multiplexcd 1.0

Functions to peform multiplex community detection

multiplexcd provides functions to perform multiplex community detection.

Installation

This module relies on igraph’s python extension as well as numpy and scipy. To install, run:

pip install multiplexcd

Test

Test that the module is running correctly by running:

python test.py

Usage

Once the package has been installed with the necessary dependencies, the module performs three basic tasks. The core purpose is to generate a list of community ids for each vertex in each network:

g = igraph.Graph()
h = igraph.Graph(directed=True)

g_vertex_names = ['a', 'b', 'c', 'd', 'e']
h_vertex_names = ['a', 'b', 'c', 'd', 'e', 'f']

g_edges = [('a', 'b'), ('a', 'c'), ('b', 'c'), ('a', 'd'),
           ('d', 'e')]
h_edges = [('a', 'b'), ('a', 'c'), ('b', 'c'), ('b', 'a'),
           ('c', 'b'), ('d', 'e'), ('d', 'f'), ('e', 'f'),
           ('e', 'd'), ('f', 'd'), ('f', 'e')]

g.add_vertices(g_vertex_names)
h.add_vertices(h_vertex_names)

g.add_edges(g_edges)
h.add_edges(h_edges)

omega = 1.0
net_list = [g, h]
net_types = ['s', 'd']

community_ids = multiplexcd.multiplex_leading_eigenvector(
                    net_list, omega, net_types)

where the omega and net_types parameters define the specific form of the multiplex modularity matrix, which can be generated directly as shown below.:

g.vs['memb'] = [0, 0, 0, 1, 1]
h.vs['memb'] = [0, 0, 0, 1, 1, 1]

community_ids = g.vs['memb'] + h.vs['memb']

B, mu = multiplexcd.get_modularity_matrix(
                    net_list, omega, net_types)

This matrix may be used to get the multiplex modularity score for an arbitrary list of community ids.:

Q = multiplexcd.multiplex_modularity(B, mu, community_ids)

Finally, the module provides a function to transform a list of distinct networks into a single, multislice representation with manually specified links between the same node in multiple networks.:

multislice = multiplexcd.make_multislice_graph([g, h], omega)

This is especially useful for identifying connected components in the multiplex network at the cost of converting every graph into a single-mode, undirected network.

Author

Michael Siemon

License

This project is licensed under the MIT License - see the LICENSE.md file for details.