Designing and implementing algorithms for the closest string problem

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

2 Scopus Citations
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Author(s)

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Detail(s)

Original languageEnglish
Pages (from-to)32-43
Journal / PublicationTheoretical Computer Science
Volume786
Online published18 May 2018
Publication statusPublished - Sept 2019

Abstract

Given a set of n strings of length L and a radius d, the closest string problem (CSP for short) asks for a string tsol that is within a Hamming distance of d to each of the given strings. It is known that the problem is NP-hard and its optimization version admits a polynomial time approximation scheme (PTAS). A number of parameterized algorithms have been then developed to solve the problem when d is small. Among them, the relatively new ones have not been implemented before and their performance in practice was unknown. In this study, we implement all of them by careful engineering. For those that have been implemented before, our implementation is much faster. For some of those that have not been implemented before, our experimental results show that there exist huge gaps between their theoretical and practical performances. We also design a new parameterized algorithm for the binary case of CSP. The algorithm is deterministic and runs in (n2+ n2d⋅6.16d) time, while the previously best deterministic algorithm runs in (nL + nd3⋅6.731d) time.

Research Area(s)

  • Algorithm engineering, Computational biology, Fixed-parameter algorithms, The closest string problem

Citation Format(s)

Designing and implementing algorithms for the closest string problem. / Yuasa, Shota; Chen, Zhi-Zhong; Ma, Bin et al.
In: Theoretical Computer Science, Vol. 786, 09.2019, p. 32-43.

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review