Finding witnesses by peeling

Yonatan Aumann, Moshe Lewenstein, Noa Lewenstein, Dekel Tsur

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

3 Scopus citations

Abstract

In the k-matches problem, we are given a pattern and a text, and for each text location the goal is to list all, but not more than k, matches between the pattern and the text. This problem is one of several string matching problems that ask to not only to find where the pattern matches the text, under different "match" definitions, but also to provide witnesses to the match. Other such problems include: k-aligned ones [4], k-witnesses, and k-mismatches [18]. In addition, the solution to several other string matching problems relies on the efficient solution of the witness finding problems. In this paper we provide a general efficient method for solving such witness finding problems. We do so by casting the problem as a generalization of group testing, which we then solve by a process which we call peeling. Using this general framework we obtain improved results for all of the above problems. We also show that our method also solves a couple of problems outside the pattern matching domain.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 18th Annual Symposium, CPM 2007, Proceedings
PublisherSpringer Verlag
Pages28-39
Number of pages12
ISBN (Print)9783540734369
DOIs
StatePublished - 1 Jan 2007
Event18th Annual Symposium on Combinatorial Pattern Matching, CPM 2007 - London, ON, Canada
Duration: 9 Jul 200711 Jul 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4580 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference18th Annual Symposium on Combinatorial Pattern Matching, CPM 2007
Country/TerritoryCanada
CityLondon, ON
Period9/07/0711/07/07

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