NetworkX

```
# -*- coding: utf-8 -*-
"""
Algorithms for chordal graphs.
A graph is chordal if every cycle of length at least 4 has a chord
(an edge joining two nodes not adjacent in the cycle).
http://en.wikipedia.org/wiki/Chordal_graph
"""
import networkx as nx
import random
import sys
__authors__ = "\n".join(['Jesus Cerquides <cerquide@iiia.csic.es>'])
# Copyright (C) 2010 by
# Jesus Cerquides <cerquide@iiia.csic.es>
# All rights reserved.
# BSD license.
__all__ = ['is_chordal',
'find_induced_nodes',
'chordal_graph_cliques',
'chordal_graph_treewidth',
'NetworkXTreewidthBoundExceeded']
class NetworkXTreewidthBoundExceeded(nx.NetworkXException):
"""Exception raised when a treewidth bound has been provided and it has
been exceeded"""
[docs]def is_chordal(G):
"""Checks whether G is a chordal graph.
A graph is chordal if every cycle of length at least 4 has a chord
(an edge joining two nodes not adjacent in the cycle).
Parameters
----------
G : graph
A NetworkX graph.
Returns
-------
chordal : bool
True if G is a chordal graph and False otherwise.
Raises
------
NetworkXError
The algorithm does not support DiGraph, MultiGraph and MultiDiGraph.
If the input graph is an instance of one of these classes, a
NetworkXError is raised.
Examples
--------
>>> import networkx as nx
>>> e=[(1,2),(1,3),(2,3),(2,4),(3,4),(3,5),(3,6),(4,5),(4,6),(5,6)]
>>> G=nx.Graph(e)
>>> nx.is_chordal(G)
True
Notes
-----
The routine tries to go through every node following maximum cardinality
search. It returns False when it finds that the separator for any node
is not a clique. Based on the algorithms in [1]_.
References
----------
.. [1] R. E. Tarjan and M. Yannakakis, Simple linear-time algorithms
to test chordality of graphs, test acyclicity of hypergraphs, and
selectively reduce acyclic hypergraphs, SIAM J. Comput., 13 (1984),
pp. 566–579.
"""
if G.is_directed():
raise nx.NetworkXError('Directed graphs not supported')
if G.is_multigraph():
raise nx.NetworkXError('Multiply connected graphs not supported.')
if len(_find_chordality_breaker(G))==0:
return True
else:
return False
[docs]def find_induced_nodes(G,s,t,treewidth_bound=sys.maxsize):
"""Returns the set of induced nodes in the path from s to t.
Parameters
----------
G : graph
A chordal NetworkX graph
s : node
Source node to look for induced nodes
t : node
Destination node to look for induced nodes
treewith_bound: float
Maximum treewidth acceptable for the graph H. The search
for induced nodes will end as soon as the treewidth_bound is exceeded.
Returns
-------
I : Set of nodes
The set of induced nodes in the path from s to t in G
Raises
------
NetworkXError
The algorithm does not support DiGraph, MultiGraph and MultiDiGraph.
If the input graph is an instance of one of these classes, a
NetworkXError is raised.
The algorithm can only be applied to chordal graphs. If
the input graph is found to be non-chordal, a NetworkXError is raised.
Examples
--------
>>> import networkx as nx
>>> G=nx.Graph()
>>> G = nx.generators.classic.path_graph(10)
>>> I = nx.find_induced_nodes(G,1,9,2)
>>> list(I)
[1, 2, 3, 4, 5, 6, 7, 8, 9]
Notes
-----
G must be a chordal graph and (s,t) an edge that is not in G.
If a treewidth_bound is provided, the search for induced nodes will end
as soon as the treewidth_bound is exceeded.
The algorithm is inspired by Algorithm 4 in [1]_.
A formal definition of induced node can also be found on that reference.
References
----------
.. [1] Learning Bounded Treewidth Bayesian Networks.
Gal Elidan, Stephen Gould; JMLR, 9(Dec):2699--2731, 2008.
http://jmlr.csail.mit.edu/papers/volume9/elidan08a/elidan08a.pdf
"""
if not is_chordal(G):
raise nx.NetworkXError("Input graph is not chordal.")
H = nx.Graph(G)
H.add_edge(s,t)
I = set()
triplet = _find_chordality_breaker(H,s,treewidth_bound)
while triplet:
(u,v,w) = triplet
I.update(triplet)
for n in triplet:
if n!=s:
H.add_edge(s,n)
triplet = _find_chordality_breaker(H,s,treewidth_bound)
if I:
# Add t and the second node in the induced path from s to t.
I.add(t)
for u in G[s]:
if len(I & set(G[u]))==2:
I.add(u)
break
return I
[docs]def chordal_graph_cliques(G):
"""Returns the set of maximal cliques of a chordal graph.
The algorithm breaks the graph in connected components and performs a
maximum cardinality search in each component to get the cliques.
Parameters
----------
G : graph
A NetworkX graph
Returns
-------
cliques : A set containing the maximal cliques in G.
Raises
------
NetworkXError
The algorithm does not support DiGraph, MultiGraph and MultiDiGraph.
If the input graph is an instance of one of these classes, a
NetworkXError is raised.
The algorithm can only be applied to chordal graphs. If the
input graph is found to be non-chordal, a NetworkXError is raised.
Examples
--------
>>> import networkx as nx
>>> e= [(1,2),(1,3),(2,3),(2,4),(3,4),(3,5),(3,6),(4,5),(4,6),(5,6),(7,8)]
>>> G = nx.Graph(e)
>>> G.add_node(9)
>>> setlist = nx.chordal_graph_cliques(G)
"""
if not is_chordal(G):
raise nx.NetworkXError("Input graph is not chordal.")
cliques = set()
for C in nx.connected.connected_component_subgraphs(G):
cliques |= _connected_chordal_graph_cliques(C)
return cliques
[docs]def chordal_graph_treewidth(G):
"""Returns the treewidth of the chordal graph G.
Parameters
----------
G : graph
A NetworkX graph
Returns
-------
treewidth : int
The size of the largest clique in the graph minus one.
Raises
------
NetworkXError
The algorithm does not support DiGraph, MultiGraph and MultiDiGraph.
If the input graph is an instance of one of these classes, a
NetworkXError is raised.
The algorithm can only be applied to chordal graphs. If
the input graph is found to be non-chordal, a NetworkXError is raised.
Examples
--------
>>> import networkx as nx
>>> e = [(1,2),(1,3),(2,3),(2,4),(3,4),(3,5),(3,6),(4,5),(4,6),(5,6),(7,8)]
>>> G = nx.Graph(e)
>>> G.add_node(9)
>>> nx.chordal_graph_treewidth(G)
3
References
----------
.. [1] http://en.wikipedia.org/wiki/Tree_decomposition#Treewidth
"""
if not is_chordal(G):
raise nx.NetworkXError("Input graph is not chordal.")
max_clique = -1
for clique in nx.chordal_graph_cliques(G):
max_clique = max(max_clique,len(clique))
return max_clique - 1
def _is_complete_graph(G):
"""Returns True if G is a complete graph."""
if G.number_of_selfloops()>0:
raise nx.NetworkXError("Self loop found in _is_complete_graph()")
n = G.number_of_nodes()
if n < 2:
return True
e = G.number_of_edges()
max_edges = ((n * (n-1))/2)
return e == max_edges
def _find_missing_edge(G):
""" Given a non-complete graph G, returns a missing edge."""
nodes=set(G)
for u in G:
missing=nodes-set(list(G[u].keys())+[u])
if missing:
return (u,missing.pop())
def _max_cardinality_node(G,choices,wanna_connect):
"""Returns a the node in choices that has more connections in G
to nodes in wanna_connect.
"""
# max_number = None
max_number = -1
for x in choices:
number=len([y for y in G[x] if y in wanna_connect])
if number > max_number:
max_number = number
max_cardinality_node = x
return max_cardinality_node
def _find_chordality_breaker(G,s=None,treewidth_bound=sys.maxsize):
""" Given a graph G, starts a max cardinality search
(starting from s if s is given and from a random node otherwise)
trying to find a non-chordal cycle.
If it does find one, it returns (u,v,w) where u,v,w are the three
nodes that together with s are involved in the cycle.
"""
unnumbered = set(G)
if s is None:
s = random.choice(list(unnumbered))
unnumbered.remove(s)
numbered = set([s])
# current_treewidth = None
current_treewidth = -1
while unnumbered:# and current_treewidth <= treewidth_bound:
v = _max_cardinality_node(G,unnumbered,numbered)
unnumbered.remove(v)
numbered.add(v)
clique_wanna_be = set(G[v]) & numbered
sg = G.subgraph(clique_wanna_be)
if _is_complete_graph(sg):
# The graph seems to be chordal by now. We update the treewidth
current_treewidth = max(current_treewidth,len(clique_wanna_be))
if current_treewidth > treewidth_bound:
raise nx.NetworkXTreewidthBoundExceeded(\
"treewidth_bound exceeded: %s"%current_treewidth)
else:
# sg is not a clique,
# look for an edge that is not included in sg
(u,w) = _find_missing_edge(sg)
return (u,v,w)
return ()
def _connected_chordal_graph_cliques(G):
"""Return the set of maximal cliques of a connected chordal graph."""
if G.number_of_nodes() == 1:
x = frozenset(G.nodes())
return set([x])
else:
cliques = set()
unnumbered = set(G.nodes())
v = random.choice(list(unnumbered))
unnumbered.remove(v)
numbered = set([v])
clique_wanna_be = set([v])
while unnumbered:
v = _max_cardinality_node(G,unnumbered,numbered)
unnumbered.remove(v)
numbered.add(v)
new_clique_wanna_be = set(G.neighbors(v)) & numbered
sg = G.subgraph(clique_wanna_be)
if _is_complete_graph(sg):
new_clique_wanna_be.add(v)
if not new_clique_wanna_be >= clique_wanna_be:
cliques.add(frozenset(clique_wanna_be))
clique_wanna_be = new_clique_wanna_be
else:
raise nx.NetworkXError("Input graph is not chordal.")
cliques.add(frozenset(clique_wanna_be))
return cliques
```