Quality Metrics for Graph Clustering for Biological Networks
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Last seen 7 months ago

I have a unweighted protein-protein interaction network and I will do cluster analysis with Louvain community detection, MCL, MCODE etc. I am planning to use "modularity" for quality metric but I want to use more metrics too. Silhouette Index and Dunn Index are not possible to use in this case as I known because my network is not constructed based on a high dimension numerical data (such as gene expression). I only have nodes and edges as relations. Most of the quality metrics I found require numerical data. Is there any other methods that I can use in this case?

Does bioconductor offers any packages about network clustering evaluation methods?

Thank you in advance

R protein-interaction networks network • 108 views

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