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Towards Reproducible Descriptions of Neuronal Network Models

机译:走向神经网络模型的可再现描述

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摘要

Progress in science depends on the effective exchange of ideas among scientists. New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely. This applies to simulation studies as well as to experiments and theories. But after more than 50 years of neuronal network simulations, we still lack a clear and common understanding of the role of computational models in neuroscience as well as established practices for describing network models in publications. This hinders the critical evaluation of network models as well as their re-use.We analyze here 14 research papers proposing neuronal network models of different complexity and find widely varying approaches to model descriptions, with regard to both the means of description and the ordering and placement of material. We further observe great variation in the graphical representation of networks and the notation used in equations. Based on our observations, we propose a good model description practice, composed of guidelines for the organization of publications, a checklist for model descriptions, templates for tables presenting model structure, and guidelines for diagrams of networks. The main purpose of this good practice is to trigger a debate about the communication of neuronal network models in a manner comprehensible to humans, as opposed to machine-readable model description languages.We believe that the good model description practice proposed here, together with a number of other recent initiatives on data-, model-, and software-sharing, may lead to a deeper and more fruitful exchange of ideas among computational neuroscientists in years to come. We further hope that work on standardized ways of describing—and thinking about—complex neuronal networks will lead the scientific community to a clearer understanding of high-level concepts in network dynamics, and will thus lead to deeper insights into the function of the brain.
机译:科学的进步取决于科学家之间有效的思想交流。只有精确地提出新思想,才能以有意义的方式对其进行评估和批评。这适用于模拟研究以及实验和理论。但是,经过50多年的神经网络仿真之后,我们仍然对计算模型在神经科学中的作用以及在出版物中描述网络模型的既定实践缺乏清晰而普遍的理解。这阻碍了对网络模型及其重新使用的严格评估。我们在这里分析了14篇提出不同复杂度的神经网络模型的研究论文,并在描述方法,排序和排序方面发现了多种多样的模型描述方法。放置材料。我们进一步观察到网络的图形表示形式和方程式中使用的表示法存在很大差异。根据我们的观察,我们提出了一个良好的模型描述实践,包括出版物组织指南,模型描述清单,模型结构表格模板以及网络图指南。这种良好做法的主要目的是以与人类可读的模型描述语言相反的方式引发对人类神经网络模型通信的辩论。我们认为,此处提出的良好模型描述做法与近期在数据共享,模型共享和软件共享方面的其他许多举措,可能会导致未来几年内计算神经科学家之间进行更深入,更富有成果的思想交流。我们进一步希望,以标准化的方式描述和思考复杂的神经元网络,将使科学界对网络动力学中的高级概念有更清晰的理解,从而对大脑的功能有更深入的了解。

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