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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

0:4f3585e2f14b

"""Functions for computing large cliques."""
import networkx as nx
from networkx.utils import not_implemented_for
from networkx.algorithms.approximation import ramsey

__all__ = ["clique_removal", "max_clique", "large_clique_size"]


def max_clique(G):
    r"""Find the Maximum Clique

    Finds the $O(|V|/(log|V|)^2)$ apx of maximum clique/independent set
    in the worst case.

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

    Returns
    -------
    clique : set
        The apx-maximum clique of the graph

    Notes
    ------
    A clique in an undirected graph G = (V, E) is a subset of the vertex set
    `C \subseteq V` such that for every two vertices in C there exists an edge
    connecting the two. This is equivalent to saying that the subgraph
    induced by C is complete (in some cases, the term clique may also refer
    to the subgraph).

    A maximum clique is a clique of the largest possible size in a given graph.
    The clique number `\omega(G)` of a graph G is the number of
    vertices in a maximum clique in G. The intersection number of
    G is the smallest number of cliques that together cover all edges of G.

    https://en.wikipedia.org/wiki/Maximum_clique

    References
    ----------
    .. [1] Boppana, R., & Halldórsson, M. M. (1992).
        Approximating maximum independent sets by excluding subgraphs.
        BIT Numerical Mathematics, 32(2), 180–196. Springer.
        doi:10.1007/BF01994876
    """
    if G is None:
        raise ValueError("Expected NetworkX graph!")

    # finding the maximum clique in a graph is equivalent to finding
    # the independent set in the complementary graph
    cgraph = nx.complement(G)
    iset, _ = clique_removal(cgraph)
    return iset


def clique_removal(G):
    r""" Repeatedly remove cliques from the graph.

    Results in a $O(|V|/(\log |V|)^2)$ approximation of maximum clique
    and independent set. Returns the largest independent set found, along
    with found maximal cliques.

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

    Returns
    -------
    max_ind_cliques : (set, list) tuple
        2-tuple of Maximal Independent Set and list of maximal cliques (sets).

    References
    ----------
    .. [1] Boppana, R., & Halldórsson, M. M. (1992).
        Approximating maximum independent sets by excluding subgraphs.
        BIT Numerical Mathematics, 32(2), 180–196. Springer.
    """
    graph = G.copy()
    c_i, i_i = ramsey.ramsey_R2(graph)
    cliques = [c_i]
    isets = [i_i]
    while graph:
        graph.remove_nodes_from(c_i)
        c_i, i_i = ramsey.ramsey_R2(graph)
        if c_i:
            cliques.append(c_i)
        if i_i:
            isets.append(i_i)
    # Determine the largest independent set as measured by cardinality.
    maxiset = max(isets, key=len)
    return maxiset, cliques


@not_implemented_for("directed")
@not_implemented_for("multigraph")
def large_clique_size(G):
    """Find the size of a large clique in a graph.

    A *clique* is a subset of nodes in which each pair of nodes is
    adjacent. This function is a heuristic for finding the size of a
    large clique in the graph.

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

    Returns
    -------
    int
       The size of a large clique in the graph.

    Notes
    -----
    This implementation is from [1]_. Its worst case time complexity is
    :math:`O(n d^2)`, where *n* is the number of nodes in the graph and
    *d* is the maximum degree.

    This function is a heuristic, which means it may work well in
    practice, but there is no rigorous mathematical guarantee on the
    ratio between the returned number and the actual largest clique size
    in the graph.

    References
    ----------
    .. [1] Pattabiraman, Bharath, et al.
       "Fast Algorithms for the Maximum Clique Problem on Massive Graphs
       with Applications to Overlapping Community Detection."
       *Internet Mathematics* 11.4-5 (2015): 421--448.
       <https://doi.org/10.1080/15427951.2014.986778>

    See also
    --------

    :func:`networkx.algorithms.approximation.clique.max_clique`
        A function that returns an approximate maximum clique with a
        guarantee on the approximation ratio.

    :mod:`networkx.algorithms.clique`
        Functions for finding the exact maximum clique in a graph.

    """
    degrees = G.degree

    def _clique_heuristic(G, U, size, best_size):
        if not U:
            return max(best_size, size)
        u = max(U, key=degrees)
        U.remove(u)
        N_prime = {v for v in G[u] if degrees[v] >= best_size}
        return _clique_heuristic(G, U & N_prime, size + 1, best_size)

    best_size = 0
    nodes = (u for u in G if degrees[u] >= best_size)
    for u in nodes:
        neighbors = {v for v in G[u] if degrees[v] >= best_size}
        best_size = _clique_heuristic(G, neighbors, 1, best_size)
    return best_size