Multitype drug interaction prediction based on the deep fusion of drug features and topological relationships

PLoS One. 2022 Aug 29;17(8):e0273764. doi: 10.1371/journal.pone.0273764. eCollection 2022.

Abstract

Drug-drug interaction (DDI) prediction has received considerable attention from industry and academia. Most existing methods predict DDIs from drug attributes or relationships with neighbors, which does not guarantee that informative drug embeddings for prediction will be obtained. To address this limitation, we propose a multitype drug interaction prediction method based on the deep fusion of drug features and topological relationships, abbreviated DM-DDI. The proposed method adopts a deep fusion strategy to combine drug features and topologies to learn representative drug embeddings for DDI prediction. Specifically, a deep neural network model is first used on the drug feature matrix to extract feature information, while a graph convolutional network model is employed to capture structural information from the adjacency matrix. Then, we adopt delivery operations that allow the two models to exchange information between layers, as well as an attention mechanism for a weighted fusion of the two learned embeddings before the output layer. Finally, the unified drug embeddings for the downstream task are obtained. We conducted extensive experiments on real-world datasets, the experimental results demonstrated that DM-DDI achieved more accurate prediction results than state-of-the-art baselines. Furthermore, in two tasks that are more similar to real-world scenarios, DM-DDI outperformed other prediction methods for unknown drugs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Drug Interactions
  • Neural Networks, Computer*
  • Pharmaceutical Preparations

Substances

  • Pharmaceutical Preparations

Grants and funding

This research was funded by the Science Foundation of Fujian Province (No. 2021J011188, 2019Y0057), the Xiamen Science and Technology Planning Project (No.3502Z20206073), the Research Project of Xiamen Overseas Students (No.XRS202017206), the Open Fund of Engineering Research Center of Big Data Application in Private Health Medicine, Fujian Provincial University (KF2020003), and the XMUT Scientific Research Project (No.YSK20002R, No. YKJCX2021053). The funders had no role in study design,data collection and analysis, decision to publish, or preparation of the manuscript.