Waltman, Ludo, and Nees Jan van Eck. Acad. Blondel, V. D., Guillaume, J.-L., Lambiotte, R. & Lefebvre, E. Fast unfolding of communities in large networks. An iteration of the Leiden algorithm in which the partition does not change is called a stable iteration. Community detection - Tim Stuart Importantly, the output of the local moving stage will depend on the order that the nodes are considered in. Clustering with the Leiden Algorithm in R Neurosci. Note that this code is designed for Seurat version 2 releases. Modularity optimization. This contrasts with the Leiden algorithm. b, The elephant graph (in a) is clustered using the Leiden clustering algorithm 51 (resolution r = 0.5). 2018. The Leiden community detection algorithm outperforms other clustering methods. Technol. See the documentation for these functions. ADS In fact, by implementing the refinement phase in the right way, several attractive guarantees can be given for partitions produced by the Leiden algorithm. Local Resolution-Limit-Free Potts Model for Community Detection. Phys. Google Scholar. https://doi.org/10.1038/s41598-019-41695-z, DOI: https://doi.org/10.1038/s41598-019-41695-z. Iterating the Louvain algorithm can therefore be seen as a double-edged sword: it improves the partition in some way, but degrades it in another way. J. Introduction The Louvain method is an algorithm to detect communities in large networks. Algorithmics 16, 2.1, https://doi.org/10.1145/1963190.1970376 (2011). However, it is also possible to start the algorithm from a different partition15. In fact, for the Web of Science and Web UK networks, Fig. 2013. When a disconnected community has become a node in an aggregate network, there are no more possibilities to split up the community. Fortunato, Santo, and Marc Barthlemy. Is modularity with a resolution parameter equivalent to leidenalg.RBConfigurationVertexPartition? We gratefully acknowledge computational facilities provided by the LIACS Data Science Lab Computing Facilities through Frank Takes. In the Louvain algorithm, a node may be moved to a different community while it may have acted as a bridge between different components of its old community. In fact, when we keep iterating the Leiden algorithm, it will converge to a partition for which it is guaranteed that: A community is uniformly -dense if there are no subsets of the community that can be separated from the community. Preprocessing and clustering 3k PBMCs Scanpy documentation E 92, 032801, https://doi.org/10.1103/PhysRevE.92.032801 (2015). After the first iteration of the Louvain algorithm, some partition has been obtained.
