Conference Paper

Calculating elementary flux modes with variable neighbourhood search

Book Series cp
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
  • Volumen: 9656
  • Fecha: 01 January 2016
  • Páginas: 304-314
  • ISSN: 16113349 03029743
  • ISBN: 9783319317434
  • Source Type: Book Series
  • DOI: 10.1007/978-3-319-31744-1_27
  • Document Type: Conference Paper
  • Publisher: Springer
© Springer International Publishing Switzerland 2016.In this work, we calculate Elementary Flux Modes (EFMs) from metabolic networks using a trajectory-based metaheuristic, Variable Neighbourhood Search (VNS). This method is based on the local exploration around an incumbent solution and the subsequent visits to ¿neighbourhoods¿ (i.e., other areas of the search space) when the exploration is not successful on improving an objective function. This strategy ensures a suitable balance between exploration and exploitation, which is the key point in metaheuristic-based optimization. Making use of linear programming and the Simplex method, a VNS-based metaheuristic has been designed and implemented. This algorithm iteratively solves the linear programs resulting from the formulation of different hypotheses about the metabolic network. These solutions are, when feasible, EFMs. The application of the proposed method on a benchmark problem corroborates its efficacy.

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