融合分子序列与结构信息,提升少样本药物性质预测效果
AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery
- 双层次注意力动态融合SMILES序列与分子图特征
- 5/10样本下在三个基准上达顶尖性能
- 可解释性方法揭示关键活性基团,适合药物研发者
准确的分子性质预测(MPP)是现代药物研发的关键步骤。然而实验验证数据稀缺,给基于AI的研究范式带来挑战。在少样本学习场景下,分子表征质量直接决定模型性能上限。我们提出AdaptMol,一种集成自适应多模态融合的原型网络,用于分子表征。该框架采用双层次注意力机制,动态融合来自两个模态的特征:SMILES序列和分子图。(1)局部层面,从分子图中提取原子相互作用和子结构等细节拓扑信息;(2)全局层面,SMILES序列提供分子整体表示。为验证多模态自适应融合的必要性,我们提出一种基于识别分子活性子结构的可解释方法,证明其能高效表征分子。在三个常用基准上,5/10样本设置下的大量实验表明,AdaptMol在多数情况下达到当前最优性能。所提出的可解释方法指导了两模态融合,凸显了两种模态的重要性。
原文摘要 · Abstract (English)
Accurate molecular property prediction (MPP) is a critical step in modern drug development. However, the scarcity of experimental validation data poses a significant challenge to AI-driven research paradigms. Under few-shot learning scenarios, the quality of molecular representations directly dictates the theoretical upper limit of model performance. We present AdaptMol, a prototypical network integrating Adaptive multimodal fusion for Molecular representation. This framework employs a dual-level attention mechanism to dynamically integrate global and local molecular features derived from two modalities: SMILES sequences and molecular graphs. (1) At the local level, structural features such as atomic interactions and substructures are extracted from molecular graphs, emphasizing fine-grained topological information; (2) At the global level, the SMILES sequence provides a holistic representation of the molecule. To validate the necessity of multimodal adaptive fusion, we propose an interpretable approach based on identifying molecular active substructures to demonstrate that multimodal adaptive fusion can efficiently represent molecules. Extensive experiments on three commonly used benchmarks under 5-shot and 10-shot settings demonstrate that AdaptMol achieves state-of-the-art performance in most cases. The rationale-extracted method guides the fusion of two modalities and highlights the importance of both modalities.
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