Drug-target interaction prediction based on metapaths and simplified neighbor aggregation
Di Yu, Xinyu Yang, Yifan Shang, Sisi Yuan, Yuansheng Liu, Yiping Liu · Methods · 2025
Drug-target interaction (DTI) prediction is critical in drug repositioning and discovery. In current metapath-based prediction methods, attention mechanisms are often used to differentiate the importance of various neighbors, enhancing the model's expressiveness. However, in biological networks with small-scale imbalanced data, attention mechanisms are prone to interference from noise and missing data, leading to instability in weight learning, reduced efficiency, and an increased risk of overfitting. To address these issues, we propose the use of average aggregation to mitigate noise, simplify model complexity, and improve stability. Specifically, we introduce a simplified mean aggregation method for DTI prediction. This approach uses average aggregation, effectively reducing noise interference, lowering model complexity, and preventing overfitting, making it especially suitable for current biological networks. Extensive testing on three heterogeneous biological datasets shows that SNADTI outperforms 12 leading methods across two evaluation metrics, significantly reducing training time and validating its effectiveness in DTI prediction. Complexity analysis reveals that our method offers a substantial computational speed advantage over other methods on the same dataset, highlighting its enhanced efficiency. Experimental results demonstrate that SNADTI excels in prediction accuracy, stability, and reproducibility, confirming its practicality and effectiveness in DTI prediction.