Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks
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arXiv
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| Autores principales: | , , |
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| Formato: | Preprint |
| Publicado: |
2025
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| _version_ | 1866909598275862528 |
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| author | Wang, Xinyu Bi, Jinbo Song, Minghu |
| author_facet | Wang, Xinyu Bi, Jinbo Song, Minghu |
| contents | SMILES-based molecule generation has emerged as a powerful approach in drug discovery. Deep reinforcement learning (RL) using large language model (LLM) has been incorporated into the molecule generation process to achieve high matching score in term of likelihood of desired molecule candidates. However, a critical challenge in this approach is catastrophic forgetting during the RL phase, where knowledge such as molecule validity, which often exceeds 99\% during pretraining, significantly deteriorates. Current RL algorithms applied in drug discovery, such as REINVENT, use prior models as anchors to retian pretraining knowledge, but these methods lack robust exploration mechanisms. To address these issues, we propose Partial SMILES Validation-PPO (PSV-PPO), a novel RL algorithm that incorporates real-time partial SMILES validation to prevent catastrophic forgetting while encouraging exploration. Unlike traditional RL approaches that validate molecule structures only after generating entire sequences, PSV-PPO performs stepwise validation at each auto-regressive step, evaluating not only the selected token candidate but also all potential branches stemming from the prior partial sequence. This enables early detection of invalid partial SMILES across all potential paths. As a result, PSV-PPO maintains high validity rates even during aggressive exploration of the vast chemical space. Our experiments on the PMO and GuacaMol benchmark datasets demonstrate that PSV-PPO significantly reduces the number of invalid generated structures while maintaining competitive exploration and optimization performance. While our work primarily focuses on maintaining validity, the framework of PSV-PPO can be extended in future research to incorporate additional forms of valuable domain knowledge, further enhancing reinforcement learning applications in drug discovery. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_00530 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Wang, Xinyu Bi, Jinbo Song, Minghu Machine Learning Computational Engineering, Finance, and Science Biomolecules SMILES-based molecule generation has emerged as a powerful approach in drug discovery. Deep reinforcement learning (RL) using large language model (LLM) has been incorporated into the molecule generation process to achieve high matching score in term of likelihood of desired molecule candidates. However, a critical challenge in this approach is catastrophic forgetting during the RL phase, where knowledge such as molecule validity, which often exceeds 99\% during pretraining, significantly deteriorates. Current RL algorithms applied in drug discovery, such as REINVENT, use prior models as anchors to retian pretraining knowledge, but these methods lack robust exploration mechanisms. To address these issues, we propose Partial SMILES Validation-PPO (PSV-PPO), a novel RL algorithm that incorporates real-time partial SMILES validation to prevent catastrophic forgetting while encouraging exploration. Unlike traditional RL approaches that validate molecule structures only after generating entire sequences, PSV-PPO performs stepwise validation at each auto-regressive step, evaluating not only the selected token candidate but also all potential branches stemming from the prior partial sequence. This enables early detection of invalid partial SMILES across all potential paths. As a result, PSV-PPO maintains high validity rates even during aggressive exploration of the vast chemical space. Our experiments on the PMO and GuacaMol benchmark datasets demonstrate that PSV-PPO significantly reduces the number of invalid generated structures while maintaining competitive exploration and optimization performance. While our work primarily focuses on maintaining validity, the framework of PSV-PPO can be extended in future research to incorporate additional forms of valuable domain knowledge, further enhancing reinforcement learning applications in drug discovery. |
| title | Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks |
| topic | Machine Learning Computational Engineering, Finance, and Science Biomolecules |
| url | https://arxiv.org/abs/2505.00530 |