def triangulate(self, C, randomized=False):
'''
Find a minimum triangulation of a graph
Args:
C : a graph in networkx format
randomized : has no effect
Return:
F : a set of edges such that C + F is a minimum triangulation
'''
logging.info("=== MT.triangulate ===")
if nx.is_chordal(C):
logging.debug("Component is already chordal")
return []
# use LEX-M to determine the size of a minimal triangulation to have an upper bound for the minimum triangulation
lexm_triang = LEX_M.triangulate_LexM(C)
size_minimal = lexm_triang["size"]
logging.debug("size of minimal: "+str(size_minimal))
F = []
# iterate through all subsets of chord edges by increasing set size.
# for each subset, check if self.G + additional edges is chordal
# return first set of edges that makes self.G chordal. this is a minimum triangulation.
k = 1
found_minimum = False
#print (self.chordedge_candidates)
while not found_minimum and k < size_minimal:
# check timeout:
if self.timeout > 0 and time.time() > self.timeout:
raise ta.TimeLimitExceededException("Time Limit Exceeded!")
logging.debug("Current iteration: consider edgesets of size "+str(k))
edgesets_size_k = itertools.combinations(self.chordedge_candidates, k)
k_edgeset = 0
for edgeset in edgesets_size_k:
#print (edgeset)
k_edgeset += 1
if k_edgeset%10000 == 0:
# check timeout every 10k sets:
if self.timeout > 0 and time.time() > self.timeout:
raise ta.TimeLimitExceededException("Time Limit Exceeded!")
H = C.copy()
H.add_edges_from(edgeset)
if nx.is_chordal(H):
F += [e for e in edgeset]
found_minimum = True
break
k += 1
if not found_minimum:
F += [e for e in lexm_triang["H"].edges() if e not in C.edges()]
return F
def is_chordal(edge_list): """ Check if the graph is chordal/triangulated. Parameters ---------- *edge_list* : a list of lists (optional) The edges to check (if not self.E) Returns ------- *nx.is_chordal(G)* : a boolean Whether the graph is chordal or not Effects ------- None Notes ----- Again, do we need networkx for this? Eventually should write this check on our own. """ G = nx.Graph(list(edge_list)) return nx.is_chordal(G)
def test_logmu_monte_carlo():
p = 4
matspace = [range(2) for i in range(p * p)]
graphs = {}
graph_jtreps = {}
for adjmatvec in itertools.product(*matspace):
adjmat = np.matrix(adjmatvec).reshape(p, p)
if np.diag(adjmat).sum() == 0:
g = nx.from_numpy_matrix(adjmat)
if nx.is_chordal(g):
if check_symmetric(adjmat):
# print libg.mu(g)
graphs[adjmatvec] = trilearn.graph.decomposable.n_junction_trees(g)
jt = trilearn.graph.decomposable.junction_tree(g)
S = jt.get_separators()
graph_jtreps[adjmatvec] = {"graph": g,
"jts": set(),
"mu": np.exp(jtlib.log_n_junction_trees(jt, S))}
for i in range(100):
jtlib.randomize(jt)
graph_jtreps[adjmatvec]["jts"].add(jt.tuple())
#print graphs
#print "Exact number of chordal graphs: " + str(len(graph_jtreps))
#print "Exact number of junction trees: " + str(np.sum([val for key, val in graphs.iteritems()]))
sum = 0
for graph, val in graph_jtreps.items():
#print val["mu"], val["jts"]
#print val["mu"] - len(val["jts"])
sum += len(val["jts"])
assert np.abs(val["mu"] - len(val["jts"]) < 0.0000001)
print(sum)
def is_chordal(edge_list):
"""
Check if the graph is chordal/triangulated.
Parameters
----------
*edge_list* : a list of lists (optional)
The edges to check (if not self.E)
Returns
-------
*nx.is_chordal(G)* : a boolean
Whether the graph is chordal or not
Effects
-------
None
Notes
-----
Again, do we need networkx for this? Eventually should
write this check on our own.
"""
G = nx.Graph(list(edge_list))
return nx.is_chordal(G)
def addMoreEdges(self, requiredMoreEdges):
"""function to add more edges in the graph: moreEdges = givenEdges - treeEdges"""
newEdges = 0
self.chordalGraph = copy.deepcopy(self.chordalTree)
while newEdges < requiredMoreEdges:
vertices = random.sample(self.chordalGraph, 2)
u = vertices[0]
v = vertices[1]
if self.ifEdgeExist(self.chordalGraph, u, v):
continue
else:
I_uv = list(
set(self.chordalGraph[u]).intersection(
self.chordalGraph[v]))
if I_uv:
x = random.choice(I_uv)
auxNodes = list(set(self.chordalGraph[x]).difference(I_uv))
auxGraph = self.createAuxGraph(self.chordalGraph, auxNodes)
if not self.isReachable(auxGraph, u, v):
self.addAnEdge(self.chordalGraph, u, v)
#print "Add edge between: "+str(u)+" and "+str(v)
newEdges += 1
print self.chordalGraph
G = nx.Graph(self.chordalGraph)
if nx.is_chordal(G):
print "========================"
print "This is a Chordal graph."
print "========================"
def pairwise_score_TVD(self, graph):
if not nx.is_chordal(graph):
graph = utils.tools.triangulate(graph)
# junction tree size
size = 0
exceed = False
for clique in nx.find_cliques(graph):
temp_size = self.domain.project(clique).size()
# if temp_size > self.config['max_clique_size'] or len(clique) > 15:
if temp_size > self.config['max_clique_size']:
# print(clique, 'clique size exceeds', temp_size)
exceed = True
size += temp_size
if size > self.config['max_parameter_size']:
# print('total clique size exceeds')
exceed = True
if exceed:
return self.min_score, 0, size
noisy_TVD = 0
for attr1, attr2 in graph.edges:
noisy_TVD += utils.tools.dp_TVD(self.TVD_map, self.data,
self.domain, [attr1, attr2],
self.TVD_noise)[1]
score = noisy_TVD - self.config['size_penalty'] * size
score -= nx.number_connected_components(
graph) * self.config['connectivity_penalty']
return score, noisy_TVD, size
def pairwise_score_MI(self, graph):
if not nx.is_chordal(graph):
graph = utils.tools.triangulate(graph)
# junction tree size
size = 0
for clique in nx.find_cliques(graph):
temp_size = self.domain.project(clique).size()
# if temp_size > self.config['max_clique_size'] or len(clique) > 15:
if temp_size > self.config['max_clique_size']:
# print(temp_size)
return self.min_score, 0, size
size += temp_size
if size > self.config['max_parameter_size']:
# print(size, '!')
return self.min_score, 0, size
noisy_MI = 0
for attr1, attr2 in graph.edges:
noisy_MI += utils.tools.dp_mutual_info(self.MI_map,
self.entropy_map, self.data,
self.domain, [attr1, attr2],
self.MI_noise)[1]
score = noisy_MI - self.config['size_penalty'] * size
score -= nx.number_connected_components(
graph) * self.config['connectivity_penalty']
return score, noisy_MI, size
def test_triangulation_of_3_clique_maps_on_itself(self):
m = np.ones((3, 3))
np.fill_diagonal(m, 0)
g = nx.Graph(m)
t = triangulate_variable_elimination(g)
self.assertTrue((m == nx.to_numpy_array(t)).all())
self.assertTrue(nx.is_chordal(t))
def addMoreEdges(self, requiredMoreEdges):
"""function to create connected trampolines"""
newEdges = 0
while newEdges < requiredMoreEdges:
trampolines = random.sample(range(len(self.trampoAllNodes)),2)
u = random.choice(self.trampoAllNodes[trampolines[0]])
v = random.choice(self.trampoAllNodes[trampolines[1]])
if self.ifEdgeExist(self.trampolinesConnected, u, v):
continue
else:
I_uv = list(set(self.trampolinesConnected[u]).intersection(self.trampolinesConnected[v]))
if I_uv:
x = random.choice(I_uv)
auxNodes = list(set(self.trampolinesConnected[x]).difference(I_uv))
auxGraph = self.createAuxGraph(self.trampolinesConnected, auxNodes)
if not self.isReachable(auxGraph, u, v):
self.addAnEdge(self.trampolinesConnected, u, v)
print "Added edge between: "+str(u)+" and "+str(v)
newEdges += 1
self.plotGraph(self.trampolinesConnected, "Connected Trampolines")
print self.trampolinesConnected
G = nx.Graph(self.trampolinesConnected)
if not nx.is_chordal(G):
print "============================"
print "This is NOT a Chordal graph."
print "============================"
print str(newEdges)+" edges added to connect trampolines"
def naive_decomposable_graph(n):
""" Naive implementation for generating a random decomposable graph.
Note that this will only for for small numbers (~10) of n.
Args:
n (int): order of the samples graph.
Returns:
NetworkX graph: A decomposable graph.
Example:
>>> g = dlib.naive_decomposable_graph(4)
>>> g.edges
EdgeView([(0, 1), (0, 3)])
>>> g.nodes
NodeView((0, 1, 2, 3))
"""
m = np.zeros(n * n, dtype=int)
m.resize(n, n)
for i in range(n - 1):
for j in range(i + 1, n):
e = np.random.randint(2)
m[i, j] = e
m[j, i] = e
graph = nx.from_numpy_matrix(m)
while not nx.is_chordal(graph):
for i in range(n - 1):
for j in range(i + 1, n):
e = np.random.randint(2)
m[i, j] = e
m[j, i] = e
graph = nx.from_numpy_matrix(m)
return graph
def triangulate_ig(g, debug=True):
g_nx = ig_to_nx(g)
g_nx, h_nx, F = triangulate_nx(g_nx, debug=debug)
assert nx.is_chordal(h_nx)
gc = g.copy()
gc.add_edges(F)
return gc
def is_triangulated(self):
"""
Just checks if the graph is triangulated
Parameters
----------
See Also
--------
maxCardinalitySearch
Example
--------
>>> from pgmpy.base import UndirectedGraph
>>> G = UndirectedGraph([(0, 1), (0, 3), (0, 8), (1, 2), (1, 4),
... (1,8), (2, 4), (2, 6), (2, 7), (3, 8),
... (3, 9), (4, 7),(4, 8), (5, 8), (5, 9),
... (5, 10), (6, 7), (7, 10),(8, 10)])
>>> G.jt_techniques(2,False,True)
4
>>> G.is_triangulated()
True
"""
ret = nx.is_chordal(self)
return ret
def LB_Triang(self, vertexList, edgeList, graphToRecognize):
"""This function is implemented based on the algorithm LB-Triang from the paper "A WIDE-RANGE EFFICIENT ALGORITHM FOR
MINIMAL TRIANGULATION" by Anne Berry for recognition chordal graphs and add edges (if necessary) by making each vertex
LB-simplicial."""
# graphToRecognize = {0: [1, 4], 1:[0, 2], 2:[1, 3], 3:[2, 4], 4:[0, 3]}
# vertexList, edgeList = self.createEdgeList(graphToRecognize)
# random.shuffle(vertexList)
vertexVisibility = [0] * len(vertexList)
isChordal = False
for v in vertexList:
print("The vertex " + str(vertexList.index(v)) + "-" + str(v) +
" is verifying...")
openNeighbors = graphToRecognize[v]
print("My openNeighbors is;", openNeighbors)
closedNeighbors = copy.deepcopy(openNeighbors)
closedNeighbors.append(v)
print("Closed Neighb:", closedNeighbors)
cNMinusE = list(set(vertexList).difference(
set(closedNeighbors))) # V-S
print("cNMinusE:", cNMinusE)
eAddedCount = 0
if cNMinusE:
VMinusSGraph = self.createAuxGraph(graphToRecognize,
cNMinusE) # G(V-S)
componentsOri = sorted(
nx.connected_components(nx.Graph(VMinusSGraph)))
print("Component(s) in the graph: " + str(componentsOri))
componentsCompAll = []
for co in componentsOri:
openNCO = []
for v1 in co:
openNV1 = graphToRecognize[v1]
print("openNV1", openNV1)
openNCO = openNCO + openNV1
print("pehle wala openNCO", openNCO)
openNCO = list(set(openNCO).difference(co))
print("Baad wala openNCO:", openNCO)
eCounter = self.createCompleteGraph(openNCO)
# if eCounter >= 1:
# self.plotGraph(self.H, str(eCounter)+" edge(s) added.")
# print "================================================"
# else:
# print "================================================"
else:
print("The vertex " + str(v) +
" does not generate any minimal separator.")
print("================================================")
###For recognition, if the generated graph is a chordal graph or not.
graph = nx.Graph(self.H)
if nx.is_chordal(graph):
print(
"*********After adding edges the generated graph is Chordal graph.*********"
)
else:
print(
"*********After adding edges the generated graph is NOT Chordal graph.*********"
)
def test_triangulation_of_square_adds_one_edge(self):
g = nx.Graph()
g.add_nodes_from(range(4))
g.add_edges_from([(0, 1), (1, 2), (2, 3), (3, 0)])
t = triangulate_variable_elimination(g)
self.assertTrue(t.number_of_edges() == 5)
self.assertTrue(nx.is_chordal(t))
def test_is_chordal(self):
assert not nx.is_chordal(self.non_chordal_G)
assert nx.is_chordal(self.chordal_G)
assert nx.is_chordal(self.connected_chordal_G)
assert nx.is_chordal(nx.complete_graph(3))
assert nx.is_chordal(nx.cycle_graph(3))
assert not nx.is_chordal(nx.cycle_graph(5))
with pytest.raises(nx.NetworkXError, match="Input graph is not chordal"):
nx.is_chordal(self.self_loop_G)
def test_triangulate():
# Generate random graphs from nodes count
nodes = [2, 10, 25, 50, 75, 100]
graphs = [nx.gnp_random_graph(n, 0.5, directed=False) for n in nodes]
wi_graphs = [mb.Graph.from_networkx(G) for G in graphs]
wi_triang = [mb.triangulate(graph) for graph in wi_graphs]
wi_triang = [nx.is_chordal(graph.to_networkx()) for graph in wi_triang]
assert (all(wi_triang))
def score(self, graph, entropy_map):
graph = graph.copy()
if not nx.is_chordal(graph):
graph = utils.tools.triangulate(graph)
clique_list = [
tuple(sorted(clique)) for clique in nx.find_cliques(graph)
]
clique_graph = nx.Graph()
clique_graph.add_nodes_from(clique_list)
for clique1, clique2 in itertools.combinations(clique_list, 2):
clique_graph.add_edge(clique1,
clique2,
weight=-len(set(clique1) & set(clique2)))
junction_tree = nx.minimum_spanning_tree(clique_graph)
# print(' clique list', len(clique_list), clique_list)
# junction tree size
size = 0
for clique in clique_list:
temp_size = self.domain.project(clique).size()
# if temp_size > self.config['max_clique_size'] or len(clique) > 15:
if temp_size > self.config['max_clique_size']:
return self.min_score, 0, size
size += temp_size
if size > self.config['max_parameter_size']:
return self.min_score, 0, size
# KL divergence
# model entropy is for debugging and can not be used for constructing model as they are not dp
KL_divergence = 0
model_entropy = 0
entropy, noisy_entropy = utils.tools.dp_entropy(
entropy_map, self.data, self.domain, clique_list[0],
self.entropy_noise)
KL_divergence += noisy_entropy
model_entropy += entropy
for start, clique in nx.dfs_edges(junction_tree,
source=clique_list[0]):
# print(clique, self.data.shape)
entropy, noisy_entropy = utils.tools.dp_entropy(
entropy_map, self.data, self.domain, clique,
self.entropy_noise)
KL_divergence += noisy_entropy
model_entropy += entropy
separator = set(start) & set(clique)
if len(separator) != 0:
entropy, noisy_entropy = utils.tools.dp_entropy(
entropy_map, self.data, self.domain, separator,
self.entropy_noise)
KL_divergence -= noisy_entropy
model_entropy -= entropy
# print('KL', KL_divergence, size)
score = -KL_divergence - self.config['size_penalty'] * size
return score, model_entropy, size
def markov_add_or_remove(g, num_steps):
all_edges = set(combinations(g.nodes, 2))
for _ in range(num_steps):
flag = random.randint(0, 1)
if flag == 0:
u, v = random.sample(g.edges, 1)[0]
g.remove_edge(u, v)
while not nx.is_connected(g) or not nx.is_chordal(g):
g.add_edge(u, v)
u, v = random.sample(g.edges, 1)[0]
g.remove_edge(u, v)
else:
u, v = random.sample(all_edges - g.edges, 1)[0]
g.add_edge(u, v)
while not nx.is_connected(g) or not nx.is_chordal(g):
g.remove_edge(u, v)
u, v = random.sample(all_edges - g.edges, 1)[0]
g.add_edge(u, v)
def test_complete_to_chordal_graph(self):
fgrg = nx.fast_gnp_random_graph
test_graphs = [
nx.barbell_graph(6, 2),
nx.cycle_graph(15),
nx.wheel_graph(20),
nx.grid_graph([10, 4]),
nx.ladder_graph(15),
nx.star_graph(5),
nx.bull_graph(),
fgrg(20, 0.3, seed=1),
]
for G in test_graphs:
H, a = nx.complete_to_chordal_graph(G)
assert nx.is_chordal(H)
assert len(a) == H.number_of_nodes()
if nx.is_chordal(G):
assert G.number_of_edges() == H.number_of_edges()
assert set(a.values()) == {0}
else:
assert len(set(a.values())) == H.number_of_nodes()
def run(self):
self.alpha = {}
for C in self.component_subgraphs:
# get triangulation for each connected component of the reduced graph G_c:
self.edges_of_triangulation += self.triangulate(C)
self.H = self.G.copy()
self.H.add_edges_from(self.edges_of_triangulation)
if not nx.is_chordal(self.H):
raise ta.TriangulationNotSuccessfulException(
"Resulting graph is somehow not chordal!")
def test_is_chordal(self):
assert not nx.is_chordal(self.non_chordal_G)
assert nx.is_chordal(self.chordal_G)
assert nx.is_chordal(self.connected_chordal_G)
assert nx.is_chordal(nx.complete_graph(3))
assert nx.is_chordal(nx.cycle_graph(3))
assert not nx.is_chordal(nx.cycle_graph(5))
def test_is_chordal(self):
assert_false(nx.is_chordal(self.non_chordal_G))
assert_true(nx.is_chordal(self.chordal_G))
assert_true(nx.is_chordal(self.connected_chordal_G))
assert_true(nx.is_chordal(nx.complete_graph(3)))
assert_true(nx.is_chordal(nx.cycle_graph(3)))
assert_false(nx.is_chordal(nx.cycle_graph(5)))
def test_is_chordal(self):
assert_false(nx.is_chordal(self.non_chordal_G))
assert_true(nx.is_chordal(self.chordal_G))
assert_true(nx.is_chordal(self.connected_chordal_G))
assert_true(nx.is_chordal(nx.complete_graph(3)))
assert_true(nx.is_chordal(nx.cycle_graph(3)))
assert_false(nx.is_chordal(nx.cycle_graph(5)))
def test_bayesian_model(self):
self.graph.add_edges_from([("a", "b"), ("b", "c"), ("c", "d"),
("d", "a")])
phi1 = DiscreteFactor(["a", "b"], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(["b", "c"], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(["c", "d"], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(["d", "a"], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
bm = self.graph.to_bayesian_model()
self.assertIsInstance(bm, BayesianModel)
self.assertListEqual(sorted(bm.nodes()), ["a", "b", "c", "d"])
self.assertTrue(nx.is_chordal(bm.to_undirected()))
def test_bayesian_model(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = Factor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = Factor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = Factor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = Factor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
bm = self.graph.to_bayesian_model()
self.assertIsInstance(bm, BayesianModel)
self.assertListEqual(sorted(bm.nodes()), ['a', 'b', 'c', 'd'])
self.assertTrue(nx.is_chordal(bm.to_undirected()))
def compute_chromatic(masses, window):
G = nx.Graph()
for i in range(0, len(masses)):
G.add_node(i)
for i in range(0, len(masses)):
for j in range(i + 1, len(masses)):
if abs(masses[j] - masses[i]) <= window*2.0:
G.add_edge(i, j)
else:
break
assert(nx.is_chordal(G))
setlist = nx.chordal_graph_cliques(G)
return max([len(x) for x in setlist])
def Chordal(P, tipo, ruta):
RUTA = ruta + '/NetWX/files/'
path = Path(RUTA)
path.mkdir(parents=True, exist_ok=True)
P_is_chordal = []
for i in range(len(P)):
P_is_chordal.append(is_chordal(P[i]))
P_is_chordal = DataFrame(is_chordal)
P_is_chordal.to_csv(RUTA + tipo + " - is chordal.txt",
sep='\t',
header=None,
index=False)
def tree_insertion(num_nodes, num_edges, return_tree=False):
tree = nx.random_tree(num_nodes)
chordal = Graph(tree)
while len(chordal.edges) < num_edges:
u, v = random.sample(chordal.nodes, 2)
chordal.add_edge(u, v)
while not nx.is_chordal(chordal):
chordal.remove_edge(u, v)
u, v = random.sample(chordal.nodes, 2)
chordal.add_edge(u, v)
if not return_tree:
return chordal
return tree, chordal
def test_bayesian_model(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
bm = self.graph.to_bayesian_model()
self.assertIsInstance(bm, BayesianModel)
self.assertListEqual(sorted(bm.nodes()), ['a', 'b', 'c', 'd'])
self.assertTrue(nx.is_chordal(bm.to_undirected()))
def get_clique_tree(nodes: Iterable[int], edges: List[Tuple[int,
int]]) -> nx.Graph:
"""
Given a set of int nodes i and edges (i,j), returns a clique tree.
Clique tree is an object G for which:
- G.nodes[i]['members'] contains the set of original nodes in the ith
maximal clique
- G[i][j]['members'] contains the set of original nodes in the seperator
set between maximal cliques i and j
Note: This method is currently only implemented for chordal graphs; TODO:
add a step to triangulate non-chordal graphs.
Parameters
----------
nodes
A list of nodes indices
edges
A list of tuples, where each tuple has indices for connected nodes
Returns
-------
networkx.Graph
An object G representing clique tree
"""
# Form the original graph G1
G1 = nx.Graph()
G1.add_nodes_from(nodes)
G1.add_edges_from(edges)
# Check if graph is chordal
# TODO: Add step to triangulate graph if not
if not nx.is_chordal(G1):
raise NotImplementedError("Graph triangulation not implemented.")
# Create maximal clique graph G2
# Each node is a maximal clique C_i
# Let w = |C_i \cap C_j|; C_i, C_j have an edge with weight w if w > 0
G2 = nx.Graph()
for i, c in enumerate(nx.chordal_graph_cliques(G1)):
G2.add_node(i, members=c)
for i in G2.nodes:
for j in G2.nodes:
S = G2.nodes[i]["members"].intersection(G2.nodes[j]["members"])
w = len(S)
if w > 0:
G2.add_edge(i, j, weight=w, members=S)
# Return a minimum spanning tree of G2
return nx.minimum_spanning_tree(G2)
def is_triangulated(self):
"""
Checks whether the undirected graph is triangulated or not.
Examples
--------
>>> from pgmpy.base import UndirectedGraph
>>> G = UndirectedGraph()
>>> G.add_edges_from([('x1', 'x2'), ('x1', 'x3'), ('x1', 'x4'),
... ('x2', 'x4'), ('x3', 'x4')])
>>> G.is_triangulated()
True
"""
return nx.is_chordal(self)
def is_triangulated(self):
"""
Checks whether the undirected graph is triangulated or not.
Examples
--------
>>> from pgmpy.base import UndirectedGraph
>>> G = UndirectedGraph()
>>> G.add_edges_from([('x1', 'x2'), ('x1', 'x3'), ('x1', 'x4'),
... ('x2', 'x4'), ('x3', 'x4')])
>>> G.is_triangulated()
True
"""
return nx.is_chordal(self)
def markov_add_remove(g, num_steps):
# The input should be a UCCG.
all_edges = set(combinations(g.nodes, 2))
for _ in range(num_steps):
u, v = random.sample(g.edges, 1)[0]
a, b = random.sample(all_edges - g.edges, 1)[0]
g.remove_edge(u, v)
g.add_edge(a, b)
while not nx.is_connected(g) or not nx.is_chordal(g):
g.add_edge(u, v)
g.remove_edge(a, b)
u, v = random.sample(g.edges, 1)[0]
a, b = random.sample(all_edges - g.edges, 1)[0]
g.remove_edge(u, v)
g.add_edge(a, b)
def print_is_of_type_attrs(graph):
print("\n====== is of type X? ======")
print("Directed? ->", "Yes" if nx.is_directed(graph) else "No")
print("Directed acyclic? ->", "Yes" if nx.is_directed_acyclic_graph(graph) else "No")
print("Weighted? ->", "Yes" if nx.is_weighted(graph) else "No")
if nx.is_directed(graph):
print("Aperiodic? ->", "Yes" if nx.is_aperiodic(graph) else "No")
print("Arborescence? ->", "Yes" if nx.is_arborescence(graph) else "No")
print("Weakly Connected? ->", "Yes" if nx.is_weakly_connected(graph) else "No")
print("Semi Connected? ->", "Yes" if nx.is_semiconnected(graph) else "No")
print("Strongly Connected? ->", "Yes" if nx.is_strongly_connected(graph) else "No")
else:
print("Connected? ->", "Yes" if nx.is_connected(graph) else "No")
print("Bi-connected? ->", "Yes" if nx.is_biconnected(graph) else "No")
if not graph.is_multigraph():
print("Chordal? -> ", "Yes" if nx.is_chordal(graph) else "No")
print("Forest? -> ", "Yes" if nx.is_chordal(graph) else "No")
print("Distance regular? -> ", "Yes" if nx.is_distance_regular(graph) else "No")
print("Eulerian? -> ", "Yes" if nx.is_eulerian(graph) else "No")
print("Strongly regular? -> ", "Yes" if nx.is_strongly_regular(graph) else "No")
print("Tree? -> ", "Yes" if nx.is_tree(graph) else "No")
def test_hypertree(self):
"""
Méthode qui va retourner True ou False si le graphe est ou n'est pas un
hypetree. Pour ça, elle va vérifier la chordalité et les cliques du
graphe
"""
primal = self.getPrimal()
isClique = self.checkClique() #O(m²n²)
isChodal = nx.is_chordal(primal) #O(m*n)
if isChodal and isClique:
plt.show()
return True
else:
plt.show()
return False
def is_triangulated(self):
"""
Checks whether the undirected graph is triangulated (also known
as chordal) or not.
Chordal Graph: A chordal graph is one in which all cycles of four
or more vertices have a chord.
Examples
--------
>>> from pgmpy.base import UndirectedGraph
>>> G = UndirectedGraph()
>>> G.add_edges_from(ebunch=[('x1', 'x2'), ('x1', 'x3'),
... ('x2', 'x4'), ('x3', 'x4')])
>>> G.is_triangulated()
False
>>> G.add_edge(u='x1', v='x4')
>>> G.is_triangulated()
True
"""
return nx.is_chordal(self)
def is_chordal(g, **kwargs):
return nx.is_chordal(g)
import networkx as nx
f = open("stats_chord.txt",'r')
lignes = f.readlines()
f.close()
for ligne in lignes:
ligne = ligne.split(',')
for i in ligne :
i = i.replace("\n", "")
G = nx.parse_edgelist(ligne, nodetype = int)
print nx.is_chordal(G)