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Efficient Moment Matrix Generation for Arbitrary Chemical Networks

机译:任意化学网络的有效时刻矩阵生成

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摘要

As stochastic simulations become increasingly common in biological research, tools for analysis of such systems are in demand. The deterministic analogue to stochastic models, a set of probability moment equations equivalent to the Chemical Master Equation (CME), offers the possibility of a priori analysis of systems without the need for computationally costly Monte Carlo simulations. Despite the drawbacks of the method, in particular non-linearity in even the simplest of cases, the use of moment equations combined with moment-closure techniques has been used effectively in many fields. The techniques currently available to generate moment equations rely upon analytical expressions that are not efficient upon scaling. Additionally, the resulting moment-dependent matrix is lower diagonal and demands massive memory allocation in extreme cases. Here it is demonstrated that by utilizing factorial moments and the probability generating function (the Z-transform of the probability distribution) a recursive algorithm is produced. The resulting method is scalable and particularly efficient when high-order moments are required. The matrix produced is banded and often demands substantially less memory resources.
机译:随着随机模拟在生物学研究中变得越来越普遍,需要用于分析此类系统的工具。随机模型的确定性类似物(一组等效于化学主方程(CME)的概率矩方程)为系统进行先验分析提供了可能,而无需进行计算上昂贵的蒙特卡洛模拟。尽管存在该方法的缺点,尤其是在最简单的情况下还是非线性的,但在许多领域中,有效地结合使用了力矩方程和力矩闭合技术。当前可用于生成力矩方程的技术依赖于在缩放时效率不高的解析表达式。另外,所得的矩相关矩阵较低的对角线,在极端情况下需要大量的内存分配。在此证明,通过利用阶乘矩和概率生成函数(概率分布的Z变换),可以生成递归算法。当需要高阶矩时,所得方法是可扩展的,并且特别有效。产生的矩阵是带状的,通常需要的存储资源要少得多。

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