arXiv:2505.00530cs.LGcs.CE2025-05被引 3

用分步验证提升药物生成中的分子有效性,防止强化学习遗忘

Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks

  • 在每步生成时实时校验部分SMILES结构,提前发现无效路径
  • 在PMO和GuacaMol数据集上无效分子数减少超90%,有效性保持在99%以上
  • 适合需要高化学合理性生成的药物发现场景,尤其适合强化学习框架

基于SMILES的分子生成已成为药物发现的重要方法。利用大语言模型的深度强化学习(RL)已被引入分子生成过程,以提高目标分子候选物的生成概率匹配度。然而,该方法在强化学习阶段面临灾难性遗忘问题:预训练中超过99%的分子有效性在训练过程中显著下降。现有算法如REINVENT虽使用先验模型作为锚点以保留知识,但缺乏有效的探索机制。为此,我们提出部分SMILES验证-近端策略优化(PSV-PPO),一种新型强化学习算法,通过实时分步验证防止灾难性遗忘并促进探索。与传统方法仅在完整序列生成后验证不同,PSV-PPO在每个自回归步骤进行验证,不仅评估当前候选符号,还检查从先前部分序列延伸出的所有可能分支。这使得能在所有潜在路径中早期检测无效的局部结构。实验结果表明,在PMO和GuacaMol基准数据集上,PSV-PPO显著减少了无效生成结构数量,同时保持了良好的探索与优化性能。尽管本工作聚焦于维持有效性,该框架未来可扩展以融入更多领域知识,进一步推动强化学习在药物发现中的应用。

原文摘要 · Abstract (English)

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.

分子生成强化学习药物设计SMILES

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