arXiv:2506.21028cs.LG2025-06NeurIPS被引 5

融合结构、文本与分类信息,提升分子属性预测精度

TRIDENT: Tri-Modal Molecular Representation Learning with Taxonomic Annotations and Local Correspondence

  • 三模态联合学习:SMILES、文本描述与分类标注协同建模
  • 在11项任务上达顶尖性能,全局与局部对齐提升表征质量
  • 适合药物发现、分子设计等需要细粒度结构-功能关联的研究

分子属性预测旨在学习将化学结构映射到功能属性的表示。尽管多模态学习已成为构建分子表示的强大范式,但以往研究大多忽视了分子的文本和分类信息。我们提出TRIDENT框架,整合分子SMILES、文本描述及分类功能注释以学习丰富的分子表示。为此,我们构建了一个包含结构化多层次功能注释的分子-文本配对数据集。不同于传统对比损失,TRIDENT采用基于体积的对齐目标,在全局层面联合对齐三模态特征,实现跨模态的软性、几何感知对齐。此外,引入新颖的局部对齐目标,捕捉分子子结构与其对应子文本描述间的详细关系。基于动量机制的动态平衡策略,使模型同时学习宏观功能语义与微观结构-功能映射。TRIDENT在11个下游任务中取得领先表现,验证了结合SMILES、文本与分类功能注释在分子属性预测中的价值。

原文摘要 · Abstract (English)

Molecular property prediction aims to learn representations that map chemical structures to functional properties. While multimodal learning has emerged as a powerful paradigm to learn molecular representations, prior works have largely overlooked textual and taxonomic information of molecules for representation learning. We introduce TRIDENT, a novel framework that integrates molecular SMILES, textual descriptions, and taxonomic functional annotations to learn rich molecular representations. To achieve this, we curate a comprehensive dataset of molecule-text pairs with structured, multi-level functional annotations. Instead of relying on conventional contrastive loss, TRIDENT employs a volume-based alignment objective to jointly align tri-modal features at the global level, enabling soft, geometry-aware alignment across modalities. Additionally, TRIDENT introduces a novel local alignment objective that captures detailed relationships between molecular substructures and their corresponding sub-textual descriptions. A momentum-based mechanism dynamically balances global and local alignment, enabling the model to learn both broad functional semantics and fine-grained structure-function mappings. TRIDENT achieves state-of-the-art performance on 11 downstream tasks, demonstrating the value of combining SMILES, textual, and taxonomic functional annotations for molecular property prediction.

分子表示多模态学习属性预测

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