def test_add(self):
"""Test that Add can be invoked."""
value1 = np.random.uniform(size=(2, 3)).astype(np.float32)
value2 = np.random.uniform(size=(2, 3)).astype(np.float32)
value3 = np.random.uniform(size=(2, 3)).astype(np.float32)
with self.test_session() as sess:
out_tensor = Add(weights=[1, 2, 1])(
tf.constant(value1), tf.constant(value2), tf.constant(value3))
assert np.array_equal(value1 + 2 * value2 + value3, out_tensor.eval())
def test_reshape_inputs(self):
"""Test that layers can automatically reshape inconsistent inputs."""
value1 = np.random.uniform(size=(2, 3)).astype(np.float32)
value2 = np.random.uniform(size=(1, 6, 1)).astype(np.float32)
with self.test_session() as sess:
out_tensor = Add()(tf.constant(value1), tf.constant(value2))
result = out_tensor.eval()
assert result.shape == (1, 6, 1)
assert np.array_equal(value1.reshape((1, 6, 1)) + value2, result)
def test_add(self):
"""Test that Add can be invoked."""
value1 = np.random.uniform(size=(2, 3)).astype(np.float32)
value2 = np.random.uniform(size=(2, 3)).astype(np.float32)
value3 = np.random.uniform(size=(2, 3)).astype(np.float32)
with self.session() as sess:
out_tensor = Add(weights=[1, 2, 1])(tf.constant(value1),
tf.constant(value2),
tf.constant(value3))
assert np.array_equal(value1 + 2 * value2 + value3, out_tensor.eval())
def identity_block(self, input, kernel_size, filters):
filters1, filters2, filters3 = filters
output = Conv2D(num_outputs=filters1,
kernel_size=1,
activation='linear',
padding='same',
in_layers=[input])
output = BatchNorm(in_layers=[output])
output = ReLU(output)
output = Conv2D(num_outputs=filters2,
kernel_size=kernel_size,
activation='linear',
padding='same',
in_layers=[input])
output = BatchNorm(in_layers=[output])
output = ReLU(output)
output = Conv2D(num_outputs=filters3,
kernel_size=1,
activation='linear',
padding='same',
in_layers=[input])
output = BatchNorm(in_layers=[output])
output = Add(in_layers=[output, input])
output = ReLU(output)
return output
def test_Constant_pickle(): tg = TensorGraph() feature = Feature(shape=(tg.batch_size, 1)) layer = Constant(np.array([15.0])) output = Add(in_layers=[feature, layer]) tg.add_output(output) tg.set_loss(output) tg.build() tg.save()
def build_graph(self):
print("building")
features = Feature(shape=(None, self.n_features))
last_layer = features
for layer_size in self.encoder_layers:
last_layer = Dense(in_layers=last_layer,
activation_fn=tf.nn.elu,
out_channels=layer_size)
self.mean = Dense(in_layers=last_layer,
activation_fn=None,
out_channels=1)
self.std = Dense(in_layers=last_layer,
activation_fn=None,
out_channels=1)
readout = CombineMeanStd([self.mean, self.std], training_only=True)
last_layer = readout
for layer_size in self.decoder_layers:
last_layer = Dense(in_layers=readout,
activation_fn=tf.nn.elu,
out_channels=layer_size)
self.reconstruction = Dense(in_layers=last_layer,
activation_fn=None,
out_channels=self.n_features)
weights = Weights(shape=(None, self.n_features))
reproduction_loss = L2Loss(
in_layers=[features, self.reconstruction, weights])
reproduction_loss = ReduceSum(in_layers=reproduction_loss, axis=0)
global_step = TensorWrapper(self._get_tf("GlobalStep"))
kl_loss = KLDivergenceLoss(
in_layers=[self.mean, self.std, global_step],
annealing_start_step=self.kl_annealing_start_step,
annealing_stop_step=self.kl_annealing_stop_step)
loss = Add(in_layers=[kl_loss, reproduction_loss], weights=[0.5, 1])
self.add_output(self.mean)
self.add_output(self.reconstruction)
self.set_loss(loss)
def conv_block(self, input, kernel_size, filters, strides=2):
filters1, filters2, filters3 = filters
output = Conv2D(num_outputs=filters1,
kernel_size=1,
stride=strides,
activation='linear',
padding='same',
in_layers=[input])
output = BatchNorm(in_layers=[output])
output = ReLU(output)
output = Conv2D(num_outputs=filters2,
kernel_size=kernel_size,
activation='linear',
padding='same',
in_layers=[output])
output = BatchNorm(in_layers=[output])
output = ReLU(output)
output = Conv2D(num_outputs=filters3,
kernel_size=1,
activation='linear',
padding='same',
in_layers=[output])
output = BatchNorm(in_layers=[output])
shortcut = Conv2D(num_outputs=filters3,
kernel_size=1,
stride=strides,
activation='linear',
padding='same',
in_layers=[input])
shortcut = BatchNorm(in_layers=[shortcut])
output = Add(in_layers=[shortcut, output])
output = ReLU(output)
return output
def sluice_model(batch_size, tasks):
model = TensorGraph(model_dir=model_dir,
batch_size=batch_size,
use_queue=False,
tensorboard=True)
atom_features = Feature(shape=(None, 75))
degree_slice = Feature(shape=(None, 2), dtype=tf.int32)
membership = Feature(shape=(None, ), dtype=tf.int32)
sluice_loss = []
deg_adjs = []
for i in range(0, 10 + 1):
deg_adj = Feature(shape=(None, i + 1), dtype=tf.int32)
deg_adjs.append(deg_adj)
gc1 = GraphConv(64,
activation_fn=tf.nn.relu,
in_layers=[atom_features, degree_slice, membership] +
deg_adjs)
as1 = AlphaShare(in_layers=[gc1, gc1])
sluice_loss.append(gc1)
batch_norm1a = BatchNorm(in_layers=[as1[0]])
batch_norm1b = BatchNorm(in_layers=[as1[1]])
gp1a = GraphPool(in_layers=[batch_norm1a, degree_slice, membership] +
deg_adjs)
gp1b = GraphPool(in_layers=[batch_norm1b, degree_slice, membership] +
deg_adjs)
gc2a = GraphConv(64,
activation_fn=tf.nn.relu,
in_layers=[gp1a, degree_slice, membership] + deg_adjs)
gc2b = GraphConv(64,
activation_fn=tf.nn.relu,
in_layers=[gp1b, degree_slice, membership] + deg_adjs)
as2 = AlphaShare(in_layers=[gc2a, gc2b])
sluice_loss.append(gc2a)
sluice_loss.append(gc2b)
batch_norm2a = BatchNorm(in_layers=[as2[0]])
batch_norm2b = BatchNorm(in_layers=[as2[1]])
gp2a = GraphPool(in_layers=[batch_norm2a, degree_slice, membership] +
deg_adjs)
gp2b = GraphPool(in_layers=[batch_norm2b, degree_slice, membership] +
deg_adjs)
densea = Dense(out_channels=128, activation_fn=None, in_layers=[gp2a])
denseb = Dense(out_channels=128, activation_fn=None, in_layers=[gp2b])
batch_norm3a = BatchNorm(in_layers=[densea])
batch_norm3b = BatchNorm(in_layers=[denseb])
as3 = AlphaShare(in_layers=[batch_norm3a, batch_norm3b])
sluice_loss.append(batch_norm3a)
sluice_loss.append(batch_norm3b)
gg1a = GraphGather(batch_size=batch_size,
activation_fn=tf.nn.tanh,
in_layers=[as3[0], degree_slice, membership] + deg_adjs)
gg1b = GraphGather(batch_size=batch_size,
activation_fn=tf.nn.tanh,
in_layers=[as3[1], degree_slice, membership] + deg_adjs)
costs = []
labels = []
count = 0
for task in tasks:
if count < len(tasks) / 2:
classification = Dense(out_channels=2,
activation_fn=None,
in_layers=[gg1a])
print("first half:")
print(task)
else:
classification = Dense(out_channels=2,
activation_fn=None,
in_layers=[gg1b])
print('second half')
print(task)
count += 1
softmax = SoftMax(in_layers=[classification])
model.add_output(softmax)
label = Label(shape=(None, 2))
labels.append(label)
cost = SoftMaxCrossEntropy(in_layers=[label, classification])
costs.append(cost)
entropy = Concat(in_layers=costs)
task_weights = Weights(shape=(None, len(tasks)))
task_loss = WeightedError(in_layers=[entropy, task_weights])
s_cost = SluiceLoss(in_layers=sluice_loss)
total_loss = Add(in_layers=[task_loss, s_cost])
model.set_loss(total_loss)
def feed_dict_generator(dataset, batch_size, epochs=1):
for epoch in range(epochs):
for ind, (X_b, y_b, w_b, ids_b) in enumerate(
dataset.iterbatches(batch_size, pad_batches=True)):
d = {}
for index, label in enumerate(labels):
d[label] = to_one_hot(y_b[:, index])
d[task_weights] = w_b
multiConvMol = ConvMol.agglomerate_mols(X_b)
d[atom_features] = multiConvMol.get_atom_features()
d[degree_slice] = multiConvMol.deg_slice
d[membership] = multiConvMol.membership
for i in range(1, len(multiConvMol.get_deg_adjacency_lists())):
d[deg_adjs[i -
1]] = multiConvMol.get_deg_adjacency_lists()[i]
yield d
return model, feed_dict_generator, labels, task_weights