Edge swap graph.

edgeswap.py

# Copyright (c) 2011-2012 Christopher D. Lasher
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##########################################
# Matt Cummins Note (29th September 2019).
# Made a couple of minor edits to get this code working in 2019 networkx with Python 3
##########################################

class EdgeSwapGraph(nx.Graph):
    """An interaction graph which can produce a "random" graph from
    itself by an iterative edge-swap technique that preserves the degree
    distribution of the original graph.
    """
    def randomize_by_edge_swaps(self, num_iterations):
        """Randomizes the graph by swapping edges in such a way that
        preserves the degree distribution of the original graph.
        The underlying idea stems from the following. Say we have this
        original formation of edges in the original graph:
            head1   head2
              |       |
              |       |
              |       |
            tail1   tail2
        Then we wish to swap the edges between these four nodes as one
        of the two following possibilities:
            head1   head2       head1---head2
                 \ /
                  X
                 / \
            tail1   tail2       tail1---tail2
        We approach both by following through the first of the two
        possibilities, but before committing to the edge creation, give
        a chance that we flip the nodes `head1` and `tail1`.
        See the following references for the algorithm:
        - F. Viger and M. Latapy, "Efficient and Simple Generation of
          Random Simple Connected Graphs with Prescribed Degree
          Sequence," Computing and Combinatorics, 2005.
        - M. Mihail and N.K. Vishnoi, "On Generating Graphs with
          Prescribed Vertex Degrees for Complex Network Modeling,"
          ARACNE 2002, 2002, pp. 1–11.
        - R. Milo, N. Kashtan, S. Itzkovitz, M.E.J. Newman, and U.
          Alon, "On the uniform generation of random graphs with
          prescribed degree sequences," cond-mat/0312028, Dec. 2003.
        :Parameters:
        - `num_iterations`: the number of iterations for edge swapping
          to perform; this value will be multiplied by the number of
          edges in the graph to get the total number of iterations
        """
        newgraph = self.copy()
        edge_list = list(newgraph.edges())

        num_edges = len(edge_list)
        total_iterations = num_edges * num_iterations

        for i in range(total_iterations):
            rand_index1 = int(round(random.random() * (num_edges - 1)))
            rand_index2 = int(round(random.random() * (num_edges - 1)))
            original_edge1 = edge_list[rand_index1]
            original_edge2 = edge_list[rand_index2]
            head1, tail1 = original_edge1
            head2, tail2 = original_edge2

            # Flip a coin to see if we should swap head1 and tail1 for
            # the connections
            if random.random() >= 0.5:
                head1, tail1 = tail1, head1

            # The plan now is to pair head1 with tail2, and head2 with
            # tail1
            #
            # To avoid self-loops in the graph, we have to check that,
            # by pairing head1 with tail2 (respectively, head2 with
            # tail1) that head1 and tail2 are not actually the same
            # node. For example, suppose we have the edges (a, b) and
            # (b, c) to swap.
            #
            #   b
            #  / \
            # a   c
            #
            # We would have new edges (a, c) and (b, b) if we didn't do
            # this check.

            if head1 == tail2 or head2 == tail1:
                continue

            # Trying to avoid multiple edges between same pair of nodes;
            # for example, suppose we had the following
            #
            # a   c
            # |*  |           | original edge pair being looked at
            # | * |
            # |  *|           * existing edge, not in the pair
            # b   d
            #
            # Then we might accidentally create yet another (a, d) edge.
            # Note that this also solves the case of the following,
            # missed by the first check, for edges (a, b) and (a, c)
            #
            #   a
            #  / \
            # b   c
            #
            # These edges already exist.

            if newgraph.has_edge(head1, tail2) or newgraph.has_edge(
                    head2, tail1):
                continue

            # Suceeded checks, perform the swap
            original_edge1_data = newgraph[head1][tail1]
            original_edge2_data = newgraph[head2][tail2]

            newgraph.remove_edges_from((original_edge1, original_edge2))

            new_edge1 = (head1, tail2, original_edge1_data)
            new_edge2 = (head2, tail1, original_edge2_data)
            newgraph.add_edges_from((new_edge1, new_edge2))

            # Now update the entries at the indices randomly selected
            edge_list[rand_index1] = (head1, tail2)
            edge_list[rand_index2] = (head2, tail1)

        assert len(newgraph.edges()) == num_edges
        return newgraph