okstra 0.108.0 → 0.110.0

package/runtime/python/okstra_vendor/networkx/algorithms/sparsifiers.py

@@ -0,0 +1,296 @@
+"""Functions for computing sparsifiers of graphs."""
+
+import math
+
+import networkx as nx
+from networkx.utils import not_implemented_for, py_random_state
+
+__all__ = ["spanner"]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@py_random_state(3)
+@nx._dispatchable(edge_attrs="weight", returns_graph=True)
+def spanner(G, stretch, weight=None, seed=None):
+    """Returns a spanner of the given graph with the given stretch.
+
+    A spanner of a graph G = (V, E) with stretch t is a subgraph
+    H = (V, E_S) such that E_S is a subset of E and the distance between
+    any pair of nodes in H is at most t times the distance between the
+    nodes in G.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        An undirected simple graph.
+
+    stretch : float
+        The stretch of the spanner.
+
+    weight : object
+        The edge attribute to use as distance.
+
+    seed : integer, random_state, or None (default)
+        Indicator of random number generation state.
+        See :ref:`Randomness<randomness>`.
+
+    Returns
+    -------
+    NetworkX graph
+        A spanner of the given graph with the given stretch.
+
+    Raises
+    ------
+    ValueError
+        If a stretch less than 1 is given.
+
+    Notes
+    -----
+    This function implements the spanner algorithm by Baswana and Sen,
+    see [1].
+
+    This algorithm is a randomized las vegas algorithm: The expected
+    running time is O(km) where k = (stretch + 1) // 2 and m is the
+    number of edges in G. The returned graph is always a spanner of the
+    given graph with the specified stretch. For weighted graphs the
+    number of edges in the spanner is O(k * n^(1 + 1 / k)) where k is
+    defined as above and n is the number of nodes in G. For unweighted
+    graphs the number of edges is O(n^(1 + 1 / k) + kn).
+
+    References
+    ----------
+    [1] S. Baswana, S. Sen. A Simple and Linear Time Randomized
+    Algorithm for Computing Sparse Spanners in Weighted Graphs.
+    Random Struct. Algorithms 30(4): 532-563 (2007).
+    """
+    if stretch < 1:
+        raise ValueError("stretch must be at least 1")
+
+    k = (stretch + 1) // 2
+
+    # initialize spanner H with empty edge set
+    H = nx.empty_graph()
+    H.add_nodes_from(G.nodes)
+
+    # phase 1: forming the clusters
+    # the residual graph has V' from the paper as its node set
+    # and E' from the paper as its edge set
+    residual_graph = _setup_residual_graph(G, weight)
+    # clustering is a dictionary that maps nodes in a cluster to the
+    # cluster center
+    clustering = {v: v for v in G.nodes}
+    sample_prob = math.pow(G.number_of_nodes(), -1 / k)
+    size_limit = 2 * math.pow(G.number_of_nodes(), 1 + 1 / k)
+
+    i = 0
+    while i < k - 1:
+        # step 1: sample centers
+        sampled_centers = set()
+        for center in set(clustering.values()):
+            if seed.random() < sample_prob:
+                sampled_centers.add(center)
+
+        # combined loop for steps 2 and 3
+        edges_to_add = set()
+        edges_to_remove = set()
+        new_clustering = {}
+        for v in residual_graph.nodes:
+            if clustering[v] in sampled_centers:
+                continue
+
+            # step 2: find neighboring (sampled) clusters and
+            # lightest edges to them
+            lightest_edge_neighbor, lightest_edge_weight = _lightest_edge_dicts(
+                residual_graph, clustering, v
+            )
+            neighboring_sampled_centers = (
+                set(lightest_edge_weight.keys()) & sampled_centers
+            )
+
+            # step 3: add edges to spanner
+            if not neighboring_sampled_centers:
+                # connect to each neighboring center via lightest edge
+                for neighbor in lightest_edge_neighbor.values():
+                    edges_to_add.add((v, neighbor))
+                # remove all incident edges
+                for neighbor in residual_graph.adj[v]:
+                    edges_to_remove.add((v, neighbor))
+
+            else:  # there is a neighboring sampled center
+                closest_center = min(
+                    neighboring_sampled_centers, key=lightest_edge_weight.get
+                )
+                closest_center_weight = lightest_edge_weight[closest_center]
+                closest_center_neighbor = lightest_edge_neighbor[closest_center]
+
+                edges_to_add.add((v, closest_center_neighbor))
+                new_clustering[v] = closest_center
+
+                # connect to centers with edge weight less than
+                # closest_center_weight
+                for center, edge_weight in lightest_edge_weight.items():
+                    if edge_weight < closest_center_weight:
+                        neighbor = lightest_edge_neighbor[center]
+                        edges_to_add.add((v, neighbor))
+
+                # remove edges to centers with edge weight less than
+                # closest_center_weight
+                for neighbor in residual_graph.adj[v]:
+                    nbr_cluster = clustering[neighbor]
+                    nbr_weight = lightest_edge_weight[nbr_cluster]
+                    if (
+                        nbr_cluster == closest_center
+                        or nbr_weight < closest_center_weight
+                    ):
+                        edges_to_remove.add((v, neighbor))
+
+        # check whether iteration added too many edges to spanner,
+        # if so repeat
+        if len(edges_to_add) > size_limit:
+            # an iteration is repeated O(1) times on expectation
+            continue
+
+        # iteration succeeded
+        i = i + 1
+
+        # actually add edges to spanner
+        for u, v in edges_to_add:
+            _add_edge_to_spanner(H, residual_graph, u, v, weight)
+
+        # actually delete edges from residual graph
+        residual_graph.remove_edges_from(edges_to_remove)
+
+        # copy old clustering data to new_clustering
+        for node, center in clustering.items():
+            if center in sampled_centers:
+                new_clustering[node] = center
+        clustering = new_clustering
+
+        # step 4: remove intra-cluster edges
+        for u in residual_graph.nodes:
+            for v in list(residual_graph.adj[u]):
+                if clustering[u] == clustering[v]:
+                    residual_graph.remove_edge(u, v)
+
+        # update residual graph node set
+        for v in list(residual_graph.nodes):
+            if v not in clustering:
+                residual_graph.remove_node(v)
+
+    # phase 2: vertex-cluster joining
+    for v in residual_graph.nodes:
+        lightest_edge_neighbor, _ = _lightest_edge_dicts(residual_graph, clustering, v)
+        for neighbor in lightest_edge_neighbor.values():
+            _add_edge_to_spanner(H, residual_graph, v, neighbor, weight)
+
+    return H
+
+
+def _setup_residual_graph(G, weight):
+    """Setup residual graph as a copy of G with unique edges weights.
+
+    The node set of the residual graph corresponds to the set V' from
+    the Baswana-Sen paper and the edge set corresponds to the set E'
+    from the paper.
+
+    This function associates distinct weights to the edges of the
+    residual graph (even for unweighted input graphs), as required by
+    the algorithm.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        An undirected simple graph.
+
+    weight : object
+        The edge attribute to use as distance.
+
+    Returns
+    -------
+    NetworkX graph
+        The residual graph used for the Baswana-Sen algorithm.
+    """
+    residual_graph = G.copy()
+
+    # establish unique edge weights, even for unweighted graphs
+    for u, v in G.edges():
+        if not weight:
+            residual_graph[u][v]["weight"] = (id(u), id(v))
+        else:
+            residual_graph[u][v]["weight"] = (G[u][v][weight], id(u), id(v))
+
+    return residual_graph
+
+
+def _lightest_edge_dicts(residual_graph, clustering, node):
+    """Find the lightest edge to each cluster.
+
+    Searches for the minimum-weight edge to each cluster adjacent to
+    the given node.
+
+    Parameters
+    ----------
+    residual_graph : NetworkX graph
+        The residual graph used by the Baswana-Sen algorithm.
+
+    clustering : dictionary
+        The current clustering of the nodes.
+
+    node : node
+        The node from which the search originates.
+
+    Returns
+    -------
+    lightest_edge_neighbor, lightest_edge_weight : dictionary, dictionary
+        lightest_edge_neighbor is a dictionary that maps a center C to
+        a node v in the corresponding cluster such that the edge from
+        the given node to v is the lightest edge from the given node to
+        any node in cluster. lightest_edge_weight maps a center C to the
+        weight of the aforementioned edge.
+
+    Notes
+    -----
+    If a cluster has no node that is adjacent to the given node in the
+    residual graph then the center of the cluster is not a key in the
+    returned dictionaries.
+    """
+    lightest_edge_neighbor = {}
+    lightest_edge_weight = {}
+    for neighbor in residual_graph.adj[node]:
+        nbr_center = clustering[neighbor]
+        weight = residual_graph[node][neighbor]["weight"]
+        if (
+            nbr_center not in lightest_edge_weight
+            or weight < lightest_edge_weight[nbr_center]
+        ):
+            lightest_edge_neighbor[nbr_center] = neighbor
+            lightest_edge_weight[nbr_center] = weight
+    return lightest_edge_neighbor, lightest_edge_weight
+
+
+def _add_edge_to_spanner(H, residual_graph, u, v, weight):
+    """Add the edge {u, v} to the spanner H and take weight from
+    the residual graph.
+
+    Parameters
+    ----------
+    H : NetworkX graph
+        The spanner under construction.
+
+    residual_graph : NetworkX graph
+        The residual graph used by the Baswana-Sen algorithm. The weight
+        for the edge is taken from this graph.
+
+    u : node
+        One endpoint of the edge.
+
+    v : node
+        The other endpoint of the edge.
+
+    weight : object
+        The edge attribute to use as distance.
+    """
+    H.add_edge(u, v)
+    if weight:
+        H[u][v][weight] = residual_graph[u][v]["weight"][0]

package/runtime/python/okstra_vendor/networkx/algorithms/structuralholes.py

@@ -0,0 +1,374 @@
+"""Functions for computing measures of structural holes."""
+
+import networkx as nx
+
+__all__ = ["constraint", "local_constraint", "effective_size"]
+
+
+@nx._dispatchable(edge_attrs="weight")
+def mutual_weight(G, u, v, weight=None):
+    """Returns the sum of the weights of the edge from `u` to `v` and
+    the edge from `v` to `u` in `G`.
+
+    `weight` is the edge data key that represents the edge weight. If
+    the specified key is `None` or is not in the edge data for an edge,
+    that edge is assumed to have weight 1.
+
+    Pre-conditions: `u` and `v` must both be in `G`.
+
+    """
+    try:
+        a_uv = G[u][v].get(weight, 1)
+    except KeyError:
+        a_uv = 0
+    try:
+        a_vu = G[v][u].get(weight, 1)
+    except KeyError:
+        a_vu = 0
+    return a_uv + a_vu
+
+
+@nx._dispatchable(edge_attrs="weight")
+def normalized_mutual_weight(G, u, v, norm=sum, weight=None):
+    """Returns normalized mutual weight of the edges from `u` to `v`
+    with respect to the mutual weights of the neighbors of `u` in `G`.
+
+    `norm` specifies how the normalization factor is computed. It must
+    be a function that takes a single argument and returns a number.
+    The argument will be an iterable of mutual weights
+    of pairs ``(u, w)``, where ``w`` ranges over each (in- and
+    out-)neighbor of ``u``. Commons values for `normalization` are
+    ``sum`` and ``max``.
+
+    `weight` can be ``None`` or a string, if None, all edge weights
+    are considered equal. Otherwise holds the name of the edge
+    attribute used as weight.
+
+    """
+    scale = norm(mutual_weight(G, u, w, weight) for w in set(nx.all_neighbors(G, u)))
+    return 0 if scale == 0 else mutual_weight(G, u, v, weight) / scale
+
+
+@nx._dispatchable(edge_attrs="weight")
+def effective_size(G, nodes=None, weight=None):
+    r"""Returns the effective size of all nodes in the graph ``G``.
+
+    The *effective size* of a node's ego network is based on the concept
+    of redundancy. A person's ego network has redundancy to the extent
+    that her contacts are connected to each other as well. The
+    nonredundant part of a person's relationships is the effective
+    size of her ego network [1]_.  Formally, the effective size of a
+    node $u$, denoted $e(u)$, is defined by
+
+    .. math::
+
+       e(u) = \sum_{v \in N(u) \setminus \{u\}}
+       \left(1 - \sum_{w \in N(v)} p_{uw} m_{vw}\right)
+
+    where $N(u)$ is the set of neighbors of $u$ and $p_{uw}$ is the
+    normalized mutual weight of the (directed or undirected) edges
+    joining $u$ and $v$, for each vertex $u$ and $v$ [1]_. And $m_{vw}$
+    is the mutual weight of $v$ and $w$ divided by $v$ highest mutual
+    weight with any of its neighbors. The *mutual weight* of $u$ and $v$
+    is the sum of the weights of edges joining them (edge weights are
+    assumed to be one if the graph is unweighted).
+
+    For the case of unweighted and undirected graphs, Borgatti proposed
+    a simplified formula to compute effective size [2]_
+
+    .. math::
+
+       e(u) = n - \frac{2t}{n}
+
+    where `t` is the number of ties in the ego network (not including
+    ties to ego) and `n` is the number of nodes (excluding ego).
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph containing ``v``. Directed graphs are treated like
+        undirected graphs when computing neighbors of ``v``.
+
+    nodes : container, optional
+        Container of nodes in the graph ``G`` to compute the effective size.
+        If None, the effective size of every node is computed.
+
+    weight : None or string, optional
+      If None, all edge weights are considered equal.
+      Otherwise holds the name of the edge attribute used as weight.
+
+    Returns
+    -------
+    dict
+        Dictionary with nodes as keys and the effective size of the node as values.
+
+    Notes
+    -----
+    Isolated nodes, including nodes which only have self-loop edges, do not
+    have a well-defined effective size::
+
+        >>> G = nx.path_graph(3)
+        >>> G.add_edge(4, 4)
+        >>> nx.effective_size(G)
+        {0: 1.0, 1: 2.0, 2: 1.0, 4: nan}
+
+    Burt also defined the related concept of *efficiency* of a node's ego
+    network, which is its effective size divided by the degree of that
+    node [1]_. So you can easily compute efficiency:
+
+    >>> G = nx.DiGraph()
+    >>> G.add_edges_from([(0, 1), (0, 2), (1, 0), (2, 1)])
+    >>> esize = nx.effective_size(G)
+    >>> efficiency = {n: v / G.degree(n) for n, v in esize.items()}
+
+    See also
+    --------
+    constraint
+
+    References
+    ----------
+    .. [1] Burt, Ronald S.
+           *Structural Holes: The Social Structure of Competition.*
+           Cambridge: Harvard University Press, 1995.
+
+    .. [2] Borgatti, S.
+           "Structural Holes: Unpacking Burt's Redundancy Measures"
+           CONNECTIONS 20(1):35-38.
+           http://www.analytictech.com/connections/v20(1)/holes.htm
+
+    """
+
+    def redundancy(G, u, v, weight=None):
+        nmw = normalized_mutual_weight
+        r = sum(
+            nmw(G, u, w, weight=weight) * nmw(G, v, w, norm=max, weight=weight)
+            for w in set(nx.all_neighbors(G, u))
+        )
+        return 1 - r
+
+    # Check if scipy is available
+    try:
+        # Needed for errstate
+        import numpy as np
+
+        # make sure nx.adjacency_matrix will not raise
+        import scipy as sp
+
+        has_scipy = True
+    except:
+        has_scipy = False
+
+    if nodes is None and has_scipy:
+        # In order to compute constraint of all nodes,
+        # algorithms based on sparse matrices can be much faster
+
+        # Obtain the adjacency matrix
+        P = nx.adjacency_matrix(G, weight=weight)
+
+        # Calculate mutual weights
+        mutual_weights1 = P + P.T
+        mutual_weights2 = mutual_weights1.copy()
+
+        with np.errstate(divide="ignore"):
+            # Mutual_weights1 = Normalize mutual weights by row sums
+            mutual_weights1 /= mutual_weights1.sum(axis=1)[:, np.newaxis]
+
+            # Mutual_weights2 = Normalize mutual weights by row max
+            mutual_weights2 /= mutual_weights2.max(axis=1).toarray()
+
+        # Calculate effective sizes
+        r = 1 - (mutual_weights1 @ mutual_weights2.T).toarray()
+        effective_size = ((mutual_weights1 > 0) * r).sum(axis=1)
+
+        # Special treatment: isolated nodes (ignoring selfloops) marked with "nan"
+        sum_mutual_weights = mutual_weights1.sum(axis=1) - mutual_weights1.diagonal()
+        isolated_nodes = sum_mutual_weights == 0
+        effective_size[isolated_nodes] = float("nan")
+        # Use tolist() to automatically convert numpy scalars -> Python scalars
+        return dict(zip(G, effective_size.tolist()))
+
+    # Results for only requested nodes
+    effective_size = {}
+    if nodes is None:
+        nodes = G
+    # Use Borgatti's simplified formula for unweighted and undirected graphs
+    if not G.is_directed() and weight is None:
+        for v in nodes:
+            # Effective size is not defined for isolated nodes, including nodes
+            # with only self-edges
+            if all(u == v for u in G[v]):
+                effective_size[v] = float("nan")
+                continue
+            E = nx.ego_graph(G, v, center=False, undirected=True)
+            effective_size[v] = len(E) - (2 * E.size()) / len(E)
+    else:
+        for v in nodes:
+            # Effective size is not defined for isolated nodes, including nodes
+            # with only self-edges
+            if all(u == v for u in G[v]):
+                effective_size[v] = float("nan")
+                continue
+            effective_size[v] = sum(
+                redundancy(G, v, u, weight) for u in set(nx.all_neighbors(G, v))
+            )
+    return effective_size
+
+
+@nx._dispatchable(edge_attrs="weight")
+def constraint(G, nodes=None, weight=None):
+    r"""Returns the constraint on all nodes in the graph ``G``.
+
+    The *constraint* is a measure of the extent to which a node *v* is
+    invested in those nodes that are themselves invested in the
+    neighbors of *v*. Formally, the *constraint on v*, denoted `c(v)`,
+    is defined by
+
+    .. math::
+
+       c(v) = \sum_{w \in N(v) \setminus \{v\}} \ell(v, w)
+
+    where $N(v)$ is the subset of the neighbors of `v` that are either
+    predecessors or successors of `v` and $\ell(v, w)$ is the local
+    constraint on `v` with respect to `w` [1]_. For the definition of local
+    constraint, see :func:`local_constraint`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph containing ``v``. This can be either directed or undirected.
+
+    nodes : container, optional
+        Container of nodes in the graph ``G`` to compute the constraint. If
+        None, the constraint of every node is computed.
+
+    weight : None or string, optional
+      If None, all edge weights are considered equal.
+      Otherwise holds the name of the edge attribute used as weight.
+
+    Returns
+    -------
+    dict
+        Dictionary with nodes as keys and the constraint on the node as values.
+
+    See also
+    --------
+    local_constraint
+
+    References
+    ----------
+    .. [1] Burt, Ronald S.
+           "Structural holes and good ideas".
+           American Journal of Sociology (110): 349–399.
+
+    """
+
+    # Check if scipy is available
+    try:
+        # Needed for errstate
+        import numpy as np
+
+        # make sure nx.adjacency_matrix will not raise
+        import scipy as sp
+
+        has_scipy = True
+    except:
+        has_scipy = False
+
+    if nodes is None and has_scipy:
+        # In order to compute constraint of all nodes,
+        # algorithms based on sparse matrices can be much faster
+
+        # Obtain the adjacency matrix
+        P = nx.adjacency_matrix(G, weight=weight)
+
+        # Calculate mutual weights
+        mutual_weights = P + P.T
+
+        # Normalize mutual weights by row sums
+        sum_mutual_weights = mutual_weights.sum(axis=1)
+        with np.errstate(divide="ignore"):
+            mutual_weights /= sum_mutual_weights[:, np.newaxis]
+
+        # Calculate local constraints and constraints
+        local_constraints = (mutual_weights + mutual_weights @ mutual_weights) ** 2
+        constraints = ((mutual_weights > 0) * local_constraints).sum(axis=1)
+
+        # Special treatment: isolated nodes marked with "nan"
+        isolated_nodes = sum_mutual_weights - 2 * mutual_weights.diagonal() == 0
+        constraints[isolated_nodes] = float("nan")
+        # Use tolist() to automatically convert numpy scalars -> Python scalars
+        return dict(zip(G, constraints.tolist()))
+
+    # Result for only requested nodes
+    constraint = {}
+    if nodes is None:
+        nodes = G
+    for v in nodes:
+        # Constraint is not defined for isolated nodes
+        if len(G[v]) == 0:
+            constraint[v] = float("nan")
+            continue
+        constraint[v] = sum(
+            local_constraint(G, v, n, weight) for n in set(nx.all_neighbors(G, v))
+        )
+    return constraint
+
+
+@nx._dispatchable(edge_attrs="weight")
+def local_constraint(G, u, v, weight=None):
+    r"""Returns the local constraint on the node ``u`` with respect to
+    the node ``v`` in the graph ``G``.
+
+    Formally, the *local constraint on u with respect to v*, denoted
+    $\ell(u, v)$, is defined by
+
+    .. math::
+
+       \ell(u, v) = \left(p_{uv} + \sum_{w \in N(v)} p_{uw} p_{wv}\right)^2,
+
+    where $N(v)$ is the set of neighbors of $v$ and $p_{uv}$ is the
+    normalized mutual weight of the (directed or undirected) edges
+    joining $u$ and $v$, for each vertex $u$ and $v$ [1]_. The *mutual
+    weight* of $u$ and $v$ is the sum of the weights of edges joining
+    them (edge weights are assumed to be one if the graph is
+    unweighted).
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph containing ``u`` and ``v``. This can be either
+        directed or undirected.
+
+    u : node
+        A node in the graph ``G``.
+
+    v : node
+        A node in the graph ``G``.
+
+    weight : None or string, optional
+      If None, all edge weights are considered equal.
+      Otherwise holds the name of the edge attribute used as weight.
+
+    Returns
+    -------
+    float
+        The constraint of the node ``v`` in the graph ``G``.
+
+    See also
+    --------
+    constraint
+
+    References
+    ----------
+    .. [1] Burt, Ronald S.
+           "Structural holes and good ideas".
+           American Journal of Sociology (110): 349–399.
+
+    """
+    nmw = normalized_mutual_weight
+    direct = nmw(G, u, v, weight=weight)
+    indirect = sum(
+        nmw(G, u, w, weight=weight) * nmw(G, w, v, weight=weight)
+        for w in set(nx.all_neighbors(G, u))
+    )
+    return (direct + indirect) ** 2