arXiv:2602.13419q-bio.QMcs.AI2026-02

用符号逻辑约束大模型,精准保护分子敏感位点,实现可控制的逆合成设计。

Protect$^*$: Steerable Retrosynthesis through Neuro-Symbolic State Encoding

  • 结合55+个SMARTS规则与40+种保护基,用符号逻辑锁定分子危险位点。
  • 在红霉素B等复杂天然产物上验证,成功发现新合成路径且零无效步骤。
  • 支持自动模式与专家干预模式,适合药物研发中需高精度控制的场景。

大语言模型在逆合成任务中展现巨大潜力,但缺乏对复杂化学空间的精细控制能力,易生成无效或不理想的合成路径。本文提出Protect$^*$,一种神经符号框架,将大语言模型的生成能力锚定在严格的化学逻辑之上。该方法融合55+个SMARTS模式和40+种已知保护基的规则推理,通过“自动模式”以符号逻辑确定性地识别并保护反应性位点,或在“人机协同模式”下引入专家战略约束。通过“主动状态追踪”,将硬性符号约束以关联标准原子映射的保护状态注入神经推理过程。在红霉素B等复杂天然产物案例中验证,该方法成功发现新合成路径,实现专家级自主性与可靠性。

原文摘要 · Abstract (English)

Large Language Models (LLMs) have shown remarkable potential in scientific domains like retrosynthesis; yet, they often lack the fine-grained control necessary to navigate complex problem spaces without error. A critical challenge is directing an LLM to avoid specific, chemically sensitive sites on a molecule - a task where unconstrained generation can lead to invalid or undesirable synthetic pathways. In this work, we introduce Protect$^*$, a neuro-symbolic framework that grounds the generative capabilities of Large Language Models (LLMs) in rigorous chemical logic. Our approach combines automated rule-based reasoning - using a comprehensive database of 55+ SMARTS patterns and 40+ characterized protecting groups - with the generative intuition of neural models. The system operates via a hybrid architecture: an ``automatic mode'' where symbolic logic deterministically identifies and guards reactive sites, and a ``human-in-the-loop mode'' that integrates expert strategic constraints. Through ``active state tracking,'' we inject hard symbolic constraints into the neural inference process via a dedicated protection state linked to canonical atom maps. We demonstrate this neuro-symbolic approach through case studies on complex natural products, including the discovery of a novel synthetic pathway for Erythromycin B, showing that grounding neural generation in symbolic logic enables reliable, expert-level autonomy.

逆合成神经符号化学生成可控生成

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