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Using mixed mode programming to parallelize an indicator-based evolutionary algorithm for inferring multiobjective phylogenetic histories

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Abstract

Multiple problems in bioinformatics research involve the optimization of time-consuming objective functions over exponentially growing search spaces. The capabilities shown by modern parallel systems composed of clustered multicore multiprocessors represent an opportunity to address such difficult problems. A suitable paradigm to exploit these systems lies on the combination of mixed mode programming and evolutionary computation. This research focuses on the reconstruction of multiobjective phylogenetic hypotheses by using an indicator-based evolutionary algorithm. In order to overcome the main sources of complexity of the problem, we propose a parallel adaptation of this algorithm based on master–worker principles. Experimental results on six real data sets report that the design achieves an efficient exploitation of a shared–distributed memory hybrid system composed of 48 processing cores, observing improved scalability in comparison with other parallel proposals. In addition, the inferred Pareto fronts give account of the relevance of the indicator-based design, verifying significant solution quality under different multiobjective metrics and biological testing procedures.

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Acknowledgments

This work was partially funded by the Spanish Ministry of Economy and Competitiveness and the ERDF (European Regional Development Fund), under the contract TIN2012-30685 (BIO project). Sergio Santander-Jiménez was supported by the Grant FPU12/04101 from the Spanish Government. Currently, he is supported by the postdoc research grant ACCION-III-04 from the University of Extremadura, Spain.

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Authors and Affiliations

  1. Department of Computer and Communications Technologies, University of Extremadura, Escuela Politécnica, Campus Universitario s/n, 10003, Caceres, Spain

    Sergio Santander-Jiménez & Miguel A. Vega-Rodríguez

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  1. Sergio Santander-Jiménez
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  2. Miguel A. Vega-Rodríguez
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Correspondence to Sergio Santander-Jiménez.

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Communicated by C. M. Vide and A. H. Dediu.

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Santander-Jiménez, S., Vega-Rodríguez, M.A. Using mixed mode programming to parallelize an indicator-based evolutionary algorithm for inferring multiobjective phylogenetic histories. Soft Comput 21, 5601–5620 (2017). https://doi.org/10.1007/s00500-016-2219-6

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