def __init__(self, config):
"""Initialize configurations."""
self.config = config
# Data loader.
self.data = SparseMolecularDataset()
self.data.load(config.mol_data_dir)
# Model configurations.
self.z_dim = config.z_dim
self.m_dim = self.data.atom_num_types
self.b_dim = self.data.bond_num_types
self.g_conv_dim = config.g_conv_dim
self.d_conv_dim = config.d_conv_dim
self.g_repeat_num = config.g_repeat_num
self.d_repeat_num = config.d_repeat_num
self.lambda_cls = config.lambda_cls
self.lambda_rec = config.lambda_rec
self.lambda_gp = config.lambda_gp
self.post_method = config.post_method
self.metric = 'validity,sas'
# Training configurations.
self.batch_size = config.batch_size
self.num_iters = config.num_iters
self.num_iters_decay = config.num_iters_decay
self.g_lr = config.g_lr
self.d_lr = config.d_lr
self.dropout = config.dropout
self.n_critic = config.n_critic
self.beta1 = config.beta1
self.beta2 = config.beta2
self.resume_iters = config.resume_iters
# Test configurations.
self.test_iters = config.test_iters
# Miscellaneous.
self.use_tensorboard = config.use_tensorboard
self.device = torch.device(
'cuda' if torch.cuda.is_available() else 'cpu')
# Directories.
self.log_dir = config.log_dir
self.sample_dir = config.sample_dir
self.model_save_dir = config.model_save_dir
self.result_dir = config.result_dir
# Step size.
self.log_step = config.log_step
self.sample_step = config.sample_step
self.model_save_step = config.model_save_step
self.lr_update_step = config.lr_update_step
# Build the model and tensorboard.
self.build_model()
if self.use_tensorboard:
self.build_tensorboard()
def __init__(self, config, log=None):
"""Initialize configurations."""
# Log
self.log = log
# Data loader.
self.data = SparseMolecularDataset()
self.data.load(config.mol_data_dir)
# Model configurations.
self.z_dim = config.z_dim
self.m_dim = self.data.atom_num_types
self.b_dim = self.data.bond_num_types
self.f_dim = self.data.features
self.g_conv_dim = config.g_conv_dim
self.d_conv_dim = config.d_conv_dim
self.lambda_wgan = config.lambda_wgan
self.lambda_rec = config.lambda_rec
self.post_method = config.post_method
self.metric = 'validity,qed'
# Training configurations.
self.batch_size = config.batch_size
self.num_epochs = config.num_epochs
self.num_steps = (len(self.data) // self.batch_size)
self.g_lr = config.g_lr
self.d_lr = config.d_lr
self.dropout_rate = config.dropout
self.n_critic = config.n_critic
self.resume_epoch = config.resume_epoch
# Training or testing.
self.mode = config.mode
# Miscellaneous.
self.device = torch.device(
'cuda' if torch.cuda.is_available() else 'cpu')
print('Device: ', self.device)
# Directories.
self.log_dir_path = config.log_dir_path
self.model_dir_path = config.model_dir_path
self.img_dir_path = config.img_dir_path
# Step size.
self.model_save_step = config.model_save_step
# VAE KL weight.
self.kl_la = 1.
# Build the model.
self.build_model()
class SparseMolecular(data.Dataset):
"""Dataset class for the CelebA dataset."""
def __init__(self, data_dir):
"""Initialize and preprocess the CelebA dataset."""
self.data = SparseMolecularDataset()
self.data.load(data_dir)
def __getitem__(self, index):
"""Return one image and its corresponding attribute label."""
return index, self.data.data[index], self.data.smiles[index], \
self.data.data_S[index], self.data.data_A[index], \
self.data.data_X[index], self.data.data_D[index], \
self.data.data_F[index], self.data.data_Le[index], \
self.data.data_Lv[index]
def __len__(self):
"""Return the number of images."""
return len(self.data)
class Solver(object):
"""Solver for training and testing StarGAN."""
def __init__(self, config):
"""Initialize configurations."""
# Data loader.
self.data = SparseMolecularDataset()
self.data.load(config.mol_data_dir)
# Model configurations.
self.z_dim = config.qubits
self.m_dim = self.data.atom_num_types
self.b_dim = self.data.bond_num_types
self.g_conv_dim = config.g_conv_dim
self.d_conv_dim = config.d_conv_dim
self.g_repeat_num = config.g_repeat_num
self.d_repeat_num = config.d_repeat_num
self.lambda_cls = config.lambda_cls
self.lambda_rec = config.lambda_rec
self.lambda_gp = config.lambda_gp
self.post_method = config.post_method
self.metric = 'validity,sas'
# Training configurations.
self.batch_size = config.batch_size
self.num_iters = config.num_iters
self.num_iters_decay = config.num_iters_decay
self.g_lr = config.g_lr
self.d_lr = config.d_lr
self.dropout = config.dropout
self.n_critic = config.n_critic
self.beta1 = config.beta1
self.beta2 = config.beta2
self.resume_iters = config.resume_iters
# Test configurations.
self.test_iters = config.test_iters
# Miscellaneous.
self.use_tensorboard = config.use_tensorboard
self.device = torch.device(
'cuda' if torch.cuda.is_available() else 'cpu')
# Directories.
self.log_dir = config.log_dir
self.sample_dir = config.sample_dir
self.model_save_dir = config.model_save_dir
self.result_dir = config.result_dir
# Step size.
self.log_step = config.log_step
self.sample_step = config.sample_step
self.model_save_step = config.model_save_step
self.lr_update_step = config.lr_update_step
# Build the model and tensorboard.
self.build_model()
if self.use_tensorboard:
self.build_tensorboard()
def build_model(self):
"""Create a generator and a discriminator."""
self.G = Generator(self.g_conv_dim, self.z_dim, self.data.vertexes,
self.data.bond_num_types, self.data.atom_num_types,
self.dropout)
self.D = Discriminator(self.d_conv_dim, self.m_dim, self.b_dim,
self.dropout)
self.V = Discriminator(self.d_conv_dim, self.m_dim, self.b_dim,
self.dropout)
self.g_optimizer = torch.optim.Adam(
list(self.G.parameters()) + list(self.V.parameters()), self.g_lr,
[self.beta1, self.beta2])
self.d_optimizer = torch.optim.Adam(self.D.parameters(), self.d_lr,
[self.beta1, self.beta2])
self.print_network(self.G, 'G')
self.print_network(self.D, 'D')
self.G.to(self.device)
self.D.to(self.device)
self.V.to(self.device)
def print_network(self, model, name):
"""Print out the network information."""
num_params = 0
for p in model.parameters():
num_params += p.numel()
print(model)
print(name)
print("The number of parameters: {}".format(num_params))
def restore_model(self, resume_iters):
"""Restore the trained generator and discriminator."""
print(
'Loading the trained models from step {}...'.format(resume_iters))
G_path = os.path.join(self.model_save_dir,
'{}-G.ckpt'.format(resume_iters))
D_path = os.path.join(self.model_save_dir,
'{}-D.ckpt'.format(resume_iters))
V_path = os.path.join(self.model_save_dir,
'{}-V.ckpt'.format(resume_iters))
self.G.load_state_dict(
torch.load(G_path, map_location=lambda storage, loc: storage))
self.D.load_state_dict(
torch.load(D_path, map_location=lambda storage, loc: storage))
self.V.load_state_dict(
torch.load(V_path, map_location=lambda storage, loc: storage))
def build_tensorboard(self):
"""Build a tensorboard logger."""
from torch.utils.tensorboard.logger import Logger #from logger import Logger
self.logger = Logger(self.log_dir)
def update_lr(self, g_lr, d_lr):
"""Decay learning rates of the generator and discriminator."""
for param_group in self.g_optimizer.param_groups:
param_group['lr'] = g_lr
for param_group in self.d_optimizer.param_groups:
param_group['lr'] = d_lr
def reset_grad(self):
"""Reset the gradient buffers."""
self.g_optimizer.zero_grad()
self.d_optimizer.zero_grad()
def denorm(self, x):
"""Convert the range from [-1, 1] to [0, 1]."""
out = (x + 1) / 2
return out.clamp_(0, 1)
def gradient_penalty(self, y, x):
"""Compute gradient penalty: (L2_norm(dy/dx) - 1)**2."""
weight = torch.ones(y.size()).to(self.device)
dydx = torch.autograd.grad(outputs=y,
inputs=x,
grad_outputs=weight,
retain_graph=True,
create_graph=True,
only_inputs=True)[0]
dydx = dydx.view(dydx.size(0), -1)
dydx_l2norm = torch.sqrt(torch.sum(dydx**2, dim=1))
return torch.mean((dydx_l2norm - 1)**2)
def label2onehot(self, labels, dim):
"""Convert label indices to one-hot vectors."""
out = torch.zeros(list(labels.size()) + [dim]).to(self.device)
out.scatter_(len(out.size()) - 1, labels.unsqueeze(-1), 1.)
return out
def classification_loss(self, logit, target, dataset='CelebA'):
"""Compute binary or softmax cross entropy loss."""
if dataset == 'CelebA':
return F.binary_cross_entropy_with_logits(
logit, target, size_average=False) / logit.size(0)
elif dataset == 'RaFD':
return F.cross_entropy(logit, target)
def sample_z(self, batch_size):
return np.random.normal(0, 1, size=(batch_size, self.z_dim))
def postprocess(self, inputs, method, temperature=1.):
def listify(x):
return x if type(x) == list or type(x) == tuple else [x]
def delistify(x):
return x if len(x) > 1 else x[0]
if method == 'soft_gumbel':
softmax = [
F.gumbel_softmax(
e_logits.contiguous().view(-1, e_logits.size(-1)) /
temperature,
hard=False).view(e_logits.size())
for e_logits in listify(inputs)
]
elif method == 'hard_gumbel':
softmax = [
F.gumbel_softmax(
e_logits.contiguous().view(-1, e_logits.size(-1)) /
temperature,
hard=True).view(e_logits.size())
for e_logits in listify(inputs)
]
else:
softmax = [
F.softmax(e_logits / temperature, -1)
for e_logits in listify(inputs)
]
return [delistify(e) for e in (softmax)]
def reward(self, mols):
rr = 1.
for m in ('logp,sas,qed,unique'
if self.metric == 'all' else self.metric).split(','):
if m == 'np':
rr *= MolecularMetrics.natural_product_scores(mols, norm=True)
elif m == 'logp':
rr *= MolecularMetrics.water_octanol_partition_coefficient_scores(
mols, norm=True)
elif m == 'sas':
rr *= MolecularMetrics.synthetic_accessibility_score_scores(
mols, norm=True)
elif m == 'qed':
rr *= MolecularMetrics.quantitative_estimation_druglikeness_scores(
mols, norm=True)
elif m == 'novelty':
rr *= MolecularMetrics.novel_scores(mols, data)
elif m == 'dc':
rr *= MolecularMetrics.drugcandidate_scores(mols, data)
elif m == 'unique':
rr *= MolecularMetrics.unique_scores(mols)
elif m == 'diversity':
rr *= MolecularMetrics.diversity_scores(mols, data)
elif m == 'validity':
rr *= MolecularMetrics.valid_scores(mols)
else:
raise RuntimeError('{} is not defined as a metric'.format(m))
return rr.reshape(-1, 1)
def train(self):
# Learning rate cache for decaying.
g_lr = self.g_lr
d_lr = self.d_lr
# Start training from scratch or resume training.
start_iters = 0
if self.resume_iters:
start_iters = self.resume_iters
self.restore_model(self.resume_iters)
# Start training.
print('Start training...')
start_time = time.time()
for i in range(start_iters, self.num_iters):
if (i + 1) % self.log_step == 0:
mols, _, _, a, x, _, _, _, _ = self.data.next_validation_batch(
)
z = self.sample_z(a.shape[0])
print('[Valid]', '')
else:
mols, _, _, a, x, _, _, _, _ = self.data.next_train_batch(
self.batch_size)
z = self.sample_z(self.batch_size)
# =================================================================================== #
# 1. Preprocess input data #
# =================================================================================== #
a = torch.from_numpy(a).to(self.device).long() # Adjacency.
x = torch.from_numpy(x).to(self.device).long() # Nodes.
a_tensor = self.label2onehot(a, self.b_dim)
x_tensor = self.label2onehot(x, self.m_dim)
z = torch.from_numpy(z).to(self.device).float()
# =================================================================================== #
# 2. Train the discriminator #
# =================================================================================== #
# Compute loss with real images.
logits_real, features_real = self.D(a_tensor, None, x_tensor)
d_loss_real = -torch.mean(logits_real)
# Compute loss with fake images.
edges_logits, nodes_logits = self.G(z)
# Postprocess with Gumbel softmax
(edges_hat, nodes_hat) = self.postprocess(
(edges_logits, nodes_logits), self.post_method)
logits_fake, features_fake = self.D(edges_hat, None, nodes_hat)
d_loss_fake = torch.mean(logits_fake)
# Compute loss for gradient penalty.
eps = torch.rand(logits_real.size(0), 1, 1, 1).to(self.device)
x_int0 = (eps * a_tensor +
(1. - eps) * edges_hat).requires_grad_(True)
x_int1 = (eps.squeeze(-1) * x_tensor +
(1. - eps.squeeze(-1)) * nodes_hat).requires_grad_(True)
grad0, grad1 = self.D(x_int0, None, x_int1)
d_loss_gp = self.gradient_penalty(
grad0, x_int0) + self.gradient_penalty(grad1, x_int1)
# Backward and optimize.
d_loss = d_loss_fake + d_loss_real + self.lambda_gp * d_loss_gp
self.reset_grad()
d_loss.backward()
self.d_optimizer.step()
# Logging.
loss = {}
loss['D/loss_real'] = d_loss_real.item()
loss['D/loss_fake'] = d_loss_fake.item()
loss['D/loss_gp'] = d_loss_gp.item()
# =================================================================================== #
# 3. Train the generator #
# =================================================================================== #
if (i + 1) % self.n_critic == 0:
# Z-to-target
edges_logits, nodes_logits = self.G(z)
# Postprocess with Gumbel softmax
(edges_hat, nodes_hat) = self.postprocess(
(edges_logits, nodes_logits), self.post_method)
logits_fake, features_fake = self.D(edges_hat, None, nodes_hat)
g_loss_fake = -torch.mean(logits_fake)
# Real Reward
rewardR = torch.from_numpy(self.reward(mols)).to(self.device)
# Fake Reward
(edges_hard, nodes_hard) = self.postprocess(
(edges_logits, nodes_logits), 'hard_gumbel')
edges_hard, nodes_hard = torch.max(edges_hard,
-1)[1], torch.max(
nodes_hard, -1)[1]
mols = [
self.data.matrices2mol(n_.data.cpu().numpy(),
e_.data.cpu().numpy(),
strict=True)
for e_, n_ in zip(edges_hard, nodes_hard)
]
rewardF = torch.from_numpy(self.reward(mols)).to(self.device)
# Value loss
value_logit_real, _ = self.V(a_tensor, None, x_tensor,
torch.sigmoid)
value_logit_fake, _ = self.V(edges_hat, None, nodes_hat,
torch.sigmoid)
g_loss_value = torch.mean((value_logit_real - rewardR)**2 +
(value_logit_fake - rewardF)**2)
#rl_loss= -value_logit_fake
#f_loss = (torch.mean(features_real, 0) - torch.mean(features_fake, 0)) ** 2
# Backward and optimize.
g_loss = g_loss_fake + g_loss_value
self.reset_grad()
g_loss.backward()
self.g_optimizer.step()
# Logging.
loss['G/loss_fake'] = g_loss_fake.item()
loss['G/loss_value'] = g_loss_value.item()
# =================================================================================== #
# 4. Miscellaneous #
# =================================================================================== #
# Print out training information.
if (i + 1) % self.log_step == 0:
et = time.time() - start_time
et = str(datetime.timedelta(seconds=et))[:-7]
log = "Elapsed [{}], Iteration [{}/{}]".format(
et, i + 1, self.num_iters)
# Log update
m0, m1 = all_scores(
mols, self.data,
norm=True) # 'mols' is output of Fake Reward
m0 = {
k: np.array(v)[np.nonzero(v)].mean()
for k, v in m0.items()
}
m0.update(m1)
loss.update(m0)
for tag, value in loss.items():
log += ", {}: {:.4f}".format(tag, value)
print(log)
if self.use_tensorboard:
for tag, value in loss.items():
self.logger.scalar_summary(tag, value, i + 1)
# Save model checkpoints.
if (i + 1) % self.model_save_step == 0:
G_path = os.path.join(self.model_save_dir,
'{}-G.ckpt'.format(i + 1))
D_path = os.path.join(self.model_save_dir,
'{}-D.ckpt'.format(i + 1))
V_path = os.path.join(self.model_save_dir,
'{}-V.ckpt'.format(i + 1))
torch.save(self.G.state_dict(), G_path)
torch.save(self.D.state_dict(), D_path)
torch.save(self.V.state_dict(), V_path)
print('Saved model checkpoints into {}...'.format(
self.model_save_dir))
# Decay learning rates.
if (i + 1) % self.lr_update_step == 0 and (i + 1) > (
self.num_iters - self.num_iters_decay):
g_lr -= (self.g_lr / float(self.num_iters_decay))
d_lr -= (self.d_lr / float(self.num_iters_decay))
self.update_lr(g_lr, d_lr)
print('Decayed learning rates, g_lr: {}, d_lr: {}.'.format(
g_lr, d_lr))
def test(self):
# Load the trained generator.
self.restore_model(self.test_iters)
with torch.no_grad():
mols, _, _, a, x, _, _, _, _ = self.data.next_test_batch()
z = self.sample_z(a.shape[0])
# Z-to-target
edges_logits, nodes_logits = self.G(z)
# Postprocess with Gumbel softmax
(edges_hat, nodes_hat) = self.postprocess(
(edges_logits, nodes_logits), self.post_method)
logits_fake, features_fake = self.D(edges_hat, None, nodes_hat)
g_loss_fake = -torch.mean(logits_fake)
# Fake Reward
(edges_hard, nodes_hard) = self.postprocess(
(edges_logits, nodes_logits), 'hard_gumbel')
edges_hard, nodes_hard = torch.max(edges_hard, -1)[1], torch.max(
nodes_hard, -1)[1]
mols = [
self.data.matrices2mol(n_.data.cpu().numpy(),
e_.data.cpu().numpy(),
strict=True)
for e_, n_ in zip(edges_hard, nodes_hard)
]
# Log update
m0, m1 = all_scores(mols, self.data,
norm=True) # 'mols' is output of Fake Reward
m0 = {k: np.array(v)[np.nonzero(v)].mean() for k, v in m0.items()}
m0.update(m1)
for tag, value in m0.items():
log += ", {}: {:.4f}".format(tag, value)
def __init__(self, data_dir):
"""Initialize and preprocess the CelebA dataset."""
self.data = SparseMolecularDataset()
self.data.load(data_dir)
class Solver(object):
"""Solver for training and testing StarGAN."""
def __init__(self, config, log=None):
"""Initialize configurations."""
# Log
self.log = log
# Data loader.
self.data = SparseMolecularDataset()
self.data.load(config.mol_data_dir)
# Model configurations.
self.z_dim = config.z_dim
self.m_dim = self.data.atom_num_types
self.b_dim = self.data.bond_num_types
self.g_conv_dim = config.g_conv_dim
self.d_conv_dim = config.d_conv_dim
self.la = config.lambda_wgan
self.lambda_rec = config.lambda_rec
self.la_gp = config.lambda_gp
self.post_method = config.post_method
self.metric = 'validity,qed'
# Training configurations.
self.batch_size = config.batch_size
self.num_epochs = config.num_epochs
self.num_steps = (len(self.data) // self.batch_size)
self.g_lr = config.g_lr
self.d_lr = config.d_lr
self.dropout = config.dropout
if self.la > 0:
self.n_critic = config.n_critic
else:
self.n_critic = 1
self.resume_epoch = config.resume_epoch
# Training or testing.
self.mode = config.mode
# Miscellaneous.
self.device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
print('Device: ', self.device)
# Directories.
self.log_dir_path = config.log_dir_path
self.model_dir_path = config.model_dir_path
self.img_dir_path = config.img_dir_path
# Step size.
self.model_save_step = config.model_save_step
# Build the model.
self.build_model()
def build_model(self):
"""Create a generator and a discriminator."""
self.G = Generator(self.g_conv_dim, self.z_dim,
self.data.vertexes,
self.data.bond_num_types,
self.data.atom_num_types,
self.dropout)
self.D = Discriminator(self.d_conv_dim, self.m_dim, self.b_dim - 1, self.dropout)
self.V = Discriminator(self.d_conv_dim, self.m_dim, self.b_dim - 1, self.dropout)
self.g_optimizer = torch.optim.RMSprop(self.G.parameters(), self.g_lr)
self.d_optimizer = torch.optim.RMSprop(self.D.parameters(), self.d_lr)
self.v_optimizer = torch.optim.RMSprop(self.V.parameters(), self.g_lr)
self.print_network(self.G, 'G', self.log)
self.print_network(self.D, 'D', self.log)
self.print_network(self.V, 'V', self.log)
self.G.to(self.device)
self.D.to(self.device)
self.V.to(self.device)
@staticmethod
def print_network(model, name, log=None):
"""Print out the network information."""
num_params = 0
for p in model.parameters():
num_params += p.numel()
print(model)
print(name)
print("The number of parameters: {}".format(num_params))
if log is not None:
log.info(model)
log.info(name)
log.info("The number of parameters: {}".format(num_params))
def restore_model(self, resume_iters):
"""Restore the trained generator and discriminator."""
print('Loading the trained models from step {}...'.format(resume_iters))
G_path = os.path.join(self.model_dir_path, '{}-G.ckpt'.format(resume_iters))
D_path = os.path.join(self.model_dir_path, '{}-D.ckpt'.format(resume_iters))
V_path = os.path.join(self.model_dir_path, '{}-V.ckpt'.format(resume_iters))
self.G.load_state_dict(torch.load(G_path, map_location=lambda storage, loc: storage))
self.D.load_state_dict(torch.load(D_path, map_location=lambda storage, loc: storage))
self.V.load_state_dict(torch.load(V_path, map_location=lambda storage, loc: storage))
def update_lr(self, g_lr, d_lr):
"""Decay learning rates of the generator and discriminator."""
for param_group in self.g_optimizer.param_groups:
param_group['lr'] = g_lr
for param_group in self.d_optimizer.param_groups:
param_group['lr'] = d_lr
def reset_grad(self):
"""Reset the gradient buffers."""
self.g_optimizer.zero_grad()
self.d_optimizer.zero_grad()
self.v_optimizer.zero_grad()
def gradient_penalty(self, y, x):
"""Compute gradient penalty: (L2_norm(dy/dx) - 1)**2."""
weight = torch.ones(y.size()).to(self.device)
dydx = torch.autograd.grad(outputs=y,
inputs=x,
grad_outputs=weight,
retain_graph=True,
create_graph=True,
only_inputs=True)[0]
dydx = dydx.view(dydx.size(0), -1)
dydx_l2norm = torch.sqrt(torch.sum(dydx ** 2, dim=1))
return torch.mean((dydx_l2norm - 1) ** 2)
def label2onehot(self, labels, dim):
"""Convert label indices to one-hot vectors."""
out = torch.zeros(list(labels.size()) + [dim]).to(self.device)
out.scatter_(len(out.size()) - 1, labels.unsqueeze(-1), 1.)
return out
def sample_z(self, batch_size):
return np.random.normal(0, 1, size=(batch_size, self.z_dim))
@staticmethod
def postprocess(inputs, method, temperature=1.):
def listify(x):
return x if type(x) == list or type(x) == tuple else [x]
def delistify(x):
return x if len(x) > 1 else x[0]
if method == 'soft_gumbel':
softmax = [F.gumbel_softmax(e_logits.contiguous().view(-1, e_logits.size(-1))
/ temperature, hard=False).view(e_logits.size())
for e_logits in listify(inputs)]
elif method == 'hard_gumbel':
softmax = [F.gumbel_softmax(e_logits.contiguous().view(-1, e_logits.size(-1))
/ temperature, hard=True).view(e_logits.size())
for e_logits in listify(inputs)]
else:
softmax = [F.softmax(e_logits / temperature, -1)
for e_logits in listify(inputs)]
return [delistify(e) for e in (softmax)]
def reward(self, mols):
rr = 1.
for m in ('logp,sas,qed,unique' if self.metric == 'all' else self.metric).split(','):
if m == 'np':
rr *= MolecularMetrics.natural_product_scores(mols, norm=True)
elif m == 'logp':
rr *= MolecularMetrics.water_octanol_partition_coefficient_scores(mols, norm=True)
elif m == 'sas':
rr *= MolecularMetrics.synthetic_accessibility_score_scores(mols, norm=True)
elif m == 'qed':
rr *= MolecularMetrics.quantitative_estimation_druglikeness_scores(mols, norm=True)
elif m == 'novelty':
rr *= MolecularMetrics.novel_scores(mols, self.data)
elif m == 'dc':
rr *= MolecularMetrics.drugcandidate_scores(mols, self.data)
elif m == 'unique':
rr *= MolecularMetrics.unique_scores(mols)
elif m == 'diversity':
rr *= MolecularMetrics.diversity_scores(mols, self.data)
elif m == 'validity':
rr *= MolecularMetrics.valid_scores(mols)
else:
raise RuntimeError('{} is not defined as a metric'.format(m))
return rr.reshape(-1, 1)
def train_and_validate(self):
self.start_time = time.time()
# Start training from scratch or resume training.
start_epoch = 0
if self.resume_epoch is not None:
start_epoch = self.resume_epoch
self.restore_model(self.resume_epoch)
# Start training.
if self.mode == 'train':
print('Start training...')
for i in range(start_epoch, self.num_epochs):
self.train_or_valid(epoch_i=i, train_val_test='train')
self.train_or_valid(epoch_i=i, train_val_test='val')
elif self.mode == 'test':
assert self.resume_epoch is not None
self.train_or_valid(epoch_i=start_epoch, train_val_test='val')
else:
raise NotImplementedError
def get_gen_mols(self, n_hat, e_hat, method):
(edges_hard, nodes_hard) = self.postprocess((e_hat, n_hat), method)
edges_hard, nodes_hard = torch.max(edges_hard, -1)[1], torch.max(nodes_hard, -1)[1]
mols = [self.data.matrices2mol(n_.data.cpu().numpy(), e_.data.cpu().numpy(), strict=True)
for e_, n_ in zip(edges_hard, nodes_hard)]
return mols
def get_reward(self, n_hat, e_hat, method):
(edges_hard, nodes_hard) = self.postprocess((e_hat, n_hat), method)
edges_hard, nodes_hard = torch.max(edges_hard, -1)[1], torch.max(nodes_hard, -1)[1]
mols = [self.data.matrices2mol(n_.data.cpu().numpy(), e_.data.cpu().numpy(), strict=True)
for e_, n_ in zip(edges_hard, nodes_hard)]
reward = torch.from_numpy(self.reward(mols)).to(self.device)
return reward
def save_checkpoints(self, epoch_i):
G_path = os.path.join(self.model_dir_path, '{}-G.ckpt'.format(epoch_i + 1))
D_path = os.path.join(self.model_dir_path, '{}-D.ckpt'.format(epoch_i + 1))
V_path = os.path.join(self.model_dir_path, '{}-V.ckpt'.format(epoch_i + 1))
torch.save(self.G.state_dict(), G_path)
torch.save(self.D.state_dict(), D_path)
torch.save(self.V.state_dict(), V_path)
print('Saved model checkpoints into {}...'.format(self.model_dir_path))
if self.log is not None:
self.log.info('Saved model checkpoints into {}...'.format(self.model_dir_path))
def train_or_valid(self, epoch_i, train_val_test='val'):
# The first several epochs using RL to purse stability (not used).
if epoch_i < 0:
cur_la = 0
else:
cur_la = self.la
# Recordings
losses = defaultdict(list)
scores = defaultdict(list)
# Iterations
the_step = self.num_steps
if train_val_test == 'val':
if self.mode == 'train':
the_step = 1
print('[Validating]')
for a_step in range(the_step):
if train_val_test == 'val':
mols, _, _, a, x, _, _, _, _ = self.data.next_validation_batch()
z = self.sample_z(a.shape[0])
elif train_val_test == 'train':
mols, _, _, a, x, _, _, _, _ = self.data.next_train_batch(self.batch_size)
z = self.sample_z(self.batch_size)
else:
raise NotImplementedError
# =================================================================================== #
# 1. Preprocess input data #
# =================================================================================== #
a = torch.from_numpy(a).to(self.device).long() # Adjacency.
x = torch.from_numpy(x).to(self.device).long() # Nodes.
a_tensor = self.label2onehot(a, self.b_dim)
x_tensor = self.label2onehot(x, self.m_dim)
z = torch.from_numpy(z).to(self.device).float()
# Current steps
cur_step = self.num_steps * epoch_i + a_step
# =================================================================================== #
# 2. Train the discriminator #
# =================================================================================== #
# Compute losses with real inputs.
logits_real, features_real = self.D(a_tensor, None, x_tensor)
# Z-to-target
edges_logits, nodes_logits = self.G(z)
# Postprocess with Gumbel softmax
(edges_hat, nodes_hat) = self.postprocess((edges_logits, nodes_logits), self.post_method)
logits_fake, features_fake = self.D(edges_hat, None, nodes_hat)
# Compute losses for gradient penalty.
eps = torch.rand(logits_real.size(0), 1, 1, 1).to(self.device)
x_int0 = (eps * a_tensor + (1. - eps) * edges_hat).requires_grad_(True)
x_int1 = (eps.squeeze(-1) * x_tensor + (1. - eps.squeeze(-1)) * nodes_hat).requires_grad_(True)
grad0, grad1 = self.D(x_int0, None, x_int1)
grad_penalty = self.gradient_penalty(grad0, x_int0) + self.gradient_penalty(grad1, x_int1)
d_loss_real = torch.mean(logits_real)
d_loss_fake = torch.mean(logits_fake)
loss_D = -d_loss_real + d_loss_fake + self.la_gp * grad_penalty
if cur_la > 0:
losses['l_D/R'].append(d_loss_real.item())
losses['l_D/F'].append(d_loss_fake.item())
losses['l_D'].append(loss_D.item())
# Optimise discriminator.
if train_val_test == 'train' and cur_step % self.n_critic != 0 and cur_la > 0:
self.reset_grad()
loss_D.backward()
self.d_optimizer.step()
# =================================================================================== #
# 3. Train the generator #
# =================================================================================== #
# Z-to-target
edges_logits, nodes_logits = self.G(z)
# Postprocess with Gumbel softmax
(edges_hat, nodes_hat) = self.postprocess((edges_logits, nodes_logits), self.post_method)
logits_fake, features_fake = self.D(edges_hat, None, nodes_hat)
# Value losses
value_logit_real, _ = self.V(a_tensor, None, x_tensor, torch.sigmoid)
value_logit_fake, _ = self.V(edges_hat, None, nodes_hat, torch.sigmoid)
# Feature mapping losses. Not used anywhere in the PyTorch version.
# I include it here for the consistency with the TF code.
f_loss = (torch.mean(features_real, 0) - torch.mean(features_fake, 0)) ** 2
# Real Reward
reward_r = torch.from_numpy(self.reward(mols)).to(self.device)
# Fake Reward
reward_f = self.get_reward(nodes_hat, edges_hat, self.post_method)
# Losses Update
loss_G = -logits_fake
# Original TF loss_V. Here we use absolute values instead of the squared one.
# loss_V = (value_logit_real - reward_r) ** 2 + (value_logit_fake - reward_f) ** 2
loss_V = torch.abs(value_logit_real - reward_r) + torch.abs(value_logit_fake - reward_f)
loss_RL = -value_logit_fake
loss_G = torch.mean(loss_G)
loss_V = torch.mean(loss_V)
loss_RL = torch.mean(loss_RL)
losses['l_G'].append(loss_G.item())
losses['l_RL'].append(loss_RL.item())
losses['l_V'].append(loss_V.item())
alpha = torch.abs(loss_G.detach() / loss_RL.detach()).detach()
train_step_G = cur_la * loss_G + (1 - cur_la) * alpha * loss_RL
train_step_V = loss_V
if train_val_test == 'train':
self.reset_grad()
# Optimise generator.
if cur_step % self.n_critic == 0:
train_step_G.backward(retain_graph=True)
self.g_optimizer.step()
# Optimise value network.
if cur_step % self.n_critic == 0:
train_step_V.backward()
self.v_optimizer.step()
# =================================================================================== #
# 4. Miscellaneous #
# =================================================================================== #
# Get scores.
if train_val_test == 'val':
mols = self.get_gen_mols(nodes_logits, edges_logits, self.post_method)
m0, m1 = all_scores(mols, self.data, norm=True) # 'mols' is output of Fake Reward
for k, v in m1.items():
scores[k].append(v)
for k, v in m0.items():
scores[k].append(np.array(v)[np.nonzero(v)].mean())
# Save checkpoints.
if self.mode == 'train':
if (epoch_i + 1) % self.model_save_step == 0:
self.save_checkpoints(epoch_i=epoch_i)
# Saving molecule images.
mol_f_name = os.path.join(self.img_dir_path, 'mol-{}.png'.format(epoch_i))
save_mol_img(mols, mol_f_name, is_test=self.mode == 'test')
# Print out training information.
et = time.time() - self.start_time
et = str(datetime.timedelta(seconds=et))[:-7]
log = "Elapsed [{}], Iteration [{}/{}]:".format(et, epoch_i + 1, self.num_epochs)
is_first = True
for tag, value in losses.items():
if is_first:
log += "\n{}: {:.2f}".format(tag, np.mean(value))
is_first = False
else:
log += ", {}: {:.2f}".format(tag, np.mean(value))
is_first = True
for tag, value in scores.items():
if is_first:
log += "\n{}: {:.2f}".format(tag, np.mean(value))
is_first = False
else:
log += ", {}: {:.2f}".format(tag, np.mean(value))
print(log)
if self.log is not None:
self.log.info(log)
class Solver(object):
"""Solver for training and testing StarGAN."""
def __init__(self, config, log=None):
"""Initialize configurations."""
# Log
self.log = log
# Data loader.
self.data = SparseMolecularDataset()
self.data.load(config.mol_data_dir)
# Model configurations.
self.z_dim = config.z_dim
self.m_dim = self.data.atom_num_types
self.b_dim = self.data.bond_num_types
self.f_dim = self.data.features
self.g_conv_dim = config.g_conv_dim
self.d_conv_dim = config.d_conv_dim
self.lambda_wgan = config.lambda_wgan
self.lambda_rec = config.lambda_rec
self.post_method = config.post_method
self.metric = 'validity,qed'
# Training configurations.
self.batch_size = config.batch_size
self.num_epochs = config.num_epochs
self.num_steps = (len(self.data) // self.batch_size)
self.g_lr = config.g_lr
self.d_lr = config.d_lr
self.dropout_rate = config.dropout
self.n_critic = config.n_critic
self.resume_epoch = config.resume_epoch
# Training or testing.
self.mode = config.mode
# Miscellaneous.
self.device = torch.device(
'cuda' if torch.cuda.is_available() else 'cpu')
print('Device: ', self.device)
# Directories.
self.log_dir_path = config.log_dir_path
self.model_dir_path = config.model_dir_path
self.img_dir_path = config.img_dir_path
# Step size.
self.model_save_step = config.model_save_step
# VAE KL weight.
self.kl_la = 1.
# Build the model.
self.build_model()
def build_model(self):
"""Create an encoder and a decoder."""
self.encoder = EncoderVAE(self.d_conv_dim,
self.m_dim,
self.b_dim - 1,
self.z_dim,
with_features=True,
f_dim=self.f_dim,
dropout_rate=self.dropout_rate).to(
self.device)
self.decoder = Generator(self.g_conv_dim, self.z_dim,
self.data.vertexes, self.data.bond_num_types,
self.data.atom_num_types,
self.dropout_rate).to(self.device)
self.V = Discriminator(self.d_conv_dim, self.m_dim, self.b_dim - 1,
self.dropout_rate).to(self.device)
self.vae_optimizer = torch.optim.RMSprop(
list(self.encoder.parameters()) + list(self.decoder.parameters()),
self.g_lr)
self.v_optimizer = torch.optim.RMSprop(self.V.parameters(), self.d_lr)
self.print_network(self.encoder, 'Encoder', self.log)
self.print_network(self.decoder, 'Decoder', self.log)
self.print_network(self.V, 'Value', self.log)
@staticmethod
def print_network(model, name, log=None):
"""Print out the network information."""
num_params = 0
for p in model.parameters():
num_params += p.numel()
print(model)
print(name)
print("The number of parameters: {}".format(num_params))
if log is not None:
log.info(model)
log.info(name)
log.info("The number of parameters: {}".format(num_params))
def restore_model(self, resume_iters):
"""Restore the trained generator and discriminator."""
print(
'Loading the trained models from step {}...'.format(resume_iters))
enc_path = os.path.join(self.model_dir_path,
'{}-encoder.ckpt'.format(resume_iters))
dec_path = os.path.join(self.model_dir_path,
'{}-decoder.ckpt'.format(resume_iters))
V_path = os.path.join(self.model_dir_path,
'{}-V.ckpt'.format(resume_iters))
self.encoder.load_state_dict(
torch.load(enc_path, map_location=lambda storage, loc: storage))
self.decoder.load_state_dict(
torch.load(dec_path, map_location=lambda storage, loc: storage))
self.V.load_state_dict(
torch.load(V_path, map_location=lambda storage, loc: storage))
def update_lr(self, g_lr, d_lr):
"""Decay learning rates of the generator and discriminator."""
for param_group in self.g_optimizer.param_groups:
param_group['lr'] = g_lr
for param_group in self.d_optimizer.param_groups:
param_group['lr'] = d_lr
def reset_grad(self):
"""Reset the gradient buffers."""
self.vae_optimizer.zero_grad()
self.v_optimizer.zero_grad()
def label2onehot(self, labels, dim):
"""Convert label indices to one-hot vectors."""
out = torch.zeros(list(labels.size()) + [dim]).to(self.device)
out.scatter_(len(out.size()) - 1, labels.unsqueeze(-1), 1.)
return out
def sample_z(self, batch_size):
return np.random.normal(0, 1, size=(batch_size, self.z_dim))
@staticmethod
def postprocess_logits(inputs, method, temperature=1.):
def listify(x):
return x if type(x) == list or type(x) == tuple else [x]
def delistify(x):
return x if len(x) > 1 else x[0]
if method == 'soft_gumbel':
softmax = [
F.gumbel_softmax(
e_logits.contiguous().view(-1, e_logits.size(-1)) /
temperature,
hard=False).view(e_logits.size())
for e_logits in listify(inputs)
]
elif method == 'hard_gumbel':
softmax = [
F.gumbel_softmax(
e_logits.contiguous().view(-1, e_logits.size(-1)) /
temperature,
hard=True).view(e_logits.size())
for e_logits in listify(inputs)
]
else:
softmax = [
F.softmax(e_logits / temperature, -1)
for e_logits in listify(inputs)
]
return [delistify(e) for e in (softmax)]
def reward(self, mols):
rr = 1.
for m in ('logp,sas,qed,unique'
if self.metric == 'all' else self.metric).split(','):
if m == 'np':
rr *= MolecularMetrics.natural_product_scores(mols, norm=True)
elif m == 'logp':
rr *= MolecularMetrics.water_octanol_partition_coefficient_scores(
mols, norm=True)
elif m == 'sas':
rr *= MolecularMetrics.synthetic_accessibility_score_scores(
mols, norm=True)
elif m == 'qed':
rr *= MolecularMetrics.quantitative_estimation_druglikeness_scores(
mols, norm=True)
elif m == 'novelty':
rr *= MolecularMetrics.novel_scores(mols, self.data)
elif m == 'dc':
rr *= MolecularMetrics.drugcandidate_scores(mols, self.data)
elif m == 'unique':
rr *= MolecularMetrics.unique_scores(mols)
elif m == 'diversity':
rr *= MolecularMetrics.diversity_scores(mols, self.data)
elif m == 'validity':
rr *= MolecularMetrics.valid_scores(mols)
else:
raise RuntimeError('{} is not defined as a metric'.format(m))
return rr.reshape(-1, 1)
def train_and_validate(self):
self.start_time = time.time()
# Start training from scratch or resume training.
start_epoch = 0
if self.resume_epoch:
start_epoch = self.resume_epoch
self.restore_model(self.resume_epoch)
# Start training.
if self.mode == 'train':
print('Start training...')
for i in range(start_epoch, self.num_epochs):
self.train_or_valid(epoch_i=i, train_val_test='train')
self.train_or_valid(epoch_i=i, train_val_test='val')
self.train_or_valid(epoch_i=i, train_val_test='sample')
elif self.mode == 'test':
assert self.resume_epoch is not None
self.train_or_valid(epoch_i=start_epoch, train_val_test='sample')
self.train_or_valid(epoch_i=start_epoch, train_val_test='val')
else:
raise NotImplementedError
def get_reconstruction_loss(self, n_hat, n, e_hat, e):
# This loss cares about the imbalance between nodes and edges.
# However, in practice, they don't work well.
# n_loss = torch.nn.CrossEntropyLoss(reduction='none')(n_hat.view(-1, self.m_dim), n.view(-1))
# n_loss_ = n_loss.view(n.shape)
# e_loss = torch.nn.CrossEntropyLoss(reduction='none')(e_hat.reshape((-1, self.b_dim)), e.view(-1))
# e_loss_ = e_loss.view(e.shape)
# loss_ = e_loss_ + n_loss_.unsqueeze(-1)
# reconstruction_loss = torch.mean(loss_)
# return reconstruction_loss
n_loss = torch.nn.CrossEntropyLoss(reduction='mean')(n_hat.view(
-1, self.m_dim), n.view(-1))
e_loss = torch.nn.CrossEntropyLoss(reduction='mean')(e_hat.reshape(
(-1, self.b_dim)), e.view(-1))
reconstruction_loss = n_loss + e_loss
return reconstruction_loss
@staticmethod
def get_kl_loss(mu, logvar):
kld_loss = torch.mean(
-0.5 * torch.sum(1 + logvar - mu**2 - logvar.exp(), dim=1), dim=0)
return kld_loss
def get_gen_mols(self, n_hat, e_hat, method):
(edges_hard, nodes_hard) = self.postprocess_logits((e_hat, n_hat),
method)
edges_hard, nodes_hard = torch.max(edges_hard,
-1)[1], torch.max(nodes_hard, -1)[1]
mols = [
self.data.matrices2mol(n_.data.cpu().numpy(),
e_.data.cpu().numpy(),
strict=True)
for e_, n_ in zip(edges_hard, nodes_hard)
]
return mols
def get_reward(self, n_hat, e_hat, method):
(edges_hard, nodes_hard) = self.postprocess_logits((e_hat, n_hat),
method)
edges_hard, nodes_hard = torch.max(edges_hard,
-1)[1], torch.max(nodes_hard, -1)[1]
mols = [
self.data.matrices2mol(n_.data.cpu().numpy(),
e_.data.cpu().numpy(),
strict=True)
for e_, n_ in zip(edges_hard, nodes_hard)
]
reward = torch.from_numpy(self.reward(mols)).to(self.device)
return reward
def save_checkpoints(self, epoch_i):
enc_path = os.path.join(self.model_dir_path,
'{}-encoder.ckpt'.format(epoch_i + 1))
dec_path = os.path.join(self.model_dir_path,
'{}-decoder.ckpt'.format(epoch_i + 1))
V_path = os.path.join(self.model_dir_path,
'{}-V.ckpt'.format(epoch_i + 1))
torch.save(self.encoder.state_dict(), enc_path)
torch.save(self.decoder.state_dict(), dec_path)
torch.save(self.V.state_dict(), V_path)
print('Saved model checkpoints into {}...'.format(self.model_dir_path))
if self.log is not None:
self.log.info('Saved model checkpoints into {}...'.format(
self.model_dir_path))
def get_scores(self, mols, to_print=False):
scores = defaultdict(list)
m0, m1 = all_scores(mols, self.data,
norm=True) # 'mols' is output of Fake Reward
for k, v in m1.items():
scores[k].append(v)
for k, v in m0.items():
scores[k].append(np.array(v)[np.nonzero(v)].mean())
if to_print:
log = ""
is_first = True
for tag, value in scores.items():
if is_first:
log += "{}: {:.2f}".format(tag, np.mean(value))
is_first = False
else:
log += ", {}: {:.2f}".format(tag, np.mean(value))
print(log)
return scores, log
return scores
def train_or_valid(self, epoch_i, train_val_test='val'):
# Recordings
losses = defaultdict(list)
the_step = self.num_steps
if train_val_test == 'val':
if self.mode == 'train':
the_step = 1
print('[Validating]')
if train_val_test == 'sample':
if self.mode == 'train':
the_step = 1
print('[Sampling]')
for a_step in range(the_step):
z = None
if train_val_test == 'val':
mols, _, _, a, x, _, f, _, _ = self.data.next_validation_batch(
)
elif train_val_test == 'train':
mols, _, _, a, x, _, f, _, _ = self.data.next_train_batch(
self.batch_size)
elif train_val_test == 'sample':
z = self.sample_z(self.batch_size)
z = torch.from_numpy(z).to(self.device).float()
else:
raise NotImplementedError
if train_val_test == 'train' or train_val_test == 'val':
a = torch.from_numpy(a).to(self.device).long() # Adjacency.
x = torch.from_numpy(x).to(self.device).long() # Nodes.
a_tensor = self.label2onehot(a, self.b_dim)
x_tensor = self.label2onehot(x, self.m_dim)
f = torch.from_numpy(f).to(self.device).float()
if train_val_test == 'train' or train_val_test == 'val':
z, z_mu, z_logvar = self.encoder(a_tensor, f, x_tensor)
edges_logits, nodes_logits = self.decoder(z)
(edges_hat, nodes_hat) = self.postprocess_logits(
(edges_logits, nodes_logits), self.post_method)
if train_val_test == 'train' or train_val_test == 'val':
recon_loss = self.get_reconstruction_loss(
nodes_logits, x, edges_logits, a)
kl_loss = self.get_kl_loss(z_mu, z_logvar)
loss_vae = recon_loss + self.kl_la * kl_loss
# Real Reward
reward_r = torch.from_numpy(self.reward(mols)).to(self.device)
# Fake Reward
reward_f = self.get_reward(nodes_logits, edges_logits,
'hard_gumbel')
# Value loss
value_logit_real, _ = self.V(a_tensor, None, x_tensor,
torch.sigmoid)
value_logit_fake, _ = self.V(edges_hat, None, nodes_hat,
torch.sigmoid)
loss_v = torch.mean((value_logit_real - reward_r)**2 +
(value_logit_fake - reward_f)**2)
loss_rl = torch.mean(-value_logit_fake)
alpha = torch.abs(loss_vae.detach() / loss_rl.detach())
loss_rl *= alpha
vae_loss_train = self.lambda_wgan * loss_vae + (
1 - self.lambda_wgan) * loss_rl
# vae_loss_train = loss_vae
losses['l_Rec'].append(recon_loss.item())
losses['l_KL'].append(kl_loss.item())
losses['l_VAE'].append(loss_vae.item())
losses['l_RL'].append(loss_rl.item())
losses['l_V'].append(loss_v.item())
if train_val_test == 'train':
self.reset_grad()
vae_loss_train.backward(retain_graph=True)
loss_v.backward()
self.vae_optimizer.step()
self.v_optimizer.step()
if train_val_test == 'sample':
mols = self.get_gen_mols(nodes_logits, edges_logits,
'hard_gumbel')
scores, mol_log = self.get_scores(mols, to_print=True)
# Saving molecule images.
mol_f_name = os.path.join(self.img_dir_path,
'sample-mol-{}.png'.format(epoch_i))
save_mol_img(mols, mol_f_name, is_test=self.mode == 'test')
if self.log is not None:
self.log.info(mol_log)
if train_val_test == 'val':
mols = self.get_gen_mols(nodes_logits, edges_logits,
'hard_gumbel')
scores = self.get_scores(mols)
# Save checkpoints.
if self.mode == 'train':
if (epoch_i + 1) % self.model_save_step == 0:
self.save_checkpoints(epoch_i=epoch_i)
# Saving molecule images.
mol_f_name = os.path.join(self.img_dir_path,
'mol-{}.png'.format(epoch_i))
save_mol_img(mols, mol_f_name, is_test=self.mode == 'test')
# Print out training information.
et = time.time() - self.start_time
et = str(datetime.timedelta(seconds=et))[:-7]
log = "Elapsed [{}], Iteration [{}/{}]:".format(
et, epoch_i + 1, self.num_epochs)
is_first = True
for tag, value in losses.items():
if is_first:
log += "\n{}: {:.2f}".format(tag, np.mean(value))
is_first = False
else:
log += ", {}: {:.2f}".format(tag, np.mean(value))
is_first = True
for tag, value in scores.items():
if is_first:
log += "\n{}: {:.2f}".format(tag, np.mean(value))
is_first = False
else:
log += ", {}: {:.2f}".format(tag, np.mean(value))
print(log)
if self.log is not None:
self.log.info(log)