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Improving machine learning in early drug discovery

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Abstract

The high cost for new medicines is hindering their development and machine learning is therefore being used to avoid carrying out physical experiments. Here, we present a comparison between three different machine learning approaches in a classification setting where learning and prediction follow a teaching schedule to mimic the drug discovery process. The approaches are standard SVM classification, SVM based multi-kernel classification and SVM classification based on learning using privileged information. Our two main conclusions are derived using experimental in-vitro data and compound structure descriptors. The in-vitro data is assumed to i) be completely absent in the standard SVM setting, ii) be available at all times when applying multi-kernel learning, or iii) be available as privileged information during training only. The structure descriptors are always available. One conclusion is that multi-kernel learning has higher odds than standard SVM in producing higher accuracy. The second is that learning using privileged information does not have higher odds than the standard SVM, although it may improve accuracy when the training sets are small.

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Acknowledgments

AD is supported by the Science Foundation Ireland Industry Fellowship No. 15/IFA/2925.

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Authors and Affiliations

  1. AstraZeneca, Innovative Medicines & Early Development, Quantitative Biology, Discovery Sciences, Cambridge Science Park, Cambridge, CB4 0WG, UK

    Claus Bendtsen

  2. University College Dublin Systems Biology Ireland, Belfiled, Dublin, Republic of Ireland

    Andrea Degasperi

  3. AstraZeneca, Innovative Medicines & Early Development, Predictive Compound ADME & Safety, Drug Safety & Metabolism, Pepparedsleden 1, 431 83, Mölndal, Sweden

    Ernst Ahlberg

  4. AstraZeneca, Innovative Medicines & Early Development, Quantitative Biology, Discovery Sciences, Pepparedsleden 1, 431 83, Mölndal, Sweden

    Lars Carlsson

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  1. Claus Bendtsen
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  2. Andrea Degasperi
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  4. Lars Carlsson
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Correspondence to Claus Bendtsen.

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Bendtsen, C., Degasperi, A., Ahlberg, E. et al. Improving machine learning in early drug discovery. Ann Math Artif Intell 81, 155–166 (2017). https://doi.org/10.1007/s10472-017-9541-2

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Keywords

Mathematics Subject Classification (2010)

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