def build_graph(self):
"""
Building graph structures:
"""
self.m1_features = Feature(shape=(None, self.n_features))
self.m2_features = Feature(shape=(None, self.n_features))
prev_layer1 = self.m1_features
prev_layer2 = self.m2_features
for layer_size in self.layer_sizes:
prev_layer1 = Dense(
out_channels=layer_size,
in_layers=[prev_layer1],
activation_fn=tf.nn.relu)
prev_layer2 = prev_layer1.shared([prev_layer2])
if self.dropout > 0.0:
prev_layer1 = Dropout(self.dropout, in_layers=prev_layer1)
prev_layer2 = Dropout(self.dropout, in_layers=prev_layer2)
readout_m1 = Dense(
out_channels=1, in_layers=[prev_layer1], activation_fn=None)
readout_m2 = readout_m1.shared([prev_layer2])
self.add_output(Sigmoid(readout_m1) * 4 + 1)
self.add_output(Sigmoid(readout_m2) * 4 + 1)
self.difference = readout_m1 - readout_m2
label = Label(shape=(None, 1))
loss = HingeLoss(in_layers=[label, self.difference])
self.my_task_weights = Weights(shape=(None, 1))
loss = WeightedError(in_layers=[loss, self.my_task_weights])
self.set_loss(loss)
def test_sigmoid(self):
"""Test that Sigmoid can be invoked."""
batch_size = 10
n_features = 5
in_tensor = np.random.rand(batch_size, n_features)
with self.session() as sess:
in_tensor = tf.convert_to_tensor(in_tensor, dtype=tf.float32)
out_tensor = Sigmoid()(in_tensor)
out_tensor = out_tensor.eval()
assert out_tensor.shape == (batch_size, n_features)
def test_sigmoid(self):
"""Test that Sigmoid can be invoked."""
batch_size = 10
n_features = 5
in_tensor = np.random.rand(batch_size, n_features)
with self.session() as sess:
in_tensor = tf.convert_to_tensor(in_tensor, dtype=tf.float32)
out_tensor = Sigmoid()(in_tensor)
out_tensor = out_tensor.eval()
assert out_tensor.shape == (batch_size, n_features)
def build_graph(self):
"""Constructs the graph architecture of IRV as described in:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750043/
"""
self.mol_features = Feature(shape=(None, self.n_features))
self._labels = Label(shape=(None, self.n_tasks))
self._weights = Weights(shape=(None, self.n_tasks))
predictions = IRVLayer(self.n_tasks,
self.K,
in_layers=[self.mol_features])
costs = []
outputs = []
for task in range(self.n_tasks):
task_output = Slice(task, 1, in_layers=[predictions])
sigmoid = Sigmoid(in_layers=[task_output])
outputs.append(sigmoid)
label = Slice(task, axis=1, in_layers=[self._labels])
cost = SigmoidCrossEntropy(in_layers=[label, task_output])
costs.append(cost)
all_cost = Concat(in_layers=costs, axis=1)
loss = WeightedError(in_layers=[all_cost, self._weights]) + \
IRVRegularize(predictions, self.penalty, in_layers=[predictions])
self.set_loss(loss)
outputs = Stack(axis=1, in_layers=outputs)
outputs = Concat(axis=2, in_layers=[1 - outputs, outputs])
self.add_output(outputs)
def test_Sigmoid_pickle(): tg = TensorGraph() feature = Feature(shape=(tg.batch_size, 1)) layer = Sigmoid(in_layers=feature) tg.add_output(layer) tg.set_loss(layer) tg.build() tg.save()
