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Faster Online Elastic Degenerate String Matching

Authors Kotaro Aoyama, Yuto Nakashima, Tomohiro I , Shunsuke Inenaga, Hideo Bannai , Masayuki Takeda

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ACM Subject Classification
  • Theory of computation → Pattern matching
Keywords
  • elastic degenerate pattern matching
  • boolean convolution

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Abstract

An Elastic-Degenerate String [Iliopoulus et al., LATA 2017] is a sequence of sets of strings, which was recently proposed as a way to model a set of similar sequences. We give an online algorithm for the Elastic-Degenerate String Matching (EDSM) problem that runs in O(nm sqrt{m log m} + N) time and O(m) working space, where n is the number of elastic degenerate segments of the text, N is the total length of all strings in the text, and m is the length of the pattern. This improves the previous algorithm by Grossi et al. [CPM 2017] that runs in O(nm^2 + N) time.

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Kotaro Aoyama, Yuto Nakashima, Tomohiro I, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda. Faster Online Elastic Degenerate String Matching. In 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 105, pp. 9:1-9:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018) https://doi.org/10.4230/LIPIcs.CPM.2018.9

Author Details

Kotaro Aoyama
  • Department of Electrical Engineering and Computer Science, Kyushu University, Japan
Yuto Nakashima
  • Department of Informatics, Kyushu University, Japan
Tomohiro I
  • Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Japan
Shunsuke Inenaga
  • Department of Informatics, Kyushu University, Japan
Hideo Bannai
  • Department of Informatics, Kyushu University, Japan
Masayuki Takeda
  • Department of Informatics, Kyushu University, Japan

References

  1. Karl R. Abrahamson. Generalized string matching. SIAM J. Comput., 16(6):1039-1051, 1987. URL: http://dx.doi.org/10.1137/0216067.
  2. Stephen Alstrup, Jens Peter Secher, and Maz Spork. Optimal on-line decremental connectivity in trees. Information Processing Letters, 64(4):161-164, 1997. Google Scholar
  3. Giulia Bernardini, Nadia Pisanti, Solon P. Pissis, and Giovanna Rosone. Pattern matching on elastic-degenerate text with errors. In Gabriele Fici, Marinella Sciortino, and Rossano Venturini, editors, String Processing and Information Retrieval, pages 74-90, Cham, 2017. Springer International Publishing. Google Scholar
  4. The Computational Pan-Genomics Consortium. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19(1):118-135, 2018. URL: http://dx.doi.org/10.1093/bib/bbw089.
  5. James W. Cooley and John W. Tukey. An algorithm for the machine calculation of complex Fourier series. Mathematics of Computation, 19(90):297-301, 1965. URL: http://www.jstor.org/stable/2003354.
  6. Martin Farach. Optimal suffix tree construction with large alphabets. In 38th Annual Symposium on Foundations of Computer Science, FOCS '97, Miami Beach, Florida, USA, October 19-22, 1997, pages 137-143. IEEE Computer Society, 1997. URL: http://dx.doi.org/10.1109/SFCS.1997.646102.
  7. Michael J. Fischer and Michael S. Paterson. String matching and other products. In Richard M. Karp, editor, Complexity of Computation, volume 7 of SIAM-AMS Proceedings, pages 113-125, 1974. Google Scholar
  8. Roberto Grossi, Costas S. Iliopoulos, Chang Liu, Nadia Pisanti, Solon P. Pissis, Ahmad Retha, Giovanna Rosone, Fatima Vayani, and Luca Versari. On-line pattern matching on similar texts. In Juha Kärkkäinen, Jakub Radoszewski, and Wojciech Rytter, editors, 28th Annual Symposium on Combinatorial Pattern Matching, CPM 2017, July 4-6, 2017, Warsaw, Poland, volume 78 of LIPIcs, pages 9:1-9:14. Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2017. URL: http://dx.doi.org/10.4230/LIPIcs.CPM.2017.9.
  9. Costas S. Iliopoulos, Ritu Kundu, and Solon P. Pissis. Efficient pattern matching in elastic-degenerate texts. In Frank Drewes, Carlos Martín-Vide, and Bianca Truthe, editors, Language and Automata Theory and Applications - 11th International Conference, LATA 2017, Umeå, Sweden, March 6-9, 2017, Proceedings, volume 10168 of Lecture Notes in Computer Science, pages 131-142, 2017. URL: http://dx.doi.org/10.1007/978-3-319-53733-7_9.
  10. Donald E. Knuth, James H. Morris Jr., and Vaughan R. Pratt. Fast pattern matching in strings. SIAM J. Comput., 6(2):323-350, 1977. URL: http://dx.doi.org/10.1137/0206024.
  11. Peter Weiner. Linear pattern matching algorithms. In 14th Annual Symposium on Switching and Automata Theory, Iowa City, Iowa, USA, October 15-17, 1973, pages 1-11. IEEE Computer Society, 1973. URL: http://dx.doi.org/10.1109/SWAT.1973.13.
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