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A Deep Neural Network for Predicting Synergistic Drug Combinations on Cancer

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Abstract

The exploration of drug combinations presents an opportunity to amplify therapeutic effectiveness while alleviating undesirable side effects. Nevertheless, the extensive array of potential combinations poses challenges in terms of cost and time constraints for experimental screening. Thus, it is crucial to narrow down the search space. Deep learning approaches have gained widespread popularity in predicting synergistic drug combinations tailored for specific cell lines in vitro settings. In the present study, we introduce a novel method termed GTextSyn, which utilizes the integration of gene expression data and chemical structure information for the prediction of synergistic effects in drug combinations. GTextSyn employs a sentence classification model within the domain of Natural Language Processing (NLP), wherein drugs and cell lines are regarded as entities possessing biochemical relevance. Meanwhile, combinations of drug pairs and cell lines are construed as sentences with biochemical relational significance. To assess the efficacy of GTextSyn, we conduct a comparative analysis with alternative deep learning approaches using a standard benchmark dataset. The results from a five-fold cross-validation demonstrate a 49.5% reduction in Mean Square Error (MSE) achieved by GTextSyn, surpassing the performance of the next best method in the regression task. Furthermore, we conduct a comprehensive literature survey on the predicted novel drug combinations and find substantial support from prior experimental studies for many of the combinations identified by GTextSyn.

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We provide the source code and data for GTextSyn, which are accessible at https://github.com/isDing/GTextSyn.

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Acknowledgements

This work was supported by the China Scholarship Council (CSC) Program (Grant No. [2022]715, file No.202008430202).

Funding

This article is funded by China Scholarship Council (Grant No. [2022]715, file No.202008430202), Shiyu Yan.

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  1. School of Computer, University of South China, West Changsheng Road, Hengyang, 421001, Hunan, China

    Shiyu Yan & Ding Zheng

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Yan, S., Zheng, D. A Deep Neural Network for Predicting Synergistic Drug Combinations on Cancer. Interdiscip Sci Comput Life Sci 16, 218–230 (2024). https://doi.org/10.1007/s12539-023-00596-6

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