Locally consistent parsing for text indexing in small space

Or Birenzwige, Shay Golan, Ely Porat

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

23 Scopus citations

Abstract

We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction, where a text S is given in read-only memory, along with a set of suffixes B, and the goal is to construct the compressed trie of all these suffixes ordered lexicographically, using only O(|B|) words of space. The second problem is the Longest Common Extension (LCE) problem, where again a text S of length n is given in read-only memory with some parameter 1 ≤ τ ≤ n, and the goal is to construct a data structure that uses O(nτ ) words of space and can compute for any pair of suffixes their longest common prefix length. We show how to use ideas based on the Locally Consistent Parsing technique, that were introduced by Sahinalp and Vishkin [44], in some nontrivial ways in order to improve the known results for the above problems. We introduce new Las-Vegas and deterministic algorithms for both problems. For the randomized algorithms, we introduce the first Las-Vegas SST construction algorithm that takes O(n) time. This is an improvement over the last result of Gawrychowski and Kociumaka [22] who obtained O(n) time for Monte Carlo algorithm, and O(nplog |B|) time with hight probability for Las-Vegas algorithm. In addition, we introduce a randomized Las-Vegas construction for a data structure that uses O(nτ ) words of space, can be constructed in linear time with high probability and answers LCE queries in O(τ) time. For the deterministic algorithms, we introduce an SST construction algorithm that takes O(nlog |Bn|) time (for |B| = Ω(log n)). This is the first almost linear time, O(n · polylog n), deterministic SST construction algorithm, where all previous algorithms take at least Ω (min{n|B|, |nB2|}) time. For the LCE problem, we introduce a data structure that uses O(nτ ) words of space and answers LCE queries in O(τplog n) time, with O(nlog τ) construction time (for τ = O(lognn)). This data structure improves both query time and construction time upon the results of Tanimura et al. [47].

Original languageEnglish
Title of host publication31st Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2020
EditorsShuchi Chawla
PublisherAssociation for Computing Machinery
Pages607-626
Number of pages20
ISBN (Electronic)9781611975994
StatePublished - 2020
Event31st Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2020 - Salt Lake City, United States
Duration: 5 Jan 20208 Jan 2020

Publication series

NameProceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
Volume2020-January

Conference

Conference31st Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2020
Country/TerritoryUnited States
CitySalt Lake City
Period5/01/208/01/20

Bibliographical note

Publisher Copyright:
Copyright © 2020 by SIAM

Funding

This research is supported by ISF grant no. 1278/16, by a grant from the United States - Israel Binational Science Foundation (BSF) and by an ERC grant MPM under the European Union's Horizon 2020 research and innovation programme (grant no. 683064).

FundersFunder number
United States - Israel Binational Science Foundation
European Commission
United States-Israel Binational Science Foundation
Israel Science Foundation1278/16
Horizon 2020683064

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