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Finite-state parameter space maps for pruning partitions in modularity-based community detection
Partitioning networks into communities of densely connected nodes is an important tool used widely across different applications, with numerous methods and software packages available for community detection. Modularity-based methods require parameters to be selected (or assume defaults) to control...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9508178/ https://www.ncbi.nlm.nih.gov/pubmed/36151268 http://dx.doi.org/10.1038/s41598-022-20142-6 |
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author | Gibson, Ryan A. Mucha, Peter J. |
author_facet | Gibson, Ryan A. Mucha, Peter J. |
author_sort | Gibson, Ryan A. |
collection | PubMed |
description | Partitioning networks into communities of densely connected nodes is an important tool used widely across different applications, with numerous methods and software packages available for community detection. Modularity-based methods require parameters to be selected (or assume defaults) to control the resolution and, in multilayer networks, interlayer coupling. Meanwhile, most useful algorithms are heuristics yielding different near-optimal results upon repeated runs (even at the same parameters). To address these difficulties, we combine recent developments into a simple-to-use framework for pruning a set of partitions to a subset that are self-consistent by an equivalence with the objective function for inference of a degree-corrected planted partition stochastic block model (SBM). Importantly, this combined framework reduces some of the problems associated with the stochasticity that is inherent in the use of heuristics for optimizing modularity. In our examples, the pruning typically highlights only a small number of partitions that are fixed points of the corresponding map on the set of somewhere-optimal partitions in the parameter space. We also derive resolution parameter upper bounds for fitting a constrained SBM of K blocks and demonstrate that these bounds hold in practice, further guiding parameter space regions to consider. With publicly available code (http://github.com/ragibson/ModularityPruning), our pruning procedure provides a new baseline for using modularity-based community detection in practice. |
format | Online Article Text |
id | pubmed-9508178 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-95081782022-09-25 Finite-state parameter space maps for pruning partitions in modularity-based community detection Gibson, Ryan A. Mucha, Peter J. Sci Rep Article Partitioning networks into communities of densely connected nodes is an important tool used widely across different applications, with numerous methods and software packages available for community detection. Modularity-based methods require parameters to be selected (or assume defaults) to control the resolution and, in multilayer networks, interlayer coupling. Meanwhile, most useful algorithms are heuristics yielding different near-optimal results upon repeated runs (even at the same parameters). To address these difficulties, we combine recent developments into a simple-to-use framework for pruning a set of partitions to a subset that are self-consistent by an equivalence with the objective function for inference of a degree-corrected planted partition stochastic block model (SBM). Importantly, this combined framework reduces some of the problems associated with the stochasticity that is inherent in the use of heuristics for optimizing modularity. In our examples, the pruning typically highlights only a small number of partitions that are fixed points of the corresponding map on the set of somewhere-optimal partitions in the parameter space. We also derive resolution parameter upper bounds for fitting a constrained SBM of K blocks and demonstrate that these bounds hold in practice, further guiding parameter space regions to consider. With publicly available code (http://github.com/ragibson/ModularityPruning), our pruning procedure provides a new baseline for using modularity-based community detection in practice. Nature Publishing Group UK 2022-09-23 /pmc/articles/PMC9508178/ /pubmed/36151268 http://dx.doi.org/10.1038/s41598-022-20142-6 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Gibson, Ryan A. Mucha, Peter J. Finite-state parameter space maps for pruning partitions in modularity-based community detection |
title | Finite-state parameter space maps for pruning partitions in modularity-based community detection |
title_full | Finite-state parameter space maps for pruning partitions in modularity-based community detection |
title_fullStr | Finite-state parameter space maps for pruning partitions in modularity-based community detection |
title_full_unstemmed | Finite-state parameter space maps for pruning partitions in modularity-based community detection |
title_short | Finite-state parameter space maps for pruning partitions in modularity-based community detection |
title_sort | finite-state parameter space maps for pruning partitions in modularity-based community detection |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9508178/ https://www.ncbi.nlm.nih.gov/pubmed/36151268 http://dx.doi.org/10.1038/s41598-022-20142-6 |
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