arXiv:2409.09702cs.LGcs.AI2024-09被引 8

用原子构建分子,通过低成本属性预训练生成更优药物分子

GFlowNet Pretraining with Inexpensive Rewards

  • 以原子为积木,用无监督预训练探索更广化学空间
  • 利用药物样性、拓扑极表面积等属性作代理奖励,引导生成优质分子
  • 适合药物设计领域研究者,可快速生成符合药理特性的新分子

生成流网络(GFlowNets)是一类新兴生成模型,可通过学习非归一化奖励分布来生成多样且高质量的分子结构。以往工作通常依赖预定义的分子片段作为构建块,限制了可探索的化学空间。本文提出原子生成流网络(A-GFNs),以单个原子为基本构建单元,更全面地探索类药物化学空间。我们采用离线类药物分子数据集进行无监督预训练,将A-GFNs条件化于低成本但信息丰富的分子描述符,如药物样性、拓扑极表面积和合成可及性评分,这些属性作为代理奖励,引导A-GFNs向具有理想药理性质的化学空间区域演化。进一步引入目标条件微调过程,使A-GFNs可针对特定目标属性进行优化。我们在ZINC15离线数据集上预训练A-GFNs,通过稳健评估指标验证方法有效性,结果优于其他相关基线方法。

原文摘要 · Abstract (English)

Generative Flow Networks (GFlowNets), a class of generative models have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from unnormalized reward distributions. Previous works in this direction often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using offline drug-like molecule datasets, which conditions A-GFNs on inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further our method by implementing a goal-conditioned fine-tuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on the ZINC15 offline dataset and employ robust evaluation metrics to show the effectiveness of our approach when compared to other relevant baseline methods in drug design.

分子生成生成模型药物设计无监督学习

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