def test(self, model_path=''):
print('[app][test] Test model')
try:
print('*** [app][test] Load pre-trained model ' + model_path +
' ***')
self.model = load_checkpoint(self.model, model_path, self.is_cuda)
except ValueError as e:
print('[app][test] Error while loading the model.', e)
self.save_traintest()
# print('\n[app][test] Test all')
# # acc = np.mean(self.accuracies)
# # acc = self.accuracies
# graphs = self.data[GRAPH]
# labels = self.labels
# self.run_test(graphs, labels)
graphs = load_pickle(os.path.join(self.odir, 'train'))
labels = load_pickle(os.path.join(self.odir, 'train_labels'))
print('\n[app][test] Test on train graphs ({})'.format(len(labels)),
os.path.join(self.odir, 'train'))
self.run_test_fold(graphs, labels, fold=300)
graphs = load_pickle(os.path.join(self.odir, 'test'))
labels = load_pickle(os.path.join(self.odir, 'test_labels'))
print('\n[app][test] Test on test graphs ({})'.format(len(labels)),
os.path.join(self.odir, 'test'))
self.run_test_fold(graphs, labels, fold=150)
def if_resume(self):
if self.cfg.logger.resume:
# load checkpoint
print(f"{datetime.now():%Y-%m-%d %H:%M:%S} - LOADING checkpoint!!!")
save_dir = self.cfg.directory.load
checkpoint = load_checkpoint(save_dir, self.device)
self.model.load_state_dict(checkpoint["model"])
self.optimizer.load_state_dict(checkpoint["optimizer"])
self.lr_scheduler.load_state_dict(checkpoint["lr_scheduler"])
self.epoch = checkpoint["epoch"] + 1
self.e_loss = checkpoint["e_loss"]
self.iteration = checkpoint["iteration"] + 1
self.best = checkpoint["best"]
print(
f"{datetime.now():%Y-%m-%d %H:%M:%S} " +
f"LOADING checkpoint was successful, start from epoch {self.epoch}" +
f" and loss {self.best}"
)
else:
self.epoch = 1
self.iteration = 0
self.best = np.inf
self.e_loss = []
self.logger.set_epoch(self.epoch)
def __init__(self, cfg_dir: str, data_loader: DataLoader, model,
labels_definition):
self.cfg = get_conf(cfg_dir)
self._labels_definition = labels_definition
#TODO
self.logger = self.init_logger(self.cfg.logger)
#self.dataset = CustomDataset(**self.cfg.dataset)
self.data = data_loader
#self.val_dataset = CustomDatasetVal(**self.cfg.val_dataset)
#self.val_data = DataLoader(self.val_dataset, **self.cfg.dataloader)
# self.logger.log_parameters({"tr_len": len(self.dataset),
# "val_len": len(self.val_dataset)})
self.model = model
#self.model._resnet.conv1.apply(init_weights_normal)
self.device = self.cfg.train_params.device
self.model = self.model.to(device=self.device)
if self.cfg.train_params.optimizer.lower() == "adam":
self.optimizer = optim.Adam(self.model.parameters(),
**self.cfg.adam)
elif self.cfg.train_params.optimizer.lower() == "rmsprop":
self.optimizer = optim.RMSprop(self.model.parameters(),
**self.cfg.rmsprop)
else:
raise ValueError(
f"Unknown optimizer {self.cfg.train_params.optimizer}")
self.lr_scheduler = optim.lr_scheduler.CosineAnnealingLR(
self.optimizer, T_max=100)
self.criterion = nn.BCELoss()
if self.cfg.logger.resume:
# load checkpoint
print("Loading checkpoint")
save_dir = self.cfg.directory.load
checkpoint = load_checkpoint(save_dir, self.device)
self.model.load_state_dict(checkpoint["model"])
self.optimizer.load_state_dict(checkpoint["optimizer"])
self.lr_scheduler.load_state_dict(checkpoint["lr_scheduler"])
self.epoch = checkpoint["epoch"]
self.e_loss = checkpoint["e_loss"]
self.best = checkpoint["best"]
print(
f"{datetime.now():%Y-%m-%d %H:%M:%S} "
f"Loading checkpoint was successful, start from epoch {self.epoch}"
f" and loss {self.best}")
else:
self.epoch = 1
self.best = np.inf
self.e_loss = []
# initialize the early_stopping object
self.early_stopping = EarlyStopping(
patience=self.cfg.train_params.patience,
verbose=True,
delta=self.cfg.train_params.early_stopping_delta,
)
# stochastic weight averaging
self.swa_model = AveragedModel(self.model)
self.swa_scheduler = SWALR(self.optimizer, **self.cfg.SWA)
def test(self, model_path=''):
print('Test model')
try:
print('*** Load pre-trained model ' + model_path + ' ***')
self.model = load_checkpoint(self.model, model_path)
except ValueError as e:
print('Error while loading the model.', e)
print('\nTest all')
# acc = np.mean(self.accuracies)
# acc = self.accuracies
graphs = self.data[GRAPH]
labels = self.labels
self.run_test(graphs, labels)
print('\nTest on train graphs')
graphs = load_pickle(os.path.join(self.odir, 'train'))
labels = load_pickle(os.path.join(self.odir, 'train_labels'))
self.run_test(graphs, labels)
print('\nTest on test graphs')
graphs = load_pickle(os.path.join(self.odir, 'test'))
labels = load_pickle(os.path.join(self.odir, 'test_labels'))
self.run_test(graphs, labels)
def load_model_state(self, model_path=''):
try:
print('[App][load_model_state] *** Load pre-trained model ' +
model_path + ' ***')
self.model = load_checkpoint(self.model, model_path, self.is_cuda)
except ValueError as e:
print('Error while loading the model.', e)
def test_on_data(self, model_path=''):
print('Test model')
try:
print('*** Load pre-trained model ' + model_path + ' ***')
self.model = load_checkpoint(self.model, model_path)
except ValueError as e:
print('Error while loading the model.', e)
print('\nTest on data')
# acc = np.mean(self.accuracies)
# acc = self.accuracies
graphs = self.data[GRAPH]
labels = self.labels
self.run_test(graphs, labels)
def test(self, data, load_path='', mode=NODE_CLASSIFICATION):
try:
print('*** Load pre-trained model ***')
self.model = load_checkpoint(self.model, load_path)
except ValueError as e:
print('Error while loading the model.', e)
if mode == NODE_CLASSIFICATION:
test_mask = data[TEST_MASK]
labels = data[LABELS]
acc, _ = self.model.eval_node_classification(labels, test_mask)
else:
acc = np.mean(self.accuracies)
print("\nTest Accuracy {:.4f}".format(acc))
return acc
def train(self,
save_path='',
k_fold=10,
train_list_file=None,
test_list_file=None):
if self.pretrained_weight is not None:
self.model = load_checkpoint(self.model, self.pretrained_weight,
self.is_cuda)
save_dir = save_path.split('/checkpoint')[0]
loss_fcn = torch.nn.CrossEntropyLoss()
# initialize graphs
self.accuracies = np.zeros(k_fold)
graphs = self.data[GRAPH] # load all the graphs
# debug purposes: reshuffle all the data before the splitting
random_indices = list(range(len(graphs)))
random.shuffle(random_indices)
graphs = [graphs[i] for i in random_indices]
labels = self.labels[random_indices]
graphs_names = [self.graphs_names[i] for i in random_indices]
split_train_test = True if train_list_file is None and test_list_file is None else False
print('[app][train] split_train_test', split_train_test)
'''
if split_train_test is True:
print('[app][train] train_list_file', train_list_file)
print('[app][train] test_list_file', test_list_file)
#############################
# Create new train/test set
# Split train and test
#############################
train_size = int(self.TRAIN_SIZE * len(graphs))
g_train = graphs[:train_size]
l_train = labels[:train_size]
n_train = graphs_names[:train_size]
g_test = graphs[train_size:]
l_test = labels[train_size:]
n_test = graphs_names[train_size:]
else:
#############################
# Load train and test graphs from list
#############################
train_files = []
test_files = []
g_train = []
l_train = []
n_train = []
g_test = []
l_test = []
n_test = []
with open(train_list_file, 'r') as f:
train_files = [l.strip() for l in f.readlines()]
with open(test_list_file, 'r') as f:
test_files = [l.strip() for l in f.readlines()]
for i in range(len(labels)):
graph_jsonpath = graphs_names[i]
# print(graph_jsonpath)
if graph_jsonpath in train_files:
g_train.append(graphs[i])
l_train.append(labels[i])
n_train.append(graphs_names[i])
if graph_jsonpath in test_files:
g_test.append(graphs[i])
l_test.append(labels[i])
n_test.append(graphs_names[i])
l_train = torch.Tensor(l_train).type(torch.LongTensor)
l_test = torch.Tensor(l_test).type(torch.LongTensor)
if self.is_cuda is True:
l_train = l_train.cuda()
l_test = l_test.cuda()
'''
print('[app][train] len labels', len(labels))
print('[app][train] len g_train', len(g_train))
# print('[app][train] g_train', g_train)
if not os.path.isdir(self.odir):
os.makedirs(self.odir)
save_pickle(g_train, os.path.join(self.odir, 'train'))
save_pickle(l_train, os.path.join(self.odir, 'train_labels'))
save_pickle(g_test, os.path.join(self.odir, 'test'))
save_pickle(l_test, os.path.join(self.odir, 'test_labels'))
# save graph name list to txt file
save_txt(n_train, os.path.join(self.odir, 'train_list.txt'))
save_txt(n_test, os.path.join(self.odir, 'test_list.txt'))
K = k_fold
for k in range(K):
self.model = self.ModelObj(g=self.data_graph[0],
config_params=self.model_config,
n_classes=self.data_nclasses,
n_rels=self.data_nrels,
n_entities=self.data_nentities,
is_cuda=self.is_cuda,
batch_size=1,
model_src_path=self.model_src_path)
print('*** [app][__init__] Model layers ***')
for name, param in self.model.named_parameters():
if param.requires_grad:
print('\t', name, param.data.type())
print('>>> [app][__init__] self.model.fc.weight.type',
self.model.fc.weight.type())
optimizer = torch.optim.Adam(
self.model.parameters(),
lr=self.learning_config['lr'],
weight_decay=self.learning_config['weight_decay'])
start = int(len(g_train) / K) * k
end = int(len(g_train) / K) * (k + 1)
print('\n\n\n[app][train] Process new k=' + str(k) + ' | ' +
str(start) + '-' + str(end))
# training batch
train_batch_graphs = g_train[:start] + g_train[end:]
train_batch_labels = l_train[list(range(0, start)) +
list(range(end + 1, len(g_train)))]
train_batch_samples = list(
map(list, zip(train_batch_graphs, train_batch_labels)))
train_batches = DataLoader(
train_batch_samples,
batch_size=self.learning_config['batch_size'],
shuffle=True,
collate_fn=collate)
# testing batch
val_batch_graphs = g_train[start:end]
val_batch_labels = l_train[start:end]
# print('[app][train] val_batch_graphs', val_batch_graphs)
print('[app][train] len val_batch_graphs', len(val_batch_graphs))
print('[app][train] val_batch_graphs[0].number_of_nodes()',
val_batch_graphs[0].number_of_nodes())
print('[app][train] val_batch_graphs[-1].number_of_nodes()',
val_batch_graphs[-1].number_of_nodes())
val_batch = dgl.batch(val_batch_graphs)
print('[app][train] train_batches size: ', len(train_batches))
print('[app][train] train_batch_graphs size: ',
len(train_batch_graphs))
print('[app][train] val_batch_graphs size: ',
len(val_batch_graphs))
print('[app][train] train_batches', train_batches)
print('[app][train] val_batch_labels', val_batch_labels)
dur = []
for epoch in range(self.learning_config['epochs']):
self.model.train()
if epoch >= 3:
t0 = time.time()
losses = []
training_accuracies = []
for iter_idx, (bg, label) in enumerate(train_batches):
# print('~~~ [app][train] bg', bg)
logits = self.model(bg)
if self.learning_config['cuda']:
label = label.cuda()
loss = loss_fcn(logits, label)
losses.append(loss.item())
_, indices = torch.max(logits, dim=1)
# print('~~~~ logits', logits)
# print('------------------')
print('\t [app][train] indices', indices)
# print('\t label', label)
correct = torch.sum(indices == label)
training_accuracies.append(correct.item() * 1.0 /
len(label))
optimizer.zero_grad()
loss.backward(retain_graph=True)
# loss.backward()
optimizer.step()
if epoch >= 3:
dur.append(time.time() - t0)
val_acc, val_loss, _ = self.model.eval_graph_classification(
val_batch_labels, val_batch)
print(
"[app][train] Epoch {:05d} | Time(s) {:.4f} | train_acc {:.4f} | train_loss {:.4f} | val_acc {:.4f} | val_loss {:.4f}"
.format(epoch,
np.mean(dur) if dur else 0,
np.mean(training_accuracies), np.mean(losses),
val_acc, val_loss))
is_better = self.early_stopping(val_loss, self.model,
save_path)
if is_better:
self.accuracies[k] = val_acc
if self.early_stopping.early_stop:
# Print model's state_dict
# print("*** Model's state_dict:")
# for param_tensor in self.model.state_dict():
# print(param_tensor, "\t", self.model.state_dict()[param_tensor].size())
# # Print optimizer's state_dict
# print("*** Optimizer's state_dict:")
# for var_name in optimizer.state_dict():
# print(var_name, "\t", optimizer.state_dict()[var_name])
# Save state dict
# torch.save(self.model.state_dict(), save_dir+'/model_state.pt')
# Save model
# torch.save({
# 'epoch': epoch,
# 'model_state_dict': self.model.state_dict(),
# 'optimizer_state_dict': optimizer.state_dict(),
# 'val_loss': val_loss,
# }, save_dir+'/saved')
print("[app][train] Early stopping")
break
self.early_stopping.reset()
def train(self,
save_path='',
k_fold=10,
train_list_file=None,
test_list_file=None):
if self.pretrained_weight is not None:
self.model = load_checkpoint(self.model, self.pretrained_weight)
loss_fcn = torch.nn.CrossEntropyLoss()
# initialize graphs
self.accuracies = np.zeros(k_fold)
graphs = self.data[GRAPH] # load all the graphs
# debug purposes: reshuffle all the data before the splitting
random_indices = list(range(len(graphs)))
random.shuffle(random_indices)
graphs = [graphs[i] for i in random_indices]
labels = self.labels[random_indices]
graphs_names = [self.graphs_names[i] for i in random_indices]
split_train_test = True if train_list_file is None and test_list_file is None else False
print('split_train_test', split_train_test)
print('train_list_file', train_list_file)
print('test_list_file', test_list_file)
if split_train_test is True:
#############################
# Create new train/test set
# Split train and test
#############################
train_size = int(self.TRAIN_SIZE * len(graphs))
g_train = graphs[:train_size]
l_train = labels[:train_size]
n_train = graphs_names[:train_size]
g_test = graphs[train_size:]
l_test = labels[train_size:]
n_test = graphs_names[train_size:]
else:
#############################
# Load train and test graphs from list
#############################
train_files = []
test_files = []
g_train = []
l_train = []
n_train = []
g_test = []
l_test = []
n_test = []
with open(train_list_file, 'r') as f:
train_files = [l.strip() for l in f.readlines()]
with open(test_list_file, 'r') as f:
test_files = [l.strip() for l in f.readlines()]
for i in range(len(labels)):
graph_jsonpath = graphs_names[i]
# print(graph_jsonpath)
if graph_jsonpath in train_files:
g_train.append(graphs[i])
l_train.append(labels[i])
n_train.append(graphs_names[i])
if graph_jsonpath in test_files:
g_test.append(graphs[i])
l_test.append(labels[i])
n_test.append(graphs_names[i])
l_train = torch.Tensor(l_train).type(torch.LongTensor)
l_test = torch.Tensor(l_test).type(torch.LongTensor)
if self.is_cuda is True:
l_train = l_train.cuda()
l_test = l_test.cuda()
# print('len g_train', len(g_train))
# print('g_train', g_train)
if not os.path.isdir(self.odir):
os.makedirs(self.odir)
save_pickle(g_train, os.path.join(self.odir, 'train'))
save_pickle(l_train, os.path.join(self.odir, 'train_labels'))
save_pickle(g_test, os.path.join(self.odir, 'test'))
save_pickle(l_test, os.path.join(self.odir, 'test_labels'))
# save graph name list to txt file
save_txt(n_train, os.path.join(self.odir, 'train_list.txt'))
save_txt(n_test, os.path.join(self.odir, 'test_list.txt'))
K = k_fold
for k in range(K): # K-fold cross validation
# create GNN model
# self.model = Model(g=self.data[GRAPH],
# config_params=self.model_config,
# n_classes=self.data[N_CLASSES],
# n_rels=self.data[N_RELS] if N_RELS in self.data else None,
# n_entities=self.data[N_ENTITIES] if N_ENTITIES in self.data else None,
# is_cuda=self.learning_config['cuda'],
# seq_dim=self.seq_max_length,
# batch_size=1)
optimizer = torch.optim.Adam(
self.model.parameters(),
lr=self.learning_config['lr'],
weight_decay=self.learning_config['weight_decay'])
if self.learning_config['cuda']:
self.model.cuda()
start = int(len(g_train) / K) * k
end = int(len(g_train) / K) * (k + 1)
print('\n\n\nProcess new k=' + str(k) + ' | ' + str(start) + '-' +
str(end))
# testing batch
val_batch_graphs = g_train[start:end]
val_batch_labels = l_train[start:end]
val_batch = dgl.batch(val_batch_graphs)
# training batch
train_batch_graphs = g_train[:start] + g_train[end:]
train_batch_labels = l_train[list(range(0, start)) +
list(range(end + 1, len(g_train)))]
train_batch_samples = list(
map(list, zip(train_batch_graphs, train_batch_labels)))
train_batches = DataLoader(
train_batch_samples,
batch_size=self.learning_config['batch_size'],
shuffle=True,
collate_fn=collate)
print('train_batches size: ', len(train_batches))
print('train_batch_graphs size: ', len(train_batch_graphs))
print('val_batch_graphs size: ', len(val_batch_graphs))
print('train_batches', train_batches)
print('val_batch_labels', val_batch_labels)
dur = []
for epoch in range(self.learning_config['epochs']):
self.model.train()
if epoch >= 3:
t0 = time.time()
losses = []
training_accuracies = []
for iter_idx, (bg, label) in enumerate(train_batches):
logits = self.model(bg)
if self.learning_config['cuda']:
label = label.cuda()
loss = loss_fcn(logits, label)
losses.append(loss.item())
_, indices = torch.max(logits, dim=1)
correct = torch.sum(indices == label)
training_accuracies.append(correct.item() * 1.0 /
len(label))
optimizer.zero_grad()
loss.backward(retain_graph=True)
optimizer.step()
if epoch >= 3:
dur.append(time.time() - t0)
val_acc, val_loss, _ = self.model.eval_graph_classification(
val_batch_labels, val_batch)
print(
"Epoch {:05d} | Time(s) {:.4f} | train_acc {:.4f} | train_loss {:.4f} | val_acc {:.4f} | val_loss {:.4f}"
.format(epoch,
np.mean(dur) if dur else 0,
np.mean(training_accuracies), np.mean(losses),
val_acc, val_loss))
is_better = self.early_stopping(val_loss, self.model,
save_path)
if is_better:
self.accuracies[k] = val_acc
if self.early_stopping.early_stop:
print("Early stopping")
break
self.early_stopping.reset()
def __init__(self, cfg_dir: str, data_loader_train: DataLoader,
data_loader_val: DataLoader, encoder, decoder,
labels_definition):
self.cfg = get_conf(cfg_dir)
self._labels_definition = labels_definition
self.logger = self.init_logger(self.cfg.logger)
self.task = decoder
self.data_train = data_loader_train
self.data_val = data_loader_val
self.model = encoder
self.decoder = decoder.mlp
self.sig = nn.Sigmoid()
#self.model._resnet.conv1.apply(init_weights_normal)
self.device = self.cfg.train_params.device
self.model = self.model.to(device=self.device)
self.decoder = self.decoder.to(device=self.device)
if self.cfg.train_params.optimizer.lower() == "adam":
params = list(self.model.parameters()) + list(
self.decoder.parameters())
self.optimizer = optim.Adam(params, **self.cfg.adam)
elif self.cfg.train_params.optimizer.lower() == "rmsprop":
self.optimizer = optim.RMSprop(
[self.model.parameters(),
self.decoder.parameters()], **self.cfg.rmsprop)
else:
raise ValueError(
f"Unknown optimizer {self.cfg.train_params.optimizer}")
self.lr_scheduler = optim.lr_scheduler.CosineAnnealingLR(
self.optimizer, T_max=100)
self.criterion_lbl = nn.BCELoss()
self.criterion_box = nn.MSELoss()
if self.cfg.logger.resume:
# load checkpoint
print("Loading checkpoint")
save_dir = self.cfg.directory.load
checkpoint = load_checkpoint(save_dir, self.device)
self.model.load_state_dict(checkpoint["model"])
self.optimizer.load_state_dict(checkpoint["optimizer"])
self.lr_scheduler.load_state_dict(checkpoint["lr_scheduler"])
self.epoch = checkpoint["epoch"]
self.e_loss = checkpoint["e_loss"]
self.best = checkpoint["best"]
print(
f"{datetime.now():%Y-%m-%d %H:%M:%S} "
f"Loading checkpoint was successful, start from epoch {self.epoch}"
f" and loss {self.best}")
else:
self.epoch = 1
self.best = np.inf
self.e_loss = []
# initialize the early_stopping object
self.early_stopping = EarlyStopping(
patience=self.cfg.train_params.patience,
verbose=True,
delta=self.cfg.train_params.early_stopping_delta,
)
# stochastic weight averaging
self.swa_model = AveragedModel(self.model)
