TY - GEN

T1 - Faster STR-IC-LCS Computation via RLE

AU - Kuboi, Keita

AU - Fujishige, Yuta

AU - Inenaga, Shunsuke

AU - Bannai, Hideo

AU - Takeda, Masayuki

N1 - Publisher Copyright:
© Keita Kuboi, Yuta Fujishige, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda.
Copyright:
Copyright 2017 Elsevier B.V., All rights reserved.

PY - 2017/7/1

Y1 - 2017/7/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85027283006&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85027283006&partnerID=8YFLogxK

U2 - 10.4230/LIPIcs.CPM.2017.20

DO - 10.4230/LIPIcs.CPM.2017.20

M3 - Conference contribution

AN - SCOPUS:85027283006

T3 - Leibniz International Proceedings in Informatics, LIPIcs

BT - 28th Annual Symposium on Combinatorial Pattern Matching, CPM 2017

A2 - Radoszewski, Jakub

A2 - Karkkainen, Juha

A2 - Radoszewski, Jakub

A2 - Rytter, Wojciech

PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing

T2 - 28th Annual Symposium on Combinatorial Pattern Matching, CPM 2017

Y2 - 4 July 2017 through 6 July 2017

ER -