Repetition-free longest common subsequence

Adi, Said Sadique; Braga, Marília D. V.; Fernandes, Cristina G.; Ferreira, Carlos Eduardo; Martinez, Fábio Viduani; Sagot, Marie‐France; Stefanes, Marco A.; Tjandraatmadja, Christian; Wakabayashi, Yoshiko

doi:10.1016/j.dam.2009.04.023

Cited by 31 publications

(27 citation statements)

References 2 publications

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“…There are several reasons for that. First, the Beam-ACO approach [6] was only compared to the heuristics from [1,2]. The same is the case for the evolutionary algorithm from [9], which was published at about the same time as the Beam-ACO approach.…”

Section: Our Contributionmentioning

confidence: 99%

“…In comparison much less research effort has been dedicated to solving the RFLCS problem. First heuristics were proposed in [1,2]. In addition, in recent years three metaheuristic approaches were described in the literature for solving the RFLCS problem.…”

Section: Related Workmentioning

confidence: 99%

“…Then, all X[i] with i < k 1 are set to 0, while X[k 1 ] := 1. Next, the position of the first occurrence of t [2] in x after position k 1 is determined, say k 2 . Then, all X[i] with k 1 < i < k 2 are set to 0, while X[k 2 ] := 1.…”

Section: Description Of Beam-acomentioning

confidence: 99%

“…Given exactly two input strings x and y over a finite alphabet Σ, the goal is to find a longest common subsequence with the additional restriction that no letter of the alphabet may appear more than once. The problem was introduced in [2] as a comparison measure for two sequences of biological origin. Moreover, the problem was shown to be APX-hard in [2], which implies NP-hardness.…”

Section: Introductionmentioning

confidence: 99%

“…The problem was introduced in [2] as a comparison measure for two sequences of biological origin. Moreover, the problem was shown to be APX-hard in [2], which implies NP-hardness.…”

Section: Introductionmentioning

confidence: 99%

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A comprehensive comparison of metaheuristics for the repetition-free longest common subsequence problem

Blum

Blesa

2017

J Heuristics

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This paper deals with a well-known NP-hard string problem from the bio-informatics field: the repetition-free longest common subsequence problem. This problem has enjoyed an increasing interest in recent years, which has resulted in the application of several pure as well as hybrid metaheuristics. However, the literature lacks a comprehensive comparison between those approaches. Moreover, it has been shown that general purpose integer linear programming solvers are very efficient for solving many of the problem instances that were used so far in the literature. Therefore, in this work we extend the available benchmark set, adding larger instances to which integer linear programming solvers cannot be applied anymore. Moreover, we provide a comprehensive comparison of the approaches found in the literature. Based on the results we propose a hybrid between two of the best methods which turns out to inherit the complementary strengths of both methods.

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Section: Our Contributionmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

Section: Description Of Beam-acomentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…The problem was introduced in [2] as a comparison measure for two sequences of biological origin. Moreover, the problem was shown to be APX-hard in [2], which implies NP-hardness.…”

Section: Introductionmentioning

confidence: 99%

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