def train_cleitcs(s_dataloaders, t_dataloaders, val_dataloader, test_dataloader, metric_name, seed, **kwargs):
"""
:param s_dataloaders:
:param t_dataloaders:
:param kwargs:
:return:
"""
s_train_dataloader = s_dataloaders
t_train_dataloader = t_dataloaders
autoencoder = AE(input_dim=kwargs['input_dim'],
latent_dim=kwargs['latent_dim'],
hidden_dims=kwargs['encoder_hidden_dims'],
dop=kwargs['dop']).to(kwargs['device'])
# get reference encoder
aux_ae = deepcopy(autoencoder)
aux_ae.encoder.load_state_dict(torch.load(os.path.join('./model_save/ae', f'ft_encoder_{seed}.pt')))
print('reference encoder loaded')
reference_encoder = aux_ae.encoder
# construct transmitter
transmitter = MLP(input_dim=kwargs['latent_dim'],
output_dim=kwargs['latent_dim'],
hidden_dims=[kwargs['latent_dim']]).to(kwargs['device'])
encoder = autoencoder.encoder
target_decoder = MoMLP(input_dim=kwargs['latent_dim'],
output_dim=kwargs['output_dim'],
hidden_dims=kwargs['regressor_hidden_dims'],
out_fn=torch.nn.Sigmoid).to(kwargs['device'])
target_regressor = EncoderDecoder(encoder=encoder,
decoder=target_decoder).to(kwargs['device'])
train_history = defaultdict(list)
# ae_eval_train_history = defaultdict(list)
val_history = defaultdict(list)
s_target_regression_eval_train_history = defaultdict(list)
t_target_regression_eval_train_history = defaultdict(list)
target_regression_eval_val_history = defaultdict(list)
target_regression_eval_test_history = defaultdict(list)
cleit_params = [
target_regressor.parameters(),
transmitter.parameters()
]
model_optimizer = torch.optim.AdamW(chain(*cleit_params), lr=kwargs['lr'])
for epoch in range(int(kwargs['train_num_epochs'])):
if epoch % 50 == 0:
print(f'Coral training epoch {epoch}')
for step, s_batch in enumerate(s_train_dataloader):
t_batch = next(iter(t_train_dataloader))
train_history = cleit_train_step(model=target_regressor,
transmitter=transmitter,
reference_encoder=reference_encoder,
s_batch=s_batch,
t_batch=t_batch,
device=kwargs['device'],
optimizer=model_optimizer,
alpha=kwargs['alpha'],
history=train_history)
s_target_regression_eval_train_history = evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=s_train_dataloader,
device=kwargs['device'],
history=s_target_regression_eval_train_history)
t_target_regression_eval_train_history = evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=t_train_dataloader,
device=kwargs['device'],
history=t_target_regression_eval_train_history)
target_regression_eval_val_history = evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=val_dataloader,
device=kwargs['device'],
history=target_regression_eval_val_history)
target_regression_eval_test_history = evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=target_regression_eval_test_history)
save_flag, stop_flag = model_save_check(history=target_regression_eval_val_history,
metric_name=metric_name,
tolerance_count=50)
if save_flag:
torch.save(target_regressor.state_dict(), os.path.join(kwargs['model_save_folder'], f'cleitcs_regressor_{seed}.pt'))
if stop_flag:
break
target_regressor.load_state_dict(
torch.load(os.path.join(kwargs['model_save_folder'], f'cleitcs_regressor_{seed}.pt')))
# evaluate_target_regression_epoch(regressor=target_regressor,
# dataloader=val_dataloader,
# device=kwargs['device'],
# history=None,
# seed=seed,
# output_folder=kwargs['model_save_folder'])
evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=None,
seed=seed,
output_folder=kwargs['model_save_folder'])
return target_regressor, (
train_history, s_target_regression_eval_train_history, t_target_regression_eval_train_history,
target_regression_eval_val_history, target_regression_eval_test_history)
def fine_tune_encoder(encoder,
train_dataloader,
val_dataloader,
seed,
task_save_folder,
test_dataloader=None,
metric_name='cpearsonr',
normalize_flag=False,
**kwargs):
target_decoder = MoMLP(input_dim=kwargs['latent_dim'],
output_dim=kwargs['output_dim'],
hidden_dims=kwargs['regressor_hidden_dims'],
out_fn=torch.nn.Sigmoid).to(kwargs['device'])
target_regressor = EncoderDecoder(encoder=encoder,
decoder=target_decoder,
normalize_flag=normalize_flag).to(
kwargs['device'])
target_regression_train_history = defaultdict(list)
target_regression_eval_train_history = defaultdict(list)
target_regression_eval_val_history = defaultdict(list)
target_regression_eval_test_history = defaultdict(list)
encoder_module_indices = [
i for i in range(len(list(encoder.modules())))
if str(list(encoder.modules())[i]).startswith('Linear')
]
reset_count = 1
lr = kwargs['lr']
target_regression_params = [target_regressor.decoder.parameters()]
target_regression_optimizer = torch.optim.AdamW(
chain(*target_regression_params), lr=lr)
for epoch in range(kwargs['train_num_epochs']):
if epoch % 50 == 0:
print(f'Fine tuning epoch {epoch}')
for step, batch in enumerate(train_dataloader):
target_regression_train_history = regression_train_step(
model=target_regressor,
batch=batch,
device=kwargs['device'],
optimizer=target_regression_optimizer,
history=target_regression_train_history)
target_regression_eval_train_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=train_dataloader,
device=kwargs['device'],
history=target_regression_eval_train_history)
target_regression_eval_val_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=val_dataloader,
device=kwargs['device'],
history=target_regression_eval_val_history)
if test_dataloader is not None:
target_regression_eval_test_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=target_regression_eval_test_history)
save_flag, stop_flag = model_save_check(
history=target_regression_eval_val_history,
metric_name=metric_name,
tolerance_count=10,
reset_count=reset_count)
if save_flag:
torch.save(
target_regressor.state_dict(),
os.path.join(task_save_folder, f'target_regressor_{seed}.pt'))
torch.save(target_regressor.encoder.state_dict(),
os.path.join(task_save_folder, f'ft_encoder_{seed}.pt'))
if stop_flag:
try:
ind = encoder_module_indices.pop()
print(f'Unfreezing {epoch}')
target_regressor.load_state_dict(
torch.load(
os.path.join(task_save_folder,
f'target_regressor_{seed}.pt')))
target_regression_params.append(
list(target_regressor.encoder.modules())[ind].parameters())
lr = lr * kwargs['decay_coefficient']
target_regression_optimizer = torch.optim.AdamW(
chain(*target_regression_params), lr=lr)
reset_count += 1
except IndexError:
break
target_regressor.load_state_dict(
torch.load(
os.path.join(task_save_folder, f'target_regressor_{seed}.pt')))
evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=val_dataloader,
device=kwargs['device'],
history=None,
seed=seed,
cv_flag=True,
output_folder=kwargs['model_save_folder'])
evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=None,
seed=seed,
output_folder=kwargs['model_save_folder'])
return target_regressor, (target_regression_train_history,
target_regression_eval_train_history,
target_regression_eval_val_history,
target_regression_eval_test_history)
def train_dann(s_dataloaders, t_dataloaders, val_dataloader, test_dataloader,
metric_name, seed, **kwargs):
"""
:param s_dataloaders:
:param t_dataloaders:
:param kwargs:
:return:
"""
s_train_dataloader = s_dataloaders
t_train_dataloader = t_dataloaders
autoencoder = AE(input_dim=kwargs['input_dim'],
latent_dim=kwargs['latent_dim'],
hidden_dims=kwargs['encoder_hidden_dims'],
dop=kwargs['dop']).to(kwargs['device'])
encoder = autoencoder.encoder
target_decoder = MoMLP(input_dim=kwargs['latent_dim'],
output_dim=kwargs['output_dim'],
hidden_dims=kwargs['regressor_hidden_dims'],
out_fn=torch.nn.Sigmoid).to(kwargs['device'])
target_regressor = EncoderDecoder(
encoder=encoder, decoder=target_decoder).to(kwargs['device'])
classifier = MLP(input_dim=kwargs['latent_dim'],
output_dim=1,
hidden_dims=kwargs['classifier_hidden_dims'],
dop=kwargs['dop'],
out_fn=torch.nn.Sigmoid).to(kwargs['device'])
confounder_classifier = EncoderDecoder(encoder=autoencoder.encoder,
decoder=classifier).to(
kwargs['device'])
train_history = defaultdict(list)
s_target_regression_eval_train_history = defaultdict(list)
t_target_regression_eval_train_history = defaultdict(list)
target_regression_eval_val_history = defaultdict(list)
target_regression_eval_test_history = defaultdict(list)
confounded_loss = nn.BCEWithLogitsLoss()
dann_params = [
target_regressor.parameters(),
confounder_classifier.decoder.parameters()
]
dann_optimizer = torch.optim.AdamW(chain(*dann_params), lr=kwargs['lr'])
# start alternative training
for epoch in range(int(kwargs['train_num_epochs'])):
if epoch % 50 == 0:
print(f'DANN training epoch {epoch}')
# start autoencoder training epoch
for step, s_batch in enumerate(s_train_dataloader):
t_batch = next(iter(t_train_dataloader))
train_history = dann_train_step(classifier=confounder_classifier,
model=target_regressor,
s_batch=s_batch,
t_batch=t_batch,
loss_fn=confounded_loss,
alpha=kwargs['alpha'],
device=kwargs['device'],
optimizer=dann_optimizer,
history=train_history,
scheduler=None)
s_target_regression_eval_train_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=s_train_dataloader,
device=kwargs['device'],
history=s_target_regression_eval_train_history)
t_target_regression_eval_train_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=t_train_dataloader,
device=kwargs['device'],
history=t_target_regression_eval_train_history)
target_regression_eval_val_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=val_dataloader,
device=kwargs['device'],
history=target_regression_eval_val_history)
target_regression_eval_test_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=target_regression_eval_test_history)
save_flag, stop_flag = model_save_check(
history=target_regression_eval_val_history,
metric_name=metric_name,
tolerance_count=50)
if save_flag:
torch.save(
target_regressor.state_dict(),
os.path.join(kwargs['model_save_folder'],
f'dann_regressor_{seed}.pt'))
if stop_flag:
break
target_regressor.load_state_dict(
torch.load(
os.path.join(kwargs['model_save_folder'],
f'dann_regressor_{seed}.pt')))
# evaluate_target_regression_epoch(regressor=target_regressor,
# dataloader=val_dataloader,
# device=kwargs['device'],
# history=None,
# seed=seed,
# output_folder=kwargs['model_save_folder'])
evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=None,
seed=seed,
output_folder=kwargs['model_save_folder'])
return target_regressor, (train_history,
s_target_regression_eval_train_history,
t_target_regression_eval_train_history,
target_regression_eval_val_history,
target_regression_eval_test_history)
def fine_tune_encoder(train_dataloader, val_dataloader, seed, test_dataloader=None,
metric_name='cpearsonr',
normalize_flag=False, **kwargs):
autoencoder = AE(input_dim=kwargs['input_dim'],
latent_dim=kwargs['latent_dim'],
hidden_dims=kwargs['encoder_hidden_dims'],
dop=kwargs['dop']).to(kwargs['device'])
encoder = autoencoder.encoder
target_decoder = MoMLP(input_dim=kwargs['latent_dim'],
output_dim=kwargs['output_dim'],
hidden_dims=kwargs['regressor_hidden_dims'],
out_fn=torch.nn.Sigmoid).to(kwargs['device'])
target_regressor = EncoderDecoder(encoder=encoder,
decoder=target_decoder,
normalize_flag=normalize_flag).to(kwargs['device'])
target_regression_train_history = defaultdict(list)
target_regression_eval_train_history = defaultdict(list)
target_regression_eval_val_history = defaultdict(list)
target_regression_eval_test_history = defaultdict(list)
target_regression_optimizer = torch.optim.AdamW(target_regressor.parameters(), lr=kwargs['lr'])
for epoch in range(kwargs['train_num_epochs']):
if epoch % 10 == 0:
print(f'MLP fine-tuning epoch {epoch}')
for step, batch in enumerate(train_dataloader):
target_regression_train_history = regression_train_step(model=target_regressor,
batch=batch,
device=kwargs['device'],
optimizer=target_regression_optimizer,
history=target_regression_train_history)
target_regression_eval_train_history = evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=train_dataloader,
device=kwargs['device'],
history=target_regression_eval_train_history)
target_regression_eval_val_history = evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=val_dataloader,
device=kwargs['device'],
history=target_regression_eval_val_history)
if test_dataloader is not None:
target_regression_eval_test_history = evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=target_regression_eval_test_history)
save_flag, stop_flag = model_save_check(history=target_regression_eval_val_history,
metric_name=metric_name,
tolerance_count=50)
if save_flag or epoch == 0:
torch.save(target_regressor.state_dict(),
os.path.join(kwargs['model_save_folder'], f'target_regressor_{seed}.pt'))
torch.save(target_regressor.encoder.state_dict(),
os.path.join(kwargs['model_save_folder'], f'ft_encoder_{seed}.pt'))
if stop_flag:
break
target_regressor.load_state_dict(
torch.load(os.path.join(kwargs['model_save_folder'], f'target_regressor_{seed}.pt')))
evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=val_dataloader,
device=kwargs['device'],
history=None,
seed=seed,
cv_flag=True,
output_folder=kwargs['model_save_folder'])
if test_dataloader is not None:
evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=None,
seed=seed,
output_folder=kwargs['model_save_folder'])
return target_regressor, (target_regression_train_history, target_regression_eval_train_history,
target_regression_eval_val_history, target_regression_eval_test_history)
def train_adda(s_dataloaders, t_dataloaders, val_dataloader, test_dataloader,
metric_name, seed, **kwargs):
"""
:param s_dataloaders:
:param t_dataloaders:
:param kwargs:
:return:
"""
s_train_dataloader = s_dataloaders
t_train_dataloader = t_dataloaders
autoencoder = AE(input_dim=kwargs['input_dim'],
latent_dim=kwargs['latent_dim'],
hidden_dims=kwargs['encoder_hidden_dims'],
dop=kwargs['dop']).to(kwargs['device'])
encoder = autoencoder.encoder
target_decoder = MoMLP(input_dim=kwargs['latent_dim'],
output_dim=kwargs['output_dim'],
hidden_dims=kwargs['regressor_hidden_dims'],
out_fn=torch.nn.Sigmoid).to(kwargs['device'])
target_regressor = EncoderDecoder(
encoder=encoder, decoder=target_decoder).to(kwargs['device'])
confounding_classifier = MLP(input_dim=kwargs['latent_dim'],
output_dim=1,
hidden_dims=kwargs['classifier_hidden_dims'],
dop=kwargs['dop']).to(kwargs['device'])
critic_train_history = defaultdict(list)
gen_train_history = defaultdict(list)
s_target_regression_eval_train_history = defaultdict(list)
t_target_regression_eval_train_history = defaultdict(list)
target_regression_eval_val_history = defaultdict(list)
target_regression_eval_test_history = defaultdict(list)
model_optimizer = torch.optim.AdamW(target_regressor.parameters(),
lr=kwargs['lr'])
classifier_optimizer = torch.optim.RMSprop(
confounding_classifier.parameters(), lr=kwargs['lr'])
for epoch in range(int(kwargs['train_num_epochs'])):
if epoch % 50 == 0:
print(f'ADDA training epoch {epoch}')
for step, s_batch in enumerate(s_train_dataloader):
t_batch = next(iter(t_train_dataloader))
critic_train_history = critic_train_step(
critic=confounding_classifier,
model=target_regressor,
s_batch=s_batch,
t_batch=t_batch,
device=kwargs['device'],
optimizer=classifier_optimizer,
history=critic_train_history,
# clip=0.1,
gp=10.0)
if (step + 1) % 5 == 0:
gen_train_history = gan_gen_train_step(
critic=confounding_classifier,
model=target_regressor,
s_batch=s_batch,
t_batch=t_batch,
device=kwargs['device'],
optimizer=model_optimizer,
alpha=1.0,
history=gen_train_history)
s_target_regression_eval_train_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=s_train_dataloader,
device=kwargs['device'],
history=s_target_regression_eval_train_history)
t_target_regression_eval_train_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=t_train_dataloader,
device=kwargs['device'],
history=t_target_regression_eval_train_history)
target_regression_eval_val_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=val_dataloader,
device=kwargs['device'],
history=target_regression_eval_val_history)
target_regression_eval_test_history = evaluate_target_regression_epoch(
regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=target_regression_eval_test_history)
save_flag, stop_flag = model_save_check(
history=target_regression_eval_val_history,
metric_name=metric_name,
tolerance_count=50)
if save_flag:
torch.save(
target_regressor.state_dict(),
os.path.join(kwargs['model_save_folder'],
f'adda_regressor_{seed}.pt'))
if stop_flag:
break
target_regressor.load_state_dict(
torch.load(
os.path.join(kwargs['model_save_folder'],
f'adda_regressor_{seed}.pt')))
# evaluate_target_regression_epoch(regressor=target_regressor,
# dataloader=val_dataloader,
# device=kwargs['device'],
# history=None,
# seed=seed,
# output_folder=kwargs['model_save_folder'])
evaluate_target_regression_epoch(regressor=target_regressor,
dataloader=test_dataloader,
device=kwargs['device'],
history=None,
seed=seed,
output_folder=kwargs['model_save_folder'])
return target_regressor, (critic_train_history, gen_train_history,
s_target_regression_eval_train_history,
t_target_regression_eval_train_history,
target_regression_eval_val_history,
target_regression_eval_test_history)
