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The accounting of noise to solve the problem of negative populations in approximate accelerated stochastic simulations

机译:近似加速随机模拟中用于解决负种群问题的噪声计算

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The advent of different approximate accelerated stochastic simulation methods has helped considerably in reducing the computational load of the exact simulation algorithms. However, along with the reduction in the computational load comes the risk of driving the molecular numbers to the regime of negative numbers during the simulations. Over the years, various methods have been developed in order to solve the problem by using different strategies. Some methods have employed binomial numbers to model the reactions, while others have tried the partitioning of the reaction network. In this manuscript, we have proposed a new approach where the noise inherent in the choice of the number of firings of a given reaction during a time step is taken into account. This idea of noise accounting is used in conjunction with the accelerated stochastic method: the Representative Reaction Approach (RRA). It is found that the new method is successful at solving the problem of negative numbers, and compares very favorably with other state-of-the-art stochastic simulation methods.
机译:不同近似加速随机仿真方法的出现极大地帮助减少了精确仿真算法的计算量。但是,随着计算量的减少,在模拟过程中有将分子数驱动为负数的风险。多年来,为了使用不同的策略解决问题,已经开发了各种方法。一些方法采用二项式数来模拟反应,而另一些方法则尝试对反应网络进行分区。在本手稿中,我们提出了一种新方法,其中考虑了在时间步长中选择给定反应的点火次数所固有的噪声。这种噪声核算的思想与加速随机方法:代表性反应方法(RRA)结合使用。发现该新方法成功地解决了负数问题,并且与其他最新的随机模拟方法相比非常有利。

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