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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/networkx/algorithms/communicability_alg.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,160 @@
+"""
+Communicability.
+"""
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["communicability", "communicability_exp"]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+def communicability(G):
+    r"""Returns communicability between all pairs of nodes in G.
+
+    The communicability between pairs of nodes in G is the sum of
+    walks of different lengths starting at node u and ending at node v.
+
+    Parameters
+    ----------
+    G: graph
+
+    Returns
+    -------
+    comm: dictionary of dictionaries
+        Dictionary of dictionaries keyed by nodes with communicability
+        as the value.
+
+    Raises
+    ------
+    NetworkXError
+       If the graph is not undirected and simple.
+
+    See Also
+    --------
+    communicability_exp:
+       Communicability between all pairs of nodes in G  using spectral
+       decomposition.
+    communicability_betweenness_centrality:
+       Communicability betweeness centrality for each node in G.
+
+    Notes
+    -----
+    This algorithm uses a spectral decomposition of the adjacency matrix.
+    Let G=(V,E) be a simple undirected graph.  Using the connection between
+    the powers  of the adjacency matrix and the number of walks in the graph,
+    the communicability  between nodes `u` and `v` based on the graph spectrum
+    is [1]_
+
+    .. math::
+        C(u,v)=\sum_{j=1}^{n}\phi_{j}(u)\phi_{j}(v)e^{\lambda_{j}},
+
+    where `\phi_{j}(u)` is the `u\rm{th}` element of the `j\rm{th}` orthonormal
+    eigenvector of the adjacency matrix associated with the eigenvalue
+    `\lambda_{j}`.
+
+    References
+    ----------
+    .. [1] Ernesto Estrada, Naomichi Hatano,
+       "Communicability in complex networks",
+       Phys. Rev. E 77, 036111 (2008).
+       https://arxiv.org/abs/0707.0756
+
+    Examples
+    --------
+    >>> G = nx.Graph([(0, 1), (1, 2), (1, 5), (5, 4), (2, 4), (2, 3), (4, 3), (3, 6)])
+    >>> c = nx.communicability(G)
+    """
+    import numpy
+
+    nodelist = list(G)  # ordering of nodes in matrix
+    A = nx.to_numpy_array(G, nodelist)
+    # convert to 0-1 matrix
+    A[A != 0.0] = 1
+    w, vec = numpy.linalg.eigh(A)
+    expw = numpy.exp(w)
+    mapping = dict(zip(nodelist, range(len(nodelist))))
+    c = {}
+    # computing communicabilities
+    for u in G:
+        c[u] = {}
+        for v in G:
+            s = 0
+            p = mapping[u]
+            q = mapping[v]
+            for j in range(len(nodelist)):
+                s += vec[:, j][p] * vec[:, j][q] * expw[j]
+            c[u][v] = float(s)
+    return c
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+def communicability_exp(G):
+    r"""Returns communicability between all pairs of nodes in G.
+
+    Communicability between pair of node (u,v) of node in G is the sum of
+    walks of different lengths starting at node u and ending at node v.
+
+    Parameters
+    ----------
+    G: graph
+
+    Returns
+    -------
+    comm: dictionary of dictionaries
+        Dictionary of dictionaries keyed by nodes with communicability
+        as the value.
+
+    Raises
+    ------
+    NetworkXError
+        If the graph is not undirected and simple.
+
+    See Also
+    --------
+    communicability:
+       Communicability between pairs of nodes in G.
+    communicability_betweenness_centrality:
+       Communicability betweeness centrality for each node in G.
+
+    Notes
+    -----
+    This algorithm uses matrix exponentiation of the adjacency matrix.
+
+    Let G=(V,E) be a simple undirected graph.  Using the connection between
+    the powers  of the adjacency matrix and the number of walks in the graph,
+    the communicability between nodes u and v is [1]_,
+
+    .. math::
+        C(u,v) = (e^A)_{uv},
+
+    where `A` is the adjacency matrix of G.
+
+    References
+    ----------
+    .. [1] Ernesto Estrada, Naomichi Hatano,
+       "Communicability in complex networks",
+       Phys. Rev. E 77, 036111 (2008).
+       https://arxiv.org/abs/0707.0756
+
+    Examples
+    --------
+    >>> G = nx.Graph([(0, 1), (1, 2), (1, 5), (5, 4), (2, 4), (2, 3), (4, 3), (3, 6)])
+    >>> c = nx.communicability_exp(G)
+    """
+    import scipy.linalg
+
+    nodelist = list(G)  # ordering of nodes in matrix
+    A = nx.to_numpy_array(G, nodelist)
+    # convert to 0-1 matrix
+    A[A != 0.0] = 1
+    # communicability matrix
+    expA = scipy.linalg.expm(A)
+    mapping = dict(zip(nodelist, range(len(nodelist))))
+    c = {}
+    for u in G:
+        c[u] = {}
+        for v in G:
+            c[u][v] = float(expA[mapping[u], mapping[v]])
+    return c