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Faster STR-IC-LCS Computation via RLE

Authors Keita Kuboi, Yuta Fujishige, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda

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Keywords
  • longest common subsequence
  • STR-IC-LCS
  • run-length encoding

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Abstract

The constrained LCS problem asks one to find a longest common subsequence of two input strings A and B with some constraints. The STR-IC-LCS problem is a variant of the constrained LCS problem, where the solution must include a given constraint string C as a substring. Given two strings A and B of respective lengths M and N, and a constraint string C of length at most min{M, N}, the best known algorithm for the STR-IC-LCS problem, proposed by Deorowicz (Inf. Process. Lett., 11:423-426, 2012), runs in O(MN) time. In this work, we present an O(mN + nM)-time solution to the STR-IC-LCS problem, where m and n denote the sizes of the run-length encodings of A and B, respectively. Since m <= M and n <= N always hold, our algorithm is always as fast as Deorowicz's algorithm, and is faster when input strings are compressible via RLE.

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Keita Kuboi, Yuta Fujishige, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda. Faster STR-IC-LCS Computation via RLE. In 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 78, pp. 20:1-20:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017) https://doi.org/10.4230/LIPIcs.CPM.2017.20

Author Details

Keita Kuboi
Yuta Fujishige
Shunsuke Inenaga
Hideo Bannai
Masayuki Takeda

References

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