让大模型像化学家一样推理分子性质,提升预测准确率与可解释性。
Reasoning-Enhanced Large Language Models for Molecular Property Prediction
- 融合分子图像与SMILES字符串,用两阶段训练强化化学推理能力。
- 在8个数据集上比最优基线提升7.91%(分布内)和4.53%(分布外)。
- 生成符合化学原理的推理路径,适合药物研发与材料设计人员使用。
分子性质预测对药物发现与材料科学至关重要,但现有方法普遍存在可解释性差、跨任务泛化能力弱及缺乏化学推理能力的问题。传统机器学习模型难以实现任务迁移,而专用分子语言模型又缺乏决策过程透明度。为此,我们提出MPPReasoner,一种基于Qwen2.5-VL-7B-Instruct的多模态大语言模型,通过结合分子图像与SMILES字符串实现全面的分子理解。采用两阶段训练策略:首先利用16,000条高质量推理轨迹进行监督微调(SFT),这些轨迹由专家知识与多个教师模型生成;随后引入基于原则引导奖励的强化学习(RLPGR),通过可验证的规则化奖励系统,对化学原理应用、分子结构分析与逻辑一致性进行计算验证。在8个数据集上的大量实验表明,MPPReasoner在分布内任务上优于最佳基线7.91%,在分布外任务上提升4.53%。该模型展现出优异的跨任务泛化能力,并生成符合化学常识的推理路径,显著增强预测结果的可解释性与实际应用价值。代码已公开于https://anonymous.4open.science/r/MPPReasoner-12687。
原文摘要 · Abstract (English)
Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional machine learning models struggle with task transferability, while specialized molecular language models provide little insight into their decision-making processes. To address these limitations, we propose \textbf{MPPReasoner}, a multimodal large language model that incorporates chemical reasoning for molecular property prediction. Our approach, built upon Qwen2.5-VL-7B-Instruct, integrates molecular images with SMILES strings to enable comprehensive molecular understanding. We develop a two-stage training strategy: supervised fine-tuning (SFT) using 16,000 high-quality reasoning trajectories generated through expert knowledge and multiple teacher models, followed by Reinforcement Learning from Principle-Guided Rewards (RLPGR). RLPGR employs verifiable, rule-based rewards that systematically evaluate chemical principle application, molecular structure analysis, and logical consistency through computational verification. Extensive experiments across 8 datasets demonstrate significant performance improvements, with MPPReasoner outperforming the best baselines by 7.91\% and 4.53\% on in-distribution and out-of-distribution tasks respectively. MPPReasoner exhibits exceptional cross-task generalization and generates chemically sound reasoning paths that provide valuable insights into molecular property analysis, substantially enhancing both interpretability and practical utility for chemists. Code is available at https://anonymous.4open.science/r/MPPReasoner-12687.
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