def main(args, exp_config, train_set, val_set, test_set):
if args['featurizer_type'] != 'pre_train':
exp_config['in_node_feats'] = args['node_featurizer'].feat_size()
if args['edge_featurizer'] is not None:
exp_config['in_edge_feats'] = args['edge_featurizer'].feat_size()
exp_config.update({
'n_tasks': args['n_tasks'],
'model': args['model']
})
train_loader = DataLoader(dataset=train_set, batch_size=exp_config['batch_size'], shuffle=True,
collate_fn=collate_molgraphs, num_workers=args['num_workers'])
val_loader = DataLoader(dataset=val_set, batch_size=exp_config['batch_size'],
collate_fn=collate_molgraphs, num_workers=args['num_workers'])
test_loader = DataLoader(dataset=test_set, batch_size=exp_config['batch_size'],
collate_fn=collate_molgraphs, num_workers=args['num_workers'])
if args['pretrain']:
args['num_epochs'] = 0
if args['featurizer_type'] == 'pre_train':
model = load_pretrained('{}_{}'.format(
args['model'], args['dataset'])).to(args['device'])
else:
model = load_pretrained('{}_{}_{}'.format(
args['model'], args['featurizer_type'], args['dataset'])).to(args['device'])
else:
model = load_model(exp_config).to(args['device'])
loss_criterion = nn.SmoothL1Loss(reduction='none')
optimizer = Adam(model.parameters(), lr=exp_config['lr'],
weight_decay=exp_config['weight_decay'])
stopper = EarlyStopping(patience=exp_config['patience'],
filename=args['result_path'] + '/model.pth',
metric=args['metric'])
for epoch in range(args['num_epochs']):
# Train
run_a_train_epoch(args, epoch, model, train_loader, loss_criterion, optimizer)
# Validation and early stop
val_score = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
print('epoch {:d}/{:d}, validation {} {:.4f}, best validation {} {:.4f}'.format(
epoch + 1, args['num_epochs'], args['metric'],
val_score, args['metric'], stopper.best_score))
if early_stop:
break
if not args['pretrain']:
stopper.load_checkpoint(model)
val_score = run_an_eval_epoch(args, model, val_loader)
test_score = run_an_eval_epoch(args, model, test_loader)
print('val {} {:.4f}'.format(args['metric'], val_score))
print('test {} {:.4f}'.format(args['metric'], test_score))
with open(args['result_path'] + '/eval.txt', 'w') as f:
if not args['pretrain']:
f.write('Best val {}: {}\n'.format(args['metric'], stopper.best_score))
f.write('Val {}: {}\n'.format(args['metric'], val_score))
f.write('Test {}: {}\n'.format(args['metric'], test_score))
def main(args, exp_config, train_set, val_set, test_set):
# Record settings
exp_config.update({
'model': args['model'],
'in_feats': args['node_featurizer'].feat_size(),
'n_tasks': args['n_tasks']
})
# Set up directory for saving results
args = init_trial_path(args)
train_loader = DataLoader(dataset=train_set,
batch_size=exp_config['batch_size'],
shuffle=True,
collate_fn=collate_molgraphs)
val_loader = DataLoader(dataset=val_set,
batch_size=exp_config['batch_size'],
collate_fn=collate_molgraphs)
test_loader = DataLoader(dataset=test_set,
batch_size=exp_config['batch_size'],
collate_fn=collate_molgraphs)
model = load_model(exp_config).to(args['device'])
loss_criterion = nn.SmoothL1Loss(reduction='none')
optimizer = Adam(model.parameters(),
lr=exp_config['lr'],
weight_decay=exp_config['weight_decay'])
stopper = EarlyStopping(patience=exp_config['patience'],
filename=args['trial_path'] + '/model.pth')
for epoch in range(args['num_epochs']):
# Train
run_a_train_epoch(args, epoch, model, train_loader, loss_criterion,
optimizer)
# Validation and early stop
val_score = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
print(
'epoch {:d}/{:d}, validation {} {:.4f}, best validation {} {:.4f}'.
format(epoch + 1, args['num_epochs'], args['metric'], val_score,
args['metric'], stopper.best_score))
if early_stop:
break
stopper.load_checkpoint(model)
test_score = run_an_eval_epoch(args, model, test_loader)
print('test {} {:.4f}'.format(args['metric'], test_score))
with open(args['trial_path'] + '/eval.txt', 'w') as f:
f.write('Best val {}: {}\n'.format(args['metric'], stopper.best_score))
f.write('Test {}: {}\n'.format(args['metric'], test_score))
with open(args['trial_path'] + '/configure.json', 'w') as f:
json.dump(exp_config, f, indent=2)
return args['trial_path'], stopper.best_score
def main(args):
args['device'] = torch.device(
"cuda: 0") if torch.cuda.is_available() else torch.device("cpu")
set_random_seed(args['random_seed'])
dataset = PubChemBioAssayAromaticity(
smiles_to_graph=args['smiles_to_graph'],
node_featurizer=args.get('node_featurizer', None),
edge_featurizer=args.get('edge_featurizer', None))
train_set, val_set, test_set = RandomSplitter.train_val_test_split(
dataset,
frac_train=args['frac_train'],
frac_val=args['frac_val'],
frac_test=args['frac_test'],
random_state=args['random_seed'])
train_loader = DataLoader(dataset=train_set,
batch_size=args['batch_size'],
shuffle=True,
collate_fn=collate_molgraphs)
val_loader = DataLoader(dataset=val_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
test_loader = DataLoader(dataset=test_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
if args['pre_trained']:
args['num_epochs'] = 0
model = load_pretrained(args['exp'])
else:
model = load_model(args)
loss_fn = nn.MSELoss(reduction='none')
optimizer = torch.optim.Adam(model.parameters(),
lr=args['lr'],
weight_decay=args['weight_decay'])
stopper = EarlyStopping(mode=args['mode'], patience=args['patience'])
model.to(args['device'])
for epoch in range(args['num_epochs']):
# Train
run_a_train_epoch(args, epoch, model, train_loader, loss_fn, optimizer)
# Validation and early stop
val_score = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
print(
'epoch {:d}/{:d}, validation {} {:.4f}, best validation {} {:.4f}'.
format(epoch + 1, args['num_epochs'], args['metric_name'],
val_score, args['metric_name'], stopper.best_score))
if early_stop:
break
if not args['pre_trained']:
stopper.load_checkpoint(model)
test_score = run_an_eval_epoch(args, model, test_loader)
print('test {} {:.4f}'.format(args['metric_name'], test_score))
def main(args, node_featurizer, edge_featurizer, train_set, val_set, test_set):
# Record starting time
t0 = time.time()
train_mean, train_std = get_label_mean_and_std(train_set)
train_mean, train_std = train_mean.to(args['device']), train_std.to(
args['device'])
args['train_mean'], args['train_std'] = train_mean, train_std
train_loader = DataLoader(dataset=train_set,
batch_size=args['batch_size'],
shuffle=True,
collate_fn=collate)
val_loader = DataLoader(dataset=val_set,
batch_size=args['batch_size'],
shuffle=False,
collate_fn=collate)
test_loader = DataLoader(dataset=test_set,
batch_size=args['batch_size'],
shuffle=False,
collate_fn=collate)
model = load_model(args, node_featurizer,
edge_featurizer).to(args['device'])
criterion = nn.SmoothL1Loss(reduction='none')
optimizer = Adam(model.parameters(),
lr=args['lr'],
weight_decay=args['weight_decay'])
stopper = EarlyStopping(patience=args['patience'],
filename=args['result_path'] + '/model.pth')
for epoch in range(args['num_epochs']):
loss, train_r2, train_mae = run_a_train_epoch(args, model,
train_loader, criterion,
optimizer)
print('Epoch {:d}/{:d} | training | averaged loss {:.4f} | '
'averaged r2 {:.4f} | averaged mae {:.4f}'.format(
epoch + 1, args['num_epochs'], float(np.mean(loss)),
float(np.mean(train_r2)), float(np.mean(train_mae))))
# Validation and early stop
val_r2, val_mae = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(float(np.mean(val_r2)), model)
print(
'Epoch {:d}/{:d} | validation | current r2 {:.4f} | best r2 {:.4f} | mae {:.4f}'
.format(epoch + 1, args['num_epochs'], float(np.mean(val_r2)),
stopper.best_score, float(np.mean(val_mae))))
if early_stop:
break
print('It took {:.4f}s to complete the task'.format(time.time() - t0))
stopper.load_checkpoint(model)
log_model_evaluation(args, model, train_loader, val_loader, test_loader)
def main(args):
args['device'] = torch.device(
"cuda") if torch.cuda.is_available() else torch.device("cpu")
set_random_seed(args['random_seed'])
# Interchangeable with other datasets
dataset, train_set, val_set, test_set = load_dataset_for_classification(
args)
train_loader = DataLoader(train_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs,
shuffle=True)
val_loader = DataLoader(val_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
test_loader = DataLoader(test_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
if args['pre_trained']:
args['num_epochs'] = 0
model = load_pretrained(args['exp'])
else:
args['n_tasks'] = dataset.n_tasks
model = load_model(args)
loss_criterion = BCEWithLogitsLoss(pos_weight=dataset.task_pos_weights(
torch.tensor(train_set.indices)).to(args['device']),
reduction='none')
optimizer = Adam(model.parameters(), lr=args['lr'])
stopper = EarlyStopping(patience=args['patience'])
model.to(args['device'])
for epoch in range(args['num_epochs']):
# Train
run_a_train_epoch(args, epoch, model, train_loader, loss_criterion,
optimizer)
# Validation and early stop
val_score = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
print(
'epoch {:d}/{:d}, validation {} {:.4f}, best validation {} {:.4f}'.
format(epoch + 1, args['num_epochs'], args['metric_name'],
val_score, args['metric_name'], stopper.best_score))
if early_stop:
break
if not args['pre_trained']:
stopper.load_checkpoint(model)
test_score = run_an_eval_epoch(args, model, test_loader)
print('test {} {:.4f}'.format(args['metric_name'], test_score))
def main(args):
args['device'] = torch.device(
"cuda") if torch.cuda.is_available() else torch.device("cpu")
set_random_seed(args['random_seed'])
train_set, val_set, test_set = load_dataset_for_regression(args)
train_loader = DataLoader(dataset=train_set,
batch_size=args['batch_size'],
shuffle=True,
collate_fn=collate_molgraphs)
val_loader = DataLoader(dataset=val_set,
batch_size=args['batch_size'],
shuffle=True,
collate_fn=collate_molgraphs)
if test_set is not None:
test_loader = DataLoader(dataset=test_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
if args['pre_trained']:
args['num_epochs'] = 0
model = load_pretrained(args['exp'])
else:
model = load_model(args)
loss_fn = nn.MSELoss(reduction='none')
optimizer = torch.optim.Adam(model.parameters(),
lr=args['lr'],
weight_decay=args['weight_decay'])
stopper = EarlyStopping(mode='lower', patience=args['patience'])
model.to(args['device'])
for epoch in range(args['num_epochs']):
# Train
run_a_train_epoch(args, epoch, model, train_loader, loss_fn, optimizer)
# Validation and early stop
val_score = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
print(
'epoch {:d}/{:d}, validation {} {:.4f}, best validation {} {:.4f}'.
format(epoch + 1, args['num_epochs'], args['metric_name'],
val_score, args['metric_name'], stopper.best_score))
if early_stop:
break
if test_set is not None:
if not args['pre_trained']:
stopper.load_checkpoint(model)
test_score = run_an_eval_epoch(args, model, test_loader)
print('test {} {:.4f}'.format(args['metric_name'], test_score))
def main(args, train_set, val_set, test_set):
# Set up directory for saving results
args = init_trial_path(args)
train_loader = DataLoader(dataset=train_set,
batch_size=args['batch_size'],
shuffle=True,
collate_fn=collate_molgraphs)
val_loader = DataLoader(dataset=val_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
test_loader = DataLoader(dataset=test_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
model = load_model(args).to(args['device'])
loss_criterion = nn.BCEWithLogitsLoss(reduction='none')
optimizer = Adam(model.parameters(),
lr=args['lr'],
weight_decay=args['weight_decay'])
stopper = EarlyStopping(patience=args['patience'],
filename=args['trial_path'] + '/model.pth')
for epoch in range(args['num_epochs']):
# Train
run_a_train_epoch(args, epoch, model, train_loader, loss_criterion,
optimizer)
# Validation and early stop
val_score = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
print(
'epoch {:d}/{:d}, validation {} {:.4f}, best validation {} {:.4f}'.
format(epoch + 1, args['num_epochs'], args['metric'], val_score,
args['metric'], stopper.best_score))
if early_stop:
break
test_score = run_an_eval_epoch(args, model, test_loader)
print('test {} {:.4f}'.format(args['metric'], test_score))
with open(args['trial_path'] + '/eval.txt', 'w') as f:
f.write('Best val {}: {}\n'.format(args['metric'], stopper.best_score))
f.write('Test {}: {}\n'.format(args['metric'], test_score))
return args, stopper.best_score
def main(args):
args['device'] = torch.device(
"cuda") if torch.cuda.is_available() else torch.device("cpu")
set_random_seed(args['random_seed'])
train_g, train_y, val_g, val_y = load_data(0)
train_set = list(zip(train_g, train_y))
val_set = list(zip(val_g, val_y))
train_loader = DataLoader(dataset=train_set,
batch_size=args['batch_size'],
shuffle=True,
collate_fn=collate_molgraphs)
val_loader = DataLoader(dataset=val_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
model = load_model(args)
loss_fn = nn.MSELoss(reduction='none')
optimizer = torch.optim.Adam(model.parameters(),
lr=args['lr'],
weight_decay=args['weight_decay'])
stopper = EarlyStopping(mode=args['mode'], patience=args['patience'])
model.to(args['device'])
for epoch in range(args['num_epochs']):
# Train
run_a_train_epoch(args, epoch, model, train_loader, loss_fn, optimizer)
# Validation and early stop
val_score, prc_auc = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
validation_score.append(val_score)
print(
'epoch {:d}/{:d}, validation {} {:.4f}, prc_auc_score {:.4f}, best validation {} {:.4f}'
.format(epoch + 1, args['num_epochs'], args['metric_name'],
val_score, prc_auc, args['metric_name'],
stopper.best_score))
if early_stop:
break
def train(self, model, train_loader, val_loader, epochs, lr, patience,
metric):
args = dict(
patience=patience,
num_epochs=epochs,
lr=lr,
device=self.device,
metric_name=metric,
)
self.args = args
stopper = EarlyStopping(patience=args["patience"])
loss_fn = nn.MSELoss(reduction="none")
optimizer = optim.Adam(model.parameters(), lr=args["lr"])
for epoch in range(args["num_epochs"]):
self.run_a_train_epoch(args, epoch, model, train_loader, loss_fn,
optimizer)
# Validation and early stop
if val_loader is not None:
val_score = self.run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
print(
"epoch {:d}/{:d}, validation {} {:.4f}, best validation {} {:.4f}"
.format(
epoch + 1,
args["num_epochs"],
args["metric_name"],
val_score,
args["metric_name"],
stopper.best_score,
))
if early_stop:
self.model = model
self.args = args
break
self.model = model
self.args = args
train_set = list(zip(train_g, train_y))
val_set = list(zip(val_g, val_y))
train_loader = DataLoader(dataset=train_set,
batch_size=args['batch_size'],
shuffle=True,
collate_fn=collate_molgraphs)
val_loader = DataLoader(dataset=val_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
model = load_model(args)
loss_fn = nn.MSELoss(reduction='none')
optimizer = torch.optim.Adam(model.parameters(),
lr=args['lr'],
weight_decay=args['weight_decay'])
stopper = EarlyStopping(mode=args['mode'], patience=args['patience'])
model.to(args['device'])
for epoch in range(args['num_epochs']):
# Train
run_a_train_epoch(args, epoch, model, train_loader, loss_fn, optimizer)
# Validation and early stop
val_score, prc_auc = run_an_eval_epoch(args, model, val_loader)
early_stop = stopper.step(val_score, model)
validation_score.append(val_score)
print(
'epoch {:d}/{:d}, validation {} {:.4f}, prc_auc_score {:.4f}, best validation {} {:.4f}'
.format(epoch + 1, args['num_epochs'], args['metric_name'], val_score,
prc_auc, args['metric_name'], stopper.best_score))
def main(args):
torch.cuda.set_device(args['gpu'])
set_random_seed(args['random_seed'])
dataset, train_set, val_set, test_set = load_dataset_for_classification(
args) # 6264, 783, 784
train_loader = DataLoader(train_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs,
shuffle=True)
val_loader = DataLoader(val_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
test_loader = DataLoader(test_set,
batch_size=args['batch_size'],
collate_fn=collate_molgraphs)
if args['pre_trained']:
args['num_epochs'] = 0
model = load_pretrained(args['exp'])
else:
args['n_tasks'] = dataset.n_tasks
if args['method'] == 'twp':
model = load_mymodel(args)
print(model)
else:
model = load_model(args)
for name, parameters in model.named_parameters():
print(name, ':', parameters.size())
method = args['method']
life_model = importlib.import_module(f'LifeModel.{method}_model')
life_model_ins = life_model.NET(model, args)
data_loader = DataLoader(train_set,
batch_size=len(train_set),
collate_fn=collate_molgraphs,
shuffle=True)
life_model_ins.data_loader = data_loader
loss_criterion = BCEWithLogitsLoss(
pos_weight=dataset.task_pos_weights.cuda(), reduction='none')
model.cuda()
score_mean = []
score_matrix = np.zeros([args['n_tasks'], args['n_tasks']])
prev_model = None
for task_i in range(12):
print('\n********' + str(task_i))
stopper = EarlyStopping(patience=args['patience'])
for epoch in range(args['num_epochs']):
# Train
if args['method'] == 'lwf':
life_model_ins.observe(train_loader, loss_criterion, task_i,
args, prev_model)
else:
life_model_ins.observe(train_loader, loss_criterion, task_i,
args)
# Validation and early stop
val_score = run_an_eval_epoch(args, model, val_loader, task_i)
early_stop = stopper.step(val_score, model)
if early_stop:
print(epoch)
break
if not args['pre_trained']:
stopper.load_checkpoint(model)
score_matrix[task_i] = run_eval_epoch(args, model, test_loader)
prev_model = copy.deepcopy(life_model_ins).cuda()
print('AP: ', round(np.mean(score_matrix[-1, :]), 4))
backward = []
for t in range(args['n_tasks'] - 1):
b = score_matrix[args['n_tasks'] - 1][t] - score_matrix[t][t]
backward.append(round(b, 4))
mean_backward = round(np.mean(backward), 4)
print('AF: ', mean_backward)
def test_early_stopping_low():
model1 = nn.Linear(2, 3)
stopper = EarlyStopping(mode='lower', patience=1, filename='test.pkl')
# Save model in the first step
stopper.step(1., model1)
model1.weight.data = model1.weight.data + 1
model2 = nn.Linear(2, 3)
stopper.load_checkpoint(model2)
assert not torch.allclose(model1.weight, model2.weight)
# Save model checkpoint with performance improvement
model1.weight.data = model1.weight.data + 1
stopper.step(0.5, model1)
stopper.load_checkpoint(model2)
assert torch.allclose(model1.weight, model2.weight)
# Stop when no improvement observed
model1.weight.data = model1.weight.data + 1
assert stopper.step(2, model1)
stopper.load_checkpoint(model2)
assert not torch.allclose(model1.weight, model2.weight)
remove_file('test.pkl')
def main(args):
# fix random seeds
torch.manual_seed(args.seed)
np.random.seed(args.seed)
random.seed(args.seed)
# load CSV dataset
smlstr = []
logCMC = []
with open("../data/dataset.csv") as csvDataFile:
csvReader = csv.reader(csvDataFile)
for row in csvReader:
smlstr.append(row[0])
logCMC.append(row[1])
smlstr = np.asarray(smlstr)
logCMC = np.asarray(logCMC, dtype="float")
dataset_size = len(smlstr)
all_ind = np.arange(dataset_size)
# split into training and testing
if args.randSplit:
train_full_ind, test_ind, \
smlstr_train, smlstr_test, \
logCMC_train, logCMC_test = train_test_split(all_ind, smlstr, logCMC,
test_size=args.test_size,
random_state=args.seed)
else:
if args.dataset in ["nonionic","all"]:
if args.dataset == "nonionic":
test_ind = np.array([8,14,26,31,43,54,57,68,72,80,99,110]) # for nonionic surfactants only
elif args.dataset == "all":
test_ind = np.array([8,14,26,31,43,54,57,68,72,80,99,110,125,132,140,150,164,171,178,185,192,197])
train_full_ind = np.asarray([x for x in all_ind if x not in test_ind])
np.random.shuffle(test_ind)
np.random.shuffle(train_full_ind)
smlstr_train = smlstr[train_full_ind]
smlstr_test = smlstr[test_ind]
logCMC_train = logCMC[train_full_ind]
logCMC_test = logCMC[test_ind]
else:
print("Using Random Splits")
args.randSplit = True
train_full_ind, test_ind, \
smlstr_train, smlstr_test, \
logCMC_train, logCMC_test = train_test_split(all_ind, smlstr, logCMC,
test_size=args.test_size,
random_state=args.seed)
# save train/test data and index corresponding to the original dataset
pickle.dump(smlstr_train,open("../gnn_logs/smlstr_train.p","wb"))
pickle.dump(smlstr_test,open("../gnn_logs/smlstr_test.p","wb"))
pickle.dump(logCMC_train,open("../gnn_logs/logCMC_train.p","wb"))
pickle.dump(logCMC_test,open("../gnn_logs/logCMC_test.p","wb"))
pickle.dump(train_full_ind,open("../gnn_logs/original_ind_train_full.p","wb"))
pickle.dump(test_ind,open("../gnn_logs/original_ind_test.p","wb"))
rows = zip(train_full_ind,smlstr_train,logCMC_train)
with open("../gnn_logs/dataset_train.csv",'w',newline='') as f:
writer = csv.writer(f,delimiter=',')
for row in rows:
writer.writerow(row)
rows = zip(test_ind,smlstr_test,logCMC_test)
with open("../gnn_logs/dataset_test.csv",'w',newline='') as f:
writer = csv.writer(f,delimiter=',')
for row in rows:
writer.writerow(row)
train_size = len(smlstr_train)
indices = list(range(train_size))
if args.skip_cv == False:
# K-fold CV setup
kf = KFold(n_splits=args.cv, random_state=args.seed, shuffle=True)
cv_index = 0
index_list_train = []
index_list_valid = []
for train_indices, valid_indices in kf.split(indices):
index_list_train.append(train_indices)
index_list_valid.append(valid_indices)
model = args.gnn_model(args.dim_input, args.unit_per_layer,1,False)
model_arch = 'GCNReg'
loss_fn = nn.MSELoss()
# check gpu availability
if args.gpu >= 0:
model = model.cuda(args.gpu)
loss_fn = loss_fn.cuda(args.gpu)
cudnn.enabled = True
cudnn.benchmark = True
cudnn.deterministic = False
optimizer = torch.optim.Adam(model.parameters(), args.lr)
# training
if args.single_feat:
from dgllife.utils import BaseAtomFeaturizer,atomic_number
train_full_dataset = graph_dataset(smlstr_train,logCMC_train,node_enc=BaseAtomFeaturizer({'h': atomic_number}))
test_dataset = graph_dataset(smlstr_test,logCMC_test,node_enc=BaseAtomFeaturizer({'h': atomic_number}))
args.dim_input = 1
else:
train_full_dataset = graph_dataset(smlstr_train,logCMC_train)
test_dataset = graph_dataset(smlstr_test,logCMC_test)
train_sampler = SubsetRandomSampler(train_indices)
valid_sampler = SubsetRandomSampler(valid_indices)
train_loader = torch.utils.data.DataLoader(train_full_dataset, batch_size=args.batch_size,
sampler=train_sampler,
collate_fn=collate,
shuffle=False)
val_loader = torch.utils.data.DataLoader(train_full_dataset, batch_size=args.batch_size,
sampler=valid_sampler,
collate_fn=collate,
shuffle=False)
train_dataset = graph_dataset(smlstr_train[train_indices],logCMC_train[train_indices])
valid_dataset = graph_dataset(smlstr_train[valid_indices],logCMC_train[valid_indices])
fname = r"ep{}bs{}lr{}kf{}hu{}cvid{}".format(args.epochs, args.batch_size,
args.lr,
args.cv,
args.unit_per_layer, cv_index)
best_rmse = 1000
if args.train:
print("Training the model ...")
stopper = EarlyStopping(mode='lower', patience=args.patience, filename=r'../gnn_logs/{}es.pth.tar'.format(fname)) # early stop model
for epoch in range(args.start_epoch, args.epochs):
train_loss = train(train_loader, model, loss_fn, optimizer, epoch, args, fname)
rmse = validate(val_loader, model, epoch, args, fname)
is_best = rmse < best_rmse
best_rmse = min(rmse, best_rmse)
if is_best:
save_checkpoint({
'epoch': epoch + 1,
'model_arch': model_arch,
'state_dict': model.state_dict(),
'best_rmse': best_rmse,
'optimizer': optimizer.state_dict(),
}, fname)
if args.early_stop:
early_stop = stopper.step(train_loss, model)
if early_stop:
print("**********Early Stopping!")
break
# test
print("Testing the model ...")
checkpoint = torch.load(r"../gnn_logs/{}.pth.tar".format(fname))
args.start_epoch = 0
best_rmse = checkpoint['best_rmse']
model = args.gnn_model(args.dim_input, args.unit_per_layer,1,True)
if args.gpu >= 0:
model = model.cuda(args.gpu)
model.load_state_dict(checkpoint['state_dict'])
# if args.gpu < 0:
# model = model.cpu()
# else:
# model = model.cuda(args.gpu)
print("=> loaded checkpoint '{}' (epoch {}, rmse {})"
.format(fname, checkpoint['epoch'], best_rmse))
cudnn.deterministic = True
stage = 'testtest'
predict(test_dataset, model, -1, args, fname, stage)
stage = 'testtrain'
predict(train_dataset, model, -1, args, fname, stage)
stage = 'testval'
predict(valid_dataset, model, -1, args, fname, stage)
cv_index += 1
pickle.dump(index_list_train,open("../gnn_logs/ind_train_list.p","wb"))
pickle.dump(index_list_valid,open("../gnn_logs/ind_val_list.p","wb"))
cv_index += 1
else:
model = args.gnn_model(args.dim_input, args.unit_per_layer,1,False)
model_arch = 'GCNReg'
loss_fn = nn.MSELoss()
# check gpu availability
if args.gpu >= 0:
model = model.cuda(args.gpu)
loss_fn = loss_fn.cuda(args.gpu)
cudnn.enabled = True
cudnn.benchmark = True
cudnn.deterministic = False
optimizer = torch.optim.Adam(model.parameters(), args.lr)
# training
if args.single_feat:
from dgllife.utils import BaseAtomFeaturizer,atomic_number
train_full_dataset = graph_dataset(smlstr_train,logCMC_train,node_enc=BaseAtomFeaturizer({'h': atomic_number}))
test_dataset = graph_dataset(smlstr_test,logCMC_test,node_enc=BaseAtomFeaturizer({'h': atomic_number}))
args.dim_input = 1
else:
train_full_dataset = graph_dataset(smlstr_train,logCMC_train)
test_dataset = graph_dataset(smlstr_test,logCMC_test)
train_loader = torch.utils.data.DataLoader(train_full_dataset, batch_size=args.batch_size,
collate_fn=collate,
shuffle=False)
test_loader = torch.utils.data.DataLoader(test_dataset, batch_size=args.batch_size,
collate_fn=collate,
shuffle=False)
train_dataset = graph_dataset(smlstr_train,logCMC_train)
fname = r"ep{}bs{}lr{}hu{}".format(args.epochs, args.batch_size,
args.lr,
args.unit_per_layer)
best_rmse = 1000
if args.train:
print("Training the model ...")
stopper = EarlyStopping(mode='lower', patience=args.patience, filename=r'../gnn_logs/{}es.pth.tar'.format(fname)) # early stop model
for epoch in range(args.start_epoch, args.epochs):
train_loss = train(train_loader, model, loss_fn, optimizer, epoch, args, fname)
rmse = validate(test_loader, model, epoch, args, fname)
is_best = rmse < best_rmse
best_rmse = min(rmse, best_rmse)
if is_best:
save_checkpoint({
'epoch': epoch + 1,
'model_arch': model_arch,
'state_dict': model.state_dict(),
'best_rmse': best_rmse,
'optimizer': optimizer.state_dict(),
}, fname)
if args.early_stop:
early_stop = stopper.step(train_loss, model)
if early_stop:
print("**********Early Stopping!")
break
# test
print("Testing the model ...")
checkpoint = torch.load(r"../gnn_logs/{}.pth.tar".format(fname))
args.start_epoch = 0
best_rmse = checkpoint['best_rmse']
model = args.gnn_model(args.dim_input, args.unit_per_layer,1,True)
if args.gpu >= 0:
model = model.cuda(args.gpu)
model.load_state_dict(checkpoint['state_dict'])
# if args.gpu < 0:
# model = model.cpu()
# else:
# model = model.cuda(args.gpu)
print("=> loaded checkpoint '{}' (epoch {}, rmse {})"
.format(fname, checkpoint['epoch'], best_rmse))
cudnn.deterministic = True
stage = 'testtest'
predict(test_dataset, model, -1, args, fname, stage)
stage = 'testtrain'
predict(train_dataset, model, -1, args, fname, stage)
if args.early_stop:
checkpoint = torch.load(r"../gnn_logs/{}es.pth.tar".format(fname))
args.start_epoch = 0
model = args.gnn_model(args.dim_input, args.unit_per_layer,1,True)
if args.gpu >= 0:
model = model.cuda(args.gpu)
model.load_state_dict(checkpoint['model_state_dict'])
train_dataset = graph_dataset(smlstr_train,logCMC_train)
test_dataset = graph_dataset(smlstr_test,logCMC_test)
cudnn.deterministic = True
stage = 'testtest'
predict(test_dataset, model, -1, args, r"{}es".format(fname), stage)
stage = 'testtrain'
predict(train_dataset, model, -1, args, r"{}es".format(fname), stage)
return
def test_early_stopping_high_metric():
for metric in ['r2', 'roc_auc_score']:
model1 = nn.Linear(2, 3)
stopper = EarlyStopping(mode=None,
patience=1,
filename='test.pkl',
metric=metric)
# Save model in the first step
stopper.step(1., model1)
model1.weight.data = model1.weight.data + 1
model2 = nn.Linear(2, 3)
stopper.load_checkpoint(model2)
assert not torch.allclose(model1.weight, model2.weight)
# Save model checkpoint with performance improvement
model1.weight.data = model1.weight.data + 1
stopper.step(2., model1)
stopper.load_checkpoint(model2)
assert torch.allclose(model1.weight, model2.weight)
# Stop when no improvement observed
model1.weight.data = model1.weight.data + 1
assert stopper.step(0.5, model1)
stopper.load_checkpoint(model2)
assert not torch.allclose(model1.weight, model2.weight)
remove_file('test.pkl')
