基于动态网络子图行为分析的布尔网络简化方法
Reducing Boolean Networks via Analysis of Dynamic Network Subgraph Behavior
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中文总结 AI 辅助
本研究通过枚举两节点布尔子图并刻画其同步与异步状态转移图，提出基于行为的网络分类框架，开发 BORNA 工具，为简化布尔网络动力学及扩展调控系统分析提供基础。
中文摘要 AI 辅助
布尔网络为调控系统建模提供了紧凑框架，但其快速扩张的状态空间使系统动力学分析颇具挑战性。本研究系统枚举所有非同构的两节点符号调控子图及其可容许的布尔更新规则，并详尽刻画其在同步与异步更新下的状态转移图（STG）。通过提取定量动力学描述符，研究从静态 wiring diagram（接线图）转向基于行为的网络结构分类：同步分析识别出确定性不动点与循环吸引子 regime（ regime 译为“状态域”），异步分析则通过异步 STG 的终端强连通分量捕捉单节点更新的动力学行为；对比两种更新方案可区分在不同更新假设下均稳健的动力学行为与依赖同步更新的行为。尽管图-规则组合具有多样性，诸多实现却收敛至有限的动力学类别，揭示结构与动力学表示间存在大量冗余。研究进一步提出可检验框架，探究此类局部动力学类别是否可用于表征大型布尔模型中的选定子网络；为便于探索与复现，开发了交互式网络应用 BORNA，可用于探索完整网络目录、STG 及同步与异步模拟，网址为 this https URL。上述结果为最小布尔网络动力学提供了系统参考，并为将基于行为的分析扩展至更大调控系统奠定了基础。
英文摘要
Boolean networks provide a compact framework for modeling regulatory systems, yet their rapidly expanding state spaces make systematic dynamical analysis challenging. Here, we systematically enumerate all non-isomorphic two-node signed regulatory subgraphs with their admissible Boolean update rules and exhaustively characterize their state-transition graphs (STGs) under both synchronous and asynchronous updating. By extracting quantitative dynamical descriptors, we move beyond static wiring diagrams toward a behavior-based classification of network structures. The synchronous analysis identifies deterministic fixed-point and cyclic attractor regimes, while the asynchronous analysis captures one-node-at-a-time dynamics through terminal strongly connected components of the asynchronous STGs. Comparing the two update schemes distinguishes dynamical behaviors that are robust across update assumptions from those that depend on synchronous updating. Despite the diversity of graph-rule combinations, many realizations converge to a limited repertoire of dynamical classes, revealing substantial redundancy between structural and dynamical representations. We further propose a testable framework for investigating whether such local dynamical classes can be used to characterize selected subnetworks within larger Boolean models. To facilitate exploration and reproducibility, we developed BORNA, an interactive web application for exploring the complete network catalogue, STGs, and synchronous and asynchronous simulations, available at https://jafarilab.github.io/BORNA/. Together, these results provide a systematic reference for minimal Boolean network dynamics and a foundation for extending behavior-based analysis to larger regulatory systems.
