Enhancing Molecular Property Prediction with Knowledge from Large Language Models

• URL: http://arxiv.org/abs/2509.20664v1
• Date: Thu, 25 Sep 2025 01:48:54 GMT
• Title: Enhancing Molecular Property Prediction with Knowledge from Large Language Models
• Authors: Peng Zhou, Lai Hou Tim, Zhixiang Cheng, Kun Xie, Chaoyi Li, Wei Liu, Xiangxiang Zeng,
• Abstract summary: We propose a novel framework that integrates knowledge extracted from large language models with structural features derived from pre-trained molecular models to enhance molecular property prediction.<n>Our approach prompts LLMs to generate both domain-relevant knowledge and executable code for molecular vectorization, producing knowledge-based features that are subsequently fused with structural representations.
• Score: 15.273538257961905
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Predicting molecular properties is a critical component of drug discovery. Recent advances in deep learning, particularly Graph Neural Networks (GNNs), have enabled end-to-end learning from molecular structures, reducing reliance on manual feature engineering. However, while GNNs and self-supervised learning approaches have advanced molecular property prediction (MPP), the integration of human prior knowledge remains indispensable, as evidenced by recent methods that leverage large language models (LLMs) for knowledge extraction. Despite their strengths, LLMs are constrained by knowledge gaps and hallucinations, particularly for less-studied molecular properties. In this work, we propose a novel framework that, for the first time, integrates knowledge extracted from LLMs with structural features derived from pre-trained molecular models to enhance MPP. Our approach prompts LLMs to generate both domain-relevant knowledge and executable code for molecular vectorization, producing knowledge-based features that are subsequently fused with structural representations. We employ three state-of-the-art LLMs, GPT-4o, GPT-4.1, and DeepSeek-R1, for knowledge extraction. Extensive experiments demonstrate that our integrated method outperforms existing approaches, confirming that the combination of LLM-derived knowledge and structural information provides a robust and effective solution for MPP.

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