Quick greedy computation for minimum common string partitions

Isaac Goldstein, Moshe Lewenstein

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

5 Scopus citations

Abstract

In the minimum common string partition problem one is given two strings S and T with the same character statistics and one seeks the smallest partition of S into substrings so that T can also be partitioned into the same substring multiset. The problem is fundamental in several variants of edit distance with block operations, e.g. signed reversal distance with duplicates and edit distance with moves. The minimum common string partition problem is known to be NP-complete and the best approximation known is of order O(lognlog* n). Since this problem is of utmost practical importance one seeks a heuristic that will (1) usually have a low approximation factor and (2) will run fast. A simple greedy algorithm is known and it has been well-studied from an approximation point of view. It has been shown to have a bad worst case approximation factor. However, all the bad approximation factors presented so far stem from complicated recursive construction. In practice the greedy algorithm seems to have small approximation factors. However, the best current implementation of greedy runs in quadratic time. We propose a novel method to implement greedy in linear time.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 22nd Annual Symposium, CPM 2011, Proceedings
Pages273-284
Number of pages12
DOIs
StatePublished - 2011
Event22nd Annual Symposium on Combinatorial Pattern Matching, CPM 2011 - Palermo, Italy
Duration: 27 Jun 201129 Jun 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6661 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference22nd Annual Symposium on Combinatorial Pattern Matching, CPM 2011
Country/TerritoryItaly
CityPalermo
Period27/06/1129/06/11

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