### 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 language | English |
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Title of host publication | SOFSEM 2016 |

Subtitle of host publication | Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings |

Editors | Rūsiņš Mārtiņš Freivalds, Gregor Engels, Barbara Catania |

Publisher | Springer Verlag |

Pages | 302-313 |

Number of pages | 12 |

ISBN (Print) | 9783662491911 |

DOIs | |

Publication status | Published - Jan 1 2016 |

Event | 42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016 - Harrachov, Czech Republic Duration: Jan 23 2016 → Jan 28 2016 |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 9587 |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Other

Other | 42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016 |
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Country | Czech Republic |

City | Harrachov |

Period | 1/23/16 → 1/28/16 |

### Fingerprint

### All Science Journal Classification (ASJC) codes

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*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.

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

*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

}

TY - GEN

T1 - Compacting a dynamic edit distance table by RLE compression

AU - Hyyrö, Heikki

AU - Inenaga, Shunsuke

PY - 2016/1/1

Y1 - 2016/1/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84956657208&partnerID=8YFLogxK

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U2 - 10.1007/978-3-662-49192-8_25

DO - 10.1007/978-3-662-49192-8_25

M3 - Conference contribution

AN - SCOPUS:84956657208

SN - 9783662491911

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 302

EP - 313

BT - SOFSEM 2016

A2 - Freivalds, Rūsiņš Mārtiņš

A2 - Engels, Gregor

A2 - Catania, Barbara

PB - Springer Verlag

ER -