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arXiv 2004.01259cs.DMmath.CO
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由正反馈顶点集求布尔网络的不动点

Finding the fixed points of a Boolean network from a positive feedback vertex set

Julio Aracena, Luis Cabreras-Crot, Lilian Salinas

摘要:

在用布尔网络对生物系统建模时,一个关键问题是求出给定网络的不动点集。一些构造的算法考虑了交互图的某些结构性质,如Akutsu等人在\cite{akutsu1998system,zhang2007algorithms}中提出的那些,其考虑了图的反馈顶点集。然而,这些方法没有考虑到其组分之间的作用类型(激活、抑制)。本文提出了一种新的算法来寻找一个布尔网络的不动点集,基于其交互图的正反馈顶点集$P$,它的工作原理,通过应用一个顺序的更新计划,在时间$O(2^{|P|} \cdot n^2)$,其中$n$是组件的数量。该算法的理论基础是我们对无正圈且有不动点的布尔网络的动力学行为给出了一个很好的刻画。用Java制作的\Afp可执行文件和一些输入文件示例可在以下网址获得:\href{http://www.inf.udec.cl/~lilian/FPCollector/}{\url{www.inf.udec.cl/~lilian/FPCollector/}}

英文摘要:

In the modeling of biological systems by Boolean networks a key problem is finding the set of fixed points of a given network. Some constructed algorithms consider certain structural properties of the interaction graph like those proposed by Akutsu et al. in \cite{akutsu1998system,zhang2007algorithms} which consider a feedback vertex set of the graph. However, these methods do not take into account the type of action (activation, inhibition) between its components. In this paper we propose a new algorithm for finding the set of fixed points of a Boolean network, based on a positive feedback vertex set $P$ of its interaction graph and which works, by applying a sequential update schedule, in time $O(2^{|P|} \cdot n^2)$, where $n$ is the number of components. The theoretical foundation of this algorithm is due a nice characterization, that we give, of the dynamical behavior of the Boolean networks without positive cycles and with a fixed point. An executable file of \Afp made in Java and some examples of input files are available at: \href{http://www.inf.udec.cl/~lilian/FPCollector/}{\url{www.inf.udec.cl/~lilian/FPCollector/}}

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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