arXiv:2505.06283cs.LGq-bio.QM2025-05

提出软因果学习框架,提升分子属性预测在分布外数据上的泛化能力。

Soft causal learning for generalized molecule property prediction: An environment perspective

  • 从环境视角建模分子图,结合化学理论生成扩展原子模式
  • 在7个数据集上实现跨分布泛化,优于现有方法
  • 适合需要强泛化能力的分子科学与药物发现研究者

分子图上的学习已成为人工智能促进科学发现的重要方向。现有基于图神经网络的方法虽能生成分子表示,但难以适应分布外(OOD)样本。尽管近期研究发现了图结构中的不变性原理,仍存在三大问题:1)原子环境扩展导致基于不变性的模型失效;2)分子子图与属性间关联复杂,因果子结构无法完全解释标签;3)环境与不变性之间存在动态交互,难以建模。为此,我们提出一种软因果学习框架,从全面建模分子环境出发,绕过对不变子图的依赖。首先将化学理论融入图生成器以模拟扩展环境,再设计基于信息瓶颈(GIB)的目标函数解耦环境与整体图结构,最后引入基于交叉注意力的软因果交互机制,实现环境与不变性之间的动态互动。我们在七个数据集上模拟多种分布外泛化场景进行实验,大量对比、消融实验及可视化案例均验证了所提方法具有优异的泛化性能。

原文摘要 · Abstract (English)

Learning on molecule graphs has become an increasingly important topic in AI for science, which takes full advantage of AI to facilitate scientific discovery. Existing solutions on modeling molecules utilize Graph Neural Networks (GNNs) to achieve representations but they mostly fail to adapt models to out-of-distribution (OOD) samples. Although recent advances on OOD-oriented graph learning have discovered the invariant rationale on graphs, they still ignore three important issues, i.e., 1) the expanding atom patterns regarding environments on graphs lead to failures of invariant rationale based models, 2) the associations between discovered molecular subgraphs and corresponding properties are complex where causal substructures cannot fully interpret the labels. 3) the interactions between environments and invariances can influence with each other thus are challenging to be modeled. To this end, we propose a soft causal learning framework, to tackle the unresolved OOD challenge in molecular science, from the perspective of fully modeling the molecule environments and bypassing the invariant subgraphs. Specifically, we first incorporate chemistry theories into our graph growth generator to imitate expaned environments, and then devise an GIB-based objective to disentangle environment from whole graphs and finally introduce a cross-attention based soft causal interaction, which allows dynamic interactions between environments and invariances. We perform experiments on seven datasets by imitating different kinds of OOD generalization scenarios. Extensive comparison, ablation experiments as well as visualized case studies demonstrate well generalization ability of our proposal.

分子科学图神经网络因果学习泛化能力

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