okstra 0.107.2 → 0.109.0

package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/projection.py

@@ -0,0 +1,526 @@
+"""One-mode (unipartite) projections of bipartite graphs."""
+
+import networkx as nx
+from networkx.exception import NetworkXAlgorithmError
+from networkx.utils import not_implemented_for
+
+__all__ = [
+    "projected_graph",
+    "weighted_projected_graph",
+    "collaboration_weighted_projected_graph",
+    "overlap_weighted_projected_graph",
+    "generic_weighted_projected_graph",
+]
+
+
+@nx._dispatchable(
+    graphs="B", preserve_node_attrs=True, preserve_graph_attrs=True, returns_graph=True
+)
+def projected_graph(B, nodes, multigraph=False):
+    r"""Returns the projection of B onto one of its node sets.
+
+    Returns the graph G that is the projection of the bipartite graph B
+    onto the specified nodes. They retain their attributes and are connected
+    in G if they have a common neighbor in B.
+
+    Parameters
+    ----------
+    B : NetworkX graph
+      The input graph should be bipartite.
+
+    nodes : list or iterable
+      Nodes to project onto (the "bottom" nodes).
+
+    multigraph: bool (default=False)
+       If True return a multigraph where the multiple edges represent multiple
+       shared neighbors.  They edge key in the multigraph is assigned to the
+       label of the neighbor.
+
+    Returns
+    -------
+    Graph : NetworkX graph or multigraph
+       A graph that is the projection onto the given nodes.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import bipartite
+    >>> B = nx.path_graph(4)
+    >>> G = bipartite.projected_graph(B, [1, 3])
+    >>> list(G)
+    [1, 3]
+    >>> list(G.edges())
+    [(1, 3)]
+
+    If nodes `a`, and `b` are connected through both nodes 1 and 2 then
+    building a multigraph results in two edges in the projection onto
+    [`a`, `b`]:
+
+    >>> B = nx.Graph()
+    >>> B.add_edges_from([("a", 1), ("b", 1), ("a", 2), ("b", 2)])
+    >>> G = bipartite.projected_graph(B, ["a", "b"], multigraph=True)
+    >>> print([sorted((u, v)) for u, v in G.edges()])
+    [['a', 'b'], ['a', 'b']]
+
+    Notes
+    -----
+    No attempt is made to verify that the input graph B is bipartite.
+    Returns a simple graph that is the projection of the bipartite graph B
+    onto the set of nodes given in list nodes.  If multigraph=True then
+    a multigraph is returned with an edge for every shared neighbor.
+
+    Directed graphs are allowed as input.  The output will also then
+    be a directed graph with edges if there is a directed path between
+    the nodes.
+
+    The graph and node properties are (shallow) copied to the projected graph.
+
+    See :mod:`bipartite documentation <networkx.algorithms.bipartite>`
+    for further details on how bipartite graphs are handled in NetworkX.
+
+    See Also
+    --------
+    is_bipartite,
+    is_bipartite_node_set,
+    sets,
+    weighted_projected_graph,
+    collaboration_weighted_projected_graph,
+    overlap_weighted_projected_graph,
+    generic_weighted_projected_graph
+    """
+    if B.is_multigraph():
+        raise nx.NetworkXError("not defined for multigraphs")
+    if B.is_directed():
+        directed = True
+        if multigraph:
+            G = nx.MultiDiGraph()
+        else:
+            G = nx.DiGraph()
+    else:
+        directed = False
+        if multigraph:
+            G = nx.MultiGraph()
+        else:
+            G = nx.Graph()
+    G.graph.update(B.graph)
+    G.add_nodes_from((n, B.nodes[n]) for n in nodes)
+    for u in nodes:
+        nbrs2 = {v for nbr in B[u] for v in B[nbr] if v != u}
+        if multigraph:
+            for n in nbrs2:
+                if directed:
+                    links = set(B[u]) & set(B.pred[n])
+                else:
+                    links = set(B[u]) & set(B[n])
+                for l in links:
+                    if not G.has_edge(u, n, l):
+                        G.add_edge(u, n, key=l)
+        else:
+            G.add_edges_from((u, n) for n in nbrs2)
+    return G
+
+
+@not_implemented_for("multigraph")
+@nx._dispatchable(graphs="B", returns_graph=True)
+def weighted_projected_graph(B, nodes, ratio=False):
+    r"""Returns a weighted projection of B onto one of its node sets.
+
+    The weighted projected graph is the projection of the bipartite
+    network B onto the specified nodes with weights representing the
+    number of shared neighbors or the ratio between actual shared
+    neighbors and possible shared neighbors if ``ratio is True`` [1]_.
+    The nodes retain their attributes and are connected in the resulting
+    graph if they have an edge to a common node in the original graph.
+
+    Parameters
+    ----------
+    B : NetworkX graph
+        The input graph should be bipartite.
+
+    nodes : list or iterable
+        Distinct nodes to project onto (the "bottom" nodes).
+
+    ratio: Bool (default=False)
+        If True, edge weight is the ratio between actual shared neighbors
+        and maximum possible shared neighbors (i.e., the size of the other
+        node set). If False, edges weight is the number of shared neighbors.
+
+    Returns
+    -------
+    Graph : NetworkX graph
+       A graph that is the projection onto the given nodes.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import bipartite
+    >>> B = nx.path_graph(4)
+    >>> G = bipartite.weighted_projected_graph(B, [1, 3])
+    >>> list(G)
+    [1, 3]
+    >>> list(G.edges(data=True))
+    [(1, 3, {'weight': 1})]
+    >>> G = bipartite.weighted_projected_graph(B, [1, 3], ratio=True)
+    >>> list(G.edges(data=True))
+    [(1, 3, {'weight': 0.5})]
+
+    Notes
+    -----
+    No attempt is made to verify that the input graph B is bipartite, or that
+    the input nodes are distinct. However, if the length of the input nodes is
+    greater than or equal to the nodes in the graph B, an exception is raised.
+    If the nodes are not distinct but don't raise this error, the output weights
+    will be incorrect.
+    The graph and node properties are (shallow) copied to the projected graph.
+
+    See :mod:`bipartite documentation <networkx.algorithms.bipartite>`
+    for further details on how bipartite graphs are handled in NetworkX.
+
+    See Also
+    --------
+    is_bipartite,
+    is_bipartite_node_set,
+    sets,
+    collaboration_weighted_projected_graph,
+    overlap_weighted_projected_graph,
+    generic_weighted_projected_graph
+    projected_graph
+
+    References
+    ----------
+    .. [1] Borgatti, S.P. and Halgin, D. In press. "Analyzing Affiliation
+        Networks". In Carrington, P. and Scott, J. (eds) The Sage Handbook
+        of Social Network Analysis. Sage Publications.
+    """
+    if B.is_directed():
+        pred = B.pred
+        G = nx.DiGraph()
+    else:
+        pred = B.adj
+        G = nx.Graph()
+    G.graph.update(B.graph)
+    G.add_nodes_from((n, B.nodes[n]) for n in nodes)
+    n_top = len(B) - len(nodes)
+
+    if n_top < 1:
+        raise NetworkXAlgorithmError(
+            f"the size of the nodes to project onto ({len(nodes)}) is >= the graph size ({len(B)}).\n"
+            "They are either not a valid bipartite partition or contain duplicates"
+        )
+
+    for u in nodes:
+        unbrs = set(B[u])
+        nbrs2 = {n for nbr in unbrs for n in B[nbr]} - {u}
+        for v in nbrs2:
+            vnbrs = set(pred[v])
+            common = unbrs & vnbrs
+            if not ratio:
+                weight = len(common)
+            else:
+                weight = len(common) / n_top
+            G.add_edge(u, v, weight=weight)
+    return G
+
+
+@not_implemented_for("multigraph")
+@nx._dispatchable(graphs="B", returns_graph=True)
+def collaboration_weighted_projected_graph(B, nodes):
+    r"""Newman's weighted projection of B onto one of its node sets.
+
+    The collaboration weighted projection is the projection of the
+    bipartite network B onto the specified nodes with weights assigned
+    using Newman's collaboration model [1]_:
+
+    .. math::
+
+        w_{u, v} = \sum_k \frac{\delta_{u}^{k} \delta_{v}^{k}}{d_k - 1}
+
+    where `u` and `v` are nodes from the bottom bipartite node set,
+    and `k` is a node of the top node set.
+    The value `d_k` is the degree of node `k` in the bipartite
+    network and `\delta_{u}^{k}` is 1 if node `u` is
+    linked to node `k` in the original bipartite graph or 0 otherwise.
+
+    The nodes retain their attributes and are connected in the resulting
+    graph if have an edge to a common node in the original bipartite
+    graph.
+
+    Parameters
+    ----------
+    B : NetworkX graph
+      The input graph should be bipartite.
+
+    nodes : list or iterable
+      Nodes to project onto (the "bottom" nodes).
+
+    Returns
+    -------
+    Graph : NetworkX graph
+       A graph that is the projection onto the given nodes.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import bipartite
+    >>> B = nx.path_graph(5)
+    >>> B.add_edge(1, 5)
+    >>> G = bipartite.collaboration_weighted_projected_graph(B, [0, 2, 4, 5])
+    >>> list(G)
+    [0, 2, 4, 5]
+    >>> for edge in sorted(G.edges(data=True)):
+    ...     print(edge)
+    (0, 2, {'weight': 0.5})
+    (0, 5, {'weight': 0.5})
+    (2, 4, {'weight': 1.0})
+    (2, 5, {'weight': 0.5})
+
+    Notes
+    -----
+    No attempt is made to verify that the input graph B is bipartite.
+    The graph and node properties are (shallow) copied to the projected graph.
+
+    See :mod:`bipartite documentation <networkx.algorithms.bipartite>`
+    for further details on how bipartite graphs are handled in NetworkX.
+
+    See Also
+    --------
+    is_bipartite,
+    is_bipartite_node_set,
+    sets,
+    weighted_projected_graph,
+    overlap_weighted_projected_graph,
+    generic_weighted_projected_graph,
+    projected_graph
+
+    References
+    ----------
+    .. [1] Scientific collaboration networks: II.
+        Shortest paths, weighted networks, and centrality,
+        M. E. J. Newman, Phys. Rev. E 64, 016132 (2001).
+    """
+    if B.is_directed():
+        pred = B.pred
+        G = nx.DiGraph()
+    else:
+        pred = B.adj
+        G = nx.Graph()
+    G.graph.update(B.graph)
+    G.add_nodes_from((n, B.nodes[n]) for n in nodes)
+    for u in nodes:
+        unbrs = set(B[u])
+        nbrs2 = {n for nbr in unbrs for n in B[nbr] if n != u}
+        for v in nbrs2:
+            vnbrs = set(pred[v])
+            common_degree = (len(B[n]) for n in unbrs & vnbrs)
+            weight = sum(1.0 / (deg - 1) for deg in common_degree if deg > 1)
+            G.add_edge(u, v, weight=weight)
+    return G
+
+
+@not_implemented_for("multigraph")
+@nx._dispatchable(graphs="B", returns_graph=True)
+def overlap_weighted_projected_graph(B, nodes, jaccard=True):
+    r"""Overlap weighted projection of B onto one of its node sets.
+
+    The overlap weighted projection is the projection of the bipartite
+    network B onto the specified nodes with weights representing
+    the Jaccard index between the neighborhoods of the two nodes in the
+    original bipartite network [1]_:
+
+    .. math::
+
+        w_{v, u} = \frac{|N(u) \cap N(v)|}{|N(u) \cup N(v)|}
+
+    or if the parameter 'jaccard' is False, the fraction of common
+    neighbors by minimum of both nodes degree in the original
+    bipartite graph [1]_:
+
+    .. math::
+
+        w_{v, u} = \frac{|N(u) \cap N(v)|}{min(|N(u)|, |N(v)|)}
+
+    The nodes retain their attributes and are connected in the resulting
+    graph if have an edge to a common node in the original bipartite graph.
+
+    Parameters
+    ----------
+    B : NetworkX graph
+        The input graph should be bipartite.
+
+    nodes : list or iterable
+        Nodes to project onto (the "bottom" nodes).
+
+    jaccard: Bool (default=True)
+
+    Returns
+    -------
+    Graph : NetworkX graph
+       A graph that is the projection onto the given nodes.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import bipartite
+    >>> B = nx.path_graph(5)
+    >>> nodes = [0, 2, 4]
+    >>> G = bipartite.overlap_weighted_projected_graph(B, nodes)
+    >>> list(G)
+    [0, 2, 4]
+    >>> list(G.edges(data=True))
+    [(0, 2, {'weight': 0.5}), (2, 4, {'weight': 0.5})]
+    >>> G = bipartite.overlap_weighted_projected_graph(B, nodes, jaccard=False)
+    >>> list(G.edges(data=True))
+    [(0, 2, {'weight': 1.0}), (2, 4, {'weight': 1.0})]
+
+    Notes
+    -----
+    No attempt is made to verify that the input graph B is bipartite.
+    The graph and node properties are (shallow) copied to the projected graph.
+
+    See :mod:`bipartite documentation <networkx.algorithms.bipartite>`
+    for further details on how bipartite graphs are handled in NetworkX.
+
+    See Also
+    --------
+    is_bipartite,
+    is_bipartite_node_set,
+    sets,
+    weighted_projected_graph,
+    collaboration_weighted_projected_graph,
+    generic_weighted_projected_graph,
+    projected_graph
+
+    References
+    ----------
+    .. [1] Borgatti, S.P. and Halgin, D. In press. Analyzing Affiliation
+        Networks. In Carrington, P. and Scott, J. (eds) The Sage Handbook
+        of Social Network Analysis. Sage Publications.
+
+    """
+    if B.is_directed():
+        pred = B.pred
+        G = nx.DiGraph()
+    else:
+        pred = B.adj
+        G = nx.Graph()
+    G.graph.update(B.graph)
+    G.add_nodes_from((n, B.nodes[n]) for n in nodes)
+    for u in nodes:
+        unbrs = set(B[u])
+        nbrs2 = {n for nbr in unbrs for n in B[nbr]} - {u}
+        for v in nbrs2:
+            vnbrs = set(pred[v])
+            if jaccard:
+                wt = len(unbrs & vnbrs) / len(unbrs | vnbrs)
+            else:
+                wt = len(unbrs & vnbrs) / min(len(unbrs), len(vnbrs))
+            G.add_edge(u, v, weight=wt)
+    return G
+
+
+@not_implemented_for("multigraph")
+@nx._dispatchable(graphs="B", preserve_all_attrs=True, returns_graph=True)
+def generic_weighted_projected_graph(B, nodes, weight_function=None):
+    r"""Weighted projection of B with a user-specified weight function.
+
+    The bipartite network B is projected on to the specified nodes
+    with weights computed by a user-specified function.  This function
+    must accept as a parameter the neighborhood sets of two nodes and
+    return an integer or a float.
+
+    The nodes retain their attributes and are connected in the resulting graph
+    if they have an edge to a common node in the original graph.
+
+    Parameters
+    ----------
+    B : NetworkX graph
+        The input graph should be bipartite.
+
+    nodes : list or iterable
+        Nodes to project onto (the "bottom" nodes).
+
+    weight_function : function
+        This function must accept as parameters the same input graph
+        that this function, and two nodes; and return an integer or a float.
+        The default function computes the number of shared neighbors.
+
+    Returns
+    -------
+    Graph : NetworkX graph
+       A graph that is the projection onto the given nodes.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import bipartite
+    >>> # Define some custom weight functions
+    >>> def jaccard(G, u, v):
+    ...     unbrs = set(G[u])
+    ...     vnbrs = set(G[v])
+    ...     return float(len(unbrs & vnbrs)) / len(unbrs | vnbrs)
+    >>> def my_weight(G, u, v, weight="weight"):
+    ...     w = 0
+    ...     for nbr in set(G[u]) & set(G[v]):
+    ...         w += G[u][nbr].get(weight, 1) + G[v][nbr].get(weight, 1)
+    ...     return w
+    >>> # A complete bipartite graph with 4 nodes and 4 edges
+    >>> B = nx.complete_bipartite_graph(2, 2)
+    >>> # Add some arbitrary weight to the edges
+    >>> for i, (u, v) in enumerate(B.edges()):
+    ...     B.edges[u, v]["weight"] = i + 1
+    >>> for edge in B.edges(data=True):
+    ...     print(edge)
+    (0, 2, {'weight': 1})
+    (0, 3, {'weight': 2})
+    (1, 2, {'weight': 3})
+    (1, 3, {'weight': 4})
+    >>> # By default, the weight is the number of shared neighbors
+    >>> G = bipartite.generic_weighted_projected_graph(B, [0, 1])
+    >>> print(list(G.edges(data=True)))
+    [(0, 1, {'weight': 2})]
+    >>> # To specify a custom weight function use the weight_function parameter
+    >>> G = bipartite.generic_weighted_projected_graph(
+    ...     B, [0, 1], weight_function=jaccard
+    ... )
+    >>> print(list(G.edges(data=True)))
+    [(0, 1, {'weight': 1.0})]
+    >>> G = bipartite.generic_weighted_projected_graph(
+    ...     B, [0, 1], weight_function=my_weight
+    ... )
+    >>> print(list(G.edges(data=True)))
+    [(0, 1, {'weight': 10})]
+
+    Notes
+    -----
+    No attempt is made to verify that the input graph B is bipartite.
+    The graph and node properties are (shallow) copied to the projected graph.
+
+    See :mod:`bipartite documentation <networkx.algorithms.bipartite>`
+    for further details on how bipartite graphs are handled in NetworkX.
+
+    See Also
+    --------
+    is_bipartite,
+    is_bipartite_node_set,
+    sets,
+    weighted_projected_graph,
+    collaboration_weighted_projected_graph,
+    overlap_weighted_projected_graph,
+    projected_graph
+
+    """
+    if B.is_directed():
+        pred = B.pred
+        G = nx.DiGraph()
+    else:
+        pred = B.adj
+        G = nx.Graph()
+    if weight_function is None:
+
+        def weight_function(G, u, v):
+            # Notice that we use set(pred[v]) for handling the directed case.
+            return len(set(G[u]) & set(pred[v]))
+
+    G.graph.update(B.graph)
+    G.add_nodes_from((n, B.nodes[n]) for n in nodes)
+    for u in nodes:
+        nbrs2 = {n for nbr in set(B[u]) for n in B[nbr]} - {u}
+        for v in nbrs2:
+            weight = weight_function(B, u, v)
+            G.add_edge(u, v, weight=weight)
+    return G

package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/redundancy.py

@@ -0,0 +1,112 @@
+"""Node redundancy for bipartite graphs."""
+
+from itertools import combinations
+
+import networkx as nx
+from networkx import NetworkXError
+
+__all__ = ["node_redundancy"]
+
+
+@nx._dispatchable
+def node_redundancy(G, nodes=None):
+    r"""Computes the node redundancy coefficients for the nodes in the bipartite
+    graph `G`.
+
+    The redundancy coefficient of a node `v` is the fraction of pairs of
+    neighbors of `v` that are both linked to other nodes. In a one-mode
+    projection these nodes would be linked together even if `v` were
+    not there.
+
+    More formally, for any vertex `v`, the *redundancy coefficient of `v`* is
+    defined by
+
+    .. math::
+
+        rc(v) = \frac{|\{\{u, w\} \subseteq N(v),
+        \: \exists v' \neq  v,\: (v',u) \in E\:
+        \mathrm{and}\: (v',w) \in E\}|}{ \frac{|N(v)|(|N(v)|-1)}{2}},
+
+    where `N(v)` is the set of neighbors of `v` in `G` [1]_.
+
+    Parameters
+    ----------
+    G : graph
+        A bipartite graph
+
+    nodes : list or iterable (optional)
+        Compute redundancy for these nodes. The default is all nodes in G.
+
+    Returns
+    -------
+    redundancy : dictionary
+        A dictionary keyed by node with the node redundancy value.
+
+    Examples
+    --------
+    Compute the redundancy coefficient of each node in a graph:
+
+    >>> from networkx.algorithms import bipartite
+    >>> G = nx.cycle_graph(4)
+    >>> rc = bipartite.node_redundancy(G)
+    >>> rc[0]
+    1.0
+
+    Compute the average redundancy for the graph:
+
+    >>> from networkx.algorithms import bipartite
+    >>> G = nx.cycle_graph(4)
+    >>> rc = bipartite.node_redundancy(G)
+    >>> sum(rc.values()) / len(G)
+    1.0
+
+    Compute the average redundancy for a set of nodes:
+
+    >>> from networkx.algorithms import bipartite
+    >>> G = nx.cycle_graph(4)
+    >>> rc = bipartite.node_redundancy(G)
+    >>> nodes = [0, 2]
+    >>> sum(rc[n] for n in nodes) / len(nodes)
+    1.0
+
+    Raises
+    ------
+    NetworkXError
+        If any of the nodes in the graph (or in `nodes`, if specified) has
+        (out-)degree less than two (which would result in division by zero,
+        according to the definition of the redundancy coefficient).
+
+    References
+    ----------
+    .. [1] Latapy, Matthieu, Clémence Magnien, and Nathalie Del Vecchio (2008).
+       Basic notions for the analysis of large two-mode networks.
+       Social Networks 30(1), 31--48.
+
+    """
+    if nodes is None:
+        nodes = G
+    if any(len(G[v]) < 2 for v in nodes):
+        raise NetworkXError(
+            "Cannot compute redundancy coefficient for a node"
+            " that has fewer than two neighbors."
+        )
+    # TODO This can be trivially parallelized.
+    return {v: _node_redundancy(G, v) for v in nodes}
+
+
+def _node_redundancy(G, v):
+    """Returns the redundancy of the node `v` in the bipartite graph `G`.
+
+    If `G` is a graph with `n` nodes, the redundancy of a node is the ratio
+    of the "overlap" of `v` to the maximum possible overlap of `v`
+    according to its degree. The overlap of `v` is the number of pairs of
+    neighbors that have mutual neighbors themselves, other than `v`.
+
+    `v` must have at least two neighbors in `G`.
+
+    """
+    n = len(G[v])
+    overlap = sum(
+        1 for (u, w) in combinations(G[v], 2) if (set(G[u]) & set(G[w])) - {v}
+    )
+    return (2 * overlap) / (n * (n - 1))

package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/spectral.py

@@ -0,0 +1,69 @@
+"""
+Spectral bipartivity measure.
+"""
+
+import networkx as nx
+
+__all__ = ["spectral_bipartivity"]
+
+
+@nx._dispatchable(edge_attrs="weight")
+def spectral_bipartivity(G, nodes=None, weight="weight"):
+    """Returns the spectral bipartivity.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+
+    nodes : list or container  optional(default is all nodes)
+      Nodes to return value of spectral bipartivity contribution.
+
+    weight : string or None  optional (default = 'weight')
+      Edge data key to use for edge weights. If None, weights set to 1.
+
+    Returns
+    -------
+    sb : float or dict
+       A single number if the keyword nodes is not specified, or
+       a dictionary keyed by node with the spectral bipartivity contribution
+       of that node as the value.
+
+    Examples
+    --------
+    >>> from networkx.algorithms import bipartite
+    >>> G = nx.path_graph(4)
+    >>> bipartite.spectral_bipartivity(G)
+    1.0
+
+    Notes
+    -----
+    This implementation uses Numpy (dense) matrices which are not efficient
+    for storing large sparse graphs.
+
+    See Also
+    --------
+    color
+
+    References
+    ----------
+    .. [1] E. Estrada and J. A. Rodríguez-Velázquez, "Spectral measures of
+       bipartivity in complex networks", PhysRev E 72, 046105 (2005)
+    """
+    import scipy as sp
+
+    nodelist = list(G)  # ordering of nodes in matrix
+    A = nx.to_numpy_array(G, nodelist, weight=weight)
+    expA = sp.linalg.expm(A)
+    expmA = sp.linalg.expm(-A)
+    coshA = 0.5 * (expA + expmA)
+    if nodes is None:
+        # return single number for entire graph
+        return float(coshA.diagonal().sum() / expA.diagonal().sum())
+    else:
+        # contribution for individual nodes
+        index = dict(zip(nodelist, range(len(nodelist))))
+        sb = {}
+        for n in nodes:
+            i = index[n]
+            sb[n] = coshA.item(i, i) / expA.item(i, i)
+        return sb