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TP-DDI: A Two-Pathway Deep Neural Network for Drug–Drug Interaction Prediction

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Abstract

Adverse drug–drug interactions (DDIs) can severely damage the body. Thus, it is essential to accurately predict DDIs. DDIs are complex processes in which many factors can cause interactions. Rather than merely considering one or two of the factors, we design a two-pathway drug–drug interaction framework named TP-DDI that uses multimodal data for DDI prediction. TP-DDI effectively explores the combined effect of a topological structure-based pathway and a biomedical object similarity-based pathway to obtain multimodal drug representations. For the topology-based pathway, we focus on drug chemistry structures through the self-attention mechanism, which can capture hidden critical relationships, especially between pairs of atoms at remote topological distances. For the similarity-based pathway, our model can emphasize useful biomedical objects according to the channel weights. Finally, the fusion of multimodal data provides a holistic view of DDIs by learning the complementary features. On a real-world dataset, experiments show that TP-DDI can achieve better performance than the state-of-the-art models. Moreover, we can find the most critical substructures with certain interpretability in the newly predicted DDIs.

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Acknowledgements

We would like to express our sincere acknowledgements to the anonymous reviewers and all authors of the cited references.

Funding

This work was supported by the National Natural Science Foundation of China (no. 61873156).

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Authors and Affiliations

  1. School of Computer Engineering and Science, Shanghai University, Shanghai, 200444, China

    Jiang Xie, Chang Zhao, Jiaming Ouyang, Hongjian He, Dingkai Huang & Mengjiao Liu

  2. School of Life Sciences, Shanghai University, Shanghai, 200444, China

    Jiao Wang

  3. College of Information Technology, Shanghai Jianqiao University, Shanghai, 201306, China

    Wenjun Zhang

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  1. Jiang Xie
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Correspondence to Jiao Wang or Wenjun Zhang.

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Xie, J., Zhao, C., Ouyang, J. et al. TP-DDI: A Two-Pathway Deep Neural Network for Drug–Drug Interaction Prediction. Interdiscip Sci Comput Life Sci 14, 895–905 (2022). https://doi.org/10.1007/s12539-022-00524-0

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