def benchmark_dataset(dataset, title, fname, testname, xlabels, ylabels=None):
global benchmark_data
print(f'Benchmarking {title}.. ')
dataloader = torch.utils.data.DataLoader(
dataset, batch_size=10,
shuffle=False, num_workers=4,
)
tracked_metrics = [
metrics.Accuracy(),
metrics.RocAuc(),
metrics.FScore()
]
logs, cm = trainer.test(
model=model, test_dataloader=dataloader,
criterion=criterion, metrics=tracked_metrics, device=device
)
with open(f'logs/{vars.corda_version}/{name}/{fname}-metric.txt', 'w') as f:
f.write(f'{fname}: ' + trainer.summarize_metrics(logs) + '\n')
ax = sns.heatmap(
cm.get(normalized=True), annot=True, fmt=".2f",
xticklabels=xlabels, yticklabels=ylabels or xlabels,
vmin=0., vmax=1.
)
ax.set_title(title)
plt.xlabel('predicted')
plt.ylabel('ground')
hm = ax.get_figure()
hm.savefig(f'logs/{vars.corda_version}/{name}/{fname}.png')
hm.clf()
fpr, tpr, thresholds = tracked_metrics[1].get_curve()
auc = tracked_metrics[1].get()
f = plt.figure()
plt.plot(fpr, tpr, color='darkorange', lw=2, label=f'ROC curve (auc = {auc:.2f})')
plt.title(f'{title} ROC')
plt.legend(loc='lower right')
plt.savefig(f'logs/{vars.corda_version}/{name}/{fname}-roc.png')
plt.clf()
plt.cla()
plt.close()
specificity, fpr, fnr, sensitivity = cm.get(normalized=True).ravel()
dor = (sensitivity*specificity)/((1-sensitivity)*(1-specificity))
fscore = tracked_metrics[2].get()
ba = (sensitivity+specificity)/2.
data = {
'arch': args.arch, 'pretrain': args.pretrain, 'train': args.train.upper(),
'test': testname, 'accuracy': tracked_metrics[0].get(), 'auc': auc,
'sensitivity': sensitivity, 'specificity': specificity, 'fscore': fscore,
'ba': ba, 'missrate': fnr, 'dor': dor
}
for k,v in data.items():
benchmark_data[k].append(v)
def test_accuracy():
m = metrics.Accuracy()
m.reset()
m.add(torch.tensor([1]).to(DEVICE), torch.tensor([[.0, .1]]).to(DEVICE))
assert m.get() == 1
m.add(torch.tensor([0]).to(DEVICE), torch.tensor([[.0, .1]]).to(DEVICE))
assert m.get() == 0.5
m.add(torch.tensor([0]).to(DEVICE), torch.tensor([[.1, .0]]).to(DEVICE))
m.add(torch.tensor([0]).to(DEVICE), torch.tensor([[.1, .0]]).to(DEVICE))
assert m.get() == 0.75
def benchmark_dataset(dataset, title, fname, xlabels, ylabels=None):
print(f'Benchmarking {title}.. ', end='', flush=True)
dataloader = torch.utils.data.DataLoader(
dataset,
batch_size=10,
shuffle=False,
num_workers=4,
)
tracked_metrics = [metrics.Accuracy(), metrics.RocAuc(), metrics.FScore()]
logs, cm = trainer.test(model=model,
test_dataloader=dataloader,
criterion=criterion,
metrics=tracked_metrics,
device=device)
with open(f'logs/{vars.corda_version}/{name}/{fname}-metric.txt',
'w') as f:
f.write(f'{fname}: ' + trainer.summarize_metrics(logs) + '\n')
ax = sns.heatmap(cm.get(normalized=True),
annot=True,
fmt=".2f",
xticklabels=xlabels,
yticklabels=ylabels or xlabels)
ax.set_title(title)
plt.xlabel('predicted')
plt.ylabel('ground')
hm = ax.get_figure()
hm.savefig(f'logs/{vars.corda_version}/{name}/{fname}.png')
hm.clf()
fpr, tpr, thresholds = tracked_metrics[1].get_curve()
auc = tracked_metrics[1].get()
f = plt.figure()
plt.plot(fpr,
tpr,
color='darkorange',
lw=2,
label=f'ROC curve (auc = {auc:.2f})')
plt.title(f'{title} ROC')
plt.legend(loc='lower right')
plt.savefig(f'logs/{vars.corda_version}/{name}/{fname}-roc.png')
plt.clf()
plt.cla()
plt.close()
).to(device)
elif args.arch == 'resnet50':
model = covid_classifier.CovidClassifier50(
encoder=feature_extractor,
pretrained=False,
freeze_conv=False
).to(device)
#model = covid_classifier.LeNet1024NoPoolingDeep().to(device)
print(f'Using lr {lr}')
# TRAINING
# %%
tracked_metrics = [
metrics.Accuracy(),
metrics.RocAuc(),
metrics.FScore()
]
def focal_loss(output, target, gamma=2., weight=None):
bce = F.binary_cross_entropy(output, target, reduction='none', weight=weight)
pt = target*output + (1-target)*(1-output)
return (torch.pow((1-pt), gamma) * bce).mean()
criterion = focal_loss
optimizer = torch.optim.SGD(model.parameters(), lr=lr, weight_decay=1e-3)
lr_scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, patience=15, verbose=True)
best_model = trainer.fit(
model=model, train_dataloader=train_dataloader,
trainer = Trainer(
model=model,
logger=log,
prefix="classifier",
checkpoint_dir=ARGS.checkpoint_dir,
summary_dir=ARGS.summary_dir,
n_summaries=4,
start_scratch=ARGS.start_scratch,
)
metrics = {
"tp": m.TruePositives(ARGS.device),
"tn": m.TrueNegatives(ARGS.device),
"fp": m.FalsePositives(ARGS.device),
"fn": m.FalseNegatives(ARGS.device),
"accuracy": m.Accuracy(ARGS.device),
"f1": m.F1Score(ARGS.device),
"precision": m.Precision(ARGS.device),
"TPR": m.Recall(ARGS.device),
"FPR": m.FPR(ARGS.device),
}
optimizer = optim.Adam(model.parameters(),
lr=ARGS.lr,
betas=(ARGS.beta1, 0.999))
metric_mode = "max"
lr_scheduler = optim.lr_scheduler.ReduceLROnPlateau(
optimizer,
mode=metric_mode,
patience=patience_lr,
print(f'using lr {lr}')
# %%
model = pneumonia_classifier.PneumoniaClassifierChest(
pretrained=True).to(device)
# %%
criterion = functools.partial(F.cross_entropy, reduction='mean')
optimizer = torch.optim.SGD(model.parameters(), lr=lr, weight_decay=0.001)
lr_scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer,
patience=15,
verbose=True)
# %%
tracked_metrics = [
metrics.Accuracy(multiclass=True),
]
name = f'resnet18-pneumonia-classifier-s{seed}-3-classes-unprocessed'
utils.ensure_dir(f'logs/{vars.corda_version}/{name}')
# %%
best_model = trainer.fit(model=model,
train_dataloader=train_dataloader,
val_dataloader=val_dataloader,
test_dataloader=test_dataloader,
test_every=10,
criterion=criterion,
optimizer=optimizer,
scheduler=lr_scheduler,
metrics=tracked_metrics,
def train_seg_wrapper(ctx, epoch, lr, model_prefix, symbol, class_num, workspace, init_weight_file,
im_root, mask_root, flist_path, use_g_labels, rgb_mean, crop_size, scale_range, label_shrink_scale,
epoch_size, max_epoch, batch_size, wd, momentum):
arg_dict = {}
aux_dict = {}
if use_g_labels:
seg_net = symbol.create_training(class_num=class_num, gweight=1.0/batch_size, workspace=workspace)
else:
seg_net = symbol.create_training(class_num=class_num, workspace=workspace)
if epoch == 0:
if not os.path.exists(init_weight_file):
logging.warn("No model file found at %s. Start from scratch!" % init_weight_file)
else:
arg_dict, aux_dict, _ = misc.load_checkpoint(init_weight_file)
param_types = ["_weight", "_bias", "_gamma", "_beta", "_moving_mean", "_moving_var"]
#copy params for global branch
if use_g_labels:
for arg in arg_dict.keys():
for param_type in param_types:
if param_type in arg:
arg_name = arg[:arg.rfind(param_type)]
arg_dict[arg_name + "_g" + param_type] = arg_dict[arg].copy()
if arg_name in ["fc6", "fc7"]:
arg_dict[arg_name + "_1" + param_type] = arg_dict[arg].copy()
arg_dict[arg_name + "_2" + param_type] = arg_dict[arg].copy()
arg_dict[arg_name + "_3" + param_type] = arg_dict[arg].copy()
arg_dict[arg_name + "_4" + param_type] = arg_dict[arg].copy()
break
for aux in aux_dict.keys():
for param_type in param_types:
if param_type in aux:
aux_name = aux[:aux.rfind(param_type)]
aux_dict[aux_name + "_g" + param_type] = aux_dict[aux].copy()
break
else:
arg_dict, aux_dict, _ = misc.load_checkpoint(model_prefix, epoch)
data_iter = SegTrainingIter(
im_root=im_root,
mask_root=mask_root,
file_list_path=flist_path,
provide_g_labels=use_g_labels,
class_num=class_num,
rgb_mean=rgb_mean,
crop_size=crop_size,
shuffle=True,
scale_range=scale_range,
label_shrink_scale=label_shrink_scale,
random_flip=True,
data_queue_size=8,
epoch_size=epoch_size,
batch_size=batch_size,
round_batch=True
)
initializer = mx.initializer.Normal()
initializer.set_verbosity(True)
if use_g_labels:
mod = mx.mod.Module(seg_net, context=ctx, label_names=["softmax_label", "g_logistic_label"])
else:
mod = mx.mod.Module(seg_net, context=ctx, label_names=["softmax_label"])
mod.bind(data_shapes=data_iter.provide_data,
label_shapes=data_iter.provide_label)
mod.init_params(initializer=initializer, arg_params=arg_dict, aux_params=aux_dict, allow_missing=(epoch == 0))
opt_params = {"learning_rate":lr,
"wd": wd,
'momentum': momentum,
'rescale_grad': 1.0/len(ctx)}
if use_g_labels:
eval_metrics = [metrics.Accuracy(), metrics.Loss(), metrics.MultiLogisticLoss(l_index=1, p_index=1)]
else:
eval_metrics = [metrics.Accuracy(), metrics.Loss()]
mod.fit(data_iter,
optimizer="sgd",
optimizer_params=opt_params,
num_epoch=max_epoch,
epoch_end_callback=callbacks.module_checkpoint(model_prefix),
batch_end_callback=callbacks.Speedometer(batch_size, frequent=10),
eval_metric=eval_metrics,
begin_epoch=epoch+1)
if args.arch == 'resnet18':
model = covid_classifier.CovidClassifier(encoder=feature_extractor,
pretrained=False,
freeze_conv=False).to(device)
elif args.arch == 'resnet50':
model = covid_classifier.CovidClassifier50(encoder=feature_extractor,
pretrained=False,
freeze_conv=False).to(device)
#model = covid_classifier.LeNet1024NoPoolingDeep().to(device)
print(f'Using lr {lr}')
# TRAINING
# %%
tracked_metrics = [metrics.Accuracy(), metrics.RocAuc(), metrics.FScore()]
def focal_loss(output, target, gamma=2., weight=None):
bce = F.binary_cross_entropy(output,
target,
reduction='none',
weight=weight)
pt = target * output + (1 - target) * (1 - output)
return (torch.pow((1 - pt), gamma) * bce).mean()
criterion = focal_loss
optimizer = torch.optim.SGD(model.parameters(), lr=lr, weight_decay=1e-3)
lr_scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer,
patience=15,