Affiliation:
1. Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315000, China
Abstract
The combined use of multiple medications is common in treatment, which may lead to severe drug–drug interactions (DDIs). Deep learning methods have been widely used to predict DDIs in recent years. However, current models need help to fully understand the characteristics of drugs and the relationships between these characteristics, resulting in inaccurate and inefficient feature representations. Beyond that, existing studies predominantly focus on analyzing a single DDIs, failing to explore multiple similar DDIs simultaneously, thus limiting the discovery of common mechanisms underlying DDIs. To address these limitations, this research proposes a method based on M-Transformer and knowledge graph for predicting DDIs, comprising a dual-pathway approach and neural network. In the first pathway, we leverage the interpretability of the transformer to capture the intricate relationships between drug features using the multi-head attention mechanism, identifying and discarding redundant information to obtain a more refined and information-dense drug representation. However, due to the potential difficulty for a single transformer model to understand features from multiple semantic spaces, we adopted M-Transformer to understand the structural and pharmacological information of the drug as well as the connections between them. In the second pathway, we constructed a drug–drug interaction knowledge graph (DDIKG) using drug representation vectors obtained from M-Transformer as nodes and DDI types as edges. Subsequently, drug edges with similar interactions were aggregated using a graph neural network (GNN). This facilitates the exploration and extraction of shared mechanisms underlying drug–drug interactions. Extensive experiments demonstrate that our MTrans model accurately predicts DDIs and outperforms state-of-the-art models.
Funder
Natural Science Foundation of Zhejiang Province
Science and Technology Innovation 2025 Major Project of Ningbo
Natural Science Foundation of Ningbo
Research and Development of a Digital Infrastructure Cloud Operation and Maintenance Platform Based on 5G and AI
China Innovation Challenge (Ningbo) Major Project