skyork skyork - 1 month ago 27
Python Question

Overlapping community detection with igraph or other libaries

I would like to detect overlapping communities in small networks/graphs. By overlapping, I mean that a node can be included within more than one communities/clusters in the output of the detection algorithm.

I have looked at various community detection algorithms curretly provided by

igraph
, but I think none of them handles overlapping communities.

Ideally, I would like to be able to programmatically utilize some implementation of such algorithm(s) in Python. However, implementation in other languages is OK too.

Answer

I have implemented the hierarchical link clustering algorithm of Ahn et al a while ago using the Python interface of igraph; see its source code here.

Also, implementing CFinder in Python using igraph is fairly easy; this is what I came up with:

#!/usr/bin/env python
from itertools import combinations

import igraph
import optparse

parser = optparse.OptionParser(usage="%prog [options] infile")
parser.add_option("-k", metavar="K", default=3, type=int,
        help="use a clique size of K")

options, args = parser.parse_args()

if not args:
    parser.error("Required input file as first argument")

k = options.k
g = igraph.load(args[0], format="ncol", directed=False)
cls = map(set, g.maximal_cliques(min=k))

edgelist = []
for i, j in combinations(range(len(cls)), 2):
    if len(cls[i].intersection(cls[j])) >= k-1:
        edgelist.append((i, j))

cg = igraph.Graph(edgelist, directed=False)
clusters = cg.clusters()
for cluster in clusters:
    members = set()
    for i in cluster:
        members.update(cls[i])
    print "\t".join(g.vs[members]["name"])