Semi-dynamic compact index for short patterns and succinct van Emde Boas tree

Yoshiaki Matsuoka, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We present a compact semi-dynamic text index which allows us to find short patterns efficiently. For parameters k ≤ q ≤ logσ n − logσ logσ n and alphabet size σ = O(polylog(n)), all occ occurrences of a pattern of length at most q−k+1 can be obtained in O(k×occ +logσ n) time, where n is the length of the text. Adding characters to the end of the text is supported in amortized constant time. Our index requires (n/k) log(n/k) + n log σ + o(n) bits of space, which is compact (i.e., O(n log σ)) when k = Θ(logσ n). As a byproduct, we present a succinct van Emde Boas tree which supports insertion, deletion, predecessor, and successor on a dynamic set of integers over the universe [0,m − 1] in O(log logm) time and requires only m + o(m) bits of space.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 26th Annual Symposium, CPM 2015, Proceedings
EditorsUgo Vaccaro, Ely Porat, Ferdinando Cicalese
PublisherSpringer Verlag
Pages355-366
Number of pages12
ISBN (Print)9783319199283
DOIs
Publication statusPublished - Jan 1 2015
Event26th Annual Symposium on Combinatorial Pattern Matching, CPM 2015 - Ischia Island, Italy
Duration: Jun 29 2015Jul 1 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9133
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other26th Annual Symposium on Combinatorial Pattern Matching, CPM 2015
CountryItaly
CityIschia Island
Period6/29/157/1/15

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All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Matsuoka, Y., I, T., Inenaga, S., Bannai, H., & Takeda, M. (2015). Semi-dynamic compact index for short patterns and succinct van Emde Boas tree. In U. Vaccaro, E. Porat, & F. Cicalese (Eds.), Combinatorial Pattern Matching - 26th Annual Symposium, CPM 2015, Proceedings (pp. 355-366). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9133). Springer Verlag. https://doi.org/10.1007/978-3-319-19929-0_30