okstra 0.108.0 → 0.110.0

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/load.py

@@ -0,0 +1,200 @@
+"""Load centrality."""
+
+from operator import itemgetter
+
+import networkx as nx
+
+__all__ = ["load_centrality", "edge_load_centrality"]
+
+
+@nx._dispatchable(edge_attrs="weight")
+def newman_betweenness_centrality(G, v=None, cutoff=None, normalized=True, weight=None):
+    """Compute load centrality for nodes.
+
+    The load centrality of a node is the fraction of all shortest
+    paths that pass through that node.
+
+    Parameters
+    ----------
+    G : graph
+      A networkx graph.
+
+    normalized : bool, optional (default=True)
+      If True the betweenness values are normalized by b=b/(n-1)(n-2) where
+      n is the number of nodes in G.
+
+    weight : None or string, optional (default=None)
+      If None, edge weights are ignored.
+      Otherwise holds the name of the edge attribute used as weight.
+      The weight of an edge is treated as the length or distance between the two sides.
+
+    cutoff : bool, optional (default=None)
+      If specified, only consider paths of length <= cutoff.
+
+    Returns
+    -------
+    nodes : dictionary
+       Dictionary of nodes with centrality as the value.
+
+    See Also
+    --------
+    betweenness_centrality
+
+    Notes
+    -----
+    Load centrality is slightly different than betweenness. It was originally
+    introduced by [2]_. For this load algorithm see [1]_.
+
+    References
+    ----------
+    .. [1] Mark E. J. Newman:
+       Scientific collaboration networks. II.
+       Shortest paths, weighted networks, and centrality.
+       Physical Review E 64, 016132, 2001.
+       http://journals.aps.org/pre/abstract/10.1103/PhysRevE.64.016132
+    .. [2] Kwang-Il Goh, Byungnam Kahng and Doochul Kim
+       Universal behavior of Load Distribution in Scale-Free Networks.
+       Physical Review Letters 87(27):1–4, 2001.
+       https://doi.org/10.1103/PhysRevLett.87.278701
+    """
+    if v is not None:  # only one node
+        betweenness = 0.0
+        for source in G:
+            ubetween = _node_betweenness(G, source, cutoff, False, weight)
+            betweenness += ubetween[v] if v in ubetween else 0
+        if normalized:
+            order = G.order()
+            if order <= 2:
+                return betweenness  # no normalization b=0 for all nodes
+            betweenness *= 1.0 / ((order - 1) * (order - 2))
+    else:
+        betweenness = {}.fromkeys(G, 0.0)
+        for source in betweenness:
+            ubetween = _node_betweenness(G, source, cutoff, False, weight)
+            for vk in ubetween:
+                betweenness[vk] += ubetween[vk]
+        if normalized:
+            order = G.order()
+            if order <= 2:
+                return betweenness  # no normalization b=0 for all nodes
+            scale = 1.0 / ((order - 1) * (order - 2))
+            for v in betweenness:
+                betweenness[v] *= scale
+    return betweenness  # all nodes
+
+
+def _node_betweenness(G, source, cutoff=False, normalized=True, weight=None):
+    """Node betweenness_centrality helper:
+
+    See betweenness_centrality for what you probably want.
+    This actually computes "load" and not betweenness.
+    See https://networkx.lanl.gov/ticket/103
+
+    This calculates the load of each node for paths from a single source.
+    (The fraction of number of shortests paths from source that go
+    through each node.)
+
+    To get the load for a node you need to do all-pairs shortest paths.
+
+    If weight is not None then use Dijkstra for finding shortest paths.
+    """
+    # get the predecessor and path length data
+    if weight is None:
+        (pred, length) = nx.predecessor(G, source, cutoff=cutoff, return_seen=True)
+    else:
+        (pred, length) = nx.dijkstra_predecessor_and_distance(G, source, cutoff, weight)
+
+    # order the nodes by path length
+    onodes = [(l, vert) for (vert, l) in length.items()]
+    onodes.sort()
+    onodes[:] = [vert for (l, vert) in onodes if l > 0]
+
+    # initialize betweenness
+    between = {}.fromkeys(length, 1.0)
+
+    while onodes:
+        v = onodes.pop()
+        if v in pred:
+            num_paths = len(pred[v])  # Discount betweenness if more than
+            for x in pred[v]:  # one shortest path.
+                if x == source:  # stop if hit source because all remaining v
+                    break  # also have pred[v]==[source]
+                between[x] += between[v] / num_paths
+    #  remove source
+    for v in between:
+        between[v] -= 1
+    # rescale to be between 0 and 1
+    if normalized:
+        l = len(between)
+        if l > 2:
+            # scale by 1/the number of possible paths
+            scale = 1 / ((l - 1) * (l - 2))
+            for v in between:
+                between[v] *= scale
+    return between
+
+
+load_centrality = newman_betweenness_centrality
+
+
+@nx._dispatchable
+def edge_load_centrality(G, cutoff=False):
+    """Compute edge load.
+
+    WARNING: This concept of edge load has not been analysed
+    or discussed outside of NetworkX that we know of.
+    It is based loosely on load_centrality in the sense that
+    it counts the number of shortest paths which cross each edge.
+    This function is for demonstration and testing purposes.
+
+    Parameters
+    ----------
+    G : graph
+        A networkx graph
+
+    cutoff : bool, optional (default=False)
+        If specified, only consider paths of length <= cutoff.
+
+    Returns
+    -------
+    A dict keyed by edge 2-tuple to the number of shortest paths
+    which use that edge. Where more than one path is shortest
+    the count is divided equally among paths.
+    """
+    betweenness = {}
+    for u, v in G.edges():
+        betweenness[(u, v)] = 0.0
+        betweenness[(v, u)] = 0.0
+
+    for source in G:
+        ubetween = _edge_betweenness(G, source, cutoff=cutoff)
+        for e, ubetweenv in ubetween.items():
+            betweenness[e] += ubetweenv  # cumulative total
+    return betweenness
+
+
+def _edge_betweenness(G, source, nodes=None, cutoff=False):
+    """Edge betweenness helper."""
+    # get the predecessor data
+    (pred, length) = nx.predecessor(G, source, cutoff=cutoff, return_seen=True)
+    # order the nodes by path length
+    onodes = [n for n, d in sorted(length.items(), key=itemgetter(1))]
+    # initialize betweenness, doesn't account for any edge weights
+    between = {}
+    for u, v in G.edges(nodes):
+        between[(u, v)] = 1.0
+        between[(v, u)] = 1.0
+
+    while onodes:  # work through all paths
+        v = onodes.pop()
+        if v in pred:
+            # Discount betweenness if more than one shortest path.
+            num_paths = len(pred[v])
+            for w in pred[v]:
+                if w in pred:
+                    # Discount betweenness, mult path
+                    num_paths = len(pred[w])
+                    for x in pred[w]:
+                        between[(w, x)] += between[(v, w)] / num_paths
+                        between[(x, w)] += between[(w, v)] / num_paths
+    return between

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/percolation.py

@@ -0,0 +1,128 @@
+"""Percolation centrality measures."""
+
+import networkx as nx
+from networkx.algorithms.centrality.betweenness import (
+    _single_source_dijkstra_path_basic as dijkstra,
+)
+from networkx.algorithms.centrality.betweenness import (
+    _single_source_shortest_path_basic as shortest_path,
+)
+
+__all__ = ["percolation_centrality"]
+
+
+@nx._dispatchable(node_attrs="attribute", edge_attrs="weight")
+def percolation_centrality(G, attribute="percolation", states=None, weight=None):
+    r"""Compute the percolation centrality for nodes.
+
+    Percolation centrality of a node $v$, at a given time, is defined
+    as the proportion of ‘percolated paths’ that go through that node.
+
+    This measure quantifies relative impact of nodes based on their
+    topological connectivity, as well as their percolation states.
+
+    Percolation states of nodes are used to depict network percolation
+    scenarios (such as during infection transmission in a social network
+    of individuals, spreading of computer viruses on computer networks, or
+    transmission of disease over a network of towns) over time. In this
+    measure usually the percolation state is expressed as a decimal
+    between 0.0 and 1.0.
+
+    When all nodes are in the same percolated state this measure is
+    equivalent to betweenness centrality.
+
+    Parameters
+    ----------
+    G : graph
+      A NetworkX graph.
+
+    attribute : None or string, optional (default='percolation')
+      Name of the node attribute to use for percolation state, used
+      if `states` is None. If a node does not set the attribute the
+      state of that node will be set to the default value of 1.
+      If all nodes do not have the attribute all nodes will be set to
+      1 and the centrality measure will be equivalent to betweenness centrality.
+
+    states : None or dict, optional (default=None)
+      Specify percolation states for the nodes, nodes as keys states
+      as values.
+
+    weight : None or string, optional (default=None)
+      If None, all edge weights are considered equal.
+      Otherwise holds the name of the edge attribute used as weight.
+      The weight of an edge is treated as the length or distance between the two sides.
+
+
+    Returns
+    -------
+    nodes : dictionary
+       Dictionary of nodes with percolation centrality as the value.
+
+    See Also
+    --------
+    betweenness_centrality
+
+    Notes
+    -----
+    The algorithm is from Mahendra Piraveenan, Mikhail Prokopenko, and
+    Liaquat Hossain [1]_
+    Pair dependencies are calculated and accumulated using [2]_
+
+    For weighted graphs the edge weights must be greater than zero.
+    Zero edge weights can produce an infinite number of equal length
+    paths between pairs of nodes.
+
+    References
+    ----------
+    .. [1] Mahendra Piraveenan, Mikhail Prokopenko, Liaquat Hossain
+       Percolation Centrality: Quantifying Graph-Theoretic Impact of Nodes
+       during Percolation in Networks
+       http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053095
+    .. [2] Ulrik Brandes:
+       A Faster Algorithm for Betweenness Centrality.
+       Journal of Mathematical Sociology 25(2):163-177, 2001.
+       https://doi.org/10.1080/0022250X.2001.9990249
+    """
+    percolation = dict.fromkeys(G, 0.0)  # b[v]=0 for v in G
+
+    nodes = G
+
+    if states is None:
+        states = nx.get_node_attributes(nodes, attribute, default=1)
+
+    # sum of all percolation states
+    p_sigma_x_t = 0.0
+    for v in states.values():
+        p_sigma_x_t += v
+
+    for s in nodes:
+        # single source shortest paths
+        if weight is None:  # use BFS
+            S, P, sigma, _ = shortest_path(G, s)
+        else:  # use Dijkstra's algorithm
+            S, P, sigma, _ = dijkstra(G, s, weight)
+        # accumulation
+        percolation = _accumulate_percolation(
+            percolation, S, P, sigma, s, states, p_sigma_x_t
+        )
+
+    n = len(G)
+
+    for v in percolation:
+        percolation[v] *= 1 / (n - 2)
+
+    return percolation
+
+
+def _accumulate_percolation(percolation, S, P, sigma, s, states, p_sigma_x_t):
+    delta = dict.fromkeys(S, 0)
+    while S:
+        w = S.pop()
+        coeff = (1 + delta[w]) / sigma[w]
+        for v in P[w]:
+            delta[v] += sigma[v] * coeff
+        if w != s:
+            # percolation weight
+            pw_s_w = states[s] / (p_sigma_x_t - states[w])
+            percolation[w] += delta[w] * pw_s_w
+    return percolation

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/reaching.py

@@ -0,0 +1,209 @@
+"""Functions for computing reaching centrality of a node or a graph."""
+
+import networkx as nx
+from networkx.utils import pairwise
+
+__all__ = ["global_reaching_centrality", "local_reaching_centrality"]
+
+
+def _average_weight(G, path, weight=None):
+    """Returns the average weight of an edge in a weighted path.
+
+    Parameters
+    ----------
+    G : graph
+      A networkx graph.
+
+    path: list
+      A list of vertices that define the path.
+
+    weight : None or string, optional (default=None)
+      If None, edge weights are ignored.  Then the average weight of an edge
+      is assumed to be the multiplicative inverse of the length of the path.
+      Otherwise holds the name of the edge attribute used as weight.
+    """
+    path_length = len(path) - 1
+    if path_length <= 0:
+        return 0
+    if weight is None:
+        return 1 / path_length
+    total_weight = sum(G.edges[i, j][weight] for i, j in pairwise(path))
+    return total_weight / path_length
+
+
+@nx._dispatchable(edge_attrs="weight")
+def global_reaching_centrality(G, weight=None, normalized=True):
+    """Returns the global reaching centrality of a directed graph.
+
+    The *global reaching centrality* of a weighted directed graph is the
+    average over all nodes of the difference between the local reaching
+    centrality of the node and the greatest local reaching centrality of
+    any node in the graph [1]_. For more information on the local
+    reaching centrality, see :func:`local_reaching_centrality`.
+    Informally, the local reaching centrality is the proportion of the
+    graph that is reachable from the neighbors of the node.
+
+    Parameters
+    ----------
+    G : DiGraph
+        A networkx DiGraph.
+
+    weight : None or string, optional (default=None)
+        Attribute to use for edge weights. If ``None``, each edge weight
+        is assumed to be one. A higher weight implies a stronger
+        connection between nodes and a *shorter* path length.
+
+    normalized : bool, optional (default=True)
+        Whether to normalize the edge weights by the total sum of edge
+        weights.
+
+    Returns
+    -------
+    h : float
+        The global reaching centrality of the graph.
+
+    Examples
+    --------
+    >>> G = nx.DiGraph()
+    >>> G.add_edge(1, 2)
+    >>> G.add_edge(1, 3)
+    >>> nx.global_reaching_centrality(G)
+    1.0
+    >>> G.add_edge(3, 2)
+    >>> nx.global_reaching_centrality(G)
+    0.75
+
+    See also
+    --------
+    local_reaching_centrality
+
+    References
+    ----------
+    .. [1] Mones, Enys, Lilla Vicsek, and Tamás Vicsek.
+           "Hierarchy Measure for Complex Networks."
+           *PLoS ONE* 7.3 (2012): e33799.
+           https://doi.org/10.1371/journal.pone.0033799
+    """
+    if nx.is_negatively_weighted(G, weight=weight):
+        raise nx.NetworkXError("edge weights must be positive")
+    total_weight = G.size(weight=weight)
+    if total_weight <= 0:
+        raise nx.NetworkXError("Size of G must be positive")
+    # If provided, weights must be interpreted as connection strength
+    # (so higher weights are more likely to be chosen). However, the
+    # shortest path algorithms in NetworkX assume the provided "weight"
+    # is actually a distance (so edges with higher weight are less
+    # likely to be chosen). Therefore we need to invert the weights when
+    # computing shortest paths.
+    #
+    # If weight is None, we leave it as-is so that the shortest path
+    # algorithm can use a faster, unweighted algorithm.
+    if weight is not None:
+
+        def as_distance(u, v, d):
+            return total_weight / d.get(weight, 1)
+
+        shortest_paths = dict(nx.shortest_path(G, weight=as_distance))
+    else:
+        shortest_paths = dict(nx.shortest_path(G))
+
+    centrality = local_reaching_centrality
+    # TODO This can be trivially parallelized.
+    lrc = [
+        centrality(G, node, paths=paths, weight=weight, normalized=normalized)
+        for node, paths in shortest_paths.items()
+    ]
+
+    max_lrc = max(lrc)
+    return sum(max_lrc - c for c in lrc) / (len(G) - 1)
+
+
+@nx._dispatchable(edge_attrs="weight")
+def local_reaching_centrality(G, v, paths=None, weight=None, normalized=True):
+    """Returns the local reaching centrality of a node in a directed
+    graph.
+
+    The *local reaching centrality* of a node in a directed graph is the
+    proportion of other nodes reachable from that node [1]_.
+
+    Parameters
+    ----------
+    G : DiGraph
+        A NetworkX DiGraph.
+
+    v : node
+        A node in the directed graph `G`.
+
+    paths : dictionary (default=None)
+        If this is not `None` it must be a dictionary representation
+        of single-source shortest paths, as computed by, for example,
+        :func:`networkx.shortest_path` with source node `v`. Use this
+        keyword argument if you intend to invoke this function many
+        times but don't want the paths to be recomputed each time.
+
+    weight : None or string, optional (default=None)
+        Attribute to use for edge weights.  If `None`, each edge weight
+        is assumed to be one. A higher weight implies a stronger
+        connection between nodes and a *shorter* path length.
+
+    normalized : bool, optional (default=True)
+        Whether to normalize the edge weights by the total sum of edge
+        weights.
+
+    Returns
+    -------
+    h : float
+        The local reaching centrality of the node ``v`` in the graph
+        ``G``.
+
+    Examples
+    --------
+    >>> G = nx.DiGraph()
+    >>> G.add_edges_from([(1, 2), (1, 3)])
+    >>> nx.local_reaching_centrality(G, 3)
+    0.0
+    >>> G.add_edge(3, 2)
+    >>> nx.local_reaching_centrality(G, 3)
+    0.5
+
+    See also
+    --------
+    global_reaching_centrality
+
+    References
+    ----------
+    .. [1] Mones, Enys, Lilla Vicsek, and Tamás Vicsek.
+           "Hierarchy Measure for Complex Networks."
+           *PLoS ONE* 7.3 (2012): e33799.
+           https://doi.org/10.1371/journal.pone.0033799
+    """
+    # Corner case: graph with single node containing a self-loop
+    if (total_weight := G.size(weight=weight)) > 0 and len(G) == 1:
+        raise nx.NetworkXError(
+            "local_reaching_centrality of a single node with self-loop not well-defined"
+        )
+    if paths is None:
+        if nx.is_negatively_weighted(G, weight=weight):
+            raise nx.NetworkXError("edge weights must be positive")
+        if total_weight <= 0:
+            raise nx.NetworkXError("Size of G must be positive")
+        if weight is not None:
+            # Interpret weights as lengths.
+            def as_distance(u, v, d):
+                return total_weight / d.get(weight, 1)
+
+            paths = nx.shortest_path(G, source=v, weight=as_distance)
+        else:
+            paths = nx.shortest_path(G, source=v)
+    # If the graph is unweighted, simply return the proportion of nodes
+    # reachable from the source node ``v``.
+    if weight is None and G.is_directed():
+        return (len(paths) - 1) / (len(G) - 1)
+    if normalized and weight is not None:
+        norm = G.size(weight=weight) / G.size()
+    else:
+        norm = 1
+    # TODO This can be trivially parallelized.
+    avgw = (_average_weight(G, path, weight=weight) for path in paths.values())
+    sum_avg_weight = sum(avgw) / norm
+    return sum_avg_weight / (len(G) - 1)

package/runtime/python/okstra_vendor/networkx/algorithms/centrality/second_order.py

@@ -0,0 +1,141 @@
+"""Copyright (c) 2015 – Thomson Licensing, SAS
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted (subject to the limitations in the
+disclaimer below) provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+* Neither the name of Thomson Licensing, or Technicolor, nor the names
+of its contributors may be used to endorse or promote products derived
+from this software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+GRANTED BY THIS LICENSE.  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT
+HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+"""
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+# Authors: Erwan Le Merrer (erwan.lemerrer@technicolor.com)
+
+__all__ = ["second_order_centrality"]
+
+
+@not_implemented_for("directed")
+@nx._dispatchable(edge_attrs="weight")
+def second_order_centrality(G, weight="weight"):
+    """Compute the second order centrality for nodes of G.
+
+    The second order centrality of a given node is the standard deviation of
+    the return times to that node of a perpetual random walk on G:
+
+    Parameters
+    ----------
+    G : graph
+      A NetworkX connected and undirected graph.
+
+    weight : string or None, optional (default="weight")
+        The name of an edge attribute that holds the numerical value
+        used as a weight. If None then each edge has weight 1.
+
+    Returns
+    -------
+    nodes : dictionary
+       Dictionary keyed by node with second order centrality as the value.
+
+    Examples
+    --------
+    >>> G = nx.star_graph(10)
+    >>> soc = nx.second_order_centrality(G)
+    >>> print(sorted(soc.items(), key=lambda x: x[1])[0][0])  # pick first id
+    0
+
+    Raises
+    ------
+    NetworkXException
+        If the graph G is empty, non connected or has negative weights.
+
+    See Also
+    --------
+    betweenness_centrality
+
+    Notes
+    -----
+    Lower values of second order centrality indicate higher centrality.
+
+    The algorithm is from Kermarrec, Le Merrer, Sericola and Trédan [1]_.
+
+    This code implements the analytical version of the algorithm, i.e.,
+    there is no simulation of a random walk process involved. The random walk
+    is here unbiased (corresponding to eq 6 of the paper [1]_), thus the
+    centrality values are the standard deviations for random walk return times
+    on the transformed input graph G (equal in-degree at each nodes by adding
+    self-loops).
+
+    Complexity of this implementation, made to run locally on a single machine,
+    is O(n^3), with n the size of G, which makes it viable only for small
+    graphs.
+
+    References
+    ----------
+    .. [1] Anne-Marie Kermarrec, Erwan Le Merrer, Bruno Sericola, Gilles Trédan
+       "Second order centrality: Distributed assessment of nodes criticity in
+       complex networks", Elsevier Computer Communications 34(5):619-628, 2011.
+    """
+    import numpy as np
+
+    n = len(G)
+
+    if n == 0:
+        raise nx.NetworkXException("Empty graph.")
+    if not nx.is_connected(G):
+        raise nx.NetworkXException("Non connected graph.")
+    if any(d.get(weight, 0) < 0 for u, v, d in G.edges(data=True)):
+        raise nx.NetworkXException("Graph has negative edge weights.")
+
+    # balancing G for Metropolis-Hastings random walks
+    G = nx.DiGraph(G)
+    in_deg = dict(G.in_degree(weight=weight))
+    d_max = max(in_deg.values())
+    for i, deg in in_deg.items():
+        if deg < d_max:
+            G.add_edge(i, i, weight=d_max - deg)
+
+    P = nx.to_numpy_array(G)
+    P /= P.sum(axis=1)[:, np.newaxis]  # to transition probability matrix
+
+    def _Qj(P, j):
+        P = P.copy()
+        P[:, j] = 0
+        return P
+
+    M = np.empty([n, n])
+
+    for i in range(n):
+        M[:, i] = np.linalg.solve(
+            np.identity(n) - _Qj(P, i), np.ones([n, 1])[:, 0]
+        )  # eq 3
+
+    return dict(
+        zip(
+            G.nodes,
+            (float(np.sqrt(2 * np.sum(M[:, i]) - n * (n + 1))) for i in range(n)),
+        )
+    )  # eq 6