def test_shapes(self):
"""Simple test that Graph topology placeholders have correct shapes."""
n_atoms = 5
n_feat = 10
batch_size = 3
max_deg = 6
min_deg = 0
topology = GraphTopology(n_feat)
# Degrees from 1 to max_deg inclusive
# TODO(rbharath): Should this be 0 to max_deg inclusive?
deg_adj_lists_placeholders = topology.get_deg_adjacency_lists_placeholders(
)
assert len(deg_adj_lists_placeholders) == max_deg
for ind, deg_adj_list in enumerate(deg_adj_lists_placeholders):
deg = ind + 1
# Should have shape (?, deg)
assert deg_adj_list.get_shape()[1] == deg
# Shape of atom_features should be (?, n_feat)
atom_features = topology.get_atom_features_placeholder()
assert atom_features.get_shape()[1] == n_feat
# Shape of deg_slice placeholder should be (max_deg+1-min_deg, 2)
deg_slice = topology.get_deg_slice_placeholder()
print("deg_slice.get_shape()")
print(deg_slice.get_shape())
assert deg_slice.get_shape() == (max_deg + 1 - min_deg, 2)
def test_shapes(self):
"""Simple test that Graph topology placeholders have correct shapes."""
n_atoms = 5
n_feat = 10
batch_size = 3
max_deg = 6
min_deg = 0
topology = GraphTopology(n_feat)
# Degrees from 1 to max_deg inclusive
# TODO(rbharath): Should this be 0 to max_deg inclusive?
deg_adj_lists_placeholders = topology.get_deg_adjacency_lists_placeholders()
assert len(deg_adj_lists_placeholders) == max_deg
for ind, deg_adj_list in enumerate(deg_adj_lists_placeholders):
deg = ind + 1
# Should have shape (?, deg)
assert deg_adj_list.get_shape()[1] == deg
# Shape of atom_features should be (?, n_feat)
atom_features = topology.get_atom_features_placeholder()
assert atom_features.get_shape()[1] == n_feat
# Shape of deg_slice placeholder should be (max_deg+1-min_deg, 2)
deg_slice = topology.get_deg_slice_placeholder()
print("deg_slice.get_shape()")
print(deg_slice.get_shape())
assert deg_slice.get_shape() == (max_deg+1-min_deg, 2)
def test_graph_pool(self):
"""Tests that GraphPool transforms shapes correctly."""
n_atoms = 5
n_feat = 10
batch_size = 3
nb_filter = 7
with self.test_session() as sess:
graph_topology = GraphTopology(n_feat)
graph_pool_layer = GraphPool()
X = graph_topology.get_input_placeholders()
out = graph_pool_layer(X)
def __init__(self, n_feat):
"""
Parameters
----------
n_feat: int
Number of features per atom.
"""
#self.graph_topology = GraphTopology(n_atoms, n_feat)
self.graph_topology = GraphTopology(n_feat)
self.output = self.graph_topology.get_atom_features_placeholder()
# Keep track of the layers
self.layers = []
class SequentialGraphModel(object):
"""An analog of Keras Sequential class for Graph data.
Like the Sequential class from Keras, but automatically passes topology
placeholders from GraphTopology to each graph layer (from keras_layers) added
to the network. Non graph layers don't get the extra placeholders.
"""
def __init__(self, n_feat):
"""
Parameters
----------
n_feat: int
Number of features per atom.
"""
#self.graph_topology = GraphTopology(n_atoms, n_feat)
self.graph_topology = GraphTopology(n_feat)
self.output = self.graph_topology.get_atom_features_placeholder()
# Keep track of the layers
self.layers = []
def add(self, layer):
"""Adds a new layer to model."""
# For graphical layers, add connectivity placeholders
if type(layer).__name__ in ['GraphConv', 'GraphGather', 'GraphPool']:
if (len(self.layers) > 0 and hasattr(self.layers[-1], "__name__")):
assert self.layers[-1].__name__ != "GraphGather", \
'Cannot use GraphConv or GraphGather layers after a GraphGather'
self.output = layer(
[self.output] +
self.graph_topology.get_topology_placeholders())
else:
self.output = layer(self.output)
# Add layer to the layer list
self.layers.append(layer)
def get_graph_topology(self):
return self.graph_topology
def get_num_output_features(self):
"""Gets the output shape of the featurization layers of the network"""
return self.layers[-1].output_shape[1]
def return_outputs(self):
return self.output
def return_inputs(self):
return self.graph_topology.get_input_placeholders()
def get_layer(self, layer_id):
return self.layers[layer_id]
def test_graph_convolution(self):
"""Tests that Graph Convolution transforms shapes correctly."""
n_atoms = 5
n_feat = 10
nb_filter = 7
with self.test_session() as sess:
graph_topology = GraphTopology(n_feat)
graph_conv_layer = GraphConv(nb_filter)
X = graph_topology.get_input_placeholders()
out = graph_conv_layer(X)
# Output should be of shape (?, nb_filter)
assert out.get_shape()[1] == nb_filter
class SequentialGraph(object):
"""An analog of Keras Sequential class for Graph data.
Like the Sequential class from Keras, but automatically passes topology
placeholders from GraphTopology to each graph layer (from keras_layers) added
to the network. Non graph layers don't get the extra placeholders.
"""
def __init__(self, n_feat):
"""
Parameters
----------
n_feat: int
Number of features per atom.
"""
#self.graph_topology = GraphTopology(n_atoms, n_feat)
self.graph_topology = GraphTopology(n_feat)
self.output = self.graph_topology.get_atom_features_placeholder()
# Keep track of the layers
self.layers = []
def add(self, layer):
"""Adds a new layer to model."""
# For graphical layers, add connectivity placeholders
if type(layer).__name__ in ['GraphConv', 'GraphGather', 'GraphPool']:
if (len(self.layers) > 0 and hasattr(self.layers[-1], "__name__")):
assert self.layers[-1].__name__ != "GraphGather", \
'Cannot use GraphConv or GraphGather layers after a GraphGather'
self.output = layer(
[self.output] + self.graph_topology.get_topology_placeholders())
else:
self.output = layer(self.output)
# Add layer to the layer list
self.layers.append(layer)
def get_graph_topology(self):
return self.graph_topology
def get_num_output_features(self):
"""Gets the output shape of the featurization layers of the network"""
return self.layers[-1].output_shape[1]
def return_outputs(self):
return self.output
def return_inputs(self):
return self.graph_topology.get_input_placeholders()
def get_layer(self, layer_id):
return self.layers[layer_id]
def test_graph_gather(self):
"""Tests that GraphGather transforms shapes correctly."""
n_atoms = 5
n_feat = 10
batch_size = 3
nb_filter = 7
with self.test_session() as sess:
graph_topology = GraphTopology(n_feat)
graph_gather_layer = GraphGather(batch_size)
X = graph_topology.get_input_placeholders()
out = graph_gather_layer(X)
# Output should be of shape (batch_size, n_feat)
assert out.get_shape() == (batch_size, n_feat)
def __init__(self, n_feat):
"""
Parameters
----------
n_feat: int
Number of atomic features.
"""
# Create graph topology and x
self.test_graph_topology = GraphTopology(n_feat, name='test')
self.support_graph_topology = GraphTopology(n_feat, name='support')
self.test = self.test_graph_topology.get_atom_features_placeholder()
self.support = self.support_graph_topology.get_atom_features_placeholder()
# Keep track of the layers
self.layers = []
# Whether or not we have used the GraphGather layer yet
self.bool_pre_gather = True
def test_attn_lstm_embedding(self):
"""Test that attention LSTM computation works properly."""
max_depth = 5
n_test = 5
n_support = 11
n_feat = 10
nb_filter = 7
with self.test_session() as sess:
graph_topology_test = GraphTopology(n_feat)
graph_topology_support = GraphTopology(n_feat)
test = graph_topology_test.get_input_placeholders()[0]
support = graph_topology_support.get_input_placeholders()[0]
attn_embedding_layer = AttnLSTMEmbedding(n_test, n_support,
max_depth)
# Try concatenating the two lists of placeholders
feed_dict = {
test: np.zeros((n_test, n_feat)),
support: np.zeros((n_support, n_feat))
}
test_out, support_out = attn_embedding_layer([test, support])
assert test_out.get_shape() == (n_test, n_feat)
assert support_out.get_shape()[1] == (n_feat)
class SequentialSupportGraph(object):
"""An analog of Keras Sequential model for test/support models."""
def __init__(self, n_feat):
"""
Parameters
----------
n_feat: int
Number of atomic features.
"""
# Create graph topology and x
self.test_graph_topology = GraphTopology(n_feat, name='test')
self.support_graph_topology = GraphTopology(n_feat, name='support')
self.test = self.test_graph_topology.get_atom_features_placeholder()
self.support = self.support_graph_topology.get_atom_features_placeholder()
# Keep track of the layers
self.layers = []
# Whether or not we have used the GraphGather layer yet
self.bool_pre_gather = True
def add(self, layer):
"""Adds a layer to both test/support stacks.
Note that the layer transformation is performed independently on the
test/support tensors.
"""
self.layers.append(layer)
# Update new value of x
if type(layer).__name__ in ['GraphConv', 'GraphGather', 'GraphPool']:
assert self.bool_pre_gather, "Cannot apply graphical layers after gather."
self.test = layer([self.test] + self.test_graph_topology.topology)
self.support = layer([self.support] + self.support_graph_topology.topology)
else:
self.test = layer(self.test)
self.support = layer(self.support)
if type(layer).__name__ == 'GraphGather':
self.bool_pre_gather = False # Set flag to stop adding topology
def add_test(self, layer):
"""Adds a layer to test."""
self.layers.append(layer)
# Update new value of x
if type(layer).__name__ in ['GraphConv', 'GraphPool', 'GraphGather']:
self.test = layer([self.test] + self.test_graph_topology.topology)
else:
self.test = layer(self.test)
def add_support(self, layer):
"""Adds a layer to support."""
self.layers.append(layer)
# Update new value of x
if type(layer).__name__ in ['GraphConv', 'GraphPool', 'GraphGather']:
self.support = layer([self.support] + self.support_graph_topology.topology)
else:
self.support = layer(self.support)
def join(self, layer):
"""Joins test and support to a two input two output layer"""
self.layers.append(layer)
self.test, self.support = layer([self.test, self.support])
def get_test_output(self):
return self.test
def get_support_output(self):
return self.support
def return_outputs(self):
return [self.test] + [self.support]
def return_inputs(self):
return (self.test_graph_topology.get_inputs()
+ self.support_graph_topology.get_inputs())