arXiv subjects

Yoel Shkolnisky

Publications and source records attributed to Yoel Shkolnisky.

At least 19 recordsLinked to original sources

arXiv2026

nvPAX: Constrained Optimization for Dynamic Power Allocation in Hierarchical and Multi-Tenant Systems

Power oversubscription is increasingly central to datacenter operation as power density grows, making it necessary to dynamically allocate limited power budgets across devices based on real-time demand. Existing approaches typically assume flat power domains, whereas in practice power distribution is hierarchical and allocation decisions must additionally respect tenant-level contractual constraints. We present nvPAX, a constrained-optimization policy that computes feasible power allocations at every control step via a three-phase hybrid QP/LP procedure. Phase I allocates power with minimum deviation from each device's power request, while respecting job priorities. Phase II fairly distributes excess power among active devices. Phase III fairly distributes any remaining power to idle devices. The rationale behind the three phases is to allow power oversubscription while maximizing datacenter utilization. On a trace-driven large-scale simulation using GPU power telemetry from a production datacenter, nvPAX runs with a mean wall-clock time of 264.69 ms per allocation interval and achieves a mean satisfaction ratio of 98.92%, outperforming static equal-share allocation and providing robustness beyond greedy proportional allocation in the presence of non-uniform hierarchical bottlenecks.

cs.DC↗

arXiv2026

SHREC: A Spectral Embedding-Based Approach for Ab-Initio Reconstruction of Helical Molecules

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, reconstructing helical assemblies presents unique challenges due to their inherent symmetry and the need to determine unknown helical symmetry parameters. Traditional approaches require an accurate initial estimation of these parameters, which is often obtained through trial and error or prior knowledge. These requirements can lead to incorrect reconstructions, limiting the reliability of ab initio helical reconstruction. In this work, we present SHREC (Spectral Helical REConstruction), an algorithm that directly recovers the projection angles of helical segments from their two-dimensional cryo-EM images, without requiring prior knowledge of helical symmetry parameters. Our approach leverages the insight that projections of helical segments form a one-dimensional manifold, which can be recovered using spectral embedding techniques. Experimental validation on publicly available datasets demonstrates that SHREC achieves high resolution reconstructions while accurately recovering helical parameters, requiring only knowledge of the specimen's axial symmetry group. By eliminating the need for initial symmetry estimates, SHREC offers a more robust and automated pathway for determining helical structures in cryo-EM.

q-bio.QM↗

arXiv2026

SOLVAR: Fast covariance-based heterogeneity analysis with pose refinement for cryo-EM

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 characterizing continuous heterogeneity, where molecules adopt a continuum of conformational states. Covariance-based methods offer a principled approach to modeling structural variability. However, estimating the covariance matrix efficiently remains a challenging computational task. In this paper, we present SOLVAR (Stochastic Optimization for Low-rank Variability Analysis), which leverages a low-rank assumption on the covariance matrix to provide a tractable estimator for its principal components, despite the apparently prohibitive large size of the covariance matrix. Under this low-rank assumption, our estimator can be formulated as an optimization problem that can be solved quickly and accurately. Moreover, our framework enables refinement of the poses of the input particle images, a capability absent from most heterogeneity-analysis methods, and all covariance-based methods. Numerical experiments on both synthetic and experimental datasets demonstrate that the algorithm accurately captures dominant components of variability while maintaining computational efficiency. SOLVAR achieves state-of-the-art performance across multiple datasets in a recent heterogeneity benchmark. The code of the algorithm is freely available at https://github.com/RoeyYadgar/SOLVAR.

stat.ML↗

arXiv2024

Object detection under the linear subspace model with application to cryo-EM images

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 linear subspace model, which assumes that the objects can be expanded in some known basis (such as the Fourier basis). In this paper, we develop an object detection algorithm that under the linear subspace model is asymptotically guaranteed to detect all objects, while controlling the family wise error rate or the false discovery rate. Numerical simulations show that the algorithm also controls the error rate with high power in the non-asymptotic regime, even in highly challenging regimes. We apply the proposed algorithm to experimental electron microscopy data set, and show that it outperforms existing standard software.

math.ST↗

arXiv2023

G-invariant diffusion maps

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 embedding data sets that were sampled from a manifold which is closed under the action of a continuous matrix group. An example of such a data set is images whose planar rotations are arbitrary. The G-invariant graph Laplacian, introduced in Part I of this work, admits eigenfunctions in the form of tensor products between the elements of the irreducible unitary representations of the group and eigenvectors of certain matrices. We employ these eigenfunctions to derive diffusion maps that intrinsically account for the group action on the data. In particular, we construct both equivariant and invariant embeddings, which can be used to cluster and align the data points. We demonstrate the utility of our construction in the problem of random computerized tomography.

cs.LG↗

arXiv2023

The G-invariant graph Laplacian

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 consider data sets whose data points lie on a manifold that is closed under the action of a known unitary matrix Lie group G. We propose to construct the graph Laplacian by incorporating the distances between all the pairs of points generated by the action of G on the data set. We deem the latter construction the ``G-invariant Graph Laplacian'' (G-GL). We show that the G-GL converges to the Laplace-Beltrami operator on the data manifold, while enjoying a significantly improved convergence rate compared to the standard graph Laplacian which only utilizes the distances between the points in the given data set. Furthermore, we show that the G-GL admits a set of eigenfunctions that have the form of certain products between the group elements and eigenvectors of certain matrices, which can be estimated from the data efficiently using FFT-type algorithms. We demonstrate our construction and its advantages on the problem of filtering data on a noisy manifold closed under the action of the special unitary group SU(2).

cs.LG↗

arXiv2022

Signal enhancement for two-dimensional cryo-EM data processing

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 develop an efficient algorithm for signal enhancement of cryo-EM images. The enhanced images can be used for a variety of downstream tasks, such as 2-D classification, removing uninformative images, constructing {ab initio} models, generating templates for particle picking, providing a quick assessment of the data set, dimensionality reduction, and symmetry detection. The algorithm includes built-in quality measures to assess its performance and alleviate the risk of model bias. We demonstrate the effectiveness of the proposed algorithm on several experimental data sets. In particular, we show that the quality of the resulting images is high enough to produce ab initio models of $\sim 10$ Åresolution. The algorithm is accompanied by a publicly available, documented and easy-to-use code.

eess.IV↗

arXiv2022

A common lines approach for ab-initio modeling of molecules with tetrahedral and octahedral symmetry

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 projection-images. In this work, we propose an algorithm for ab-initio reconstruction for molecules with tetrahedral or octahedral symmetry. The algorithm exploits the multiple common lines between each pair of projection-images as well as self common lines within each image. It is robust to noise in the input images as it integrates the information from all images at once. The applicability of the proposed algorithm is demonstrated using experimental cryo-electron microscopy data.

physics.comp-ph↗

arXiv2022

Three-Dimensional Alignment of Density Maps in Cryo-Electron Microscopy

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 aligning three-dimensional density maps that exploits common lines between projection images of the maps. The algorithm is fully automatic and handles rotations, reflections (handedness), and translations between the maps. In addition, the algorithm is applicable to any type of molecular symmetry without requiring any information regarding the symmetry of the maps. We evaluate our alignment algorithm on publicly available density maps, demonstrating its accuracy and efficiency. The algorithm is available at https://github.com/ShkolniskyLab/emalign.

eess.IV↗

arXiv2022

A Perturbation-Based Kernel Approximation Framework

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 approximation methods were proposed to overcome this issue, with the most prominent method being the Nystr{ö}m method. In this paper, we derive a perturbation-based kernel approximation framework building upon results from classical perturbation theory. We provide an error analysis for this framework, and prove that in fact, it generalizes the Nystr{ö}m method and several of its variants. Furthermore, we show that our framework gives rise to new kernel approximation schemes, that can be tuned to take advantage of the structure of the approximated kernel matrix. We support our theoretical results numerically and demonstrate the advantages of our approximation framework on both synthetic and real-world data.

cs.LG↗

arXiv2022

ASOCEM: Automatic Segmentation Of Contaminations in cryo-EM

Particle picking is currently a critical step in the cryo-electron microscopy single particle reconstruction pipeline. Contaminations in the acquired micrographs severely degrade the performance of particle pickers, resulting is many ``non-particles'' in the collected stack of particles. In this paper, we present ASOCEM (Automatic Segmentation Of Contaminations in cryo-EM), an automatic method to detect and segment contaminations, which requires as an input only the approximated particle size. In particular, it does not require any parameter tuning nor manual intervention. Our method is based on the observation that the statistical distribution of contaminated regions is different from that of the rest of the micrograph. This nonrestrictive assumption allows to automatically detect various types of contaminations, from the carbon edges of the supporting grid to high contrast blobs of different sizes. We demonstrate the efficiency of our algorithm using various experimental data sets containing various types of contaminations. ASOCEM is integrated as part of the KLT picker \cite{ELDAR2020107473} and is available at \url{https://github.com/ShkolniskyLab/kltpicker2}.

cs.CV↗

arXiv2020

Multi-reference factor analysis: low-rank covariance estimation under unknown translations

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 problem allows to discover low-rank structures masked by the existence of translations (which act as nuisance parameters), with direct application to Principal Components Analysis (PCA). We assume that the underlying signal is of length $L$ and follows a standard factor model with mean zero and $r$ normally-distributed factors. To recover the covariance matrix in this case, we propose to employ the second- and fourth-order shift-invariant moments of the signal known as the $\textit{power spectrum}$ and the $\textit{trispectrum}$. We prove that they are sufficient for recovering the covariance matrix (under a certain technical condition) when $r<\sqrt{L}$. Correspondingly, we provide a polynomial-time procedure for estimating the covariance matrix from many (translated and noisy) observations, where no explicit knowledge of $r$ is required, and prove the procedure's statistical consistency. While our results establish that covariance estimation is possible from the power spectrum and the trispectrum for low-rank covariance matrices, we prove that this is not the case for full-rank covariance matrices. We conduct numerical experiments that corroborate our theoretical findings, and demonstrate the favorable performance of our algorithms in various settings, including in high levels of noise.

math.ST↗

arXiv2020

Super-resolution SAXS based on PSF engineering and sub-pixel detector translations

Small-angle X-ray scattering (SAXS) technique enables convenient nanoscopic characterization for various systems and conditions. Nonetheless, lab-based SAXS systems intrinsically suffer from insufficient x-ray flux and limited angular resolution. Here, we develop a two-step reconstruction methodology to enhance the angular resolution for given experimental conditions. Using minute hardware additions, we show that translating the x-ray detector in subpixel steps and modifying the incoming beam shape results in a set of 2D scattering images which is sufficient for super-resolution SAXS reconstruction. The technique is verified experimentally to show above 25\% increase in resolution. Such advantages have a direct impact on the ability to resolve faster and finer nanoscopic structures and can be implemented in most existing SAXS apparatuses.

physics.ins-det↗

arXiv2019

KLT Picker: Particle Picking Using Data-Driven Optimal Templates

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 challenging, especially for low SNR micrographs. We present the KLT (Karhunen Loeve Transform) picker, which is fully automatic and requires as an input only the approximated particle size. In particular, it does not require any manual picking. Our method is designed especially to handle low SNR micrographs. It is based on learning a set of optimal templates through the use of multi-variate statistical analysis via the Karhunen Loeve Transform. We evaluate the KLT picker on publicly available data sets and present high-quality results with minimal manual effort.

physics.data-an↗

arXiv2019

ROIPCA: An online memory-restricted PCA algorithm based on rank-one updates

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 too large to fit in memory, or when data arrive as a stream of items. In this paper, we propose ROIPCA and fROIPCA, two online PCA algorithms that are based on rank-one updates. While ROIPCA is typically more accurate, fROIPCA is faster and has comparable accuracy. We show the relation between fROIPCA and an existing popular gradient algorithm for online PCA, and in particular, prove that fROIPCA is in fact a gradient algorithm with an optimal learning rate. We demonstrate numerically the advantages of our algorithms over existing state-of-the-art algorithms in terms of accuracy and runtime.

cs.LG↗

arXiv2019

A max-cut approach to heterogeneity in cryo-electron microscopy

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 challenges of the field remains the processing of heterogeneous data sets, produced from samples containing particles at several different conformational states. For such data sets, the algorithms must include some classification procedure to identify homogeneous groups within the data, so that the images in each group correspond to the same underlying structure. The fundamental importance of the heterogeneity problem in cryo-electron microscopy has drawn many research efforts, and resulted in significant progress in classification algorithms for heterogeneous data sets. While these algorithms are extremely useful and effective in practice, they lack rigorous mathematical analysis and performance guarantees. In this paper, we attempt to make the first steps towards rigorous mathematical analysis of the heterogeneity problem in cryo-electron microscopy. To that end, we present an algorithm for processing heterogeneous data sets, and prove accuracy and stability bounds for it. We also suggest an extension of this algorithm that combines the classification and reconstruction steps. We demonstrate it on simulated data, and compare its performance to the state-of-the-art algorithm in RELION.

cs.CV↗

arXiv2019

Symmetric rank-one updates from partial spectrum with an application to out-of-sample extension

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 known. We address this variant using an efficient scheme for updating the known eigenpairs with guaranteed error bounds. Then, we apply our scheme to the extension of the top eigenvectors of the graph Laplacian to a new data sample. In particular, we model this extension as a perturbation problem and show how to solve it using our rank-one updating scheme. We provide a theoretical analysis of this extension method, and back it up with numerical results that illustrate its advantages.

math.NA↗

arXiv2019

A common lines approach for ab-initio modeling of cyclically-symmetric molecules

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-images. In this paper, we propose a robust "angular reconstitution" algorithm for molecules with $n$-fold cyclic symmetry, that estimates the orientation parameters of the projections-images. Our suggested method utilizes self common lines which induce identical lines within the Fourier transform of each projection-image. We show that the location of self common lines admits quite a few favorable geometrical constraints, thus allowing to detect them even in a noisy setting. In addition, for molecules with higher order rotational symmetry, our proposed method exploits the fact that there exist numerous common lines between any two Fourier transformed projection-images of such molecules, thus allowing to determine their relative orientation even under high levels of noise. The efficacy of our proposed method is demonstrated using numerical experiments conducted on simulated and experimental data.

cs.CG↗