def test_flatten(self):
"""Test that Flatten can be invoked."""
in_dim_1 = 2
in_dim_2 = 2
out_dim = 4
batch_size = 10
in_tensor = np.random.rand(batch_size, in_dim_1, in_dim_2)
with self.session() as sess:
in_tensor = tf.convert_to_tensor(in_tensor, dtype=tf.float32)
out_tensor = Flatten()(in_tensor)
out_tensor = out_tensor.eval()
assert out_tensor.shape == (batch_size, out_dim)
def test_neighbor_list_vina(self):
"""Test under conditions closer to Vina usage."""
N_atoms = 5
M_nbrs = 2
ndim = 3
start = 0
stop = 4
nbr_cutoff = 1
X = NumpyDataset(start + np.random.rand(N_atoms, ndim) * (stop - start))
coords = Feature(shape=(N_atoms, ndim))
# Now an (N, M) shape
nbr_list = NeighborList(
N_atoms, M_nbrs, ndim, nbr_cutoff, start, stop, in_layers=[coords])
nbr_list = ToFloat(in_layers=[nbr_list])
flattened = Flatten(in_layers=[nbr_list])
dense = Dense(out_channels=1, in_layers=[flattened])
output = ReduceSum(in_layers=[dense])
tg = dc.models.TensorGraph(learning_rate=0.1, use_queue=False)
tg.set_loss(output)
databag = Databag({coords: X})
tg.fit_generator(databag.iterbatches(epochs=1))
def create_layers(self, state, **kwargs):
d1 = Flatten(in_layers=state)
d2 = Dense(
in_layers=[d1],
activation_fn=tf.nn.relu,
normalizer_fn=tf.nn.l2_normalize,
normalizer_params={"dim": 1},
out_channels=64)
d3 = Dense(
in_layers=[d2],
activation_fn=tf.nn.relu,
normalizer_fn=tf.nn.l2_normalize,
normalizer_params={"dim": 1},
out_channels=32)
d4 = Dense(
in_layers=[d3],
activation_fn=tf.nn.relu,
normalizer_fn=tf.nn.l2_normalize,
normalizer_params={"dim": 1},
out_channels=16)
d4 = BatchNorm(in_layers=[d4])
d5 = Dense(in_layers=[d4], activation_fn=None, out_channels=9)
value = Dense(in_layers=[d4], activation_fn=None, out_channels=1)
value = Squeeze(squeeze_dims=1, in_layers=[value])
probs = SoftMax(in_layers=[d5])
return {'action_prob': probs, 'value': value}
def _build_graph(self):
self.one_hot_seq = Feature(shape=(None, self.pad_length,
self.num_amino_acids),
dtype=tf.float32)
conv1 = Conv1D(kernel_size=2,
filters=512,
in_layers=[self.one_hot_seq])
maxpool1 = MaxPool1D(strides=2, padding="VALID", in_layers=[conv1])
conv2 = Conv1D(kernel_size=3, filters=512, in_layers=[maxpool1])
flattened = Flatten(in_layers=[conv2])
dense1 = Dense(out_channels=400,
in_layers=[flattened],
activation_fn=tf.nn.tanh)
dropout = Dropout(dropout_prob=self.dropout_p, in_layers=[dense1])
output = Dense(out_channels=1, in_layers=[dropout], activation_fn=None)
self.add_output(output)
if self.mode == "regression":
label = Label(shape=(None, 1))
loss = L2Loss(in_layers=[label, output])
else:
raise NotImplementedError(
"Classification support not added yet. Missing details in paper."
)
weights = Weights(shape=(None, ))
weighted_loss = WeightedError(in_layers=[loss, weights])
self.set_loss(weighted_loss)
def test_graph_save(self):
n_samples = 10
n_features = 11
n_tasks = 1
batch_size = 10
X = np.random.rand(batch_size, n_samples, n_features)
y = np.ones(shape=(n_samples, n_tasks))
ids = np.arange(n_samples)
dataset = dc.data.NumpyDataset(X, y, None, ids)
g = TensorGraph(model_dir='/tmp/tmpss5_ki5_')
inLayer = Input(shape=(None, n_samples, n_features))
g.add_feature(inLayer)
flatten = Flatten()
g.add_layer(flatten, parents=[inLayer])
dense = Dense(out_channels=1)
g.add_layer(dense, parents=[flatten])
g.add_output(dense)
label_out = Input(shape=(None, 1))
g.add_label(label_out)
loss = LossLayer()
g.add_layer(loss, parents=[dense, label_out])
g.set_loss(loss)
g.fit(dataset, nb_epoch=100)
g.save()
g1 = TensorGraph.load_from_dir('/tmp/tmpss5_ki5_')
print(g1)
print(g1.predict_on_batch(X))
def test_Flatten_pickle(): tg = TensorGraph() feature = Feature(shape=(tg.batch_size, 1)) layer = Flatten(in_layers=feature) tg.add_output(layer) tg.set_loss(layer) tg.build() tg.save()
def build_graph(self):
self.vertex_features = Feature(shape=(None, self.max_atoms, 75))
self.adj_matrix = Feature(shape=(None, self.max_atoms, 1, self.max_atoms))
self.mask = Feature(shape=(None, self.max_atoms, 1))
gcnn1 = BatchNorm(
GraphCNN(
num_filters=64,
in_layers=[self.vertex_features, self.adj_matrix, self.mask]))
gcnn1 = Dropout(self.dropout, in_layers=gcnn1)
gcnn2 = BatchNorm(
GraphCNN(num_filters=64, in_layers=[gcnn1, self.adj_matrix, self.mask]))
gcnn2 = Dropout(self.dropout, in_layers=gcnn2)
gc_pool, adj_matrix = GraphCNNPool(
num_vertices=32, in_layers=[gcnn2, self.adj_matrix, self.mask])
gc_pool = BatchNorm(gc_pool)
gc_pool = Dropout(self.dropout, in_layers=gc_pool)
gcnn3 = BatchNorm(GraphCNN(num_filters=32, in_layers=[gc_pool, adj_matrix]))
gcnn3 = Dropout(self.dropout, in_layers=gcnn3)
gc_pool2, adj_matrix2 = GraphCNNPool(
num_vertices=8, in_layers=[gcnn3, adj_matrix])
gc_pool2 = BatchNorm(gc_pool2)
gc_pool2 = Dropout(self.dropout, in_layers=gc_pool2)
flattened = Flatten(in_layers=gc_pool2)
readout = Dense(
out_channels=256, activation_fn=tf.nn.relu, in_layers=flattened)
costs = []
self.my_labels = []
for task in range(self.n_tasks):
if self.mode == 'classification':
classification = Dense(
out_channels=2, activation_fn=None, in_layers=[readout])
softmax = SoftMax(in_layers=[classification])
self.add_output(softmax)
label = Label(shape=(None, 2))
self.my_labels.append(label)
cost = SoftMaxCrossEntropy(in_layers=[label, classification])
costs.append(cost)
if self.mode == 'regression':
regression = Dense(
out_channels=1, activation_fn=None, in_layers=[readout])
self.add_output(regression)
label = Label(shape=(None, 1))
self.my_labels.append(label)
cost = L2Loss(in_layers=[label, regression])
costs.append(cost)
if self.mode == "classification":
entropy = Stack(in_layers=costs, axis=-1)
elif self.mode == "regression":
entropy = Stack(in_layers=costs, axis=1)
self.my_task_weights = Weights(shape=(None, self.n_tasks))
loss = WeightedError(in_layers=[entropy, self.my_task_weights])
self.set_loss(loss)
def __init__(self,
img_rows=224,
img_cols=224,
weights="imagenet",
classes=1000,
**kwargs):
super(ResNet50, self).__init__(use_queue=False, **kwargs)
self.img_cols = img_cols
self.img_rows = img_rows
self.weights = weights
self.classes = classes
input = Feature(shape=(None, self.img_rows, self.img_cols, 3))
labels = Label(shape=(None, self.classes))
conv1 = Conv2D(num_outputs=64,
kernel_size=7,
stride=2,
activation='linear',
padding='same',
in_layers=[input])
bn1 = BatchNorm(in_layers=[conv1])
ac1 = ReLU(bn1)
pool1 = MaxPool2D(ksize=[1, 3, 3, 1], in_layers=[bn1])
cb1 = self.conv_block(pool1, 3, [64, 64, 256], 1)
id1 = self.identity_block(cb1, 3, [64, 64, 256])
id1 = self.identity_block(id1, 3, [64, 64, 256])
cb2 = self.conv_block(id1, 3, [128, 128, 512])
id2 = self.identity_block(cb2, 3, [128, 128, 512])
id2 = self.identity_block(id2, 3, [128, 128, 512])
id2 = self.identity_block(id2, 3, [128, 128, 512])
cb3 = self.conv_block(id2, 3, [256, 256, 1024])
id3 = self.identity_block(cb3, 3, [256, 256, 1024])
id3 = self.identity_block(id3, 3, [256, 256, 1024])
id3 = self.identity_block(id3, 3, [256, 256, 1024])
id3 = self.identity_block(cb3, 3, [256, 256, 1024])
id3 = self.identity_block(id3, 3, [256, 256, 1024])
cb4 = self.conv_block(id3, 3, [512, 512, 2048])
id4 = self.identity_block(cb4, 3, [512, 512, 2048])
id4 = self.identity_block(id4, 3, [512, 512, 2048])
pool2 = AvgPool2D(ksize=[1, 7, 7, 1], in_layers=[id4])
flatten = Flatten(in_layers=[pool2])
dense = Dense(classes, in_layers=[flatten])
loss = SoftMaxCrossEntropy(in_layers=[labels, dense])
loss = ReduceMean(in_layers=[loss])
self.set_loss(loss)
self.add_output(dense)
def test_mnist(self):
from tensorflow.examples.tutorials.mnist import input_data
mnist = input_data.read_data_sets("MNIST_data/", one_hot=True)
train = dc.data.NumpyDataset(mnist.train.images, mnist.train.labels)
valid = dc.data.NumpyDataset(mnist.validation.images,
mnist.validation.labels)
# Images are square 28x28 (batch, height, width, channel)
feature = Feature(shape=(None, 784), name="Feature")
make_image = Reshape(shape=(-1, 28, 28, 1), in_layers=[feature])
conv2d_1 = Conv2D(num_outputs=32,
normalizer_fn=tf.contrib.layers.batch_norm,
in_layers=[make_image])
maxpool_1 = MaxPool(in_layers=[conv2d_1])
conv2d_2 = Conv2D(num_outputs=64,
normalizer_fn=tf.contrib.layers.batch_norm,
in_layers=[maxpool_1])
maxpool_2 = MaxPool(in_layers=[conv2d_2])
flatten = Flatten(in_layers=[maxpool_2])
dense1 = Dense(out_channels=1024,
activation_fn=tf.nn.relu,
in_layers=[flatten])
dense2 = Dense(out_channels=10, in_layers=[dense1])
label = Label(shape=(None, 10), name="Label")
smce = SoftMaxCrossEntropy(in_layers=[label, dense2])
loss = ReduceMean(in_layers=[smce])
output = SoftMax(in_layers=[dense2])
tg = dc.models.TensorGraph(model_dir='/tmp/mnist',
batch_size=1000,
use_queue=True)
tg.add_output(output)
tg.set_loss(loss)
tg.fit(train, nb_epoch=2)
prediction = np.squeeze(tg.predict_proba_on_batch(valid.X))
fpr = dict()
tpr = dict()
roc_auc = dict()
for i in range(10):
fpr[i], tpr[i], thresh = roc_curve(valid.y[:, i], prediction[:, i])
roc_auc[i] = auc(fpr[i], tpr[i])
assert_true(roc_auc[i] > 0.99)
activation_fn=tf.nn.relu,
normalizer_fn=tf.contrib.layers.batch_norm)
self.out_tensor = tf.nn.max_pool(out_tensor,
ksize=[1, 2, 2, 1],
strides=[1, 2, 2, 1],
padding='SAME')
return self.out_tensor
conv2d_1 = Conv2d(num_outputs=32)
tg.add_layer(conv2d_1, parents=[make_image])
conv2d_2 = Conv2d(num_outputs=64)
tg.add_layer(conv2d_2, parents=[conv2d_1])
flatten = Flatten()
tg.add_layer(flatten, parents=[conv2d_2])
dense1 = Dense(out_channels=1024, activation_fn=tf.nn.relu)
tg.add_layer(dense1, parents=[flatten])
dense2 = Dense(out_channels=10)
tg.add_layer(dense2, parents=[dense1])
label = Input(shape=(None, 10))
tg.add_label(label)
smce = SoftMaxCrossEntropy()
tg.add_layer(smce, parents=[label, dense2])
loss = ReduceMean()