Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 1911.04200

Communication-Efficient Jaccard Similarity for High-Performance Distributed Genome Comparisons

Maciej Besta·Raghavendra Kanakagiri·Harun Mustafa·Mikhail Karasikov·Gunnar Rätsch·Torsten Hoefler·Edgar Solomonik
View original source ↗Read source document ↗Export metadata ↓

Abstract

The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first communication-efficient distributed algorithm for computing the Jaccard similarity among pairs of large datasets. Our algorithm provides an efficient encoding of this problem into a multiplication of sparse matrices. Both the encoding and sparse matrix product are performed in a way that minimizes data movement in terms of communication and synchronization costs. We apply our algorithm to obtain similarity among all pairs of a set of large samples of genomes. This task is a key part of modern metagenomics analysis and an evergrowing need due to the increasing availability of high-throughput DNA sequencing data. The resulting scheme is the first to enable accurate Jaccard distance derivations for massive datasets, using largescale distributed-memory systems. We package our routines in a tool, called GenomeAtScale, that combines the proposed algorithm with tools for processing input sequences. Our evaluation on real data illustrates that one can use GenomeAtScale to effectively employ tens of thousands of processors to reach new frontiers in large-scale genomic and metagenomic analysis. While GenomeAtScale can be used to foster DNA research, the more general underlying SimilarityAtScale algorithm may be used for high-performance distributed similarity computations in other data analytics application domains.

Explore related subjects

cs.CEcs.DCcs.PFq-bio.GN

Keep this discovery

BibTeXRIS

Maciej Besta, Raghavendra Kanakagiri, Harun Mustafa, Mikhail Karasikov, Gunnar Rätsch, Torsten Hoefler, Edgar Solomonik. 2019-11-11. Communication-Efficient Jaccard Similarity for High-Performance Distributed Genome Comparisons. https://arxiv.org/abs/1911.04200

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

A Framework for Discharge Time Prediction of Energy Storage Units Based on Coupled Dynamics and Multi-Factor Aging Models

This paper presents a physically interpretable framework for predicting time to empty (TTE) in portable embedded systems. The framework couples usage-driven load-power decomposition, electrical power-voltage-current closure, a semi-empirical aging model, and SOC-temperature dynamics. Smartphone telemetry is mapped to battery current through an interpretable load model and conversion-efficiency correction. Battery capacity loss is modeled by combining Arrhenius temperature dependence, SEI diffusion behavior, and cycle-related power-law degradation. The coupled dynamic model then predicts TTE under different initial SOC values, ambient temperatures, and usage profiles. Chronological hold-out evaluation on a 6.9-h smartphone discharge session yielded a current RMSE of 0.0095 $\pm$ 0.0006 A, a temperature RMSE of 2.93 $\pm$ 0.24$^\circ$C, and a TTE MAPE of 4.81 $\pm$ 0.61%. Evaluation on NASA cell B0005 produced a capacity-loss RMSE of 0.031 Ah. Baseline, ablation, and counterfactual analyses further illustrate the contributions of thermal and aging corrections and the relative influence of load features. The results demonstrate the feasibility and interpretability of the proposed framework, while broader validation across devices and batteries remains necessary.

cs.CE↗
arXiv2026

Node-Shift-Encoding Genetic Algorithm with fuzzy-enhanced reference tour to solve the bi-objective service-oriented TSP

The Travelling Salesman Problem (TSP) remains a key area of research in combinatorial optimization, with applications in logistics, manufacturing, and service delivery. This paper addresses a bi-objective service-oriented TSP in which the clients' ranks in the delivery path matter. Unlike conventional depot-based TSP formulations, the considered problem does not assume a distinguished depot or a fixed tour origin. To address this setting, we adapt the Miller--Tucker--Zemlin (MTZ)-based formulation and derive an original linearization of the resulting model, enabling its solution with off-the-shelf integer linear programming solvers. This adaptation avoids the rigid tour origin imposed by the conventional MTZ formulation, for which fixing the starting node does not affect the tour cost but can affect the objective in a customer-rank-sensitive TSP. To solve this problem, we present a Node-Shift-Encoding (NSE)-based Genetic Algorithm augmented with fuzzy reasoning to update the reference tour throughout the evolutionary process. Experimental evaluation on TSPLIB benchmarks demonstrates that the proposed method achieves improved performance compared with the classical NSE approach.

cs.CE↗
arXiv2026

Geometric organization of olfactory descriptor data in the Poincar\'e disk

Odor quality is commonly represented using high dimensional descriptor profiles, yet their low dimensional organization remains unclear. We investigated whether a two-dimensional hyperbolic embedding can provide an interpretable representation of this structure. We applied hyperbolic metric multidimensional scaling to two complementary datasets: 480 Sagar rating profiles from three participants rating 160 odorants on 15 continuous descriptors, and 4983 GoodScents--Leffingwell molecules annotated with 138 binary descriptors. The embeddings substantially preserved pairwise descriptor distances, supporting subsequent analyses of radial and angular organization. In Sagar, rating profile entropy was strongly and negatively associated with hyperbolic radius, with diffuse profiles closer to the center and concentrated profiles closer to the boundary. This radial organization emerged primarily at the level of the full descriptor profile, rather than any individual descriptor, and remained robust across alternative descriptor representations, participant specific analyses, and averaged ratings. Sweet, musky, fruity, pleasantness showed the strongest directional trends. In GoodScents--Leffingwell, active label entropy, reflecting descriptor multiplicity, increased with radius, whereas orthogonalized descriptor entropy, reflecting spread across orthogonal modes, decreased with radius. Related binary descriptors occupied coherent localized high-density regions. These findings reveal complementary radial and angular organization in the hyperbolic representation of olfactory descriptor data. They support hyperbolic mapping as an interpretable descriptive framework in which radius summarizes global profile properties, while the angular component captures continuous descriptor gradients and categorical organization.

cs.CE↗