460 lines
15 KiB
Python
460 lines
15 KiB
Python
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# -*- coding: utf-8 -*-
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# Copyright (C) 2006-2019 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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# Copyright (C) 2009 by Willem Ligtenberg <W.P.A.Ligtenberg@tue.nl>
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# All rights reserved.
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# BSD license.
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#
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# Authors: Aric Hagberg (hagberg@lanl.gov)
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# Willem Ligtenberg (W.P.A.Ligtenberg@tue.nl)
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"""
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Generators for some directed graphs, including growing network (GN) graphs and
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scale-free graphs.
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"""
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from collections import Counter
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import networkx as nx
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from networkx.generators.classic import empty_graph
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from networkx.utils import discrete_sequence
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from networkx.utils import weighted_choice
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from networkx.utils import py_random_state
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__all__ = ['gn_graph', 'gnc_graph', 'gnr_graph', 'random_k_out_graph',
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'scale_free_graph']
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@py_random_state(3)
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def gn_graph(n, kernel=None, create_using=None, seed=None):
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"""Returns the growing network (GN) digraph with `n` nodes.
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The GN graph is built by adding nodes one at a time with a link to one
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previously added node. The target node for the link is chosen with
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probability based on degree. The default attachment kernel is a linear
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function of the degree of a node.
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The graph is always a (directed) tree.
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Parameters
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----------
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n : int
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The number of nodes for the generated graph.
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kernel : function
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The attachment kernel.
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create_using : NetworkX graph constructor, optional (default DiGraph)
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Graph type to create. If graph instance, then cleared before populated.
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seed : integer, random_state, or None (default)
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Indicator of random number generation state.
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See :ref:`Randomness<randomness>`.
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Examples
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--------
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To create the undirected GN graph, use the :meth:`~DiGraph.to_directed`
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method::
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>>> D = nx.gn_graph(10) # the GN graph
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>>> G = D.to_undirected() # the undirected version
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To specify an attachment kernel, use the `kernel` keyword argument::
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>>> D = nx.gn_graph(10, kernel=lambda x: x ** 1.5) # A_k = k^1.5
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References
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----------
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.. [1] P. L. Krapivsky and S. Redner,
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Organization of Growing Random Networks,
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Phys. Rev. E, 63, 066123, 2001.
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"""
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G = empty_graph(1, create_using, default=nx.DiGraph)
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if not G.is_directed():
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raise nx.NetworkXError("create_using must indicate a Directed Graph")
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if kernel is None:
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def kernel(x): return x
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if n == 1:
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return G
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G.add_edge(1, 0) # get started
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ds = [1, 1] # degree sequence
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for source in range(2, n):
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# compute distribution from kernel and degree
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dist = [kernel(d) for d in ds]
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# choose target from discrete distribution
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target = discrete_sequence(1, distribution=dist, seed=seed)[0]
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G.add_edge(source, target)
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ds.append(1) # the source has only one link (degree one)
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ds[target] += 1 # add one to the target link degree
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return G
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@py_random_state(3)
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def gnr_graph(n, p, create_using=None, seed=None):
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"""Returns the growing network with redirection (GNR) digraph with `n`
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nodes and redirection probability `p`.
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The GNR graph is built by adding nodes one at a time with a link to one
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previously added node. The previous target node is chosen uniformly at
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random. With probabiliy `p` the link is instead "redirected" to the
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successor node of the target.
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The graph is always a (directed) tree.
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Parameters
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----------
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n : int
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The number of nodes for the generated graph.
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p : float
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The redirection probability.
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create_using : NetworkX graph constructor, optional (default DiGraph)
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Graph type to create. If graph instance, then cleared before populated.
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seed : integer, random_state, or None (default)
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Indicator of random number generation state.
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See :ref:`Randomness<randomness>`.
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Examples
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--------
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To create the undirected GNR graph, use the :meth:`~DiGraph.to_directed`
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method::
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>>> D = nx.gnr_graph(10, 0.5) # the GNR graph
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>>> G = D.to_undirected() # the undirected version
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References
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----------
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.. [1] P. L. Krapivsky and S. Redner,
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Organization of Growing Random Networks,
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Phys. Rev. E, 63, 066123, 2001.
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"""
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G = empty_graph(1, create_using, default=nx.DiGraph)
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if not G.is_directed():
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raise nx.NetworkXError("create_using must indicate a Directed Graph")
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if n == 1:
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return G
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for source in range(1, n):
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target = seed.randrange(0, source)
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if seed.random() < p and target != 0:
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target = next(G.successors(target))
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G.add_edge(source, target)
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return G
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@py_random_state(2)
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def gnc_graph(n, create_using=None, seed=None):
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"""Returns the growing network with copying (GNC) digraph with `n` nodes.
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The GNC graph is built by adding nodes one at a time with a link to one
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previously added node (chosen uniformly at random) and to all of that
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node's successors.
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Parameters
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----------
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n : int
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The number of nodes for the generated graph.
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create_using : NetworkX graph constructor, optional (default DiGraph)
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Graph type to create. If graph instance, then cleared before populated.
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seed : integer, random_state, or None (default)
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Indicator of random number generation state.
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See :ref:`Randomness<randomness>`.
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References
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----------
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.. [1] P. L. Krapivsky and S. Redner,
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Network Growth by Copying,
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Phys. Rev. E, 71, 036118, 2005k.},
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"""
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G = empty_graph(1, create_using, default=nx.DiGraph)
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if not G.is_directed():
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raise nx.NetworkXError("create_using must indicate a Directed Graph")
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if n == 1:
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return G
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for source in range(1, n):
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target = seed.randrange(0, source)
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for succ in G.successors(target):
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G.add_edge(source, succ)
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G.add_edge(source, target)
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return G
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@py_random_state(7)
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def scale_free_graph(n, alpha=0.41, beta=0.54, gamma=0.05, delta_in=0.2,
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delta_out=0, create_using=None, seed=None):
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"""Returns a scale-free directed graph.
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Parameters
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----------
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n : integer
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Number of nodes in graph
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alpha : float
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Probability for adding a new node connected to an existing node
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chosen randomly according to the in-degree distribution.
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beta : float
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Probability for adding an edge between two existing nodes.
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One existing node is chosen randomly according the in-degree
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distribution and the other chosen randomly according to the out-degree
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distribution.
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gamma : float
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Probability for adding a new node connected to an existing node
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chosen randomly according to the out-degree distribution.
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delta_in : float
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Bias for choosing nodes from in-degree distribution.
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delta_out : float
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Bias for choosing nodes from out-degree distribution.
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create_using : NetworkX graph constructor, optional
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The default is a MultiDiGraph 3-cycle.
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If a graph instance, use it without clearing first.
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If a graph constructor, call it to construct an empty graph.
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seed : integer, random_state, or None (default)
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Indicator of random number generation state.
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See :ref:`Randomness<randomness>`.
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Examples
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--------
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Create a scale-free graph on one hundred nodes::
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>>> G = nx.scale_free_graph(100)
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Notes
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-----
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The sum of `alpha`, `beta`, and `gamma` must be 1.
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References
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----------
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.. [1] B. Bollobás, C. Borgs, J. Chayes, and O. Riordan,
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Directed scale-free graphs,
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Proceedings of the fourteenth annual ACM-SIAM Symposium on
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Discrete Algorithms, 132--139, 2003.
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"""
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def _choose_node(G, distribution, delta, psum):
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cumsum = 0.0
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# normalization
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r = seed.random()
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for n, d in distribution:
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cumsum += (d + delta) / psum
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if r < cumsum:
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break
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return n
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if create_using is None or not hasattr(create_using, '_adj'):
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# start with 3-cycle
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G = nx.empty_graph(3, create_using, default=nx.MultiDiGraph)
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G.add_edges_from([(0, 1), (1, 2), (2, 0)])
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else:
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G = create_using
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if not (G.is_directed() and G.is_multigraph()):
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raise nx.NetworkXError("MultiDiGraph required in create_using")
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if alpha <= 0:
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raise ValueError('alpha must be > 0.')
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if beta <= 0:
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raise ValueError('beta must be > 0.')
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if gamma <= 0:
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raise ValueError('gamma must be > 0.')
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if abs(alpha + beta + gamma - 1.0) >= 1e-9:
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raise ValueError('alpha+beta+gamma must equal 1.')
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number_of_edges = G.number_of_edges()
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while len(G) < n:
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psum_in = number_of_edges + delta_in * len(G)
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psum_out = number_of_edges + delta_out * len(G)
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r = seed.random()
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# random choice in alpha,beta,gamma ranges
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if r < alpha:
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# alpha
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# add new node v
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v = len(G)
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# choose w according to in-degree and delta_in
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w = _choose_node(G, G.in_degree(), delta_in, psum_in)
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elif r < alpha + beta:
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# beta
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# choose v according to out-degree and delta_out
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v = _choose_node(G, G.out_degree(), delta_out, psum_out)
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# choose w according to in-degree and delta_in
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w = _choose_node(G, G.in_degree(), delta_in, psum_in)
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else:
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# gamma
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# choose v according to out-degree and delta_out
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v = _choose_node(G, G.out_degree(), delta_out, psum_out)
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# add new node w
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w = len(G)
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G.add_edge(v, w)
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number_of_edges += 1
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return G
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@py_random_state(4)
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def random_uniform_k_out_graph(n, k, self_loops=True, with_replacement=True,
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seed=None):
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"""Returns a random `k`-out graph with uniform attachment.
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A random `k`-out graph with uniform attachment is a multidigraph
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generated by the following algorithm. For each node *u*, choose
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`k` nodes *v* uniformly at random (with replacement). Add a
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directed edge joining *u* to *v*.
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Parameters
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----------
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n : int
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The number of nodes in the returned graph.
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k : int
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The out-degree of each node in the returned graph.
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self_loops : bool
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If True, self-loops are allowed when generating the graph.
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with_replacement : bool
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If True, neighbors are chosen with replacement and the
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returned graph will be a directed multigraph. Otherwise,
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neighbors are chosen without replacement and the returned graph
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will be a directed graph.
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seed : integer, random_state, or None (default)
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Indicator of random number generation state.
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See :ref:`Randomness<randomness>`.
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Returns
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-------
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NetworkX graph
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A `k`-out-regular directed graph generated according to the
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above algorithm. It will be a multigraph if and only if
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`with_replacement` is True.
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Raises
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------
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ValueError
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If `with_replacement` is False and `k` is greater than
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`n`.
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See also
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--------
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random_k_out_graph
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Notes
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-----
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The return digraph or multidigraph may not be strongly connected, or
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even weakly connected.
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If `with_replacement` is True, this function is similar to
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:func:`random_k_out_graph`, if that function had parameter `alpha`
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set to positive infinity.
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"""
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if with_replacement:
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create_using = nx.MultiDiGraph()
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def sample(v, nodes):
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if not self_loops:
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nodes = nodes - {v}
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return (seed.choice(list(nodes)) for i in range(k))
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else:
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create_using = nx.DiGraph()
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def sample(v, nodes):
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if not self_loops:
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nodes = nodes - {v}
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return seed.sample(nodes, k)
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G = nx.empty_graph(n, create_using)
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nodes = set(G)
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for u in G:
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G.add_edges_from((u, v) for v in sample(u, nodes))
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return G
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@py_random_state(4)
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def random_k_out_graph(n, k, alpha, self_loops=True, seed=None):
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"""Returns a random `k`-out graph with preferential attachment.
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A random `k`-out graph with preferential attachment is a
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multidigraph generated by the following algorithm.
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1. Begin with an empty digraph, and initially set each node to have
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weight `alpha`.
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2. Choose a node `u` with out-degree less than `k` uniformly at
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random.
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3. Choose a node `v` from with probability proportional to its
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weight.
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4. Add a directed edge from `u` to `v`, and increase the weight
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of `v` by one.
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5. If each node has out-degree `k`, halt, otherwise repeat from
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step 2.
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For more information on this model of random graph, see [1].
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Parameters
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----------
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n : int
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The number of nodes in the returned graph.
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k : int
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|
The out-degree of each node in the returned graph.
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|
alpha : float
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|
A positive :class:`float` representing the initial weight of
|
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|
each vertex. A higher number means that in step 3 above, nodes
|
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|
will be chosen more like a true uniformly random sample, and a
|
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|
lower number means that nodes are more likely to be chosen as
|
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|
their in-degree increases. If this parameter is not positive, a
|
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|
|
:exc:`ValueError` is raised.
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|
self_loops : bool
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|
If True, self-loops are allowed when generating the graph.
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||
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|
seed : integer, random_state, or None (default)
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|
Indicator of random number generation state.
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||
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|
See :ref:`Randomness<randomness>`.
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|
Returns
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||
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|
-------
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||
|
|
:class:`~networkx.classes.MultiDiGraph`
|
||
|
|
A `k`-out-regular multidigraph generated according to the above
|
||
|
|
algorithm.
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||
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|
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|
Raises
|
||
|
|
------
|
||
|
|
ValueError
|
||
|
|
If `alpha` is not positive.
|
||
|
|
|
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|
|
Notes
|
||
|
|
-----
|
||
|
|
The returned multidigraph may not be strongly connected, or even
|
||
|
|
weakly connected.
|
||
|
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|
||
|
|
References
|
||
|
|
----------
|
||
|
|
[1]: Peterson, Nicholas R., and Boris Pittel.
|
||
|
|
"Distance between two random `k`-out digraphs, with and without
|
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|
|
preferential attachment."
|
||
|
|
arXiv preprint arXiv:1311.5961 (2013).
|
||
|
|
<https://arxiv.org/abs/1311.5961>
|
||
|
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|
||
|
|
"""
|
||
|
|
if alpha < 0:
|
||
|
|
raise ValueError('alpha must be positive')
|
||
|
|
G = nx.empty_graph(n, create_using=nx.MultiDiGraph)
|
||
|
|
weights = Counter({v: alpha for v in G})
|
||
|
|
for i in range(k * n):
|
||
|
|
u = seed.choice([v for v, d in G.out_degree() if d < k])
|
||
|
|
# If self-loops are not allowed, make the source node `u` have
|
||
|
|
# weight zero.
|
||
|
|
if not self_loops:
|
||
|
|
adjustment = Counter({u: weights[u]})
|
||
|
|
else:
|
||
|
|
adjustment = Counter()
|
||
|
|
v = weighted_choice(weights - adjustment, seed=seed)
|
||
|
|
G.add_edge(u, v)
|
||
|
|
weights[v] += 1
|
||
|
|
return G
|