arXiv:2601.17582q-bio.QMcs.AI2026-01被引 2

用AI自动生成满足特定功能的生物分子网络,省去人工试错。

GenAI-Net: A Generative AI Framework for Automated Biomolecular Network Design

  • AI代理提出反应方案,仿真评估是否达标
  • 可设计出多种逻辑门、振荡器和抗噪声电路
  • 适合合成生物学与系统生物学研究者使用

生物分子网络支撑合成生物学中的新兴技术——从稳健的生物制造与代谢工程,到智能治疗和细胞诊断,并为理解自然与生态系统的复杂动态提供机制语言。然而,设计能实现特定动态功能的化学反应网络(CRNs)仍主要依赖人工:尽管可通过仿真验证提出的网络,但从行为规范反推网络结构则极为困难,需大量人为洞察来探索拓扑结构与动力学参数的巨大空间,且系统具有非线性甚至随机性。本文提出GenAI-Net,一种生成式AI框架,通过将提出反应的智能体与用户定义目标的仿真评估相结合,自动化完成CRN设计。该框架在多种任务中高效生成新颖且拓扑多样的解决方案,包括剂量响应、复杂逻辑门、分类器、振荡器以及确定性与随机性环境下均表现稳定的完美适应性(含噪声抑制)。通过将功能规格转化为电路候选集与可复用的模块,GenAI-Net为可编程生物分子电路设计提供通用路径,加速了从期望功能到可实现机制的转化。

原文摘要 · Abstract (English)

Biomolecular networks underpin emerging technologies in synthetic biology-from robust biomanufacturing and metabolic engineering to smart therapeutics and cell-based diagnostics-and also provide a mechanistic language for understanding complex dynamics in natural and ecological systems. Yet designing chemical reaction networks (CRNs) that implement a desired dynamical function remains largely manual: while a proposed network can be checked by simulation, the reverse problem of discovering a network from a behavioral specification is difficult, requiring substantial human insight to navigate a vast space of topologies and kinetic parameters with nonlinear and possibly stochastic dynamics. Here we introduce GenAI-Net, a generative AI framework that automates CRN design by coupling an agent that proposes reactions to simulation-based evaluation defined by a user-specified objective. GenAI-Net efficiently produces novel, topologically diverse solutions across multiple design tasks, including dose responses, complex logic gates, classifiers, oscillators, and robust perfect adaptation in deterministic and stochastic settings (including noise reduction). By turning specifications into families of circuit candidates and reusable motifs, GenAI-Net provides a general route to programmable biomolecular circuit design and accelerates the translation from desired function to implementable mechanisms.

生成式AI生物网络合成生物学

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