A greedy randomized adaptive search procedure with path relinking for the shortest superstring problem

Theodoros Gevezes () and Leonidas Pitsoulis ()
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Theodoros Gevezes: Aristotle University of Thessaloniki
Leonidas Pitsoulis: Aristotle University of Thessaloniki

Journal of Combinatorial Optimization, 2015, vol. 29, issue 4, No 13, 859-883

Abstract: Abstract The shortest superstring problem (SSP) is an $$NP$$ NP -hard combinatorial optimization problem which has attracted the interest of many researchers, due to its applications in computational molecular biology problems such as DNA sequencing, and in computer science problems such as string compression. In this paper a new heuristic algorithm for solving large scale instances of the SSP is presented, which outperforms the natural greedy algorithm in the majority of the tested instances. The proposed method is able to provide multiple near-optimum solutions and admits a natural parallel implementation. Extended computational experiments on a set of SSP instances with known optimum solutions indicate that the new method finds the optimum solution in most of the cases, and its average error relative to the optimum is close to zero.

Keywords: Combinatorial optimization; DNA sequencing; Data compression; Heuristics; GRASP; Path relinking (search for similar items in EconPapers)
Date: 2015
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Citations: View citations in EconPapers (1)

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DOI: 10.1007/s10878-013-9622-z

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