新药相互作用预测难题,用多模态融合网络一次解决。
CoFEND: A Cross-Modal Fusion End-to-End Network for Cold-Start Drug-Drug Interaction Prediction

- 构建四类药物中心知识图谱,融合多源生物信息
- 端到端联合训练,提升冷启动预测准确率
- 双阶段可解释性分析,揭示用药双方关键因素
新药的冷启动药物-药物相互作用(DDI)预测对减少意外不良反应至关重要。核心挑战在于捕捉新药与已知药物间的相似性,而这种相似性与药物、酶、转运体、分子结构等多重生物实体间的复杂关系密切相关。现有方法存在三方面局限:仅考虑部分关系机制,忽视跨模态信息,导致相似性建模不完整或偏差;新药与已知药的相似性计算在各模态中独立进行且离线完成,与DDI预测任务错位;可解释性分析多局限于单一模态,关注主犯药物的关键因素,对受害药物的易感原因研究不足。为此,本文提出新型跨模态融合端到端学习网络(CMF-ELN),包含三个组件:首先,利用多样化多模态信息构建四类药物中心知识图谱,在重建监督下实现全面相似性建模;其次,设计四通道图自编码器,在端到端框架内融合跨模态相似性;最后,提出双阶段可解释性方案,精准定位主犯与受害药物的关键因素。在两个真实数据集上的大量实验表明,CMF-ELN显著优于现有方法,在预测准确率和机制可解释性方面均表现更优。
原文摘要 · Abstract (English)
Cold-start drug-drug interaction (DDI) prediction for new drugs is critical for minimizing unexpected adverse drug reactions. The key challenge is to capture similarity between new and known drugs. However, such similarity is closely associated with complex relationships and mechanisms among drugs, enzymes, transporters, molecular structures, and other biomedical entities. Existing methods have three limitations in capturing such similarity: (1) only partial relationships and mechanisms are considered, which overlooks cross-modal information and yields incomplete or biased similarity modeling; (2) similarity computation between new and known drugs is conducted separately across modalities and performed offline for cold-start DDI prediction, leading to misalignment between similarity computation and DDI prediction; and (3) existing interpretability analyses are typically single-modality and focus primarily on key determinants of the perpetrator drug, while the underlying causes of susceptibility for the victim drug are seldom investigated. To address these issues, this paper proposes a novel Cross-Modal-Fused End-to-End Learning Network (CMF-ELN) with three components. First, diverse multimodal information is leveraged to construct four types of drug-centered knowledge graphs, enabling comprehensive similarity modeling under reconstruction-based supervision. Second, a four-channel graph autoencoder is designed to fuse cross-modal similarity within an end-to-end learning framework. Finally, a two-stage interpretability scheme is devised to precisely localize key factors for both perpetrator and victim drugs. Extensive experiments on two real datasets demonstrate that CMF-ELN achieves significantly higher prediction accuracy and more comprehensive interpretability of mechanisms than its peers.
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。