License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.MFCS.2018.66
URN: urn:nbn:de:0030-drops-96486
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2018/9648/
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Gawrychowski, Pawel ; Landau, Gad M. ; Starikovskaya, Tatiana

Fast Entropy-Bounded String Dictionary Look-Up with Mismatches

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LIPIcs-MFCS-2018-66.pdf (0.4 MB)

Abstract

We revisit the fundamental problem of dictionary look-up with mismatches. Given a set (dictionary) of d strings of length m and an integer k, we must preprocess it into a data structure to answer the following queries: Given a query string Q of length m, find all strings in the dictionary that are at Hamming distance at most k from Q. Chan and Lewenstein (CPM 2015) showed a data structure for k = 1 with optimal query time O(m/w + occ), where w is the size of a machine word and occ is the size of the output. The data structure occupies O(w d log^{1+epsilon} d) extra bits of space (beyond the entropy-bounded space required to store the dictionary strings). In this work we give a solution with similar bounds for a much wider range of values k. Namely, we give a data structure that has O(m/w + log^k d + occ) query time and uses O(w d log^k d) extra bits of space.

BibTeX - Entry

@InProceedings{gawrychowski_et_al:LIPIcs:2018:9648,
  author =	{Pawel Gawrychowski and Gad M. Landau and Tatiana Starikovskaya},
  title =	{{Fast Entropy-Bounded String Dictionary Look-Up with Mismatches}},
  booktitle =	{43rd International Symposium on Mathematical Foundations  of Computer Science (MFCS 2018)},
  pages =	{66:1--66:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-086-6},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{117},
  editor =	{Igor Potapov and Paul Spirakis and James Worrell},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2018/9648},
  URN =		{urn:nbn:de:0030-drops-96486},
  doi =		{10.4230/LIPIcs.MFCS.2018.66},
  annote =	{Keywords: Dictionary look-up, Hamming distance, compact data structures}
}

Keywords: Dictionary look-up, Hamming distance, compact data structures
Collection: 43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018)
Issue Date: 2018
Date of publication: 27.08.2018

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