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Dynamic String Alignment

Authors Panagiotis Charalampopoulos , Tomasz Kociumaka , Shay Mozes

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Panagiotis Charalampopoulos
  • Department of Informatics, King’s College London, UK
  • Institute of Informatics, University of Warsaw, Poland
Tomasz Kociumaka
  • Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel
Shay Mozes
  • Efi Arazi School of Computer Science, The Interdisciplinary Center Herzliya, Israel

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Panagiotis Charalampopoulos, Tomasz Kociumaka, and Shay Mozes. Dynamic String Alignment. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 9:1-9:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


We consider the problem of dynamically maintaining an optimal alignment of two strings, each of length at most n, as they undergo insertions, deletions, and substitutions of letters. The string alignment problem generalizes the longest common subsequence (LCS) problem and the edit distance problem (also with non-unit costs, as long as insertions and deletions cost the same). The conditional lower bound of Backurs and Indyk [J. Comput. 2018] for computing the LCS in the static case implies that strongly sublinear update time for the dynamic string alignment problem would refute the Strong Exponential Time Hypothesis. We essentially match this lower bound when the alignment weights are constants, by showing how to process each update in 𝒪̃(n) time. When the weights are integers bounded in absolute value by some w=n^{𝒪(1)}, we can maintain the alignment in 𝒪̃(n ⋅ min {√ n,w}) time per update. For the 𝒪̃(nw)-time algorithm, we heavily rely on Tiskin’s work on semi-local LCS, and in particular, in an implicit way, on his algorithm for computing the (min,+)-product of two simple unit-Monge matrices [Algorithmica 2015]. As for the 𝒪̃(n√n)-time algorithm, we employ efficient data structures for computing distances in planar graphs.

Subject Classification

ACM Subject Classification
  • Theory of computation → Pattern matching
  • string alignment
  • edit distance
  • longest common subsequence
  • (unit-)Monge matrices
  • (min,+)-product


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