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An In Silico Method for Predicting Drug Synergy Based on Multitask Learning

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Abstract

To make better use of all kinds of knowledge to predict drug synergy, it is crucial to successfully establish a drug synergy prediction model and leverage the reconstruction of sparse known drug targets. Therefore, we present an in silico method that predicts the synergy scores of drug pairs based on multitask learning (DSML) that could fuse drug targets, protein–protein interactions, anatomical therapeutic chemical codes, a priori knowledge of drug combinations. To simultaneously reconstruct drug–target protein interactions and synergistic drug combinations, DSML benefits indirectly from the associations with relation through proteins. In cross-validation experiments, DSML improved the ability to predict drug synergy. Moreover, the reconstruction of drug–target interactions and the incorporation of multisource knowledge significantly improved drug combination predictions by a large margin. The potential drug combinations predicted by DSML demonstrate its ability to predict drug synergy.

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Acknowledgements

This work has been supported by the National Natural Science Foundation of China (Grant Nos. 62002154, 61873089, and 61502221), Hunan Provincial Natural Science Foundation of China (Grant No. 2019JJ50520), Research Foundation of Hunan Educational Committee (Grant No. 20C1579), and Scientific Research Startup Foundation of University of South China (Grant No. 190XQD096).

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Authors and Affiliations

  1. School of Computer Science, University of South China, Hengyang, 421001, Hunan, China

    Xin Chen, Lingyun Luo & Pingjian Ding

  2. Hunan Medical Big Data International Sci.&Tech. Innovation Cooperation Base, Hengyang, 421000, Hunan, China

    Lingyun Luo & Pingjian Ding

  3. College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, Hunan, China

    Cong Shen & Jiawei Luo

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  1. Xin Chen
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Correspondence to Pingjian Ding.

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Chen, X., Luo, L., Shen, C. et al. An In Silico Method for Predicting Drug Synergy Based on Multitask Learning. Interdiscip Sci Comput Life Sci 13, 299–311 (2021). https://doi.org/10.1007/s12539-021-00422-x

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