121 lines
3.8 KiB
Python
121 lines
3.8 KiB
Python
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# -*- coding: utf-8 -*-
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"""Node redundancy for bipartite graphs."""
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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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from itertools import combinations
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from networkx import NetworkXError
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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__ = ['node_redundancy']
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def node_redundancy(G, nodes=None):
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r"""Computes the node redundancy coefficients for the nodes in the bipartite
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graph `G`.
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The redundancy coefficient of a node `v` is the fraction of pairs of
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neighbors of `v` that are both linked to other nodes. In a one-mode
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projection these nodes would be linked together even if `v` were
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not there.
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More formally, for any vertex `v`, the *redundancy coefficient of `v`* is
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defined by
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.. math::
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rc(v) = \frac{|\{\{u, w\} \subseteq N(v),
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\: \exists v' \neq v,\: (v',u) \in E\:
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\mathrm{and}\: (v',w) \in E\}|}{ \frac{|N(v)|(|N(v)|-1)}{2}},
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where `N(v)` is the set of neighbors of `v` in `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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Compute redundancy for these nodes. The default is all nodes in G.
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Returns
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-------
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redundancy : dictionary
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A dictionary keyed by node with the node redundancy value.
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Examples
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--------
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Compute the redundancy coefficient of each node in a graph::
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>>> import networkx as nx
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>>> from networkx.algorithms import bipartite
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>>> G = nx.cycle_graph(4)
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>>> rc = bipartite.node_redundancy(G)
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>>> rc[0]
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1.0
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Compute the average redundancy for the graph::
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>>> import networkx as nx
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>>> from networkx.algorithms import bipartite
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>>> G = nx.cycle_graph(4)
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>>> rc = bipartite.node_redundancy(G)
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>>> sum(rc.values()) / len(G)
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1.0
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Compute the average redundancy for a set of nodes::
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>>> import networkx as nx
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>>> from networkx.algorithms import bipartite
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>>> G = nx.cycle_graph(4)
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>>> rc = bipartite.node_redundancy(G)
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>>> nodes = [0, 2]
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>>> sum(rc[n] for n in nodes) / len(nodes)
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1.0
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Raises
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------
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NetworkXError
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If any of the nodes in the graph (or in `nodes`, if specified) has
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(out-)degree less than two (which would result in division by zero,
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according to the definition of the redundancy coefficient).
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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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if any(len(G[v]) < 2 for v in nodes):
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raise NetworkXError('Cannot compute redundancy coefficient for a node'
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' that has fewer than two neighbors.')
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# TODO This can be trivially parallelized.
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return {v: _node_redundancy(G, v) for v in nodes}
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def _node_redundancy(G, v):
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"""Returns the redundancy of the node `v` in the bipartite graph `G`.
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If `G` is a graph with `n` nodes, the redundancy of a node is the ratio
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of the "overlap" of `v` to the maximum possible overlap of `v`
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according to its degree. The overlap of `v` is the number of pairs of
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neighbors that have mutual neighbors themselves, other than `v`.
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`v` must have at least two neighbors in `G`.
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"""
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n = len(G[v])
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# TODO On Python 3, we could just use `G[u].keys() & G[w].keys()` instead
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# of instantiating the entire sets.
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overlap = sum(1 for (u, w) in combinations(G[v], 2)
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if (set(G[u]) & set(G[w])) - {v})
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return (2 * overlap) / (n * (n - 1))
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