Reasoning-Enhanced Large Language Models for Molecular Property Prediction
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| Main Authors: | , , , , , , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866911216069246976 |
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| author | Zhuang, Jiaxi Shi, Yaorui Hou, Jue He, Yunong Ye, Mingwei Xu, Mingjun Su, Yuming Zhang, Linfeng Qian, Ying Zhang, Linfeng Ke, Guolin Cai, Hengxing |
| author_facet | Zhuang, Jiaxi Shi, Yaorui Hou, Jue He, Yunong Ye, Mingwei Xu, Mingjun Su, Yuming Zhang, Linfeng Qian, Ying Zhang, Linfeng Ke, Guolin Cai, Hengxing |
| contents | 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. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2510_10248 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Reasoning-Enhanced Large Language Models for Molecular Property Prediction Zhuang, Jiaxi Shi, Yaorui Hou, Jue He, Yunong Ye, Mingwei Xu, Mingjun Su, Yuming Zhang, Linfeng Qian, Ying Zhang, Linfeng Ke, Guolin Cai, Hengxing Machine Learning Artificial Intelligence 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. |
| title | Reasoning-Enhanced Large Language Models for Molecular Property Prediction |
| topic | Machine Learning Artificial Intelligence |
| url | https://arxiv.org/abs/2510.10248 |