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Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication

Authors Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone

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Author Details

Giulia Bernardini
  • Department of Informatics, Systems and Communication, University of Milano - Bicocca, Italy
Paweł Gawrychowski
  • Institute of Computer Science, University of Wrocław, Poland
Nadia Pisanti
  • Department of Computer Science, University of Pisa, Italy
  • ERABLE Team, INRIA, France
Solon P. Pissis
  • CWI, Amsterdam, The Netherlands
Giovanna Rosone
  • Department of Computer Science, University of Pisa, Italy

Funding

GR and NP are partially supported by MIUR-SIR project CMACBioSeq "Combinatorial methods for analysis and compression of biological sequences" grant n. RBSI146R5L.

Cite AsGet BibTex

Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, and Giovanna Rosone. Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication. In 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 132, pp. 21:1-21:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
https://doi.org/10.4230/LIPIcs.ICALP.2019.21

Abstract

An elastic-degenerate (ED) string is a sequence of n sets of strings of total length N, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of length m in an ED text. The EDSM problem has recently received some attention in the combinatorial pattern matching community, and an O(nm^{1.5}sqrt{log m} + N)-time algorithm is known [Aoyama et al., CPM 2018]. The standard assumption in the prior work on this question is that N is substantially larger than both n and m, and thus we would like to have a linear dependency on the former. Under this assumption, the natural open problem is whether we can decrease the 1.5 exponent in the time complexity, similarly as in the related (but, to the best of our knowledge, not equivalent) word break problem [Backurs and Indyk, FOCS 2016]. Our starting point is a conditional lower bound for the EDSM problem. We use the popular combinatorial Boolean matrix multiplication (BMM) conjecture stating that there is no truly subcubic combinatorial algorithm for BMM [Abboud and Williams, FOCS 2014]. By designing an appropriate reduction we show that a combinatorial algorithm solving the EDSM problem in O(nm^{1.5-epsilon} + N) time, for any epsilon>0, refutes this conjecture. Of course, the notion of combinatorial algorithms is not clearly defined, so our reduction should be understood as an indication that decreasing the exponent requires fast matrix multiplication. Two standard tools used in algorithms on strings are string periodicity and fast Fourier transform. Our main technical contribution is that we successfully combine these tools with fast matrix multiplication to design a non-combinatorial O(nm^{1.381} + N)-time algorithm for EDSM. To the best of our knowledge, we are the first to do so.

Subject Classification

ACM Subject Classification
  • Theory of computation → Pattern matching
Keywords
  • string algorithms
  • pattern matching
  • elastic-degenerate string
  • matrix multiplication
  • fast Fourier transform

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