def test_digraph(self):
G = nx.DiGraph()
G.add_edge(0, 1)
G.add_edge(1, 2)
G.add_edge(2, 3)
label_name = 'label'
G.node[0][label_name] = 'A'
G.node[3][label_name] = 'B'
node_classification.harmonic_function(G)
def test_digraph(self):
G = nx.DiGraph()
G.add_edge(0, 1)
G.add_edge(1, 2)
G.add_edge(2, 3)
label_name = 'label'
G.node[0][label_name] = 'A'
G.node[3][label_name] = 'B'
node_classification.harmonic_function(G)
def test_digraph(self):
with pytest.raises(nx.NetworkXNotImplemented):
G = nx.DiGraph()
G.add_edge(0, 1)
G.add_edge(1, 2)
G.add_edge(2, 3)
label_name = "label"
G.nodes[0][label_name] = "A"
G.nodes[3][label_name] = "B"
node_classification.harmonic_function(G)
def drop_label(graph, labels, percentage):
nodes = graph.nodes
indices = np.random.permutation(len(nodes))
bound = int(len(nodes) * percentage)
training_idx, test_idx = indices[:bound], indices[bound:]
train_mask = np.zeros(len(nodes))
train_mask[training_idx] = 1
for node, label, mask in zip(nodes, labels, train_mask):
if mask == 1:
graph.nodes[node]['label'] = label
else:
try:
nodes[node].pop("label")
except:
pass
harmonic_prediction = np.array(
node_classification.harmonic_function(graph))
local_global_prediction = np.array(
node_classification.local_and_global_consistency(graph))
return accuracy_score(labels[test_idx], harmonic_prediction[test_idx]), \
accuracy_score(labels[test_idx], local_global_prediction[test_idx])
def test_nodes_all_labeled(self):
G = nx.karate_club_graph()
label_name = 'club'
predicted = node_classification.harmonic_function(
G, label_name=label_name)
for i in range(len(G)):
assert_equal(predicted[i], G.node[i][label_name])
def test_nodes_all_labeled(self):
G = nx.karate_club_graph()
label_name = 'club'
predicted = node_classification.harmonic_function(
G, label_name=label_name)
for i in range(len(G)):
assert_equal(predicted[i], G.node[i][label_name])
def harmonic_func(G, label_name):
predicted = list(
node_classification.harmonic_function(G, label_name=label_name))
idx = 0
for n in G.nodes():
G.nodes[n][label_name] = predicted[idx]
idx = idx + 1
return G
def test_one_labeled_node(self):
G = nx.path_graph(4)
label_name = 'label'
G.node[0][label_name] = 'A'
predicted = node_classification.harmonic_function(
G, label_name=label_name)
assert_equal(predicted[0], 'A')
assert_equal(predicted[1], 'A')
assert_equal(predicted[2], 'A')
assert_equal(predicted[3], 'A')
def test_one_labeled_node(self):
G = nx.path_graph(4)
label_name = "label"
G.nodes[0][label_name] = "A"
predicted = node_classification.harmonic_function(
G, label_name=label_name)
assert predicted[0] == "A"
assert predicted[1] == "A"
assert predicted[2] == "A"
assert predicted[3] == "A"
def test_one_labeled_node(self):
G = nx.path_graph(4)
label_name = 'label'
G.node[0][label_name] = 'A'
predicted = node_classification.harmonic_function(
G, label_name=label_name)
assert_equal(predicted[0], 'A')
assert_equal(predicted[1], 'A')
assert_equal(predicted[2], 'A')
assert_equal(predicted[3], 'A')
def test_labeled_nodes_are_not_changed(self):
G = nx.karate_club_graph()
label_name = 'club'
label_removed = set([0, 1, 2, 3, 4, 5, 6, 7])
for i in label_removed:
del G.node[i][label_name]
predicted = node_classification.harmonic_function(
G, label_name=label_name)
label_not_removed = set(list(range(len(G)))) - label_removed
for i in label_not_removed:
assert_equal(predicted[i], G.node[i][label_name])
def test_labeled_nodes_are_not_changed(self):
G = nx.karate_club_graph()
label_name = 'club'
label_removed = set([0, 1, 2, 3, 4, 5, 6, 7])
for i in label_removed:
del G.node[i][label_name]
predicted = node_classification.harmonic_function(
G, label_name=label_name)
label_not_removed = set(list(range(len(G)))) - label_removed
for i in label_not_removed:
assert_equal(predicted[i], G.node[i][label_name])
def test_path_graph(self):
G = nx.path_graph(4)
label_name = 'label'
G.nodes[0][label_name] = 'A'
G.nodes[3][label_name] = 'B'
predicted = node_classification.harmonic_function(
G, label_name=label_name)
assert predicted[0] == 'A'
assert predicted[1] == 'A'
assert predicted[2] == 'B'
assert predicted[3] == 'B'
def classify_gcn_data(graph, dataset):
train_y = np.argmax(np.load(f'./ind.{dataset}.y'), axis=1)
test_y = np.argmax(np.load(f'./ind.{dataset}.ty'), axis=1)
test_idx = parse_index_file(f'./ind.{dataset}.test.index')
train_labels = {train_node: train_y[train_node] for train_node in range(len(train_y))}
test_labels = {test_node: test_y[test_node] for test_node in range(len(test_y))}
nx.set_node_attributes(graph, train_labels, 'train_labels')
harmonic_pred = node_classification.harmonic_function(graph, label_name='train_labels')
lg_pred = node_classification.local_and_global_consistency(graph, label_name='train_labels')
harmonic_acc = metrics.accuracy_score(test_y, np.array(harmonic_pred)[test_idx])
lg_acc = metrics.accuracy_score(test_y, np.array(lg_pred)[test_idx])
return harmonic_acc, lg_acc
def classifiy_lfr(graph, node_labels, train_portion=0.8):
nodes_idx = np.arange(len(node_labels))
np.random.shuffle(nodes_idx)
train_nodes_idx = nodes_idx[:int(train_portion * len(node_labels))]
test_nodes_idx = nodes_idx[int(train_portion * len(node_labels)):]
train_labels = {train_node: node_labels[train_node] for train_node in train_nodes_idx}
nx.set_node_attributes(graph, train_labels, 'train_labels')
harmonic_pred = node_classification.harmonic_function(graph, label_name='train_labels')
lg_pred = node_classification.local_and_global_consistency(graph, label_name='train_labels')
harmonic_acc = metrics.accuracy_score(node_labels[test_nodes_idx], np.array(harmonic_pred)[test_nodes_idx])
lg_acc = metrics.accuracy_score(node_labels[test_nodes_idx], np.array(lg_pred)[test_nodes_idx])
return harmonic_acc, lg_acc
def classify_real_graph_nodes(graph, train_portion=0.8):
all_labels = nx.get_node_attributes(graph, 'value')
nodes = np.array(list(all_labels.keys()))
nodes_idx = np.arange(len(nodes))
np.random.shuffle(nodes_idx)
train_nodes_idx = nodes_idx[:int(train_portion * len(nodes))]
test_nodes_idx = nodes_idx[int(train_portion * len(nodes)):]
train_labels = {train_node: all_labels[train_node] for train_node in nodes[train_nodes_idx]}
test_labels = {test_node: all_labels[test_node] for test_node in nodes[test_nodes_idx]}
nx.set_node_attributes(graph, train_labels, 'train_labels')
harmonic_pred = node_classification.harmonic_function(graph, label_name='train_labels')
lg_pred = node_classification.local_and_global_consistency(graph, label_name='train_labels')
harmonic_acc = metrics.accuracy_score(np.array(list(test_labels.values())), np.array(harmonic_pred)[test_nodes_idx])
lg_acc = metrics.accuracy_score(np.array(list(test_labels.values())), np.array(lg_pred)[test_nodes_idx])
return harmonic_acc, lg_acc
def q2():
graph, labels, y_train, y_val, y_test, train_mask, val_mask, test_mask = load_data_gcn(
args.data)
if args.data == 'citeseer':
nonzeros = labels.nonzero()
max_label = np.max(nonzeros[1])
diff = len(labels) - len(nonzeros[1])
res = np.full(labels.shape[0], -1)
res[nonzeros[0]] = nonzeros[1]
iso_mask = np.where(res == -1)
res[iso_mask] = np.arange(max_label + 1, max_label + 1 + diff)
labels = res
else:
labels = labels.nonzero()[1]
for node, label, mask in zip(graph.nodes, labels, train_mask):
if mask:
graph.nodes[node]['label'] = label
harmonic_prediction = np.array(
node_classification.harmonic_function(graph))
local_global_prediction = np.array(
node_classification.local_and_global_consistency(graph))
print("train accuracy of harmonic prediction: {}".format(
accuracy_score(labels[train_mask], harmonic_prediction[train_mask])))
print("train accuracy of loc-glob prediction: {}".format(
accuracy_score(labels[train_mask],
local_global_prediction[train_mask])))
print("val accuracy of harmonic prediction: {}".format(
accuracy_score(labels[val_mask], harmonic_prediction[val_mask])))
print("val accuracy of loc-glob prediction: {}".format(
accuracy_score(labels[val_mask], local_global_prediction[val_mask])))
print("test accuracy of harmonic prediction: {}".format(
accuracy_score(labels[test_mask], harmonic_prediction[test_mask])))
print("test accuracy of loc-glob prediction: {}".format(
accuracy_score(labels[test_mask], local_global_prediction[test_mask])))
def calculate_node_classification_accuracy(G, label, ground_truths, method):
nmi_list = []
ars_list = []
for i in range(10):
if method == 'harmonic':
predictions = node_classification.harmonic_function(G, label_name=label)
else:
predictions = node_classification.local_and_global_consistency(G, label_name=label)
nmi, ars = calculate_nmi_ars(ground_truths, predictions)
nmi_list.append(nmi)
ars_list.append(ars)
average_nmi = round(mean(nmi_list), 4)
average_ars = round(mean(ars_list), 4)
print('Average NMI:', average_nmi)
print('Average ARS:', average_ars)
return average_nmi, average_ars
def test_no_labels(self):
G = nx.path_graph(4)
node_classification.harmonic_function(G)
def test_no_edges(self):
G = nx.Graph()
G.add_node(1)
G.add_node(2)
node_classification.harmonic_function(G)
fu_values = np.dot(np.dot(np.linalg.inv(Duu - Wuu), Wul), fl_values)
for row in range(len(fu_values)):
fu[fu_list[row]] = fu_values[row]
labeled_list = []
for i in range(len(fu) + len(fl)):
try:
labeled_list.append(fl[i])
except KeyError:
labeled_list.append(fu[i])
return [uniq_labeles_inverse[int(round(value))] for value in labeled_list]
G = create_toroidal(16)
G.node[0]['label'] = 'blue'
G.node[255]['label'] = 'red'
gpos = nx.spring_layout(G, iterations=200)
node_color=['blue' if n == 0 else 'red' if n == 255 else 'gray' for n in G.nodes]
plt.figure(figsize=(10,10))
nx.draw(G, gpos, with_labels=False, node_size=200, node_color=node_color)
plt.show()
node_color=node_classification.harmonic_function(G)
removed = [n for n in G.nodes if n%3 == 0 ]
for n in G.nodes:
if n not in removed:
G.node[n]['label'] = node_color[n]
predicted = your_harmonic_function(G, label_name='label')
print(confusion_matrix(node_color, predicted))
print(precision_recall_fscore_support(node_color, predicted))
#predicted = _predict(F, label_dict)
return F
def setup_module(module):
"""Fixture for nose tests."""
from nose import SkipTest
try:
import numpy
except ImportError:
raise SkipTest("NumPy not available")
try:
import scipy
except ImportError:
raise SkipTest("SciPy not available")
if __name__ == '__main__':
G=nx.Graph()
G.add_nodes_from(range(1,16))
G.node[2]['label'] = 'A'
G.node[11]['label'] = 'B'
G.add_edges_from([(1,3),(3,2),(3,4),(4,6),(4,12),(4,14),(6,5),(12,10),(12,15),(10,7),(10,8),(10,9),(10,11),(10,13)])
# Se quiser usar a função da networkx para rotular logo basta usar:
predicted = node_classification.harmonic_function(G)
print(predicted)
# Se quiser os valores de pertinência em cada classe deve-se usar a
# função deste arquivo
F = harmonic_function(G)
print(F)
def test_no_edges(self):
G = nx.Graph()
G.add_node(1)
G.add_node(2)
node_classification.harmonic_function(G)
def test_no_labels(self):
with pytest.raises(nx.NetworkXError):
G = nx.path_graph(4)
node_classification.harmonic_function(G)
def test_no_nodes(self):
G = nx.Graph()
node_classification.harmonic_function(G)
def test_no_labels(self):
G = nx.path_graph(4)
node_classification.harmonic_function(G)
import networkx as nx
import matplotlib.pyplot as plt
from networkx.drawing.nx_agraph import graphviz_layout
from networkx.algorithms import node_classification
G = nx.path_graph(4)
G.edges()
G.node[0]['label'] = 'A'
G.node[3]['label'] = 'B'
node_classification.harmonic_function(G) # doctest: +SKIP
nx.draw(G,
pos=graphviz_layout(G),
node_size=1600,
cmap=plt.cm.Reds,
node_color=range(len(G)),
prog='dot',
with_labels=True)
plt.show()
def test_no_edges(self):
with pytest.raises(nx.NetworkXError):
G = nx.Graph()
G.add_node(1)
G.add_node(2)
node_classification.harmonic_function(G)
def test_no_nodes(self):
G = nx.Graph()
node_classification.harmonic_function(G)