281 lines
7.0 KiB
Python
281 lines
7.0 KiB
Python
#-*- coding: utf-8 -*-
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# Copyright (C) 2011 by
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# Jordi Torrents <jtorrents@milnou.net>
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# Aric Hagberg <hagberg@lanl.gov>
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# All rights reserved.
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# BSD license.
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import itertools
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import networkx as nx
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__author__ = """\n""".join(['Jordi Torrents <jtorrents@milnou.net>',
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'Aric Hagberg (hagberg@lanl.gov)'])
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__all__ = ['clustering',
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'average_clustering',
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'latapy_clustering',
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'robins_alexander_clustering']
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# functions for computing clustering of pairs
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def cc_dot(nu, nv):
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return float(len(nu & nv)) / len(nu | nv)
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def cc_max(nu, nv):
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return float(len(nu & nv)) / max(len(nu), len(nv))
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def cc_min(nu, nv):
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return float(len(nu & nv)) / min(len(nu), len(nv))
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modes = {'dot': cc_dot,
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'min': cc_min,
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'max': cc_max}
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def latapy_clustering(G, nodes=None, mode='dot'):
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r"""Compute a bipartite clustering coefficient for nodes.
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The bipartie clustering coefficient is a measure of local density
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of connections defined as [1]_:
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.. math::
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c_u = \frac{\sum_{v \in N(N(u))} c_{uv} }{|N(N(u))|}
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where `N(N(u))` are the second order neighbors of `u` in `G` excluding `u`,
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and `c_{uv}` is the pairwise clustering coefficient between nodes
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`u` and `v`.
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The mode selects the function for `c_{uv}` which can be:
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`dot`:
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.. math::
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c_{uv}=\frac{|N(u)\cap N(v)|}{|N(u) \cup N(v)|}
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`min`:
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.. math::
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c_{uv}=\frac{|N(u)\cap N(v)|}{min(|N(u)|,|N(v)|)}
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`max`:
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.. math::
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c_{uv}=\frac{|N(u)\cap N(v)|}{max(|N(u)|,|N(v)|)}
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Parameters
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----------
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G : graph
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A bipartite graph
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nodes : list or iterable (optional)
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Compute bipartite clustering for these nodes. The default
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is all nodes in G.
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mode : string
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The pariwise bipartite clustering method to be used in the computation.
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It must be "dot", "max", or "min".
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Returns
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-------
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clustering : dictionary
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A dictionary keyed by node with the clustering coefficient value.
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Examples
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--------
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>>> from networkx.algorithms import bipartite
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>>> G = nx.path_graph(4) # path graphs are bipartite
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>>> c = bipartite.clustering(G)
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>>> c[0]
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0.5
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>>> c = bipartite.clustering(G,mode='min')
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>>> c[0]
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1.0
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See Also
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--------
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robins_alexander_clustering
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square_clustering
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average_clustering
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References
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----------
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.. [1] Latapy, Matthieu, Clémence Magnien, and Nathalie Del Vecchio (2008).
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Basic notions for the analysis of large two-mode networks.
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Social Networks 30(1), 31--48.
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"""
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if not nx.algorithms.bipartite.is_bipartite(G):
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raise nx.NetworkXError("Graph is not bipartite")
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try:
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cc_func = modes[mode]
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except KeyError:
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raise nx.NetworkXError(
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"Mode for bipartite clustering must be: dot, min or max")
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if nodes is None:
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nodes = G
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ccs = {}
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for v in nodes:
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cc = 0.0
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nbrs2 = set([u for nbr in G[v] for u in G[nbr]]) - set([v])
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for u in nbrs2:
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cc += cc_func(set(G[u]), set(G[v]))
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if cc > 0.0: # len(nbrs2)>0
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cc /= len(nbrs2)
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ccs[v] = cc
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return ccs
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clustering = latapy_clustering
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def average_clustering(G, nodes=None, mode='dot'):
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r"""Compute the average bipartite clustering coefficient.
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A clustering coefficient for the whole graph is the average,
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.. math::
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C = \frac{1}{n}\sum_{v \in G} c_v,
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where `n` is the number of nodes in `G`.
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Similar measures for the two bipartite sets can be defined [1]_
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.. math::
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C_X = \frac{1}{|X|}\sum_{v \in X} c_v,
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where `X` is a bipartite set of `G`.
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Parameters
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----------
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G : graph
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a bipartite graph
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nodes : list or iterable, optional
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A container of nodes to use in computing the average.
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The nodes should be either the entire graph (the default) or one of the
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bipartite sets.
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mode : string
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The pariwise bipartite clustering method.
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It must be "dot", "max", or "min"
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Returns
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-------
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clustering : float
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The average bipartite clustering for the given set of nodes or the
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entire graph if no nodes are specified.
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Examples
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--------
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>>> from networkx.algorithms import bipartite
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>>> G=nx.star_graph(3) # star graphs are bipartite
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>>> bipartite.average_clustering(G)
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0.75
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>>> X,Y=bipartite.sets(G)
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>>> bipartite.average_clustering(G,X)
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0.0
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>>> bipartite.average_clustering(G,Y)
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1.0
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See Also
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--------
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clustering
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Notes
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-----
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The container of nodes passed to this function must contain all of the nodes
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in one of the bipartite sets ("top" or "bottom") in order to compute
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the correct average bipartite clustering coefficients.
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See :mod:`bipartite documentation <networkx.algorithms.bipartite>`
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for further details on how bipartite graphs are handled in NetworkX.
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References
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----------
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.. [1] Latapy, Matthieu, Clémence Magnien, and Nathalie Del Vecchio (2008).
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Basic notions for the analysis of large two-mode networks.
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Social Networks 30(1), 31--48.
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"""
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if nodes is None:
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nodes = G
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ccs = latapy_clustering(G, nodes=nodes, mode=mode)
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return float(sum(ccs[v] for v in nodes)) / len(nodes)
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def robins_alexander_clustering(G):
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r"""Compute the bipartite clustering of G.
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Robins and Alexander [1]_ defined bipartite clustering coefficient as
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four times the number of four cycles `C_4` divided by the number of
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three paths `L_3` in a bipartite graph:
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.. math::
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CC_4 = \frac{4 * C_4}{L_3}
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Parameters
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----------
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G : graph
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a bipartite graph
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Returns
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-------
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clustering : float
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The Robins and Alexander bipartite clustering for the input graph.
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Examples
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--------
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>>> from networkx.algorithms import bipartite
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>>> G = nx.davis_southern_women_graph()
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>>> print(round(bipartite.robins_alexander_clustering(G), 3))
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0.468
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See Also
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--------
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latapy_clustering
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square_clustering
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References
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----------
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.. [1] Robins, G. and M. Alexander (2004). Small worlds among interlocking
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directors: Network structure and distance in bipartite graphs.
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Computational & Mathematical Organization Theory 10(1), 69–94.
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"""
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if G.order() < 4 or G.size() < 3:
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return 0
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L_3 = _threepaths(G)
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if L_3 == 0:
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return 0
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C_4 = _four_cycles(G)
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return (4. * C_4) / L_3
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def _four_cycles(G):
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cycles = 0
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for v in G:
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for u, w in itertools.combinations(G[v], 2):
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cycles += len((set(G[u]) & set(G[w])) - set([v]))
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return cycles / 4
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def _threepaths(G):
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paths = 0
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for v in G:
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for u in G[v]:
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for w in set(G[u]) - set([v]):
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paths += len(set(G[w]) - set([v, u]))
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# Divide by two because we count each three path twice
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# one for each possible starting point
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return paths / 2
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