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Abstract

The Big Data explosion has necessitated the development of search algorithms that scale sub-linearly in time and memory. While compression algorithms and search algorithms do exist independently, few algorithms offer both, and those which do are domain-specific. We present panCAKES, a novel approach to compressive search, i.e., a way to perform \(k\)-NN and \(\rho\)-NN search on compressed data while only decompressing a small, relevant, portion of the data. panCAKES assumes the manifold hypothesis and leverages the low-dimensional structure of the data to compress and search it efficiently. panCAKES is generic over any distance function for which the distance between two points is proportional to the memory cost of storing an encoding of one in terms of the other. This property holds for many widely-used distance functions, e.g. string edit distances (Levenshtein, Needleman-Wunsch, etc.) and set dissimilarity measures (Jaccard, Dice, etc.). We benchmark panCAKES on a variety of datasets, including genomic, proteomic, and set data. We compare compression ratios to gzip, and search performance between the compressed and uncompressed versions of the same dataset. panCAKES achieves compression ratios close to those of gzip, while offering sub-linear time performance for \(k\)-NN and \(\rho\)-NN search. We conclude that panCAKES is an efficient, general-purpose algorithm for exact compressive search on large datasets that obey the manifold hypothesis. We provide an open-source implementation of panCAKES in the Rust programming language.

Details

1009240
Title
Generalized compression and compressive search of large datasets
Publication title
arXiv.org; Ithaca
Publication year
2024
Publication date
Dec 3, 2024
Section
Computer Science
Publisher
Cornell University Library, arXiv.org
Source
arXiv.org
Place of publication
Ithaca
Country of publication
United States
University/institution
Cornell University Library arXiv.org
e-ISSN
2331-8422
Source type
Working Paper
Language of publication
English
Document type
Working Paper
Publication history
 
 
Online publication date
2024-12-04
Milestone dates
2024-09-18 (Submission v1); 2024-12-03 (Submission v2)
Publication history
 
 
   First posting date
04 Dec 2024
ProQuest document ID
3106852401
Document URL
https://www.proquest.com/working-papers/generalized-compression-compressive-search-large/docview/3106852401/se-2?accountid=208611
Full text outside of ProQuest
Copyright
© 2024. This work is published under http://arxiv.org/licenses/nonexclusive-distrib/1.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Last updated
2024-12-05
Database
2 databases
  • ProQuest One Academic
  • ProQuest One Academic