论文标题
监管网络动力学的全球分析:平衡和鞍节分叉
Global analysis of regulatory network dynamics: equilibria and saddle-node bifurcations
论文作者
论文摘要
在本文中,我们描述了一种组合组合/数值方法,用于研究系统生物学中引起的网络模型中的平衡和分叉。动力学的ODE模型具有高维参数,这对通过数值方法研究全局动力学有很大的阻塞。本文的重点是证明,尽管参数维度很高,但适应和结合经典技术与最近开发的组合方法为全局动力学提供了更丰富的图像。 给定一个网络拓扑,描述了通过单调和有限函数相互调节的状态变量,我们首先使用由调节网络}(DSGRN)软件生成的{\ em动态签名来获得动力学的组合摘要。该摘要很粗糙,但全球性,我们将此信息用作第一个通过,以识别``有趣''的参数子集。我们使用我们的{\ em网络动力学建模和分析}(NDMA)Python库构建具有高参数维度的相关ode模型。我们介绍了算法,以有效研究限于这些参数子集的这些ODE模型中的动力学。最后,我们对该方法和几个有趣的动态应用程序进行统计验证,包括在$ 54 $参数模型中找到鞍节分叉。
In this paper we describe a combined combinatorial/numerical approach to studying equilibria and bifurcations in network models arising in Systems Biology. ODE models of the dynamics suffer from high dimensional parameters which presents a significant obstruction to studying the global dynamics via numerical methods. The main point of this paper is to demonstrate that adapting and combining classical techniques with recently developed combinatorial methods provides a richer picture of the global dynamics despite the high parameter dimension. Given a network topology describing state variables which regulate one another via monotone and bounded functions, we first use the {\em Dynamic Signatures Generated by Regulatory Networks} (DSGRN) software to obtain a combinatorial summary of the dynamics. This summary is coarse but global and we use this information as a first pass to identify ``interesting'' subsets of parameters in which to focus. We construct an associated ODE model with high parameter dimension using our {\em Network Dynamics Modeling and Analysis} (NDMA) Python library. We introduce algorithms for efficiently investigating the dynamics in these ODE models restricted to these parameter subsets. Finally, we perform a statistical validation of the method and several interesting dynamical applications including finding saddle-node bifurcations in a $54$ parameter model.