def train(model, args, device, writer, optimizer, data_loader, epoch):
# Set train mode
model.train()
criterion = nn.CrossEntropyLoss(reduction='mean')
metric_ftns = ['loss', 'correct', 'total', 'accuracy', 'sens', 'ppv']
metrics = MetricTracker(*[m for m in metric_ftns],
writer=writer,
mode='train')
metrics.reset()
cm = torch.zeros(args.classes, args.classes)
for batch_idx, input_tensors in enumerate(data_loader):
input_data, target = input_tensors[0].to(device), input_tensors[1].to(
device)
# Forward
output = model(input_data)
loss = criterion(output, target)
correct, total, acc = accuracy(output, target)
update_confusion_matrix(cm, output, target)
metrics.update_all_metrics({
'correct': correct,
'total': total,
'loss': loss.item(),
'accuracy': acc
})
# Backward
optimizer.zero_grad()
loss.backward()
optimizer.step()
# Save TB stats
writer_step = (epoch - 1) * len(data_loader) + batch_idx
if ((batch_idx + 1) % args.log_interval == 0):
# Calculate confusion for this bucket
ppv, sens = update_confusion_calc(cm)
metrics.update_all_metrics({'sens': sens, 'ppv': ppv})
cm = torch.zeros(args.classes, args.classes)
metrics.write_tb(writer_step)
num_samples = batch_idx * args.batch_size
print_stats(args, epoch, num_samples, data_loader, metrics)
return metrics, writer_step
def validation(args, model, testloader, epoch, writer):
model.eval()
criterion = nn.CrossEntropyLoss(reduction='mean')
metric_ftns = [
'loss', 'correct', 'total', 'accuracy', 'ppv', 'sensitivity'
]
val_metrics = MetricTracker(*[m for m in metric_ftns],
writer=writer,
mode='val')
val_metrics.reset()
confusion_matrix = torch.zeros(args.class_dict, args.class_dict)
with torch.no_grad():
for batch_idx, input_tensors in enumerate(testloader):
input_data, target = input_tensors
if (args.cuda):
input_data = input_data.cuda()
target = target.cuda()
output = model(input_data)
loss = criterion(output, target)
correct, total, acc = accuracy(output, target)
num_samples = batch_idx * args.batch_size + 1
_, pred = torch.max(output, 1)
num_samples = batch_idx * args.batch_size + 1
for t, p in zip(target.cpu().view(-1), pred.cpu().view(-1)):
confusion_matrix[t.long(), p.long()] += 1
val_metrics.update_all_metrics(
{
'correct': correct,
'total': total,
'loss': loss.item(),
'accuracy': acc
},
writer_step=(epoch - 1) * len(testloader) + batch_idx)
print_summary(args, epoch, num_samples, val_metrics, mode="Validation")
s = sensitivity(confusion_matrix.numpy())
ppv = positive_predictive_value(confusion_matrix.numpy())
print(f" s {s} ,ppv {ppv}")
val_metrics.update('sensitivity',
s,
writer_step=(epoch - 1) * len(testloader) + batch_idx)
val_metrics.update('ppv',
ppv,
writer_step=(epoch - 1) * len(testloader) + batch_idx)
print('Confusion Matrix\n{}'.format(confusion_matrix.cpu().numpy()))
return val_metrics, confusion_matrix
def train(args, model, trainloader, optimizer, epoch):
start_time = time.time()
model.train()
train_metrics = MetricTracker(*[m for m in METRICS_TRACKED], mode='train')
w2 = torch.Tensor([1.0, 1.0, 1.5])
if (args.cuda):
model.cuda()
w2 = w2.cuda()
train_metrics.reset()
# JUST FOR CHECK
counter_batches = 0
counter_covid = 0
for batch_idx, input_tensors in enumerate(trainloader):
optimizer.zero_grad()
input_data, target = input_tensors
counter_batches += 1
if (args.cuda):
input_data = input_data.cuda()
target = target.cuda()
output = model(input_data)
loss, counter = weighted_loss(output, target, w2)
counter_covid += counter
loss.backward()
optimizer.step()
correct, total, acc = accuracy(output, target)
precision_mean, recall_mean = precision_score(output, target)
num_samples = batch_idx * args.batch_size + 1
train_metrics.update_all_metrics(
{
'correct': correct,
'total': total,
'loss': loss.item(),
'accuracy': acc,
'precision_mean': precision_mean,
'recall_mean': recall_mean
},
writer_step=(epoch - 1) * len(trainloader) + batch_idx)
print_stats(args, epoch, num_samples, trainloader, train_metrics)
print("--- %s seconds ---" % (time.time() - start_time))
print_summary(args, epoch, num_samples, train_metrics, mode="Training")
return train_metrics
def validation(args, model, testloader, epoch):
model.eval()
val_metrics = MetricTracker(*[m for m in METRICS_TRACKED], mode='val')
val_metrics.reset()
w2 = torch.Tensor([1.0, 1.0,
1.5]) #w_full = torch.Tensor([1.456,1.0,15.71])
if (args.cuda):
w2 = w2.cuda()
confusion_matrix = torch.zeros(args.classes, args.classes)
with torch.no_grad():
for batch_idx, input_tensors in enumerate(testloader):
input_data, target = input_tensors
if (args.cuda):
input_data = input_data.cuda()
target = target.cuda()
output = model(input_data)
loss, counter = weighted_loss(output, target, w2)
correct, total, acc = accuracy(output, target)
precision_mean, recall_mean = precision_score(output, target)
num_samples = batch_idx * args.batch_size + 1
_, preds = torch.max(output, 1)
for t, p in zip(target.cpu().view(-1), preds.cpu().view(-1)):
confusion_matrix[t.long(), p.long()] += 1
val_metrics.update_all_metrics(
{
'correct': correct,
'total': total,
'loss': loss.item(),
'accuracy': acc,
'precision_mean': precision_mean,
'recall_mean': recall_mean
},
writer_step=(epoch - 1) * len(testloader) + batch_idx)
print_summary(args, epoch, num_samples, val_metrics, mode="Validation")
print('Confusion Matrix\n {}'.format(confusion_matrix.cpu().numpy()))
return val_metrics, confusion_matrix
def train(args, model, trainloader, optimizer, epoch, writer, log):
model.train()
criterion = nn.CrossEntropyLoss(reduction='mean')
metric_ftns = [
'loss', 'correct', 'total', 'accuracy', 'ppv', 'sensitivity'
]
train_metrics = MetricTracker(*[m for m in metric_ftns],
writer=writer,
mode='train')
train_metrics.reset()
confusion_matrix = torch.zeros(args.class_dict, args.class_dict)
for batch_idx, input_tensors in enumerate(trainloader):
optimizer.zero_grad()
input_data, target = input_tensors
if (args.cuda):
input_data = input_data.cuda()
target = target.cuda()
output = model(input_data)
loss = criterion(output, target)
loss.backward()
optimizer.step()
correct, total, acc = accuracy(output, target)
pred = torch.argmax(output, dim=1)
num_samples = batch_idx * args.batch_size + 1
train_metrics.update_all_metrics(
{
'correct': correct,
'total': total,
'loss': loss.item(),
'accuracy': acc
},
writer_step=(epoch - 1) * len(trainloader) + batch_idx)
print_stats(args, epoch, num_samples, trainloader, train_metrics)
for t, p in zip(target.cpu().view(-1), pred.cpu().view(-1)):
confusion_matrix[t.long(), p.long()] += 1
s = sensitivity(confusion_matrix.numpy())
ppv = positive_predictive_value(confusion_matrix.numpy())
print(f" s {s} ,ppv {ppv}")
# train_metrics.update('sensitivity', s, writer_step=(epoch - 1) * len(trainloader) + batch_idx)
# train_metrics.update('ppv', ppv, writer_step=(epoch - 1) * len(trainloader) + batch_idx)
print_summary(args, epoch, num_samples, train_metrics, mode="Training")
return train_metrics
def val(args, model, data_loader, epoch, writer, device):
model.eval()
criterion = nn.CrossEntropyLoss(reduction='mean')
metric_ftns = ['loss', 'correct', 'total', 'accuracy', 'ppv', 'sens']
metrics = MetricTracker(*[m for m in metric_ftns],
writer=writer,
mode='val')
metrics.reset()
cm = torch.zeros(args.classes, args.classes)
with torch.no_grad():
for batch_idx, input_tensors in enumerate(data_loader):
torch.cuda.empty_cache()
input_data, target = input_tensors[0].to(
device), input_tensors[1].to(device)
# Forward
output = model(input_data)
loss = criterion(output, target)
correct, total, acc = accuracy(output, target)
update_confusion_matrix(cm, output, target)
# Update the metrics record
metrics.update_all_metrics({
'correct': correct,
'total': total,
'loss': loss.item(),
'accuracy': acc
})
ppv, sens = update_confusion_calc(cm)
metrics.update_all_metrics({'sens': sens, 'ppv': ppv})
return metrics, cm
def train(args, model, trainloader, optimizer, epoch, writer):
model.train()
criterion = nn.CrossEntropyLoss(reduction='mean')
metric_ftns = ['loss', 'correct', 'total', 'accuracy']
train_metrics = MetricTracker(*[m for m in metric_ftns],
writer=writer,
mode='train')
train_metrics.reset()
for batch_idx, input_tensors in enumerate(trainloader):
optimizer.zero_grad()
input_data, target = input_tensors
if (args.cuda):
input_data = input_data.cuda()
target = target.cuda()
output = model(input_data)
loss = criterion(output, target)
loss.backward()
optimizer.step()
correct, total, acc = accuracy(output, target)
num_samples = batch_idx * args.batch_size + 1
train_metrics.update_all_metrics(
{
'correct': correct,
'total': total,
'loss': loss.item(),
'accuracy': acc
},
writer_step=(epoch - 1) * len(trainloader) + batch_idx)
print_stats(args, epoch, num_samples, trainloader, train_metrics)
print_summary(args, epoch, num_samples, train_metrics, mode="Training")
return train_metrics