arXiv:2606.29776cs.LGcs.AI2026-06

用大模型打造可解释的分子结构解析代理,解决未知分子难判断难题

Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent

论文配图:Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent
图 1 · 摘自论文原文
  • 基于大模型与化学知识图谱,模拟专家推理流程逐步推导结构
  • 在含新骨架测试集上准确率提升46.5%,相似度提高0.502
  • 适合天然产物结构鉴定与文献结构纠错,结果透明可验证

核磁共振(NMR)光谱是分子结构解析的金标准,但对未知分子的复杂谱图解读仍依赖人工经验。现有方法存在明显权衡:数据库检索无法识别新骨架,而从头生成模型为黑箱,缺乏原子级可解释性。本文提出NMRAgent,一种由大语言模型驱动的证据推理代理,融合专用谱图分析工具与化学知识图谱。它以实验NMR谱图和分子式为输入,规划解析流程,提出候选结构,验证峰-原子一致性,并通过公式感知的片段优化修正错误子结构。得益于其证据推理能力,NMRAgent在包含新骨架的分架基准测试中,顶1准确率提升46.5%,Tanimoto相似度达0.502。我们还成功解析了来自Hydrangea davidii和Vitex trifolia的两种未知天然产物结构,并纠正了文献中的结构误标。通过高精度预测与透明证据链结合,NMRAgent为分析化学中的可解释人工智能树立了新范式。

原文摘要 · Abstract (English)

Nuclear Magnetic Resonance (NMR) spectroscopy is the gold standard for molecular structure elucidation, yet interpreting complex spectra for unknown molecules remains a bottleneck reliant on human expertise. While artificial intelligence has advanced this field, current methods face a critical trade-off: database retrieval cannot identify novel scaffolds, while de novo molecular structure elucidation models operate as black boxes, lacking the atom-level interpretability required for rigorous scientific validation. Here, we present NMRAgent, an evidential reasoning agent powered by large language models (LLMs) that bridges this gap by integrating specialized spectral analysis tools with chemical knowledge graphs. Unlike previous approaches, NMRAgent mimics the deductive reasoning of human experts: it takes experimental NMR spectra and molecular formula as input, plans the elucidation process, proposes candidate structures, verifies peak-atom consistency, and refines misaligned substructure through formula-aware fragment optimization. Enabled by its evidential reasoning, NMRAgent outperforms state-of-the-art methods, improving top-1 accuracy by 46.5% and Tanimoto similarity by 0.502 on a scaffold-split benchmark with novel scaffolds in the test set. Besides, we demonstrate the agent's practical utility by elucidating the structures of two previously unknown natural products isolated from Hydrangea davidii and Vitex trifolia, and by correcting structural misassignments in established literature. By combining high-accuracy prediction with transparent and evidence-based reasoning, NMRAgent establishes a new paradigm for interpretable AI in analytical chemistry.

分子结构大模型可解释性核磁共振

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