TY - GEN

T1 - Faster subsequence and don't-care pattern matching on compressed texts

AU - Yamamoto, Takanori

AU - Bannai, Hideo

AU - Inenaga, Shunsuke

AU - Takeda, Masayuki

PY - 2011

Y1 - 2011

N2 - Subsequence pattern matching problems on compressed text were first considered by Cégielski et al. (Window Subsequence Problems for Compressed Texts, Proc. CSR 2006, LNCS 3967, pp. 127-136), where the principal problem is: given a string T represented as a straight line program (SLP) of size n, a string P of size m, compute the number of minimal subsequence occurrences of P in T. We present an O(nm) time algorithm for solving all variations of the problem introduced by Cégielski et al.. This improves the previous best known algorithm of Tiskin (Towards approximate matching in compressed strings: Local subsequence recognition, Proc. CSR 2011), which runs in O(nmlogm) time. We further show that our algorithms can be modified to solve a wider range of problems in the same O(nm) time complexity, and present the first matching algorithms for patterns containing VLDC (variable length don't care) symbols, as well as for patterns containing FLDC (fixed length don't care) symbols, on SLP compressed texts.

AB - Subsequence pattern matching problems on compressed text were first considered by Cégielski et al. (Window Subsequence Problems for Compressed Texts, Proc. CSR 2006, LNCS 3967, pp. 127-136), where the principal problem is: given a string T represented as a straight line program (SLP) of size n, a string P of size m, compute the number of minimal subsequence occurrences of P in T. We present an O(nm) time algorithm for solving all variations of the problem introduced by Cégielski et al.. This improves the previous best known algorithm of Tiskin (Towards approximate matching in compressed strings: Local subsequence recognition, Proc. CSR 2011), which runs in O(nmlogm) time. We further show that our algorithms can be modified to solve a wider range of problems in the same O(nm) time complexity, and present the first matching algorithms for patterns containing VLDC (variable length don't care) symbols, as well as for patterns containing FLDC (fixed length don't care) symbols, on SLP compressed texts.

UR - http://www.scopus.com/inward/record.url?scp=79960081284&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79960081284&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-21458-5_27

DO - 10.1007/978-3-642-21458-5_27

M3 - Conference contribution

AN - SCOPUS:79960081284

SN - 9783642214578

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

SP - 309

EP - 322

BT - Combinatorial Pattern Matching - 22nd Annual Symposium, CPM 2011, Proceedings

T2 - 22nd Annual Symposium on Combinatorial Pattern Matching, CPM 2011

Y2 - 27 June 2011 through 29 June 2011

ER -