def test_global(smiles_inputs, dropout):
preprocessor, inputs = smiles_inputs
atom_class = layers.Input(shape=[11], dtype=tf.int64, name='atom')
bond_class = layers.Input(shape=[None], dtype=tf.int64, name='bond')
connectivity = layers.Input(shape=[None, 2],
dtype=tf.int64,
name='connectivity')
atom_state = layers.Embedding(preprocessor.atom_classes,
16,
mask_zero=True)(atom_class)
bond_state = layers.Embedding(preprocessor.bond_classes,
16,
mask_zero=True)(bond_class)
global_state = layers.GlobalAveragePooling1D()(atom_state)
update = nfp.GlobalUpdate(
8, 2, dropout=dropout)([atom_state, bond_state, connectivity])
update_global = nfp.GlobalUpdate(8, 2, dropout=dropout)(
[atom_state, bond_state, connectivity, global_state])
model = tf.keras.Model([atom_class, bond_class, connectivity],
[update, update_global])
update_state, update_state_global = model(inputs)
assert not hasattr(update, '_keras_mask')
assert not hasattr(update_global, '_keras_mask')
assert update_state.shape == update_state_global.shape
assert not np.all(update_state == update_state_global)
def test_save_and_load_message(smiles_inputs, tmpdir: 'py.path.local'):
preprocessor, inputs = smiles_inputs
def get_inputs(max_atoms=-1, max_bonds=-1):
dataset = tf.data.Dataset.from_generator(
lambda: (preprocessor.construct_feature_matrices(smiles, train=True)
for smiles in ['CC', 'CCC', 'C(C)C', 'C']),
output_types=preprocessor.output_types,
output_shapes=preprocessor.output_shapes) \
.padded_batch(batch_size=4,
padded_shapes=preprocessor.padded_shapes(max_atoms, max_bonds),
padding_values=preprocessor.padding_values)
return list(dataset.take(1))[0]
atom_class = layers.Input(shape=[None], dtype=tf.int64, name='atom')
bond_class = layers.Input(shape=[None], dtype=tf.int64, name='bond')
connectivity = layers.Input(shape=[None, 2],
dtype=tf.int64,
name='connectivity')
atom_state = layers.Embedding(preprocessor.atom_classes,
16,
mask_zero=True)(atom_class)
bond_state = layers.Embedding(preprocessor.bond_classes,
16,
mask_zero=True)(bond_class)
global_state = nfp.GlobalUpdate(8,
2)([atom_state, bond_state, connectivity])
for _ in range(3):
new_bond_state = nfp.EdgeUpdate()(
[atom_state, bond_state, connectivity])
bond_state = layers.Add()([bond_state, new_bond_state])
new_atom_state = nfp.NodeUpdate()(
[atom_state, bond_state, connectivity])
atom_state = layers.Add()([atom_state, new_atom_state])
new_global_state = nfp.GlobalUpdate(
8, 2)([atom_state, bond_state, connectivity])
global_state = layers.Add()([new_global_state, global_state])
model = tf.keras.Model([atom_class, bond_class, connectivity],
[global_state])
outputs = model(get_inputs())
output_pad = model(get_inputs(max_atoms=20, max_bonds=40))
assert np.all(np.isclose(outputs, output_pad, atol=1E-4, rtol=1E-4))
model.save(tmpdir, include_optimizer=False)
loaded_model = tf.keras.models.load_model(tmpdir, compile=False)
loutputs = loaded_model(get_inputs())
loutputs_pad = model(get_inputs(max_atoms=20, max_bonds=40))
assert np.all(np.isclose(outputs, loutputs, atol=1E-4, rtol=1E-3))
assert np.all(np.isclose(output_pad, loutputs_pad, atol=1E-4, rtol=1E-3))
def build_fn(atom_features: int = 64,
message_steps: int = 8,
output_layers: List[int] = (512, 256, 128)):
atom = layers.Input(shape=[None], dtype=tf.int64, name='atom')
bond = layers.Input(shape=[None], dtype=tf.int64, name='bond')
connectivity = layers.Input(shape=[None, 2],
dtype=tf.int64,
name='connectivity')
# Convert from a single integer defining the atom state to a vector
# of weights associated with that class
atom_state = layers.Embedding(36,
atom_features,
name='atom_embedding',
mask_zero=True)(atom)
# Ditto with the bond state
bond_state = layers.Embedding(5,
atom_features,
name='bond_embedding',
mask_zero=True)(bond)
# Here we use our first nfp layer. This is an attention layer that looks at
# the atom and bond states and reduces them to a single, graph-level vector.
# mum_heads * units has to be the same dimension as the atom / bond dimension
global_state = nfp.GlobalUpdate(units=4, num_heads=1, name='problem')(
[atom_state, bond_state, connectivity])
for _ in range(message_steps): # Do the message passing
new_bond_state = nfp.EdgeUpdate()(
[atom_state, bond_state, connectivity, global_state])
bond_state = layers.Add()([bond_state, new_bond_state])
new_atom_state = nfp.NodeUpdate()(
[atom_state, bond_state, connectivity, global_state])
atom_state = layers.Add()([atom_state, new_atom_state])
new_global_state = nfp.GlobalUpdate(units=4, num_heads=1)(
[atom_state, bond_state, connectivity, global_state])
global_state = layers.Add()([global_state, new_global_state])
# Pass the global state through an output
output = global_state
for shape in output_layers:
output = layers.Dense(shape, activation='relu')(output)
output = layers.Dense(1)(output)
output = layers.Dense(1, activation='linear', name='scale')(output)
# Construct the tf.keras model
return tf.keras.Model([atom, bond, connectivity], [output])
def policy_model():
# Define inputs
atom_class = layers.Input(shape=[None], dtype=tf.int64,
name='atom') # batch_size, num_atoms
bond_class = layers.Input(shape=[None], dtype=tf.int64,
name='bond') # batch_size, num_bonds
connectivity = layers.Input(
shape=[None, 2], dtype=tf.int64,
name='connectivity') # batch_size, num_bonds, 2
input_tensors = [atom_class, bond_class, connectivity]
# Initialize the atom states
atom_state = layers.Embedding(preprocessor.atom_classes,
config.features,
name='atom_embedding',
mask_zero=True)(atom_class)
# Initialize the bond states
bond_state = layers.Embedding(preprocessor.bond_classes,
config.features,
name='bond_embedding',
mask_zero=True)(bond_class)
units = config.features // config.num_heads
global_state = nfp.GlobalUpdate(units=units, num_heads=config.num_heads)(
[atom_state, bond_state, connectivity])
for _ in range(config.num_messages): # Do the message passing
bond_state = nfp.EdgeUpdate()(
[atom_state, bond_state, connectivity, global_state])
atom_state = nfp.NodeUpdate()(
[atom_state, bond_state, connectivity, global_state])
global_state = nfp.GlobalUpdate(units=units,
num_heads=config.num_heads)([
atom_state, bond_state,
connectivity, global_state
])
value_logit = layers.Dense(1)(global_state)
pi_logit = layers.Dense(1)(global_state)
return tf.keras.Model(input_tensors, [value_logit, pi_logit],
name='policy_model')
def test_no_residual(smiles_inputs):
preprocessor, inputs = smiles_inputs
def get_inputs(max_atoms=-1, max_bonds=-1):
dataset = tf.data.Dataset.from_generator(
lambda: (preprocessor.construct_feature_matrices(smiles, train=True)
for smiles in ['CC', 'CCC', 'C(C)C', 'C']),
output_types=preprocessor.output_types,
output_shapes=preprocessor.output_shapes) \
.padded_batch(batch_size=4,
padded_shapes=preprocessor.padded_shapes(max_atoms, max_bonds),
padding_values=preprocessor.padding_values)
return list(dataset.take(1))[0]
atom_class = layers.Input(shape=[None], dtype=tf.int64, name='atom')
bond_class = layers.Input(shape=[None], dtype=tf.int64, name='bond')
connectivity = layers.Input(shape=[None, 2],
dtype=tf.int64,
name='connectivity')
atom_state = layers.Embedding(preprocessor.atom_classes,
16,
mask_zero=True)(atom_class)
bond_state = layers.Embedding(preprocessor.bond_classes,
16,
mask_zero=True)(bond_class)
global_state = nfp.GlobalUpdate(8,
2)([atom_state, bond_state, connectivity])
for _ in range(3):
bond_state = nfp.EdgeUpdate()([atom_state, bond_state, connectivity])
atom_state = nfp.NodeUpdate()([atom_state, bond_state, connectivity])
global_state = nfp.GlobalUpdate(
8, 2)([atom_state, bond_state, connectivity])
model = tf.keras.Model([atom_class, bond_class, connectivity],
[global_state])
output = model(get_inputs())
output_pad = model(get_inputs(max_atoms=20, max_bonds=40))
assert np.all(np.isclose(output, output_pad, atol=1E-4))
def message_block(atom_state, bond_state, connectivity, global_state, i):
new_bond_state = nfp.EdgeUpdate()(
[atom_state, bond_state, connectivity])
bond_state = layers.Add()([bond_state, new_bond_state])
new_atom_state = nfp.NodeUpdate()(
[atom_state, bond_state, connectivity])
atom_state = layers.Add()([atom_state, new_atom_state])
new_global_state = nfp.GlobalUpdate(
head_features, num_heads)([atom_state, bond_state, connectivity])
global_state = layers.Add()([new_global_state, global_state])
return atom_state, bond_state, global_state
# of weights associated with that class
atom_state = layers.Embedding(preprocessor.atom_classes,
num_features,
name='atom_embedding',
mask_zero=True)(atom)
# Ditto with the bond state
bond_state = layers.Embedding(preprocessor.bond_classes,
num_features,
name='bond_embedding',
mask_zero=True)(bond)
# Here we use our first nfp layer. This is an attention layer that looks at
# the atom and bond states and reduces them to a single, graph-level vector.
# mum_heads * units has to be the same dimension as the atom / bond dimension
global_state = nfp.GlobalUpdate(
units=units, num_heads=heads)([atom_state, bond_state, connectivity])
for _ in range(3): # Do the message passing
new_bond_state = nfp.EdgeUpdate()(
[atom_state, bond_state, connectivity, global_state])
bond_state = layers.Add()([bond_state, new_bond_state])
new_atom_state = nfp.NodeUpdate()(
[atom_state, bond_state, connectivity, global_state])
atom_state = layers.Add()([atom_state, new_atom_state])
new_global_state = nfp.GlobalUpdate(units=units, num_heads=heads)(
[atom_state, bond_state, connectivity, global_state])
global_state = layers.Add()([global_state, new_global_state])
# Since the final prediction is a single, molecule-level property (YSI), we
def build_embedding_model(preprocessor,
dropout=0.0,
atom_features=128,
num_messages=6,
num_heads=8,
name='atom_embedding_model'):
assert atom_features % num_heads == 0, "Wrong feature / head dimension"
head_features = atom_features // num_heads
# Define keras model
n_atom = layers.Input(shape=[], dtype=tf.int64, name='n_atom')
atom_class = layers.Input(shape=[None], dtype=tf.int64, name='atom')
bond_class = layers.Input(shape=[None], dtype=tf.int64, name='bond')
connectivity = layers.Input(shape=[None, 2],
dtype=tf.int64,
name='connectivity')
input_tensors = [atom_class, bond_class, connectivity, n_atom]
# Initialize the atom states
atom_state = layers.Embedding(preprocessor.atom_classes,
atom_features,
name='atom_embedding',
mask_zero=True)(atom_class)
# Initialize the bond states
bond_state = layers.Embedding(preprocessor.bond_classes,
atom_features,
name='bond_embedding',
mask_zero=True)(bond_class)
global_state = nfp.GlobalUpdate(
head_features, num_heads)([atom_state, bond_state, connectivity])
def message_block(atom_state, bond_state, connectivity, global_state, i):
new_bond_state = nfp.EdgeUpdate()(
[atom_state, bond_state, connectivity])
bond_state = layers.Add()([bond_state, new_bond_state])
new_atom_state = nfp.NodeUpdate()(
[atom_state, bond_state, connectivity])
atom_state = layers.Add()([atom_state, new_atom_state])
new_global_state = nfp.GlobalUpdate(
head_features, num_heads)([atom_state, bond_state, connectivity])
global_state = layers.Add()([new_global_state, global_state])
return atom_state, bond_state, global_state
atom_states = [atom_state]
bond_states = [bond_state]
global_states = [global_state]
for i in range(num_messages):
atom_state, bond_state, global_state = message_block(
atom_state, bond_state, connectivity, global_state, i)
atom_states += [atom_state]
bond_states += [bond_state]
global_states += [global_state]
# atom_embedding_model = tf.keras.Model(input_tensors, [atom_state, bond_state, global_state], name=name)
return input_tensors, atom_states, bond_states, global_states