285 lines
10 KiB
Python
285 lines
10 KiB
Python
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# Copyright (C) 2004-2019 by
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# Aric Hagberg <hagberg@lanl.gov>
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# Dan Schult <dschult@colgate.edu>
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# Pieter Swart <swart@lanl.gov>
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# All rights reserved.
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# BSD license.
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#
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# Authors: Aric Hagberg <aric.hagberg@gmail.com>
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# Pieter Swart <swart@lanl.gov>
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# Sasha Gutfraind <ag362@cornell.edu>
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# Dan Schult <dschult@colgate.edu>
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# Michael Lauria <michael.david.lauria@gmail.com>
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"""
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Closeness centrality measures.
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"""
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import functools
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import networkx as nx
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from networkx.exception import NetworkXError
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from networkx.utils.decorators import not_implemented_for
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__all__ = ['closeness_centrality', 'incremental_closeness_centrality']
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def closeness_centrality(G, u=None, distance=None, wf_improved=True):
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r"""Compute closeness centrality for nodes.
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Closeness centrality [1]_ of a node `u` is the reciprocal of the
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average shortest path distance to `u` over all `n-1` reachable nodes.
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.. math::
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C(u) = \frac{n - 1}{\sum_{v=1}^{n-1} d(v, u)},
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where `d(v, u)` is the shortest-path distance between `v` and `u`,
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and `n` is the number of nodes that can reach `u`. Notice that the
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closeness distance function computes the incoming distance to `u`
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for directed graphs. To use outward distance, act on `G.reverse()`.
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Notice that higher values of closeness indicate higher centrality.
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Wasserman and Faust propose an improved formula for graphs with
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more than one connected component. The result is "a ratio of the
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fraction of actors in the group who are reachable, to the average
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distance" from the reachable actors [2]_. You might think this
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scale factor is inverted but it is not. As is, nodes from small
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components receive a smaller closeness value. Letting `N` denote
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the number of nodes in the graph,
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.. math::
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C_{WF}(u) = \frac{n-1}{N-1} \frac{n - 1}{\sum_{v=1}^{n-1} d(v, u)},
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Parameters
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----------
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G : graph
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A NetworkX graph
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u : node, optional
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Return only the value for node u
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distance : edge attribute key, optional (default=None)
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Use the specified edge attribute as the edge distance in shortest
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path calculations
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wf_improved : bool, optional (default=True)
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If True, scale by the fraction of nodes reachable. This gives the
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Wasserman and Faust improved formula. For single component graphs
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it is the same as the original formula.
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Returns
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-------
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nodes : dictionary
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Dictionary of nodes with closeness centrality as the value.
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See Also
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--------
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betweenness_centrality, load_centrality, eigenvector_centrality,
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degree_centrality, incremental_closeness_centrality
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Notes
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-----
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The closeness centrality is normalized to `(n-1)/(|G|-1)` where
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`n` is the number of nodes in the connected part of graph
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containing the node. If the graph is not completely connected,
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this algorithm computes the closeness centrality for each
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connected part separately scaled by that parts size.
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If the 'distance' keyword is set to an edge attribute key then the
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shortest-path length will be computed using Dijkstra's algorithm with
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that edge attribute as the edge weight.
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The closeness centrality uses *inward* distance to a node, not outward.
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If you want to use outword distances apply the function to `G.reverse()`
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In NetworkX 2.2 and earlier a bug caused Dijkstra's algorithm to use the
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outward distance rather than the inward distance. If you use a 'distance'
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keyword and a DiGraph, your results will change between v2.2 and v2.3.
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References
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----------
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.. [1] Linton C. Freeman: Centrality in networks: I.
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Conceptual clarification. Social Networks 1:215-239, 1979.
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http://leonidzhukov.ru/hse/2013/socialnetworks/papers/freeman79-centrality.pdf
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.. [2] pg. 201 of Wasserman, S. and Faust, K.,
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Social Network Analysis: Methods and Applications, 1994,
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Cambridge University Press.
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"""
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if G.is_directed():
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G = G.reverse() # create a reversed graph view
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if distance is not None:
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# use Dijkstra's algorithm with specified attribute as edge weight
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path_length = functools.partial(
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nx.single_source_dijkstra_path_length, weight=distance)
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else:
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path_length = nx.single_source_shortest_path_length
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if u is None:
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nodes = G.nodes
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else:
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nodes = [u]
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closeness_centrality = {}
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for n in nodes:
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sp = path_length(G, n)
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totsp = sum(sp.values())
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len_G = len(G)
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_closeness_centrality = 0.0
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if totsp > 0.0 and len_G > 1:
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_closeness_centrality = (len(sp) - 1.0) / totsp
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# normalize to number of nodes-1 in connected part
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if wf_improved:
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s = (len(sp) - 1.0) / (len_G - 1)
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_closeness_centrality *= s
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closeness_centrality[n] = _closeness_centrality
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if u is not None:
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return closeness_centrality[u]
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else:
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return closeness_centrality
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@not_implemented_for('directed')
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def incremental_closeness_centrality(G,
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edge,
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prev_cc=None,
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insertion=True,
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wf_improved=True):
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r"""Incremental closeness centrality for nodes.
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Compute closeness centrality for nodes using level-based work filtering
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as described in Incremental Algorithms for Closeness Centrality by Sariyuce et al.
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Level-based work filtering detects unnecessary updates to the closeness
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centrality and filters them out.
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---
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From "Incremental Algorithms for Closeness Centrality":
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Theorem 1: Let :math:`G = (V, E)` be a graph and u and v be two vertices in V
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such that there is no edge (u, v) in E. Let :math:`G' = (V, E \cup uv)`
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Then :math:`cc[s] = cc'[s]` if and only if :math:`\left|dG(s, u) - dG(s, v)\right| \leq 1`.
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Where :math:`dG(u, v)` denotes the length of the shortest path between
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two vertices u, v in a graph G, cc[s] is the closeness centrality for a
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vertex s in V, and cc'[s] is the closeness centrality for a
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vertex s in V, with the (u, v) edge added.
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---
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We use Theorem 1 to filter out updates when adding or removing an edge.
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When adding an edge (u, v), we compute the shortest path lengths from all
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other nodes to u and to v before the node is added. When removing an edge,
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we compute the shortest path lengths after the edge is removed. Then we
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apply Theorem 1 to use previously computed closeness centrality for nodes
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where :math:`\left|dG(s, u) - dG(s, v)\right| \leq 1`. This works only for
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undirected, unweighted graphs; the distance argument is not supported.
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Closeness centrality [1]_ of a node `u` is the reciprocal of the
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sum of the shortest path distances from `u` to all `n-1` other nodes.
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Since the sum of distances depends on the number of nodes in the
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graph, closeness is normalized by the sum of minimum possible
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distances `n-1`.
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.. math::
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C(u) = \frac{n - 1}{\sum_{v=1}^{n-1} d(v, u)},
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where `d(v, u)` is the shortest-path distance between `v` and `u`,
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and `n` is the number of nodes in the graph.
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Notice that higher values of closeness indicate higher centrality.
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Parameters
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----------
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G : graph
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A NetworkX graph
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edge : tuple
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The modified edge (u, v) in the graph.
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prev_cc : dictionary
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The previous closeness centrality for all nodes in the graph.
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insertion : bool, optional
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If True (default) the edge was inserted, otherwise it was deleted from the graph.
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wf_improved : bool, optional (default=True)
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If True, scale by the fraction of nodes reachable. This gives the
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Wasserman and Faust improved formula. For single component graphs
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it is the same as the original formula.
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Returns
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-------
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nodes : dictionary
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Dictionary of nodes with closeness centrality as the value.
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See Also
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--------
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betweenness_centrality, load_centrality, eigenvector_centrality,
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degree_centrality, closeness_centrality
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Notes
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-----
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The closeness centrality is normalized to `(n-1)/(|G|-1)` where
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`n` is the number of nodes in the connected part of graph
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containing the node. If the graph is not completely connected,
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this algorithm computes the closeness centrality for each
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connected part separately.
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References
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----------
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.. [1] Freeman, L.C., 1979. Centrality in networks: I.
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Conceptual clarification. Social Networks 1, 215--239.
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http://www.soc.ucsb.edu/faculty/friedkin/Syllabi/Soc146/Freeman78.PDF
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.. [2] Sariyuce, A.E. ; Kaya, K. ; Saule, E. ; Catalyiirek, U.V. Incremental
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Algorithms for Closeness Centrality. 2013 IEEE International Conference on Big Data
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http://sariyuce.com/papers/bigdata13.pdf
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"""
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if prev_cc is not None and set(prev_cc.keys()) != set(G.nodes()):
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raise NetworkXError('prev_cc and G do not have the same nodes')
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# Unpack edge
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(u, v) = edge
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path_length = nx.single_source_shortest_path_length
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if insertion:
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# For edge insertion, we want shortest paths before the edge is inserted
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du = path_length(G, u)
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dv = path_length(G, v)
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G.add_edge(u, v)
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else:
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G.remove_edge(u, v)
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# For edge removal, we want shortest paths after the edge is removed
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du = path_length(G, u)
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dv = path_length(G, v)
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if prev_cc is None:
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return nx.closeness_centrality(G)
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nodes = G.nodes()
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closeness_centrality = {}
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for n in nodes:
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if (n in du and n in dv and abs(du[n] - dv[n]) <= 1):
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closeness_centrality[n] = prev_cc[n]
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else:
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sp = path_length(G, n)
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totsp = sum(sp.values())
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len_G = len(G)
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_closeness_centrality = 0.0
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if totsp > 0.0 and len_G > 1:
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_closeness_centrality = (len(sp) - 1.0) / totsp
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# normalize to number of nodes-1 in connected part
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if wf_improved:
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s = (len(sp) - 1.0) / (len_G - 1)
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_closeness_centrality *= s
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closeness_centrality[n] = _closeness_centrality
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# Leave the graph as we found it
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if insertion:
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G.remove_edge(u, v)
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else:
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G.add_edge(u, v)
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return closeness_centrality
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