Exact algorithms for the repetition-bounded longest common subsequence problem

Yuichi Asahiro, Jesper Andreas Jansson, Guohui Lin, Eiji Miyano, Hirotaka Ono, Tadatoshi Utashima

Research output: Journal article publicationJournal articleAcademic researchpeer-review

Abstract

In this paper, we study exact, exponential-time algorithms for a variant of the classic LONGEST COMMON SUBSEQUENCE problem called the REPETITION-BOUNDED LONGEST COMMON SUBSEQUENCE problem (or RBLCS, for short): Let an alphabet S be a finite set of symbols and an occurrence constraint Cocc be a function Cocc:S→N, assigning an upper bound on the number of occurrences of each symbol in S. Given two sequences X and Y over the alphabet S and an occurrence constraint Cocc, the goal of RBLCS is to find a longest common subsequence of X and Y such that each symbol s∈S appears at most Cocc(s) times in the obtained subsequence. The special case where Cocc(s)=1 for every symbol s∈S is known as the REPETITION-FREE LONGEST COMMON SUBSEQUENCE problem (RFLCS) and has been studied previously; e.g., in [1], Adi et al. presented a simple (exponential-time) exact algorithm for RFLCS. However, they did not analyze its time complexity in detail, and to the best of our knowledge, there are no previous results on the running times of any exact algorithms for this problem. Without loss of generality, we will assume that |X|≤|Y| and |X|=n. In this paper, we first propose a simpler algorithm for RFLCS based on the strategy used in [1] and show explicitly that its running time is O(1.44225n). Next, we provide a dynamic programming (DP) based algorithm for RBLCS and prove that its running time is O(1.44225n) for any occurrence constraint Cocc, and even less in certain special cases. In particular, for RFLCS, our DP-based algorithm runs in O(1.41422n) time, which is faster than the previous one. Furthermore, we prove NP-hardness and APX-hardness results for RBLCS on restricted instances.

Original languageEnglish
Pages (from-to)238-249
Number of pages12
JournalTheoretical Computer Science
Volume838
DOIs
Publication statusPublished - 24 Oct 2020

Keywords

  • APX-hardness
  • Dynamic programming
  • Exponential-time exact algorithms
  • NP-hardness
  • Repetition-bounded longest common subsequence problem
  • Repetition-free

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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