online memory-restricted PCA algorithm based on rank-one updates
Roy Mitz, Yoel Shkolnisky
Principal components analysis (PCA) is a fundamental algorithm in data analysis. Its memory-restricted online versions are useful in many modern applications, where the data are to…
Rank-one Multi-Reference Factor Analysis
Yariv Aizenbud, Boris Landa, Yoel Shkolnisky
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-dimensi…
Multi-reference factor analysis: low-rank covariance estimation under unknown translations
Boris Landa, Yoel Shkolnisky
We consider the problem of estimating the covariance matrix of a random signal observed through unknown translations (modeled by cyclic shifts) and corrupted by noise. Solving this…
Common lines ab-initio reconstruction of -symmetric molecules
Eitan Rosen, Yoel Shkolnisky
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 a…
A common lines approach for ab-initio modeling of cyclically-symmetric molecules
Gabi Pragier, Yoel Shkolnisky
One of the challenges in single particle reconstruction in cryo-electron microscopy is to find a three-dimensional model of a molecule using its two-dimensional noisy projection-im…
Sampling and Approximation of Bandlimited Volumetric Data
Rami Katz, Yoel Shkolnisky
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 sufficient…
Common lines modeling for reference free ab-initio reconstruction in cryo-EM
Ido Greenberg, Yoel Shkolnisky
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. T…
The steerable graph Laplacian and its application to filtering image data-sets
Boris Landa, Yoel Shkolnisky
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 nois…
Symmetric rank-one updates from partial spectrum with an application to out-of-sample extension
Roy Mitz, Nir Sharon, Yoel Shkolnisky
Rank-one update of the spectrum of a matrix is a fundamental problem in classical perturbation theory. In this paper, we consider its variant where only part of the spectrum is kno…
A max-cut approach to heterogeneity in cryo-electron microscopy
Yariv Aizenbud, Yoel Shkolnisky
The field of cryo-electron microscopy has made astounding advancements in the past few years, mainly due to advancements in electron detectors' technology. Yet, one of the key open…
Steerable Principal Components for Space-Frequency Localized Images
Boris Landa, Yoel Shkolnisky
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 fre…