comparison env/lib/python3.9/site-packages/networkx/algorithms/cuts.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

0:4f3585e2f14b

"""Functions for finding and evaluating cuts in a graph.

"""

from itertools import chain

import networkx as nx

__all__ = [
    "boundary_expansion",
    "conductance",
    "cut_size",
    "edge_expansion",
    "mixing_expansion",
    "node_expansion",
    "normalized_cut_size",
    "volume",
]


# TODO STILL NEED TO UPDATE ALL THE DOCUMENTATION!


def cut_size(G, S, T=None, weight=None):
    """Returns the size of the cut between two sets of nodes.

    A *cut* is a partition of the nodes of a graph into two sets. The
    *cut size* is the sum of the weights of the edges "between" the two
    sets of nodes.

    Parameters
    ----------
    G : NetworkX graph

    S : sequence
        A sequence of nodes in `G`.

    T : sequence
        A sequence of nodes in `G`. If not specified, this is taken to
        be the set complement of `S`.

    weight : object
        Edge attribute key to use as weight. If not specified, edges
        have weight one.

    Returns
    -------
    number
        Total weight of all edges from nodes in set `S` to nodes in
        set `T` (and, in the case of directed graphs, all edges from
        nodes in `T` to nodes in `S`).

    Examples
    --------
    In the graph with two cliques joined by a single edges, the natural
    bipartition of the graph into two blocks, one for each clique,
    yields a cut of weight one::

        >>> G = nx.barbell_graph(3, 0)
        >>> S = {0, 1, 2}
        >>> T = {3, 4, 5}
        >>> nx.cut_size(G, S, T)
        1

    Each parallel edge in a multigraph is counted when determining the
    cut size::

        >>> G = nx.MultiGraph(["ab", "ab"])
        >>> S = {"a"}
        >>> T = {"b"}
        >>> nx.cut_size(G, S, T)
        2

    Notes
    -----
    In a multigraph, the cut size is the total weight of edges including
    multiplicity.

    """
    edges = nx.edge_boundary(G, S, T, data=weight, default=1)
    if G.is_directed():
        edges = chain(edges, nx.edge_boundary(G, T, S, data=weight, default=1))
    return sum(weight for u, v, weight in edges)


def volume(G, S, weight=None):
    """Returns the volume of a set of nodes.

    The *volume* of a set *S* is the sum of the (out-)degrees of nodes
    in *S* (taking into account parallel edges in multigraphs). [1]

    Parameters
    ----------
    G : NetworkX graph

    S : sequence
        A sequence of nodes in `G`.

    weight : object
        Edge attribute key to use as weight. If not specified, edges
        have weight one.

    Returns
    -------
    number
        The volume of the set of nodes represented by `S` in the graph
        `G`.

    See also
    --------
    conductance
    cut_size
    edge_expansion
    edge_boundary
    normalized_cut_size

    References
    ----------
    .. [1] David Gleich.
           *Hierarchical Directed Spectral Graph Partitioning*.
           <https://www.cs.purdue.edu/homes/dgleich/publications/Gleich%202005%20-%20hierarchical%20directed%20spectral.pdf>

    """
    degree = G.out_degree if G.is_directed() else G.degree
    return sum(d for v, d in degree(S, weight=weight))


def normalized_cut_size(G, S, T=None, weight=None):
    """Returns the normalized size of the cut between two sets of nodes.

    The *normalized cut size* is the cut size times the sum of the
    reciprocal sizes of the volumes of the two sets. [1]

    Parameters
    ----------
    G : NetworkX graph

    S : sequence
        A sequence of nodes in `G`.

    T : sequence
        A sequence of nodes in `G`.

    weight : object
        Edge attribute key to use as weight. If not specified, edges
        have weight one.

    Returns
    -------
    number
        The normalized cut size between the two sets `S` and `T`.

    Notes
    -----
    In a multigraph, the cut size is the total weight of edges including
    multiplicity.

    See also
    --------
    conductance
    cut_size
    edge_expansion
    volume

    References
    ----------
    .. [1] David Gleich.
           *Hierarchical Directed Spectral Graph Partitioning*.
           <https://www.cs.purdue.edu/homes/dgleich/publications/Gleich%202005%20-%20hierarchical%20directed%20spectral.pdf>

    """
    if T is None:
        T = set(G) - set(S)
    num_cut_edges = cut_size(G, S, T=T, weight=weight)
    volume_S = volume(G, S, weight=weight)
    volume_T = volume(G, T, weight=weight)
    return num_cut_edges * ((1 / volume_S) + (1 / volume_T))


def conductance(G, S, T=None, weight=None):
    """Returns the conductance of two sets of nodes.

    The *conductance* is the quotient of the cut size and the smaller of
    the volumes of the two sets. [1]

    Parameters
    ----------
    G : NetworkX graph

    S : sequence
        A sequence of nodes in `G`.

    T : sequence
        A sequence of nodes in `G`.

    weight : object
        Edge attribute key to use as weight. If not specified, edges
        have weight one.

    Returns
    -------
    number
        The conductance between the two sets `S` and `T`.

    See also
    --------
    cut_size
    edge_expansion
    normalized_cut_size
    volume

    References
    ----------
    .. [1] David Gleich.
           *Hierarchical Directed Spectral Graph Partitioning*.
           <https://www.cs.purdue.edu/homes/dgleich/publications/Gleich%202005%20-%20hierarchical%20directed%20spectral.pdf>

    """
    if T is None:
        T = set(G) - set(S)
    num_cut_edges = cut_size(G, S, T, weight=weight)
    volume_S = volume(G, S, weight=weight)
    volume_T = volume(G, T, weight=weight)
    return num_cut_edges / min(volume_S, volume_T)


def edge_expansion(G, S, T=None, weight=None):
    """Returns the edge expansion between two node sets.

    The *edge expansion* is the quotient of the cut size and the smaller
    of the cardinalities of the two sets. [1]

    Parameters
    ----------
    G : NetworkX graph

    S : sequence
        A sequence of nodes in `G`.

    T : sequence
        A sequence of nodes in `G`.

    weight : object
        Edge attribute key to use as weight. If not specified, edges
        have weight one.

    Returns
    -------
    number
        The edge expansion between the two sets `S` and `T`.

    See also
    --------
    boundary_expansion
    mixing_expansion
    node_expansion

    References
    ----------
    .. [1] Fan Chung.
           *Spectral Graph Theory*.
           (CBMS Regional Conference Series in Mathematics, No. 92),
           American Mathematical Society, 1997, ISBN 0-8218-0315-8
           <http://www.math.ucsd.edu/~fan/research/revised.html>

    """
    if T is None:
        T = set(G) - set(S)
    num_cut_edges = cut_size(G, S, T=T, weight=weight)
    return num_cut_edges / min(len(S), len(T))


def mixing_expansion(G, S, T=None, weight=None):
    """Returns the mixing expansion between two node sets.

    The *mixing expansion* is the quotient of the cut size and twice the
    number of edges in the graph. [1]

    Parameters
    ----------
    G : NetworkX graph

    S : sequence
        A sequence of nodes in `G`.

    T : sequence
        A sequence of nodes in `G`.

    weight : object
        Edge attribute key to use as weight. If not specified, edges
        have weight one.

    Returns
    -------
    number
        The mixing expansion between the two sets `S` and `T`.

    See also
    --------
    boundary_expansion
    edge_expansion
    node_expansion

    References
    ----------
    .. [1] Vadhan, Salil P.
           "Pseudorandomness."
           *Foundations and Trends
           in Theoretical Computer Science* 7.1–3 (2011): 1–336.
           <https://doi.org/10.1561/0400000010>

    """
    num_cut_edges = cut_size(G, S, T=T, weight=weight)
    num_total_edges = G.number_of_edges()
    return num_cut_edges / (2 * num_total_edges)


# TODO What is the generalization to two arguments, S and T? Does the
# denominator become `min(len(S), len(T))`?
def node_expansion(G, S):
    """Returns the node expansion of the set `S`.

    The *node expansion* is the quotient of the size of the node
    boundary of *S* and the cardinality of *S*. [1]

    Parameters
    ----------
    G : NetworkX graph

    S : sequence
        A sequence of nodes in `G`.

    Returns
    -------
    number
        The node expansion of the set `S`.

    See also
    --------
    boundary_expansion
    edge_expansion
    mixing_expansion

    References
    ----------
    .. [1] Vadhan, Salil P.
           "Pseudorandomness."
           *Foundations and Trends
           in Theoretical Computer Science* 7.1–3 (2011): 1–336.
           <https://doi.org/10.1561/0400000010>

    """
    neighborhood = set(chain.from_iterable(G.neighbors(v) for v in S))
    return len(neighborhood) / len(S)


# TODO What is the generalization to two arguments, S and T? Does the
# denominator become `min(len(S), len(T))`?
def boundary_expansion(G, S):
    """Returns the boundary expansion of the set `S`.

    The *boundary expansion* is the quotient of the size
    of the node boundary and the cardinality of *S*. [1]

    Parameters
    ----------
    G : NetworkX graph

    S : sequence
        A sequence of nodes in `G`.

    Returns
    -------
    number
        The boundary expansion of the set `S`.

    See also
    --------
    edge_expansion
    mixing_expansion
    node_expansion

    References
    ----------
    .. [1] Vadhan, Salil P.
           "Pseudorandomness."
           *Foundations and Trends in Theoretical Computer Science*
           7.1–3 (2011): 1–336.
           <https://doi.org/10.1561/0400000010>

    """
    return len(nx.node_boundary(G, S)) / len(S)