Property suffix array with applications

Panagiotis Charalampopoulos, Costas S. Iliopoulos, Chang Liu, Solon P. Pissis*

*Corresponding author for this work

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

Abstract

The suffix array is one of the most prevalent data structures for string indexing; it stores the lexicographically sorted list of suffixes of a given string. Its practical advantage compared to the suffix tree is space efficiency. In Property Indexing, we are given a string x of length n and a property Π, i.e. a set of Π -valid intervals over x. A suffix-tree-like index over these valid prefixes of suffixes of x can be built in time and space O(n). We show here how to directly build a suffix-array-like index, the Property Suffix Array (PSA), in time and space O(n). We mainly draw our motivation from weighted (probabilistic) sequences: sequences of probability distributions over a given alphabet. Given a probability threshold 1z, we say that a string p of length m matches a weighted sequence X of length n at starting position i if the product of probabilities of the letters of p at positions i, …, i+ m- 1 in X is at least 1z. Our algorithm for building the PSA can be directly applied to build an O(nz) -sized suffix-array-like index over X in time and space O(nz).

Original languageEnglish
Title of host publicationLATIN 2018
Subtitle of host publicationTheoretical Informatics - 13th Latin American Symposium, Proceedings
EditorsMiguel A. Mosteiro, Michael A. Bender, Martin Farach-Colton
PublisherSpringer Verlag
Pages290-302
Number of pages13
ISBN (Print)9783319774039
DOIs
Publication statusPublished - 1 Jan 2018
Externally publishedYes
Event13th International Symposium on Latin American Theoretical Informatics, LATIN 2018 - Buenos Aires, Argentina
Duration: 16 Apr 201819 Apr 2018

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10807 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference13th International Symposium on Latin American Theoretical Informatics, LATIN 2018
CountryArgentina
CityBuenos Aires
Period16/04/1819/04/18

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  • Cite this

    Charalampopoulos, P., Iliopoulos, C. S., Liu, C., & Pissis, S. P. (2018). Property suffix array with applications. In M. A. Mosteiro, M. A. Bender, & M. Farach-Colton (Eds.), LATIN 2018: Theoretical Informatics - 13th Latin American Symposium, Proceedings (pp. 290-302). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10807 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-77404-6_22