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Approximate Circular Pattern Matching

Authors Panagiotis Charalampopoulos , Tomasz Kociumaka , Jakub Radoszewski , Solon P. Pissis , Wojciech Rytter , Tomasz Waleń , Wiktor Zuba



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Author Details

Panagiotis Charalampopoulos
  • Birkbeck, University of London, UK
  • Reichman University, Herzliya, Israel
Tomasz Kociumaka
  • Max Planck Institute for Informatics, Saarbrücken, Germany
Jakub Radoszewski
  • University of Warsaw, Poland
  • Samsung R&D, Warsaw, Poland
Solon P. Pissis
  • CWI, Amsterdam, The Netherlands
  • Vrije Universiteit, Amsterdam, The Netherlands
Wojciech Rytter
  • University of Warsaw, Poland
Tomasz Waleń
  • University of Warsaw, Poland
Wiktor Zuba
  • CWI, Amsterdam, The Netherlands

Acknowledgements

We thank Paweł Gawrychowski and Oren Weimann for suggesting the strategy for the proof of Lemma 29.

Cite AsGet BibTex

Panagiotis Charalampopoulos, Tomasz Kociumaka, Jakub Radoszewski, Solon P. Pissis, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba. Approximate Circular Pattern Matching. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 35:1-35:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)
https://doi.org/10.4230/LIPIcs.ESA.2022.35

Abstract

We investigate the complexity of approximate circular pattern matching (CPM, in short) under the Hamming and edit distance. Under each of these two basic metrics, we are given a length-n text T, a length-m pattern P, and a positive integer threshold k, and we are to report all starting positions (called occurrences) of fragments of T that are at distance at most k from some cyclic rotation of P. In the decision version of the problem, we are to check if there is any such occurrence. All previous results for approximate CPM were either average-case upper bounds or heuristics, with the exception of the work of Charalampopoulos et al. [CKP^+, JCSS'21], who considered only the Hamming distance. For the reporting version of the approximate CPM problem, under the Hamming distance we improve upon the main algorithm of [CKP^+, JCSS'21] from 𝒪(n+(n/m) ⋅ k⁴) to 𝒪(n+(n/m) ⋅ k³ log log k) time; for the edit distance, we give an 𝒪(nk²)-time algorithm. Notably, for the decision versions and wide parameter-ranges, we give algorithms whose complexities are almost identical to the state-of-the-art for standard (i.e., non-circular) approximate pattern matching: - For the decision version of the approximate CPM problem under the Hamming distance, we obtain an 𝒪(n+(n/m) ⋅ k² log k / log log k)-time algorithm, which works in 𝒪(n) time whenever k = 𝒪(√{m log log m / log m}). In comparison, the fastest algorithm for the standard counterpart of the problem, by Chan et al. [CGKKP, STOC’20], runs in 𝒪(n) time only for k = 𝒪(√m). We achieve this result via a reduction to a geometric problem by building on ideas from [CKP^+, JCSS'21] and Charalampopoulos et al. [CKW, FOCS'20]. - For the decision version of the approximate CPM problem under the edit distance, the 𝒪(nklog³ k) runtime of our algorithm near matches the 𝒪(nk) runtime of the Landau-Vishkin algorithm [LV, J. Algorithms'89] for approximate pattern matching under edit distance; the latter algorithm remains the fastest known for k = Ω(m^{2/5}). As a stepping stone, we propose an 𝒪(nklog³ k)-time algorithm for solving the Longest Prefix k'-Approximate Match problem, proposed by Landau et al. [LMS, SICOMP'98], for all k' ∈ {1,…,k}. Our algorithm is based on Tiskin’s theory of seaweeds [Tiskin, Math. Comput. Sci.'08], with recent advancements (see Charalampopoulos et al. [CKW, FOCS'22]), and on exploiting the seaweeds' relation to Monge matrices. In contrast, we obtain a conditional lower bound that suggests a polynomial separation between approximate CPM under the Hamming distance over the binary alphabet and its non-circular counterpart. We also show that a strongly subquadratic-time algorithm for the decision version of approximate CPM under edit distance would refute the Strong Exponential Time Hypothesis.

Subject Classification

ACM Subject Classification
  • Theory of computation → Pattern matching
Keywords
  • approximate circular pattern matching
  • Hamming distance
  • edit distance

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