Space-efficient string indexing for wildcard pattern matching

Moshe Lewenstein; Yakov Nekrich; Jeffrey Scott Vitter

doi:10.4230/LIPIcs.STACS.2014.506

Space-efficient string indexing for wildcard pattern matching

Moshe Lewenstein
, Yakov Nekrich
, Jeffrey Scott Vitter

Department of Computer Science

University of Kansas

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

15 Scopus citations

Abstract

In this paper we describe compressed indexes that support pattern matching queries for strings with wildcards. For a constant size alphabet our data structure uses O(n log^εn) bits for any ε> 0 and reports all occ occurrences of a wildcard string in O(m + σ^g·μ(n) + occ) time, where μ(n) = o(log log log n), σ is the alphabet size, m is the number of alphabet symbols and g is the number of wildcard symbols in the query string. We also present an O(n)-bit index with O((m + σ^g+ occ) log^εn) query time and an O(n(log log n)²)-bit index with O((m + σ^g+ occ) log log n) query time. These are the first non-trivial data structures for this problem that need o(n log n) bits of space.

Original language	English
Title of host publication	31st International Symposium on Theoretical Aspects of Computer Science, STACS 2014
Editors	Ernst W. Mayr, Natacha Portier
Publisher	Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Pages	506-517
Number of pages	12
Volume	25
ISBN (Electronic)	9783939897651
DOIs	https://doi.org/10.4230/LIPIcs.STACS.2014.506
State	Published - 1 Mar 2014
Event	31st International Symposium on Theoretical Aspects of Computer Science, STACS 2014 - Lyon, France Duration: 5 Mar 2014 → 8 Mar 2014

Conference

Conference	31st International Symposium on Theoretical Aspects of Computer Science, STACS 2014
Country/Territory	France
City	Lyon
Period	5/03/14 → 8/03/14

Bibliographical note

Publisher Copyright:
© Moshe Lewenstein, Yakov Nekrich, and Jeffrey Scott Vitter.

Funding

Funders
Natural Sciences and Engineering Research Council of Canada

Keywords

Compressed data structures
Compressed indexes
Pattern matching

Access to Document

10.4230/LIPIcs.STACS.2014.506

Cite this

Lewenstein, M., Nekrich, Y., & Vitter, J. S. (2014). Space-efficient string indexing for wildcard pattern matching. In E. W. Mayr, & N. Portier (Eds.), 31st International Symposium on Theoretical Aspects of Computer Science, STACS 2014 (Vol. 25, pp. 506-517). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.STACS.2014.506

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title = "Space-efficient string indexing for wildcard pattern matching",

abstract = "In this paper we describe compressed indexes that support pattern matching queries for strings with wildcards. For a constant size alphabet our data structure uses O(n logεn) bits for any ε> 0 and reports all occ occurrences of a wildcard string in O(m + σg·μ(n) + occ) time, where μ(n) = o(log log log n), σ is the alphabet size, m is the number of alphabet symbols and g is the number of wildcard symbols in the query string. We also present an O(n)-bit index with O((m + σg+ occ) logεn) query time and an O(n(log log n)2)-bit index with O((m + σg+ occ) log log n) query time. These are the first non-trivial data structures for this problem that need o(n log n) bits of space.",

keywords = "Compressed data structures, Compressed indexes, Pattern matching",

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note = "Publisher Copyright: {\textcopyright} Moshe Lewenstein, Yakov Nekrich, and Jeffrey Scott Vitter.; 31st International Symposium on Theoretical Aspects of Computer Science, STACS 2014 ; Conference date: 05-03-2014 Through 08-03-2014",

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Lewenstein, M, Nekrich, Y & Vitter, JS 2014, Space-efficient string indexing for wildcard pattern matching. in EW Mayr & N Portier (eds), 31st International Symposium on Theoretical Aspects of Computer Science, STACS 2014. vol. 25, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, pp. 506-517, 31st International Symposium on Theoretical Aspects of Computer Science, STACS 2014, Lyon, France, 5/03/14. https://doi.org/10.4230/LIPIcs.STACS.2014.506

Space-efficient string indexing for wildcard pattern matching. / Lewenstein, Moshe; Nekrich, Yakov; Vitter, Jeffrey Scott.
31st International Symposium on Theoretical Aspects of Computer Science, STACS 2014. ed. / Ernst W. Mayr; Natacha Portier. Vol. 25 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2014. p. 506-517.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Space-efficient string indexing for wildcard pattern matching

Abstract

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Keywords

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