Conference Paper

Parallel metaheuristics in computational biology: An asynchronous Cooperative enhanced Scatter Search method

  • David R. Penas /
  • Patricia González /
  • José A. Egea /
  • Julio R. Banga /
  • Ramón Doallo
Conference Proceeding cp
Procedia Computer Science
  • Volumen: 51
  • Número: 1
  • Fecha: 01 January 2015
  • Páginas: 630-639
  • ISSN: 18770509
  • Source Type: Conference Proceeding
  • DOI: 10.1016/j.procs.2015.05.331
  • Document Type: Conference Paper
  • Publisher: Elsevier B.V.
© The Authors. Published by Elsevier B.V. Metaheuristics are gaining increased attention as efficient solvers for hard global optimization problems arising in bioinformatics and computational systems biology. Scatter Search (SS) is one of the recent outstanding algorithms in that class. However, its application to very hard problems, like those considering parameter estimation in dynamic models of systems biology, still results in excessive computation times. In order to reduce the computational cost of the SS and improve its success, several research efforts have been made to propose different variants of the algorithm, including parallel approaches. This work presents an asynchronous Cooperative enhanced Scatter Search (aCeSS) based on the parallel execution of different enhanced Scatter Search threads and the cooperation between them. The main features of the proposed solution are: low overhead in the cooperation step, by means of an asynchronous protocol to exchange information between processes; more effectiveness of the cooperation step, since the exchange of information is driven by quality of the solution obtained in each process, rather than by a time elapsed; optimal use of available resources, thanks to a complete distributed approach that avoids idle processes at any moment. Several challenging parameter estimation problems from the domain of computational systems biology are used to assess the efficiency of the proposal and evaluate its scalability in a parallel environment.

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