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Improved statistical model checking methods for pathway analysis

机译:改进的用于路径分析的统计模型检查方法

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摘要

Statistical model checking techniques have been shown to be effective for approximate model checking on large stochastic systems, where explicit representation of the state space is impractical. Importantly, these techniques ensure the validity of results with statistical guarantees on errors. There is an increasing interest in these classes of algorithms in computational systems biology since analysis using traditional model checking techniques does not scale well. In this context, we present two improvements to existing statistical model checking algorithms. Firstly, we construct an algorithm which removes the need of the user to define the indifference region, a critical parameter in previous sequential hypothesis testing algorithms. Secondly, we extend the algorithm to account for the case when there may be a limit on the computational resources that can be spent on verifying a property; i.e, if the original algorithm is not able to make a decision even after consuming the available amount of resources, we resort to a p-value based approach to make a decision. We demonstrate the improvements achieved by our algorithms in comparison to current algorithms first with a straightforward yet representative example, followed by a real biological model on cell fate of gustatory neurons with microRNAs.
机译:统计模型检查技术已被证明对于大型随机系统中的近似模型检查有效,在这种情况下,状态空间的显式表示是不可行的。重要的是,这些技术通过对错误的统计保证来确保结果的有效性。由于使用传统的模型检查技术进行的分析不能很好地扩展,因此在计算系统生物学中对这些算法类别的兴趣日益增加。在这种情况下,我们提出了对现有统计模型检查算法的两项改进。首先,我们构造了一种算法,该算法无需用户定义无差异区域,而无差异区域是先前顺序假设检验算法中的关键参数。其次,我们扩展算法以解决可能用于验证属性的计算资源有限的情况;也就是说,如果即使在消耗了可用资源量之后原始算法仍无法做出决定,则我们采用基于p值的方法来做出决定。我们首先通过一个简单而又具有代表性的示例证明与当前算法相比,我们的算法所实现的改进,然后是带有microRNA的味觉神经元细胞命运的真实生物学模型。

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