#community detection, #modularity, #clustering, #network partitioning

Figure from: Rosvall et al 2020

Summary

Community detection is a cornerstone of network research. This class aims to convey how community detection simplifies complex data and exposes underlying processes and functional consequences in the context of ecological networks. We begin by learning various analytical approaches to define and detect communities. We delve into two methods: modularity and the map equation, both of which are central to biological networks. We also examine the significance of characterizing and interpreting network partitions via practical applications in ecological studies.

Goals

  1. Introduce the concept and analytical approaches for community detection.
  2. Demonstrate how community detection provides insights.

A guide to choosing a community detection approach

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References

Key sources

Network Science Book chapter 9: communities; http://networksciencebook.com/chapter/9. #modularity

Infomap demo: https://www.mapequation.org/demo/#Infomap

Rosvall M, Delvenne J-C, Schaub MT, Lambiotte R. Different approaches to community detection. In: Doreian P, Batagelj V, Ferligoj A, editors. Advances in network clustering and blockmodeling. Wiley; 2020. pp. 105–120. #Infomap, #modularity

Farage C, Edler D, Eklöf A, Rosvall M, Pilosof S. Identifying flow modules in ecological networks using Infomap. Methods Ecol Evol. 2021;12: 778–786. doi:10.1111/2041-210x.13569 #Infomap, #software

Technical papers

Newman MEJ, Girvan M. Finding and evaluating community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2004;69: 026113. doi:10.1103/PhysRevE.69.026113 #modularity

Barber M. Modularity and community detection in bipartite networks. Physical Review E. 2007;76: 1–9. doi:10.1103/PhysRevE.76.066102 #modularity, #bipartite

Guimerà R, Sales-Pardo M, Amaral LAN. Module identification in bipartite and directed networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2007;76: 036102. doi:10.1103/PhysRevE.76.036102 #modularity, #bipartite

Bohlin L, Edler D, Lancichinetti A, Rosvall M. Community Detection and Visualization of Networks with the Map Equation Framework. Measuring Scholarly Impact. Springer International Publishing; 2014. pp. 3–34. doi:10.1007/978-3-319-10377-8_1 #Infomap

Dormann CF, Strauss R. A method for detecting modules in quantitative bipartite networks. Methods Ecol Evol. 2014;5: 90–98. doi:10.1111/2041-210X.12139 #modularity, #bipartite

Beckett SJ. Improved community detection in weighted bipartite networks. R Soc Open Sci. 2016;3: 140536. doi:10.1098/rsos.140536 #modularity, #bipartite

Thébault E. Identifying compartments in presence-absence matrices and bipartite networks: insights into modularity measures. J Biogeogr. 2013;40: 759–768. doi:10.1111/jbi.12015 #modularity, #bipartite

Allesina S, Pascual M. Food web models: a plea for groups. Ecol Lett. 2009;12: 652–662. doi:10.1111/j.1461-0248.2009.01321.x #SBM

Research papers

Guimerà R, Nunes Amaral LA. Functional cartography of complex metabolic networks. Nature. 2005;433: 895–900. doi:10.1038/nature03288 #node roles

Olesen JM, Bascompte J, Dupont YL, Jordano P. The modularity of pollination networks. Proc Natl Acad Sci U S A. 2007;104: 19891–198916. doi:10.1073/pnas.0706375104 #modularity

Fortuna MA, Popa-Lisseanu AG, Ibáñez C, Bascompte J. The roosting spatial network of a bird-predator bat. Ecology. 2009;90: 934–944. doi:10.1890/08-0174.1 #modularity

Guimerà R, Stouffer DB, Sales-Pardo M, Leicht EA, Newman MEJ, Amaral LAN. Origin of compartmentalization in food webs. Ecology. 2010;91: 2941–2951. Available: https://www.ncbi.nlm.nih.gov/pubmed/21058554 #modularity

Stouffer DB, Bascompte J. Compartmentalization increases food-web persistence. Proc Natl Acad Sci U S A. 2011;108: 3648–3652. doi:10.1073/pnas.1014353108 #modularity, #perturbations

Sander EL, Wootton JT, Allesina S. What can interaction webs tell us about species roles? PLoS Comput Biol. 2015;11: e1004330. doi:10.1371/journal.pcbi.1004330 #SBM

Dormann CF, Fründ J, Schaefer HM. Identifying Causes of Patterns in Ecological Networks: Opportunities and Limitations. Annu Rev Ecol Evol Syst. 2017. doi:10.1146/annurev-ecolsys-110316-022928 #review

Gilarranz LJ, Rayfield B, Liñán-Cembrano G, Bascompte J, Gonzalez A. Effects of network modularity on the spread of perturbation impact in experimental metapopulations. Science. 2017;357: 199–201. doi:10.1126/science.aal4122 #modularity

Ohlsson M, Eklöf A. Spatial resolution and location impact group structure in a marine food web. Ecol Lett. 2020. doi:10.1111/ele.13567 #SBM