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Reproducing Polychronization: A Guide to Maximizing the Reproducibility of Spiking Network Models
Julich Res Ctr, Inst Neurosci & Med INM 6, Julich, Germany.;Julich Res Ctr, Inst Adv Simulat IAS 6, Julich, Germany.;Julich Res Ctr, JARA BRAIN Inst 1, Julich, Germany..
Julich Res Ctr, Inst Neurosci & Med INM 6, Julich, Germany.;Julich Res Ctr, Inst Adv Simulat IAS 6, Julich, Germany.;Julich Res Ctr, JARA BRAIN Inst 1, Julich, Germany..
KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST). Norwegian Univ Life Sci, Fac Sci & Technol, As, Norway.
Julich Res Ctr, Inst Neurosci & Med INM 6, Julich, Germany.;Julich Res Ctr, Inst Adv Simulat IAS 6, Julich, Germany.;Julich Res Ctr, JARA BRAIN Inst 1, Julich, Germany.;Ruhr Univ Bochum, Inst Cognit Neurosci, Fac Psychol, Bochum, Germany..
2018 (English)In: Frontiers in Neuroinformatics, ISSN 1662-5196, E-ISSN 1662-5196, Vol. 12, article id 46Article in journal (Refereed) Published
Abstract [en]

Any modeler who has attempted to reproduce a spiking neural network model from its description in a paper has discovered what a painful endeavor this is. Even when all parameters appear to have been specified, which is rare, typically the initial attempt to reproduce the network does not yield results that are recognizably akin to those in the original publication. Causes include inaccurately reported or hidden parameters (e.g., wrong unit or the existence of an initialization distribution), differences in implementation of model dynamics, and ambiguities in the text description of the network experiment. The very fact that adequate reproduction often cannot be achieved until a series of such causes have been tracked down and resolved is in itself disconcerting, as it reveals unreported model dependencies on specific implementation choices that either were not clear to the original authors, or that they chose not to disclose. In either case, such dependencies diminish the credibility of the model's claims about the behavior of the target system. To demonstrate these issues, we provide a worked example of reproducing a seminal study for which, unusually, source code was provided at time of publication. Despite this seemingly optimal starting position, reproducing the results was time consuming and frustrating. Further examination of the correctly reproduced model reveals that it is highly sensitive to implementation choices such as the realization of background noise, the integration timestep, and the thresholding parameter of the analysis algorithm. From this process, we derive a guideline of best practices that would substantially reduce the investment in reproducing neural network studies, whilst simultaneously increasing their scientific quality. We propose that this guideline can be used by authors and reviewers to assess and improve the reproducibility of future network models.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018. Vol. 12, article id 46
Keywords [en]
reproducibility, polychronization, spiking network models, spike-timing dependent plasticity, synchrony
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-233416DOI: 10.3389/fninf.2018.00046ISI: 000440754900001Scopus ID: 2-s2.0-85054808107OAI: oai:DiVA.org:kth-233416DiVA, id: diva2:1240351
Note

QC 20180821

Available from: 2018-08-21 Created: 2018-08-21 Last updated: 2020-03-09Bibliographically approved

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