论文标题

在单体上最小化动力学系统

Minimization of Dynamical Systems over Monoids

论文作者

Argyris, Georgios, Lafuente, Alberto Lluch, Robayo, Alexander Leguizamon, Tribastone, Mirco, Tschaikowski, Max, Vandin, Andrea

论文摘要

分合的定量概念是最大程度地限制动态模型(例如马尔可夫链和普通微分方程(ODES))的众所周知的工具。在\ emph {forward bisimulations}中,商模型中的每个状态代表等效类别,动态演化给出了原始模型中其成员的总和。在这里,我们在交换性单体上引入了用于动力学系统的广义前向分配(GFB),并开发了一种分区改进算法来计算最粗糙的算法。当monoid为$(\ mathbb {r}, +)$时,我们恢复了马尔可夫链的概率分配,而非线性ODE的最新前向双示例。使用$(\ mathbb {r},\ cdot)$,我们获得了离散时间动态系统和ODE的非线性减少,其中商模型中的每个变量代表等价类中原始变量的乘积。当域是一个有限的集合时,例如布尔值$ \ mathbb {b} $,我们可以将GFB应用于布尔网络(BN),这是一种在计算生物学中广泛使用的动力学模型。使用我们对GFB的最小化算法的原型实现,我们发现从两个众所周知的存储库中的60亿美元降低了分离和连接性,并证明了所获得的分析加速。我们还提供了对两个选定的BN获得的还原的生物学解释,并展示了GFB如何实现对否则无法分析的大型大型分析。使用算法的随机版本,我们发现从文献中无法通过精确算法来处理的21个动态加权网络上的21个动态加权网络上的产品保护(因此是非线性)。

Quantitative notions of bisimulation are well-known tools for the minimization of dynamical models such as Markov chains and ordinary differential equations (ODEs). In \emph{forward bisimulations}, each state in the quotient model represents an equivalence class and the dynamical evolution gives the overall sum of its members in the original model. Here we introduce generalized forward bisimulation (GFB) for dynamical systems over commutative monoids and develop a partition refinement algorithm to compute the coarsest one. When the monoid is $(\mathbb{R}, +)$, we recover probabilistic bisimulation for Markov chains and more recent forward bisimulations for nonlinear ODEs. Using $(\mathbb{R}, \cdot)$ we get nonlinear reductions for discrete-time dynamical systems and ODEs where each variable in the quotient model represents the product of original variables in the equivalence class. When the domain is a finite set such as the Booleans $\mathbb{B}$, we can apply GFB to Boolean networks (BN), a widely used dynamical model in computational biology. Using a prototype implementation of our minimization algorithm for GFB, we find disjunction- and conjunction-preserving reductions on 60 BN from two well-known repositories, and demonstrate the obtained analysis speed-ups. We also provide the biological interpretation of the reduction obtained for two selected BN, and we show how GFB enables the analysis of a large one that could not be analyzed otherwise. Using a randomized version of our algorithm we find product-preserving (therefore non-linear) reductions on 21 dynamical weighted networks from the literature that could not be handled by the exact algorithm.

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