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

• URL: http://arxiv.org/abs/2507.02932v1
• Date: Thu, 26 Jun 2025 12:51:59 GMT
• Title: MolProphecy: Bridging Medicinal Chemists' Knowledge and Molecular Pre-Trained Models via a Multi-Modal Framework
• Authors: Jianping Zhao, Qiong Zhou, Tian Wang, Yusi Fan, Qian Yang, Li Jiao, Chang Liu, Zhehao Guo, Qi Lu, Fengfeng Zhou, Ruochi Zhang,
• Abstract summary: MolProphecy is a framework to integrate chemists' domain knowledge into molecular property prediction models.<n>ChatGPT is a virtual chemist to simulate expert-level reasoning and decision-making.<n>MolProphecy outperforms state-of-the-art (SOTA) models on four benchmark datasets.
• Score: 21.677162643535826
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: 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.

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