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A methodology for evaluating multi-objective evolutionary feature selection for classification in the context of virtual screening

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Abstract

Virtual screening (VS) methods have been shown to increase success rates in many drug discovery campaigns, when they complement experimental approaches, such as high-throughput screening methods or classical medicinal chemistry approaches. Nevertheless, predictive capability of VS is not yet optimal, mainly due to limitations in the underlying physical principles describing drug binding phenomena. One approach that can improve VS methods is the aid of machine learning methods. When enough experimental data are available to train such methods, predictive capability can considerably increase. We show in this research work how a multi-objective evolutionary search strategy for feature selection, which can provide with small and accurate decision trees that can be very easily understood by chemists, can drastically increase the applicability and predictive ability of these techniques and therefore aid considerable in the drug discovery problem. With the proposed methodology, we find classification models with accuracy between 0.9934 and 1.00 and area under ROC between 0.96 and 1.00 evaluated in full training sets, and accuracy between 0.9849 and 0.9940 and area under ROC between 0.89 and 0.93 evaluated with tenfold cross-validation over 30 iterations, while substantially reducing the model size.

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Acknowledgements

This study was supported by computing facilities of Extremadura Research Centre for Advanced Technologies (CETA-CIEMAT), funded by the European Regional Development Fund (ERDF). CETA-CIEMAT belongs to CIEMAT and the Government of Spain. This work was partially funded by the Fundación Séneca del Centro de Coordinación de la Investigación de la Región de Murcia under Project 18946/JLI/13.

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Authors and Affiliations

  1. Department of Information and Communication Engineering, Faculty of Informatics, University of Murcia, 30100, Murcia, Spain

    Fernando Jiménez, José Palma & Gracia Sánchez

  2. Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Catholic University San Antonio of Murcia (UCAM), 30107, Murcia, Spain

    Horacio Pérez-Sánchez

  3. International Doctorate School, University of Murcia, 30100, Murcia, Spain

    Carlos Martínez

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  1. Fernando Jiménez
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Correspondence to Fernando Jiménez or Horacio Pérez-Sánchez.

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Jiménez, F., Pérez-Sánchez, H., Palma, J. et al. A methodology for evaluating multi-objective evolutionary feature selection for classification in the context of virtual screening. Soft Comput 23, 8775–8800 (2019). https://doi.org/10.1007/s00500-018-3479-0

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