Connectivity concepts in neuronal network modeling

PLoS Comput Biol. 2022 Sep 8;18(9):e1010086. doi: 10.1371/journal.pcbi.1010086. eCollection 2022 Sep.

Abstract

Sustainable research on computational models of neuronal networks requires published models to be understandable, reproducible, and extendable. Missing details or ambiguities about mathematical concepts and assumptions, algorithmic implementations, or parameterizations hinder progress. Such flaws are unfortunately frequent and one reason is a lack of readily applicable standards and tools for model description. Our work aims to advance complete and concise descriptions of network connectivity but also to guide the implementation of connection routines in simulation software and neuromorphic hardware systems. We first review models made available by the computational neuroscience community in the repositories ModelDB and Open Source Brain, and investigate the corresponding connectivity structures and their descriptions in both manuscript and code. The review comprises the connectivity of networks with diverse levels of neuroanatomical detail and exposes how connectivity is abstracted in existing description languages and simulator interfaces. We find that a substantial proportion of the published descriptions of connectivity is ambiguous. Based on this review, we derive a set of connectivity concepts for deterministically and probabilistically connected networks and also address networks embedded in metric space. Beside these mathematical and textual guidelines, we propose a unified graphical notation for network diagrams to facilitate an intuitive understanding of network properties. Examples of representative network models demonstrate the practical use of the ideas. We hope that the proposed standardizations will contribute to unambiguous descriptions and reproducible implementations of neuronal network connectivity in computational neuroscience.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Models, Neurological*
  • Neurons / physiology
  • Neurosciences*
  • Software

Grants and funding

This project has received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreement 720270 (HBP SGA1) [to MDj, MDi, HEP], 785907 (HBP SGA2) [to JS, MDj, MDi, HEP, SvA], 945539 (HBP SGA3) [to JS, MDj, HJJ, MDi, HEP, SvA], and 754304 (DEEP-EST) [to HEP]; the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 368482240/GRK2416: ‘`RTG 2416 Multi-senses Multi-scales" [to MDi]; the Priority Program (SPP 2041 ‘`Computational Connectomics”) of the Deutsche Forschungsgemeinschaft [to SvA]; the Helmholtz Association Initiative and Networking Fund under project number SO-092 (Advanced Computing Architectures, ACA) [to JS, MDi]; the Excellence Initiative of the German federal and state governments (neuroIC001): ‘`ERS: disziplinärer Paketantrag NeuroIC: NeuroModelingTalk (NMT) Approaching the complexity barrier in neuroscientific modeling" [to JS, LS, GG, MDi]; and the Helmholtz Metadata Collaboration (HMC), an incubator platform of the Helmholtz Association within the framework of the Information and Data Science strategic initiative, under the funding ZT-I-PF-3-026 [to JS]. Open access publication funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 491111487. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.