论文标题

先验可识别性分析的基准测试工具

Benchmarking tools for a priori identifiability analysis

论文作者

Barreiro, Xabier Rey, Villaverde, Alejandro F.

论文摘要

模型的结构可识别性和可观察性通过观察其输出来推断其参数和状态的可能性。这些属性应在尝试校准模型之前进行分析。不幸的是,这样的\ textIt {先验分析}的分析可能具有挑战性,因为它需要符号计算通常具有较高的计算成本。近年来,为此任务开发了许多软件工具,主要是在系统生物学社区,但也在其他学科中。这些工具具有截然不同的功能,并且仍然缺乏对其性能的批判性评估。在这里,我们介绍了可用于分析结构可识别性的计算资源的全面研究。我们考虑使用7种编程语言开发的12种软件工具(MATLAB,MAPLE,MATHEMATICA,JULIA,PYTHON,REDID和MAXIMA),并使用21个模型创建的25个案例研究来评估其性能。我们的结果揭示了他们的优势和劣势,提供了为给定问题选择最合适工具的指南,并突出了未来发展的机会。

The structural identifiability and the observability of a model determine the possibility of inferring its parameters and states by observing its outputs. These properties should be analysed before attempting to calibrate a model. Unfortunately, such \textit{a priori} analysis can be challenging, since it requires symbolic calculations that often have a high computational cost. In recent years a number of software tools have been developed for this task, mostly in the systems biology community but also in other disciplines. These tools have vastly different features and capabilities, and a critical assessment of their performance is still lacking. Here we present a comprehensive study of the computational resources available for analysing structural identifiability. We consider 12 software tools developed in 7 programming languages (Matlab, Maple, Mathematica, Julia, Python, Reduce, and Maxima), and evaluate their performance using a set of 25 case studies created from 21 models. Our results reveal their strengths and weaknesses, provide guidelines for choosing the most appropriate tool for a given problem, and highlight opportunities for future developments.

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