arXiv:2607.03007cs.LGcs.AI2026-07

让大模型先学懂分子结构,再做推理。

Back to Basics: Improving Molecular Understanding in LLMs via SMILES-Graph Translation

论文配图:Back to Basics: Improving Molecular Understanding in LLMs via SMILES-Graph Translation
图 1 · 摘自论文原文
  • 用SMILES与分子图双向转换强化结构理解
  • 在属性预测和目标优化任务上显著提升性能
  • 适合需要可靠化学结构认知的药物研发人群

近年来,分子大语言模型在分子理解与生成任务上表现优异,但往往缺乏可靠的结构基础。现有方法违背了‘结构决定功能’的化学原则:尽管下游任务表现良好,但在基本结构识别上仍表现不佳,表明其未能从标准SMILES中有效捕捉分子图。为此,我们提出MolBasic,一种以结构为核心的框架,通过SMILES-图转换强化结构感知。该框架基于多层级结构感知评测体系,以双向SMILES-图转换为核心任务,对齐序列与拓扑表示。在此基础上,采用标准化链式思维(CoT)的渐进式学习策略,引导模型从结构获取逐步迈向高级分子推理。实验表明,MolBasic显著提升了结构理解能力,并在属性预测与目标优化等下游任务中取得稳健增益,验证了结构优先范式的有效性。

原文摘要 · Abstract (English)

Recent advances in molecular large language models have led to strong performance on molecular understanding and generation tasks, yet these gains often come without reliable structural grounding. In particular, existing approaches conflict with the chemistry principle that structure determines function: despite their downstream success, current molecular LLMs perform poorly on basic structure recognition, suggesting that they fail to capture molecular graphs from canonical SMILES. To remedy this, we propose MolBasic, a structure-first framework that strengthens structural comprehension via SMILES-Graph translation. MolBasic is built around a multi-level structure perception benchmark, where bidirectional SMILES-Graph conversion serves as the core task to align sequential and topological representations. On top of this foundation, we employ a progressive learning scheme with a standardized Chain-of-Thought (CoT) to steer models from structure acquisition toward higher-level molecular reasoning. Experiments show that MolBasic substantially improves structural understanding and yields robust gains on downstream tasks, including property prediction and objective optimization, supporting our structure-first paradigm.

分子建模结构理解LLM

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