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Binding affinity prediction for binary drug–target interactions using semi-supervised transfer learning

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Abstract

In the field of drug–target interactions prediction, the majority of approaches formulated the problem as a simple binary classification task. These methods used binary drug–target interaction datasets to train their models. The prediction of drug–target interactions is inherently a regression problem and these interactions would be identified according to the binding affinity between drugs and targets. This paper deals the binary drug–target interactions and tries to identify the binary interactions based on the binding strength of a drug and its target. To this end, we propose a semi-supervised transfer learning approach to predict the binding affinity in a continuous spectrum for binary interactions. Due to the lack of training data with continuous binding affinity in the target domain, the proposed method makes use of the information available in other domains (i.e. source domain), via the transfer learning approach. The general framework of our algorithm is based on an objective function, which considers the performance in both source and target domains as well as the unlabeled data in the target domain via a regularization term. To optimize this objective function, we make use of a gradient boosting machine which constructs the final model. To assess the performance of the proposed method, we have used some benchmark datasets with binary interactions for four classes of human proteins. Our algorithm identifies interactions in a more realistic situation. According to the experimental results, our regression model performs better than the state-of-the-art methods in some procedures.

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Data availability

The target datasets used during the current study are available in the: http://web.kuicr.kyoto-u.ac.jp/supp/yoshi/drugtarget/. The source dataset used in this study is available in: https://www.bindingdb.org/bind/index.jsp.

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Authors and Affiliations

  1. School of Electrical and Computer Engineering, Shiraz University, Shiraz, Iran

    Betsabeh Tanoori, Mansoor Zolghadri Jahromi & Eghbal G. Mansoori

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  1. Betsabeh Tanoori
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Tanoori, B., Zolghadri Jahromi, M. & Mansoori, E.G. Binding affinity prediction for binary drug–target interactions using semi-supervised transfer learning. J Comput Aided Mol Des 35, 883–900 (2021). https://doi.org/10.1007/s10822-021-00404-7

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