okstra 0.107.2 → 0.109.0

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

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+"""Functions for computing the harmonic centrality of a graph."""
+
+from functools import partial
+
+import networkx as nx
+
+__all__ = ["harmonic_centrality"]
+
+
+@nx._dispatchable(edge_attrs="distance")
+def harmonic_centrality(G, nbunch=None, distance=None, sources=None):
+    r"""Compute harmonic centrality for nodes.
+
+    Harmonic centrality [1]_ of a node `u` is the sum of the reciprocal
+    of the shortest path distances from all other nodes to `u`
+
+    .. math::
+
+        C(u) = \sum_{v \neq u} \frac{1}{d(v, u)}
+
+    where `d(v, u)` is the shortest-path distance between `v` and `u`.
+
+    If `sources` is given as an argument, the returned harmonic centrality
+    values are calculated as the sum of the reciprocals of the shortest
+    path distances from the nodes specified in `sources` to `u` instead
+    of from all nodes to `u`.
+
+    Notice that higher values indicate higher centrality.
+
+    Parameters
+    ----------
+    G : graph
+      A NetworkX graph
+
+    nbunch : container (default: all nodes in G)
+      Container of nodes for which harmonic centrality values are calculated.
+
+    sources : container (default: all nodes in G)
+      Container of nodes `v` over which reciprocal distances are computed.
+      Nodes not in `G` are silently ignored.
+
+    distance : edge attribute key, optional (default=None)
+      Use the specified edge attribute as the edge distance in shortest
+      path calculations.  If `None`, then each edge will have distance equal to 1.
+
+    Returns
+    -------
+    nodes : dictionary
+      Dictionary of nodes with harmonic centrality as the value.
+
+    See Also
+    --------
+    betweenness_centrality, load_centrality, eigenvector_centrality,
+    degree_centrality, closeness_centrality
+
+    Notes
+    -----
+    If the 'distance' keyword is set to an edge attribute key then the
+    shortest-path length will be computed using Dijkstra's algorithm with
+    that edge attribute as the edge weight.
+
+    References
+    ----------
+    .. [1] Boldi, Paolo, and Sebastiano Vigna. "Axioms for centrality."
+           Internet Mathematics 10.3-4 (2014): 222-262.
+    """
+
+    nbunch = set(G.nbunch_iter(nbunch) if nbunch is not None else G.nodes)
+    sources = set(G.nbunch_iter(sources) if sources is not None else G.nodes)
+
+    centrality = {u: 0 for u in nbunch}
+
+    transposed = False
+    if len(nbunch) < len(sources):
+        transposed = True
+        nbunch, sources = sources, nbunch
+        if nx.is_directed(G):
+            G = nx.reverse(G, copy=False)
+
+    spl = partial(nx.shortest_path_length, G, weight=distance)
+    for v in sources:
+        dist = spl(v)
+        for u, d_uv in dist.items():
+            # Ignore self-loops and edges with 0 weight
+            if d_uv != 0 and u in nbunch:
+                centrality[v if transposed else u] += 1 / d_uv
+
+    return centrality

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

@@ -0,0 +1,331 @@
+"""Katz centrality."""
+
+import math
+
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["katz_centrality", "katz_centrality_numpy"]
+
+
+@not_implemented_for("multigraph")
+@nx._dispatchable(edge_attrs="weight")
+def katz_centrality(
+    G,
+    alpha=0.1,
+    beta=1.0,
+    max_iter=1000,
+    tol=1.0e-6,
+    nstart=None,
+    normalized=True,
+    weight=None,
+):
+    r"""Compute the Katz centrality for the nodes of the graph G.
+
+    Katz centrality computes the centrality for a node based on the centrality
+    of its neighbors. It is a generalization of the eigenvector centrality. The
+    Katz centrality for node $i$ is
+
+    .. math::
+
+        x_i = \alpha \sum_{j} A_{ij} x_j + \beta,
+
+    where $A$ is the adjacency matrix of graph G with eigenvalues $\lambda$.
+
+    The parameter $\beta$ controls the initial centrality and
+
+    .. math::
+
+        \alpha < \frac{1}{\lambda_{\max}}.
+
+    Katz centrality computes the relative influence of a node within a
+    network by measuring the number of the immediate neighbors (first
+    degree nodes) and also all other nodes in the network that connect
+    to the node under consideration through these immediate neighbors.
+
+    Extra weight can be provided to immediate neighbors through the
+    parameter $\beta$.  Connections made with distant neighbors
+    are, however, penalized by an attenuation factor $\alpha$ which
+    should be strictly less than the inverse largest eigenvalue of the
+    adjacency matrix in order for the Katz centrality to be computed
+    correctly. More information is provided in [1]_.
+
+    Parameters
+    ----------
+    G : graph
+      A NetworkX graph.
+
+    alpha : float, optional (default=0.1)
+      Attenuation factor
+
+    beta : scalar or dictionary, optional (default=1.0)
+      Weight attributed to the immediate neighborhood. If not a scalar, the
+      dictionary must have a value for every node.
+
+    max_iter : integer, optional (default=1000)
+      Maximum number of iterations in power method.
+
+    tol : float, optional (default=1.0e-6)
+      Error tolerance used to check convergence in power method iteration.
+
+    nstart : dictionary, optional
+      Starting value of Katz iteration for each node.
+
+    normalized : bool, optional (default=True)
+      If True normalize the resulting 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.
+      In this measure the weight is interpreted as the connection strength.
+
+    Returns
+    -------
+    nodes : dictionary
+       Dictionary of nodes with Katz centrality as the value.
+
+    Raises
+    ------
+    NetworkXError
+       If the parameter `beta` is not a scalar but lacks a value for at least
+       one node
+
+    PowerIterationFailedConvergence
+        If the algorithm fails to converge to the specified tolerance
+        within the specified number of iterations of the power iteration
+        method.
+
+    Examples
+    --------
+    >>> import math
+    >>> G = nx.path_graph(4)
+    >>> phi = (1 + math.sqrt(5)) / 2.0  # largest eigenvalue of adj matrix
+    >>> centrality = nx.katz_centrality(G, 1 / phi - 0.01)
+    >>> for n, c in sorted(centrality.items()):
+    ...     print(f"{n} {c:.2f}")
+    0 0.37
+    1 0.60
+    2 0.60
+    3 0.37
+
+    See Also
+    --------
+    katz_centrality_numpy
+    eigenvector_centrality
+    eigenvector_centrality_numpy
+    :func:`~networkx.algorithms.link_analysis.pagerank_alg.pagerank`
+    :func:`~networkx.algorithms.link_analysis.hits_alg.hits`
+
+    Notes
+    -----
+    Katz centrality was introduced by [2]_.
+
+    This algorithm it uses the power method to find the eigenvector
+    corresponding to the largest eigenvalue of the adjacency matrix of ``G``.
+    The parameter ``alpha`` should be strictly less than the inverse of largest
+    eigenvalue of the adjacency matrix for the algorithm to converge.
+    You can use ``max(nx.adjacency_spectrum(G))`` to get $\lambda_{\max}$ the largest
+    eigenvalue of the adjacency matrix.
+    The iteration will stop after ``max_iter`` iterations or an error tolerance of
+    ``number_of_nodes(G) * tol`` has been reached.
+
+    For strongly connected graphs, as $\alpha \to 1/\lambda_{\max}$, and $\beta > 0$,
+    Katz centrality approaches the results for eigenvector centrality.
+
+    For directed graphs this finds "left" eigenvectors which corresponds
+    to the in-edges in the graph. For out-edges Katz centrality,
+    first reverse the graph with ``G.reverse()``.
+
+    References
+    ----------
+    .. [1] Mark E. J. Newman:
+       Networks: An Introduction.
+       Oxford University Press, USA, 2010, p. 720.
+    .. [2] Leo Katz:
+       A New Status Index Derived from Sociometric Index.
+       Psychometrika 18(1):39–43, 1953
+       https://link.springer.com/content/pdf/10.1007/BF02289026.pdf
+    """
+    if len(G) == 0:
+        return {}
+
+    nnodes = G.number_of_nodes()
+
+    if nstart is None:
+        # choose starting vector with entries of 0
+        x = {n: 0 for n in G}
+    else:
+        x = nstart
+
+    try:
+        b = dict.fromkeys(G, float(beta))
+    except (TypeError, ValueError, AttributeError) as err:
+        b = beta
+        if set(beta) != set(G):
+            raise nx.NetworkXError(
+                "beta dictionary must have a value for every node"
+            ) from err
+
+    # make up to max_iter iterations
+    for _ in range(max_iter):
+        xlast = x
+        x = dict.fromkeys(xlast, 0)
+        # do the multiplication y^T = Alpha * x^T A + Beta
+        for n in x:
+            for nbr in G[n]:
+                x[nbr] += xlast[n] * G[n][nbr].get(weight, 1)
+        for n in x:
+            x[n] = alpha * x[n] + b[n]
+
+        # check convergence
+        error = sum(abs(x[n] - xlast[n]) for n in x)
+        if error < nnodes * tol:
+            if normalized:
+                # normalize vector
+                try:
+                    s = 1.0 / math.hypot(*x.values())
+                except ZeroDivisionError:
+                    s = 1.0
+            else:
+                s = 1
+            for n in x:
+                x[n] *= s
+            return x
+    raise nx.PowerIterationFailedConvergence(max_iter)
+
+
+@not_implemented_for("multigraph")
+@nx._dispatchable(edge_attrs="weight")
+def katz_centrality_numpy(G, alpha=0.1, beta=1.0, normalized=True, weight=None):
+    r"""Compute the Katz centrality for the graph G.
+
+    Katz centrality computes the centrality for a node based on the centrality
+    of its neighbors. It is a generalization of the eigenvector centrality. The
+    Katz centrality for node $i$ is
+
+    .. math::
+
+        x_i = \alpha \sum_{j} A_{ij} x_j + \beta,
+
+    where $A$ is the adjacency matrix of graph G with eigenvalues $\lambda$.
+
+    The parameter $\beta$ controls the initial centrality and
+
+    .. math::
+
+        \alpha < \frac{1}{\lambda_{\max}}.
+
+    Katz centrality computes the relative influence of a node within a
+    network by measuring the number of the immediate neighbors (first
+    degree nodes) and also all other nodes in the network that connect
+    to the node under consideration through these immediate neighbors.
+
+    Extra weight can be provided to immediate neighbors through the
+    parameter $\beta$.  Connections made with distant neighbors
+    are, however, penalized by an attenuation factor $\alpha$ which
+    should be strictly less than the inverse largest eigenvalue of the
+    adjacency matrix in order for the Katz centrality to be computed
+    correctly. More information is provided in [1]_.
+
+    Parameters
+    ----------
+    G : graph
+      A NetworkX graph
+
+    alpha : float
+      Attenuation factor
+
+    beta : scalar or dictionary, optional (default=1.0)
+      Weight attributed to the immediate neighborhood. If not a scalar the
+      dictionary must have an value for every node.
+
+    normalized : bool
+      If True normalize the resulting values.
+
+    weight : None or string, optional
+      If None, all edge weights are considered equal.
+      Otherwise holds the name of the edge attribute used as weight.
+      In this measure the weight is interpreted as the connection strength.
+
+    Returns
+    -------
+    nodes : dictionary
+       Dictionary of nodes with Katz centrality as the value.
+
+    Raises
+    ------
+    NetworkXError
+       If the parameter `beta` is not a scalar but lacks a value for at least
+       one node
+
+    Examples
+    --------
+    >>> import math
+    >>> G = nx.path_graph(4)
+    >>> phi = (1 + math.sqrt(5)) / 2.0  # largest eigenvalue of adj matrix
+    >>> centrality = nx.katz_centrality_numpy(G, 1 / phi)
+    >>> for n, c in sorted(centrality.items()):
+    ...     print(f"{n} {c:.2f}")
+    0 0.37
+    1 0.60
+    2 0.60
+    3 0.37
+
+    See Also
+    --------
+    katz_centrality
+    eigenvector_centrality_numpy
+    eigenvector_centrality
+    :func:`~networkx.algorithms.link_analysis.pagerank_alg.pagerank`
+    :func:`~networkx.algorithms.link_analysis.hits_alg.hits`
+
+    Notes
+    -----
+    Katz centrality was introduced by [2]_.
+
+    This algorithm uses a direct linear solver to solve the above equation.
+    The parameter ``alpha`` should be strictly less than the inverse of largest
+    eigenvalue of the adjacency matrix for there to be a solution.
+    You can use ``max(nx.adjacency_spectrum(G))`` to get $\lambda_{\max}$ the largest
+    eigenvalue of the adjacency matrix.
+
+    For strongly connected graphs, as $\alpha \to 1/\lambda_{\max}$, and $\beta > 0$,
+    Katz centrality approaches the results for eigenvector centrality.
+
+    For directed graphs this finds "left" eigenvectors which corresponds
+    to the in-edges in the graph. For out-edges Katz centrality,
+    first reverse the graph with ``G.reverse()``.
+
+    References
+    ----------
+    .. [1] Mark E. J. Newman:
+       Networks: An Introduction.
+       Oxford University Press, USA, 2010, p. 173.
+    .. [2] Leo Katz:
+       A New Status Index Derived from Sociometric Index.
+       Psychometrika 18(1):39–43, 1953
+       https://link.springer.com/content/pdf/10.1007/BF02289026.pdf
+    """
+    import numpy as np
+
+    if len(G) == 0:
+        return {}
+    try:
+        nodelist = beta.keys()
+        if set(nodelist) != set(G):
+            raise nx.NetworkXError("beta dictionary must have a value for every node")
+        b = np.array(list(beta.values()), dtype=float)
+    except AttributeError:
+        nodelist = list(G)
+        try:
+            b = np.ones((len(nodelist), 1)) * beta
+        except (TypeError, ValueError, AttributeError) as err:
+            raise nx.NetworkXError("beta must be a number") from err
+
+    A = nx.adjacency_matrix(G, nodelist=nodelist, weight=weight).todense().T
+    n = A.shape[0]
+    centrality = np.linalg.solve(np.eye(n, n) - (alpha * A), b).squeeze()
+
+    # Normalize: rely on truediv to cast to float, then tolist to make Python numbers
+    norm = np.sign(sum(centrality)) * np.linalg.norm(centrality) if normalized else 1
+    return dict(zip(nodelist, (centrality / norm).tolist()))

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

@@ -0,0 +1,150 @@
+"""
+Laplacian centrality measures.
+"""
+
+import networkx as nx
+
+__all__ = ["laplacian_centrality"]
+
+
+@nx._dispatchable(edge_attrs="weight")
+def laplacian_centrality(
+    G, normalized=True, nodelist=None, weight="weight", walk_type=None, alpha=0.95
+):
+    r"""Compute the Laplacian centrality for nodes in the graph `G`.
+
+    The Laplacian Centrality of a node ``i`` is measured by the drop in the
+    Laplacian Energy after deleting node ``i`` from the graph. The Laplacian Energy
+    is the sum of the squared eigenvalues of a graph's Laplacian matrix.
+
+    .. math::
+
+        C_L(u_i,G) = \frac{(\Delta E)_i}{E_L (G)} = \frac{E_L (G)-E_L (G_i)}{E_L (G)}
+
+        E_L (G) = \sum_{i=0}^n \lambda_i^2
+
+    Where $E_L (G)$ is the Laplacian energy of graph `G`,
+    E_L (G_i) is the Laplacian energy of graph `G` after deleting node ``i``
+    and $\lambda_i$ are the eigenvalues of `G`'s Laplacian matrix.
+    This formula shows the normalized value. Without normalization,
+    the numerator on the right side is returned.
+
+    Parameters
+    ----------
+    G : graph
+        A networkx graph
+
+    normalized : bool (default = True)
+        If True the centrality score is scaled so the sum over all nodes is 1.
+        If False the centrality score for each node is the drop in Laplacian
+        energy when that node is removed.
+
+    nodelist : list, optional (default = None)
+        The rows and columns are ordered according to the nodes in nodelist.
+        If nodelist is None, then the ordering is produced by G.nodes().
+
+    weight: string or None, optional (default=`weight`)
+        Optional parameter `weight` to compute the Laplacian matrix.
+        The edge data key used to compute each value in the matrix.
+        If None, then each edge has weight 1.
+
+    walk_type : string or None, optional (default=None)
+        Optional parameter `walk_type` used when calling
+        :func:`directed_laplacian_matrix <networkx.directed_laplacian_matrix>`.
+        One of ``"random"``, ``"lazy"``, or ``"pagerank"``. If ``walk_type=None``
+        (the default), then a value is selected according to the properties of `G`:
+        - ``walk_type="random"`` if `G` is strongly connected and aperiodic
+        - ``walk_type="lazy"`` if `G` is strongly connected but not aperiodic
+        - ``walk_type="pagerank"`` for all other cases.
+
+    alpha : real (default = 0.95)
+        Optional parameter `alpha` used when calling
+        :func:`directed_laplacian_matrix <networkx.directed_laplacian_matrix>`.
+        (1 - alpha) is the teleportation probability used with pagerank.
+
+    Returns
+    -------
+    nodes : dictionary
+       Dictionary of nodes with Laplacian centrality as the value.
+
+    Examples
+    --------
+    >>> G = nx.Graph()
+    >>> edges = [(0, 1, 4), (0, 2, 2), (2, 1, 1), (1, 3, 2), (1, 4, 2), (4, 5, 1)]
+    >>> G.add_weighted_edges_from(edges)
+    >>> sorted((v, f"{c:0.2f}") for v, c in laplacian_centrality(G).items())
+    [(0, '0.70'), (1, '0.90'), (2, '0.28'), (3, '0.22'), (4, '0.26'), (5, '0.04')]
+
+    Notes
+    -----
+    The algorithm is implemented based on [1]_ with an extension to directed graphs
+    using the ``directed_laplacian_matrix`` function.
+
+    Raises
+    ------
+    NetworkXPointlessConcept
+        If the graph `G` is the null graph.
+    ZeroDivisionError
+        If the graph `G` has no edges (is empty) and normalization is requested.
+
+    References
+    ----------
+    .. [1] Qi, X., Fuller, E., Wu, Q., Wu, Y., and Zhang, C.-Q. (2012).
+       Laplacian centrality: A new centrality measure for weighted networks.
+       Information Sciences, 194:240-253.
+       https://math.wvu.edu/~cqzhang/Publication-files/my-paper/INS-2012-Laplacian-W.pdf
+
+    See Also
+    --------
+    :func:`~networkx.linalg.laplacianmatrix.directed_laplacian_matrix`
+    :func:`~networkx.linalg.laplacianmatrix.laplacian_matrix`
+    """
+    import numpy as np
+    import scipy as sp
+
+    if len(G) == 0:
+        raise nx.NetworkXPointlessConcept("null graph has no centrality defined")
+    if G.size(weight=weight) == 0:
+        if normalized:
+            raise ZeroDivisionError("graph with no edges has zero full energy")
+        return {n: 0 for n in G}
+
+    if nodelist is not None:
+        nodeset = set(G.nbunch_iter(nodelist))
+        if len(nodeset) != len(nodelist):
+            raise nx.NetworkXError("nodelist has duplicate nodes or nodes not in G")
+        nodes = nodelist + [n for n in G if n not in nodeset]
+    else:
+        nodelist = nodes = list(G)
+
+    if G.is_directed():
+        lap_matrix = nx.directed_laplacian_matrix(G, nodes, weight, walk_type, alpha)
+    else:
+        lap_matrix = nx.laplacian_matrix(G, nodes, weight).toarray()
+
+    full_energy = np.sum(lap_matrix**2)
+
+    # calculate laplacian centrality
+    laplace_centralities_dict = {}
+    for i, node in enumerate(nodelist):
+        # remove row and col i from lap_matrix
+        all_but_i = list(np.arange(lap_matrix.shape[0]))
+        all_but_i.remove(i)
+        A_2 = lap_matrix[all_but_i, :][:, all_but_i]
+
+        # Adjust diagonal for removed row
+        new_diag = lap_matrix.diagonal() - abs(lap_matrix[:, i])
+        np.fill_diagonal(A_2, new_diag[all_but_i])
+
+        if len(all_but_i) > 0:  # catches degenerate case of single node
+            new_energy = np.sum(A_2**2)
+        else:
+            new_energy = 0.0
+
+        lapl_cent = full_energy - new_energy
+        if normalized:
+            lapl_cent = lapl_cent / full_energy
+
+        laplace_centralities_dict[node] = float(lapl_cent)
+
+    return laplace_centralities_dict