arXiv:2410.11527q-bio.BMcs.LG2024-10

提出TANGO奖励函数,直接优化分子合成可行性与药物属性。

It Takes Two to Tango: Directly Optimizing for Constrained Synthesizability in Generative Molecular Design

  • 设计TANGO奖励函数,将稀疏奖励转化为可学习的密集奖励。
  • 模型在无需先验偏见下,同时优化合成约束与药物属性。
  • 首次实现对起始原料、中间体等合成约束的生成式优化。

受限合成性是生成式分子设计中未被充分解决的挑战。尤其在同时满足多目标优化、分子可合成性及特定商业化构件存在的条件下进行分子设计,对分子再利用、可持续性和效率具有重要意义。本文提出一种新型奖励函数TANimoto Group Overlap(TANGO),基于化学原理将稀疏奖励转换为密集且可学习的奖励,这对强化学习至关重要。TANGO可增强通用分子生成模型,在强化学习框架下直接优化受限合成性,同时兼顾药物发现中的其他相关性质。该框架具备普适性,能处理起始物料、中间体和发散合成等多种约束。与多数现有工作不同,我们证明在无任何归纳偏置的通用模型上激励其学习是解决复杂优化问题的有效路径。实验表明,训练后的模型显式学习到了理想的分布。本框架是首个针对受限合成性开展生成式研究的方法。

原文摘要 · Abstract (English)

Constrained synthesizability is an unaddressed challenge in generative molecular design. In particular, designing molecules satisfying multi-parameter optimization objectives, while simultaneously being synthesizable and enforcing the presence of specific commercial building blocks in the synthesis. This is practically important for molecule re-purposing, sustainability, and efficiency. In this work, we propose a novel reward function called TANimoto Group Overlap (TANGO), which uses chemistry principles to transform a sparse reward function into a dense and learnable reward function -- crucial for reinforcement learning. TANGO can augment general-purpose molecular generative models to directly optimize for constrained synthesizability while simultaneously optimizing for other properties relevant to drug discovery using reinforcement learning. Our framework is general and addresses starting-material, intermediate, and divergent synthesis constraints. Contrary to most existing works in the field, we show that incentivizing a general-purpose (without any inductive biases) model is a productive approach to navigating challenging optimization scenarios. We demonstrate this by showing that the trained models explicitly learn a desirable distribution. Our framework is the first generative approach to tackle constrained synthesizability.

分子生成强化学习合成可行药物发现

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