arXiv:2507.02932cs.LGcs.AI2025-07被引 2

让AI模拟化学家思考,提升分子性质预测的准确与可解释性。

MolProphecy: Bridging Medicinal Chemists' Knowledge and Molecular Pre-Trained Models via a Multi-Modal Framework

  • 用大模型模拟化学家推理,生成可融入模型的知识表示。
  • 在四个数据集上显著优于现有模型,最高降15%误差、提5.39%准确率。
  • 支持真实化学家输入,无需重训练,适合药物研发协作场景。

MolProphecy 是一个以人为本的多模态框架,旨在将化学家的领域知识融入分子性质预测模型。尽管预训练分子模型已大幅提升预测精度,但难以捕捉专家设计中的隐性、解释性推理。为此,MolProphecy 采用 ChatGPT 作为虚拟化学家,模拟专家级推理与决策。生成的化学知识由大语言模型(LLM)编码为专用知识表示,并通过门控交叉注意力机制与基于图的分子特征融合,实现对人类知识与结构特征的联合推理。在 FreeSolv、BACE、SIDER 与 ClinTox 四个基准数据集上评估,MolProphecy 超越现有最先进(SOTA)模型:在 FreeSolv 上降低 15.0% 的 RMSE,BACE 上提升 5.39% 的 AUROC。分析表明,化学家知识与结构特征具有互补作用,同时提升准确率与可解释性。该框架提供一种可复用的协同药物发现方案,支持以真实化学家输入替换当前模拟代理,且无需重新训练。代码已开源:https://github.com/zhangruochi/MolProphecy。

原文摘要 · Abstract (English)

MolProphecy is a human-in-the-loop (HITL) multi-modal framework designed to integrate chemists' domain knowledge into molecular property prediction models. While molecular pre-trained models have enabled significant gains in predictive accuracy, they often fail to capture the tacit, interpretive reasoning central to expert-driven molecular design. To address this, MolProphecy employs ChatGPT as a virtual chemist to simulate expert-level reasoning and decision-making. The generated chemist knowledge is embedded by the large language model (LLM) as a dedicated knowledge representation and then fused with graph-based molecular features through a gated cross-attention mechanism, enabling joint reasoning over human-derived and structural features. Evaluated on four benchmark datasets (FreeSolv, BACE, SIDER, and ClinTox), MolProphecy outperforms state-of-the-art (SOTA) models, achieving a 15.0 percent reduction in RMSE on FreeSolv and a 5.39 percent improvement in AUROC on BACE. Analysis reveals that chemist knowledge and structural features provide complementary contributions, improving both accuracy and interpretability. MolProphecy offers a practical and generalizable approach for collaborative drug discovery, with the flexibility to incorporate real chemist input in place of the current simulated proxy--without the need for model retraining. The implementation is publicly available at https://github.com/zhangruochi/MolProphecy.

分子建模人机协作知识融合药物发现

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