arXiv:2511.02146cs.LGcs.AI2025-11

通过分离因果与虚假分子结构,提升药物协同作用预测的可解释性与泛化能力。

Disentangling Causal Substructures for Interpretable and Generalizable Drug Synergy Prediction

  • 将药物分子分解为因果与虚假子结构,聚焦真正影响协同作用的部分。
  • 在冷启动和分布外场景下表现优于基线模型,准确率显著提升。
  • 可识别关键分子结构,帮助理解药物组合的作用机制,适合药理研究者使用。

药物协同作用预测是复杂疾病(如癌症)有效联合疗法开发中的关键任务。现有方法多为黑箱模型,主要依赖药物特征与结果间的统计相关性。为此,我们提出CausalDDS框架,将药物分子解耦为因果与虚假子结构,并利用因果子结构表示预测协同作用。通过关注因果子结构,该方法有效缓解了虚假子结构引入的冗余特征干扰,提升了模型精度与可解释性。此外,CausalDDS采用条件干预机制,干预基于配对分子结构,并设计了基于充分性与独立性原则的新优化目标。大量实验表明,该方法在冷启动与分布外设置下均优于基线模型。同时,能有效识别决定药物协同作用的关键子结构,为药物组合的分子机制提供清晰洞见。这些结果凸显了CausalDDS在药物协同预测与药物发现中的实用潜力。

原文摘要 · Abstract (English)

Drug synergy prediction is a critical task in the development of effective combination therapies for complex diseases, including cancer. Although existing methods have shown promising results, they often operate as black-box predictors that rely predominantly on statistical correlations between drug characteristics and results. To address this limitation, we propose CausalDDS, a novel framework that disentangles drug molecules into causal and spurious substructures, utilizing the causal substructure representations for predicting drug synergy. By focusing on causal sub-structures, CausalDDS effectively mitigates the impact of redundant features introduced by spurious substructures, enhancing the accuracy and interpretability of the model. In addition, CausalDDS employs a conditional intervention mechanism, where interventions are conditioned on paired molecular structures, and introduces a novel optimization objective guided by the principles of sufficiency and independence. Extensive experiments demonstrate that our method outperforms baseline models, particularly in cold start and out-of-distribution settings. Besides, CausalDDS effectively identifies key substructures underlying drug synergy, providing clear insights into how drug combinations work at the molecular level. These results underscore the potential of CausalDDS as a practical tool for predicting drug synergy and facilitating drug discovery.

药物协同因果推理可解释性分子图

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