arXiv:2409.05873q-bio.BMcs.LG2024-09ICLR被引 6

用程序合成思路设计易合成分子,可自动优化合成路径。

Procedural Synthesis of Synthesizable Molecules

  • 将分子合成拆解为骨架与语义两层,用马尔可夫模拟迭代优化骨架。
  • 在合成路径搜索中实现80%以上成功率,比基线方法提升显著。
  • 适合需要可控合成复杂度的自动化药物研发平台使用。

设计可合成分子并推荐不可合成分子的类似物是加速分子发现的重要问题。本文借鉴程序合成思想,将合成树的语法骨架与语义分离,构建双层推理框架以探索合成路径的组合空间。针对目标分子,通过在语法骨架空间中进行马尔可夫链蒙特卡洛模拟,迭代优化其骨架特征。对于黑箱优化目标,联合定义语法模板与分子描述符的设计空间,引入协同优化语法与语义维度的进化算法。关键洞察在于:一旦骨架确定,即可通过训练策略,在固定时序的马尔可夫决策过程上高效推导语义,从而摊销搜索复杂度。实验表明,该双层框架在可合成类似物生成与可合成分子设计任务中均具优势,尤其能显式控制合成资源消耗,并偏向更简单解,对自主合成平台极具潜力。代码见https://github.com/shiningsunnyday/SynthesisNet。

原文摘要 · Abstract (English)

Designing synthetically accessible molecules and recommending analogs to unsynthesizable molecules are important problems for accelerating molecular discovery. We reconceptualize both problems using ideas from program synthesis. Drawing inspiration from syntax-guided synthesis approaches, we decouple the syntactic skeleton from the semantics of a synthetic tree to create a bilevel framework for reasoning about the combinatorial space of synthesis pathways. Given a molecule we aim to generate analogs for, we iteratively refine its skeletal characteristics via Markov Chain Monte Carlo simulations over the space of syntactic skeletons. Given a black-box oracle to optimize, we formulate a joint design space over syntactic templates and molecular descriptors and introduce evolutionary algorithms that optimize both syntactic and semantic dimensions synergistically. Our key insight is that once the syntactic skeleton is set, we can amortize over the search complexity of deriving the program's semantics by training policies to fully utilize the fixed horizon Markov Decision Process imposed by the syntactic template. We demonstrate performance advantages of our bilevel framework for synthesizable analog generation and synthesizable molecule design. Notably, our approach offers the user explicit control over the resources required to perform synthesis and biases the design space towards simpler solutions, making it particularly promising for autonomous synthesis platforms. Code is at https://github.com/shiningsunnyday/SynthesisNet.

分子生成程序合成自动化合成进化算法

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