arXiv:2605.05770cs.AI2026-05

用置信度量化不确定性,让生成模型更可靠地设计穿透细胞的环肽。

Confidence is the key: how conformal prediction enhances the generative design of permeable peptides

  • 用基于校准模型的置信区间评估分子预测可靠性
  • 在高置信度下优化生成,使设计效率提升且避免探索不可靠区域
  • 首次结合生成模型与共形预测,适合药物设计领域研究者

结合强化学习(RL)的生成模型如REINVENT和PepINVENT已成为从头分子设计的强大工具。这类框架在构思过程中依赖各类预测模型作为优化目标,但其有效性受限于模型适用范围。当RL探索化学空间时,可能提出超出预测模型适用范围的分子,导致预测可靠性下降,引导设计进入高奖励但高不确定性的化学区域。这在环肽中尤为突出——尽管环肽因可修饰性和大相互作用面具有治疗潜力,但相比小分子研究较少。针对环肽被动膜渗透性设计仍具挑战,对靶向胞内位点至关重要。本文提出一种以不确定性感知渗透性预测器为评分组件的RL引导生成框架。为应对预测不确定性(尤其是新化学结构带来的),引入共形预测(CP)进行不确定性量化。CP在用户设定的置信水平下评估设计结果。实验证明,以CP指导的奖励机制能显著提升肽类优化过程的可靠性与效率,同时抑制探索超出预测器适用范围的区域。该方法首次实现了生成建模与共形预测的融合,弥合了预测不确定性与强化学习探索之间的鸿沟。

原文摘要 · Abstract (English)

Generative models coupled with reinforcement learning (RL), such as REINVENT and PepINVENT, have emerged as a powerful framework for de novo molecular design. During the ideation process these generative frameworks utilize various predictive models as part of the optimization objectives. However, the utility of the predictive models can be limited by their domain of applicability. When RL is used to explore the chemical space with predictive models, it can suggest molecules that lie outside the predictor's domain of applicability. As a result, the predictions may become less reliable, potentially steering designs into high reward but also high uncertainty chemical spaces. This is particularly pronounced for cyclic peptides which show therapeutic promise due to their modifiability and large interaction surfaces but are understudied compared to small molecules. While passive membrane permeation in cyclic peptides has attracted interest, identifying optimal permeable designs remains challenging yet crucial for targeting intracellular sites. We present an RL-guided generative framework that designs permeable cyclic peptides using an uncertainty-aware permeability predictor as the scoring component. To address predictive uncertainty, especially impacted by novel chemistry, we integrate conformal prediction (CP) as our uncertainty quantification method. CP assesses designs based on the calibrated model under a user-defined confidence level. We demonstrate that rewarding generated peptides with CP-informed predictions improves both reliability and efficiency of peptide optimization process. This also discourages exploration outside the predictor's applicability domain. This approach bridges the gap between predictive uncertainty and RL-guided exploration, showing how generative modelling and conformal prediction can be combined for the first time.

生成设计环肽不确定性量化强化学习

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