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Source code for networkx.algorithms.community.quality

# quality.py - functions for measuring partitions of a graph
#
# Copyright 2015-2018 NetworkX developers.
#
# This file is part of NetworkX.
#
# NetworkX is distributed under a BSD license; see LICENSE.txt for more
# information.
"""Functions for measuring the quality of a partition (into
communities).

"""
from __future__ import division

from functools import wraps
from itertools import product

import networkx as nx
from networkx import NetworkXError
from networkx.utils import not_implemented_for
from networkx.algorithms.community.community_utils import is_partition

__all__ = ['coverage', 'modularity', 'performance']


class NotAPartition(NetworkXError):
    """Raised if a given collection is not a partition.

    """

    def __init__(self, G, collection):
        msg = '{} is not a valid partition of the graph {}'
        msg = msg.format(G, collection)
        super(NotAPartition, self).__init__(msg)


def require_partition(func):
    """Decorator that raises an exception if a partition is not a valid
    partition of the nodes of a graph.

    Raises :exc:`networkx.NetworkXError` if the partition is not valid.

    This decorator should be used on functions whose first two arguments
    are a graph and a partition of the nodes of that graph (in that
    order)::

        >>> @require_partition
        ... def foo(G, partition):
        ...     print('partition is valid!')
        ...
        >>> G = nx.complete_graph(5)
        >>> partition = [{0, 1}, {2, 3}, {4}]
        >>> foo(G, partition)
        partition is valid!
        >>> partition = [{0}, {2, 3}, {4}]
        >>> foo(G, partition)  # doctest: +IGNORE_EXCEPTION_DETAIL
        Traceback (most recent call last):
          ...
        NetworkXError: `partition` is not a valid partition of the nodes of G
        >>> partition = [{0, 1}, {1, 2, 3}, {4}]
        >>> foo(G, partition)  # doctest: +IGNORE_EXCEPTION_DETAIL
        Traceback (most recent call last):
          ...
        NetworkXError: `partition` is not a valid partition of the nodes of G

    """

    @wraps(func)
    def new_func(*args, **kw):
        # Here we assume that the first two arguments are (G, partition).
        if not is_partition(*args[:2]):
            raise nx.NetworkXError('`partition` is not a valid partition of'
                                   ' the nodes of G')
        return func(*args, **kw)
    return new_func


def intra_community_edges(G, partition):
    """Returns the number of intra-community edges according to the given
    partition of the nodes of `G`.

    `G` must be a NetworkX graph.

    `partition` must be a partition of the nodes of `G`.

    The "intra-community edges" are those edges joining a pair of nodes
    in the same block of the partition.

    """
    return sum(G.subgraph(block).size() for block in partition)


def inter_community_edges(G, partition):
    """Returns the number of inter-community edges according to the given
    partition of the nodes of `G`.

    `G` must be a NetworkX graph.

    `partition` must be a partition of the nodes of `G`.

    The *inter-community edges* are those edges joining a pair of nodes
    in different blocks of the partition.

    Implementation note: this function creates an intermediate graph
    that may require the same amount of memory as required to store
    `G`.

    """
    # Alternate implementation that does not require constructing a new
    # graph object (but does require constructing an affiliation
    # dictionary):
    #
    #     aff = dict(chain.from_iterable(((v, block) for v in block)
    #                                    for block in partition))
    #     return sum(1 for u, v in G.edges() if aff[u] != aff[v])
    #
    if G.is_directed():
        return nx.quotient_graph(G, partition, create_using=nx.MultiDiGraph()).size()
    else:
        return nx.quotient_graph(G, partition, create_using=nx.MultiGraph()).size()


def inter_community_non_edges(G, partition):
    """Returns the number of inter-community non-edges according to the
    given partition of the nodes of `G`.

    `G` must be a NetworkX graph.

    `partition` must be a partition of the nodes of `G`.

    A *non-edge* is a pair of nodes (undirected if `G` is undirected)
    that are not adjacent in `G`. The *inter-community non-edges* are
    those non-edges on a pair of nodes in different blocks of the
    partition.

    Implementation note: this function creates two intermediate graphs,
    which may require up to twice the amount of memory as required to
    store `G`.

    """
    # Alternate implementation that does not require constructing two
    # new graph objects (but does require constructing an affiliation
    # dictionary):
    #
    #     aff = dict(chain.from_iterable(((v, block) for v in block)
    #                                    for block in partition))
    #     return sum(1 for u, v in nx.non_edges(G) if aff[u] != aff[v])
    #
    return inter_community_edges(nx.complement(G), partition)


[docs]@not_implemented_for('multigraph') @require_partition def performance(G, partition): """Returns the performance of a partition. The *performance* of a partition is the ratio of the number of intra-community edges plus inter-community non-edges with the total number of potential edges. Parameters ---------- G : NetworkX graph A simple graph (directed or undirected). partition : sequence Partition of the nodes of `G`, represented as a sequence of sets of nodes. Each block of the partition represents a community. Returns ------- float The performance of the partition, as defined above. Raises ------ NetworkXError If `partition` is not a valid partition of the nodes of `G`. References ---------- .. [1] Santo Fortunato. "Community Detection in Graphs". *Physical Reports*, Volume 486, Issue 3--5 pp. 75--174 <https://arxiv.org/abs/0906.0612> """ # Compute the number of intra-community edges and inter-community # edges. intra_edges = intra_community_edges(G, partition) inter_edges = inter_community_non_edges(G, partition) # Compute the number of edges in the complete graph (directed or # undirected, as it depends on `G`) on `n` nodes. # # (If `G` is an undirected graph, we divide by two since we have # double-counted each potential edge. We use integer division since # `total_pairs` is guaranteed to be even.) n = len(G) total_pairs = n * (n - 1) if not G.is_directed(): total_pairs //= 2 return (intra_edges + inter_edges) / total_pairs
[docs]@require_partition def coverage(G, partition): """Returns the coverage of a partition. The *coverage* of a partition is the ratio of the number of intra-community edges to the total number of edges in the graph. Parameters ---------- G : NetworkX graph partition : sequence Partition of the nodes of `G`, represented as a sequence of sets of nodes. Each block of the partition represents a community. Returns ------- float The coverage of the partition, as defined above. Raises ------ NetworkXError If `partition` is not a valid partition of the nodes of `G`. Notes ----- If `G` is a multigraph, the multiplicity of edges is counted. References ---------- .. [1] Santo Fortunato. "Community Detection in Graphs". *Physical Reports*, Volume 486, Issue 3--5 pp. 75--174 <https://arxiv.org/abs/0906.0612> """ intra_edges = intra_community_edges(G, partition) total_edges = G.number_of_edges() return intra_edges / total_edges
def modularity(G, communities, weight='weight'): r"""Returns the modularity of the given partition of the graph. Modularity is defined in [1]_ as .. math:: Q = \frac{1}{2m} \sum_{ij} \left( A_{ij} - \frac{k_ik_j}{2m}\right) \delta(c_i,c_j) where $m$ is the number of edges, $A$ is the adjacency matrix of `G`, $k_i$ is the degree of $i$ and $\delta(c_i, c_j)$ is 1 if $i$ and $j$ are in the same community and 0 otherwise. Parameters ---------- G : NetworkX Graph communities : list List of sets of nodes of `G` representing a partition of the nodes. Returns ------- Q : float The modularity of the paritition. Raises ------ NotAPartition If `communities` is not a partition of the nodes of `G`. Examples -------- >>> G = nx.barbell_graph(3, 0) >>> nx.algorithms.community.modularity(G, [{0, 1, 2}, {3, 4, 5}]) 0.35714285714285704 References ---------- .. [1] M. E. J. Newman *Networks: An Introduction*, page 224. Oxford University Press, 2011. """ if not is_partition(G, communities): raise NotAPartition(G, communities) multigraph = G.is_multigraph() directed = G.is_directed() m = G.size(weight=weight) if directed: out_degree = dict(G.out_degree(weight=weight)) in_degree = dict(G.in_degree(weight=weight)) norm = 1 / m else: out_degree = dict(G.degree(weight=weight)) in_degree = out_degree norm = 1 / (2 * m) def val(u, v): try: if multigraph: w = sum(d.get(weight, 1) for k, d in G[u][v].items()) else: w = G[u][v].get(weight, 1) except KeyError: w = 0 # Double count self-loops if the graph is undirected. if u == v and not directed: w *= 2 return w - in_degree[u] * out_degree[v] * norm Q = sum(val(u, v) for c in communities for u, v in product(c, repeat=2)) return Q * norm