Compacting a dynamic edit distance table by RLE compression

Heikki Hyyrö, Shunsuke Inenaga

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

2 Citations (Scopus)

Abstract

Kim and Park [A dynamic edit distance table, J. Disc. Algo., 2:302–312, 2004] proposed a method (KP) based on a “dynamic edit distance table” that allows one to efficiently maintain edit distance information between two strings A of length m and B of length n when the strings can be modified by single-character edits to their left or right ends. This type of computation is useful e.g. in cyclic string comparison. KP uses linear time, O(m + n), to update the distance representation after each single edit. As noted in a recent extension of KP by Hyyrö et al. [Incremental string comparison, J. Disc. Algo., 34:2-17, 2015], a practical bottleneck is that the method needs Θ(mn) space to store a representation of a complete m×n edit distance table. In this paper we take the first steps towards reducing the space usage by RLE compressing A and B. Let M and N be the lengths of RLE compressed versions of A and B, respectively. We propose how to store the edit distance table using Θ(mN + Mn) space while maintaining the same time complexity as the original method that does not use compression.

Original languageEnglish
Title of host publicationSOFSEM 2016
Subtitle of host publicationTheory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings
EditorsRūsiņš Mārtiņš Freivalds, Gregor Engels, Barbara Catania
PublisherSpringer Verlag
Pages302-313
Number of pages12
ISBN (Print)9783662491911
DOIs
Publication statusPublished - Jan 1 2016
Event42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016 - Harrachov, Czech Republic
Duration: Jan 23 2016Jan 28 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9587
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016
CountryCzech Republic
CityHarrachov
Period1/23/161/28/16

Fingerprint

Edit Distance
Table
Compression
Strings
Time Complexity
Linear Time
Update

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Hyyrö, H., & Inenaga, S. (2016). Compacting a dynamic edit distance table by RLE compression. In R. M. Freivalds, G. Engels, & B. Catania (Eds.), SOFSEM 2016: Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings (pp. 302-313). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9587). Springer Verlag. https://doi.org/10.1007/978-3-662-49192-8_25

Compacting a dynamic edit distance table by RLE compression. / Hyyrö, Heikki; Inenaga, Shunsuke.

SOFSEM 2016: Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings. ed. / Rūsiņš Mārtiņš Freivalds; Gregor Engels; Barbara Catania. Springer Verlag, 2016. p. 302-313 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9587).

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

Hyyrö, H & Inenaga, S 2016, Compacting a dynamic edit distance table by RLE compression. in RM Freivalds, G Engels & B Catania (eds), SOFSEM 2016: Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9587, Springer Verlag, pp. 302-313, 42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016, Harrachov, Czech Republic, 1/23/16. https://doi.org/10.1007/978-3-662-49192-8_25
Hyyrö H, Inenaga S. Compacting a dynamic edit distance table by RLE compression. In Freivalds RM, Engels G, Catania B, editors, SOFSEM 2016: Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings. Springer Verlag. 2016. p. 302-313. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-662-49192-8_25
Hyyrö, Heikki ; Inenaga, Shunsuke. / Compacting a dynamic edit distance table by RLE compression. SOFSEM 2016: Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings. editor / Rūsiņš Mārtiņš Freivalds ; Gregor Engels ; Barbara Catania. Springer Verlag, 2016. pp. 302-313 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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