def train_model(params):
"""
function to create and train the model. This is called by hyper opt.
It returned the loss (=optimisation metric), status and a dict with
supporting information.
"""
dims = [
int(params['dim0']),
int(params['dim1']),
int(params['dim2']),
int(params['dim3']), 2
]
gae = GraphAutoEncoder(G,
learning_rate=0.01,
support_size=[5, 5],
dims=dims,
batch_size=12,
max_total_steps=250)
train_res = {}
for i in range(len(gae.dims)):
train_res["l" + str(i + 1)] = gae.train_layer(i + 1, act=tf.nn.relu)
train_res['all'] = gae.train_layer(len(gae.dims),
all_layers=True,
act=tf.nn.relu)
loss_val = train_res['all']['val_l'][-3:]
print(f"loss val {loss_val}")
loss = sum(loss_val) / len(loss_val)
train_res['loss'] = loss
return {'loss': loss, 'status': STATUS_OK, 'hist': train_res}
def test_train_layer3(self):
"""
Test with 3 hubs sampling using different support sizes per layer.
"""
graph = gb.create_directed_barbell(4, 4)
gae = GraphAutoEncoder(graph,
support_size=[3, 4, 5],
dims=[2, 3, 3, 3, 3, 2],
batch_size=3,
max_total_steps=1,
verbose=False,
seed=2,
act=tf.nn.relu)
exp = [
153.83647, 309.56152, 311.00153, 459.34726, 484.33817, 504.59387
]
for i in range(6):
res = gae.train_layer(i + 1)
self.assertAlmostEqual(
res['l'][0], exp[i], 4,
f"loss of layer {i+1} does not match with expectations")
res = gae.train_layer(6, all_layers=True)
self.assertAlmostEqual(
res['l'][0], 504.55478, 4,
"loss of the layer 6 all traning does not match with expectations")
def test_train_layer2(self):
"""
Test if the loss is reduced during training
"""
graph = gb.create_directed_barbell(4, 4)
gae = GraphAutoEncoder(graph,
support_size=[3, 3],
dims=[2, 3, 3, 2],
batch_size=3,
max_total_steps=10,
verbose=False,
seed=2,
act=tf.nn.relu)
res = gae.train_layer(1, learning_rate=0.0001)
self.assertTrue(res['val_l'][0] > res['val_l'][-1],
"loss has not decreased while training layer 1")
res = gae.train_layer(2, learning_rate=0.0001)
self.assertTrue(res['val_l'][0] > res['val_l'][-1],
"loss has not decreased while training layer 2")
res = gae.train_layer(3, learning_rate=0.0001)
self.assertTrue(res['val_l'][0] > res['val_l'][-1],
"loss has not decreased while training layer 3")
res = gae.train_layer(4, learning_rate=0.0001)
self.assertTrue(res['val_l'][0] > res['val_l'][-1],
"loss has not decreased while training layer 4")
def test_fit(self):
"""
Test if fit function results in the same results as when trained separately
"""
graph = gb.create_directed_barbell(4, 4)
gae = GraphAutoEncoder(graph,
learning_rate=0.01,
support_size=[5, 5],
dims=[3, 5, 7, 6, 2],
batch_size=12,
max_total_steps=50,
verbose=True)
train_res = {}
for i in range(len(gae.dims)):
train_res["l" + str(i + 1)] = gae.train_layer(i + 1)
train_res['all'] = gae.train_layer(len(gae.dims),
all_layers=True,
dropout=None)
embed = gae.calculate_embeddings()
gae2 = GraphAutoEncoder(graph,
learning_rate=0.01,
support_size=[5, 5],
dims=[3, 5, 7, 6, 2],
batch_size=12,
max_total_steps=50,
verbose=True)
gae2.fit(graph)
embed2 = gae2.calculate_embeddings()
embed3 = np.subtract(embed, embed2)
self.assertAlmostEqual(
np.sum(embed3), 0, 4,
"fit method results in a different model when trained separately")
def test_train_layer5(self):
"""
Test using final combination layer. Test if training works correctly and if the calculation
of the embeddings works correctly.
"""
graph = gb.create_directed_barbell(4, 4)
for in_node, out_node, lbl in graph.edges(data=True):
lbl['edge_lbl1'] = in_node / (out_node + 0.011) + 0.22
gae = GraphAutoEncoder(graph,
support_size=[3, 3],
dims=[2, 3, 3, 2, 2],
batch_size=3,
max_total_steps=10,
verbose=False,
seed=2,
weight_label='edge_lbl1',
act=tf.nn.relu)
for i in range(len(gae.dims)):
res = gae.train_layer(i + 1, act=tf.nn.relu)
self.assertAlmostEqual(
res['l'][0], 134.9637, 4,
"loss of the last layer does not match with expectations using a \
final combination layer")
res = gae.train_layer(len(gae.dims), all_layers=True, act=tf.nn.relu)
embed = gae.calculate_embeddings()
self.assertAlmostEqual(
embed[0][2], 38.221458435058594, 4,
"embedding of the first batch node differs from expected value")
def test_train_layer(self):
"""
Test if the loss of the initial setup is correct.
"""
graph = gb.create_directed_barbell(4, 4)
# ad node ids to the graph as label
labels3 = [(i, i) for i in range(13)]
labels3 = dict(labels3)
nx.set_node_attributes(graph, labels3, 'label3')
gae = GraphAutoEncoder(graph,
support_size=[3, 3],
dims=[2, 3, 3, 2],
batch_size=3,
max_total_steps=1,
verbose=False,
seed=2,
act=tf.nn.relu)
res = gae.train_layer(1)
self.assertAlmostEqual(
res['l'][0], 2158.0686, 4,
"loss of the initial setup does not match with expectations")
res = gae.train_layer(2)
self.assertAlmostEqual(
res['l'][0], 2613.2725, 4,
"loss of the initial setup does not match with expectations")
res = gae.train_layer(3)
self.assertAlmostEqual(
res['l'][0], 2693.6736, 4,
"loss of the initial setup does not match with expectations")
res = gae.train_layer(4)
self.assertAlmostEqual(
res['l'][0], 2842.3582, 3,
"loss of the initial setup does not match with expectations")
res = gae.train_layer(4, all_layers=True)
self.assertAlmostEqual(
res['l'][0], 2842.1409, 4,
"loss of the initial setup does not match with expectations")
def test_train_layer4(self):
"""
Test using multiple edge label icw a custom weight label. The test checks if the
weights are calculated correct.
"""
graph = gb.create_directed_barbell(4, 4)
for in_node, out_node, lbl in graph.edges(data=True):
lbl['edge_lbl1'] = in_node / (out_node + 0.011) + 0.22
gae = GraphAutoEncoder(graph,
support_size=[3, 3],
dims=[2, 3, 3, 2],
batch_size=3,
max_total_steps=10,
verbose=False,
seed=2,
weight_label='edge_lbl1',
act=tf.nn.relu)
res = gae.train_layer(1, learning_rate=0.0001)
self.assertAlmostEqual(
res['l'][0], 49.392754, 4,
"loss of the layer 1 does not match with expectations using a \
custom edge label")
# correction edge weight for node # 20
ndic = graph.nodes(data='label1')
for u, v, d in graph.edges(data=True):
if(v > 9) & (v < 21):
d['weight'] = 1
else:
d['weight'] = ndic[u] * ndic[v]
#%% create and train model
gae = GraphAutoEncoder(graph, learning_rate=0.01, support_size=[5, 5], dims=[3, 5, 7, 6, 2],
batch_size=30, max_total_steps=1000, verbose=True, act=tf.nn.tanh)
if TRAIN:
train_res = {}
for i in range(len(gae.dims)):
if i in [1, 2]:
train_res["l"+str(i+1)] = gae.train_layer(i+1, dropout=0.1)
else:
train_res["l"+str(i+1)] = gae.train_layer(i+1)
train_res['all'] = gae.train_layer(len(gae.dims), all_layers=True)
pickle.dump(train_res, open(RESULTS_FILE, "wb"))
gae.save_model(MODEL_FILENAME)
else:
gae.load_model(MODEL_FILENAME, graph)
embed = gae.calculate_embeddings()
# %% get tabel with node details
indeg = graph.in_degree()
outdeg = graph.out_degree()
# [(out_node, list(weight.values()))]
# in_weight_dict[in_node] = in_weight_dict.get(in_node, list()) + \
# [(out_node, weight['weight'])]
# print(in_edges_dict)
# print(in_weight_dict)
gae = GraphAutoEncoder(G,
support_size=[3, 4],
dims=[2, 6, 6, 2, 1],
batch_size=5,
max_total_steps=10,
verbose=True,
seed=2)
for i in range(len(gae.dims)):
h = gae.train_layer(i + 1, act=tf.nn.relu)
h = gae.train_layer(len(gae.dims), all_layers=True, act=tf.nn.relu)
# # print(h1['val_l'])
e = gae.calculate_embeddings()
print(f"e: \n {e}")
# fig, ax = plt.subplots()
# ax.scatter(e[:,1], e[:,2])
# for i, txt in enumerate(e[:,0]):
# ax.annotate(txt, (e[i,1], e[i,2]))
# plt.xlabel("Leprechauns")
# plt.ylabel("Gold")
# plt.legend(loc='upper left')
# plt.show()