def __init__(self):
super().__init__()
num_classes = 9
weight = torch.tensor([
0.01030928,
0.00552486,
0.00344828,
0.01388889,
0.02222222,
0.01204819,
0.02272727,
0.00307692,
0.00055249,
])
self.criterion = nn.CrossEntropyLoss(weight=weight)
# self.criterion = nn.CrossEntropyLoss()
self.metrics = {
"accuracy": Accuracy(),
"recall_macro": Recall(num_classes=num_classes, average="macro"),
"precision_macro": Precision(num_classes=num_classes,
average="macro"),
}
self.classifier = nn.Sequential(
nn.Linear(768, 256),
nn.Dropout(0.5),
nn.ReLU(),
nn.Linear(256, 128),
nn.Dropout(0.5),
nn.ReLU(),
nn.Linear(128, num_classes),
)
def __init__(self, hparams):
super(MaskRefineModel, self).__init__()
self.save_hyperparameters()
# Hyperparameters
self.hparams = hparams
self.lr = hparams.lr
# Modules
self.net = load_network(hparams)
self.criterion = TverskyLoss(hparams.tversky_alpha,
hparams.tversky_beta)
# Metrics
self.train_metrics = MetricCollection([Precision(), Recall(), F1(2)])
self.val_metrics = MetricCollection([Precision(), Recall(), F1(2)])
def __init__(self,MODEL,TRAIN_DATA,TRAIN_CODES,DEV_DATA,DEV_CODES,TEST_DATA,TEST_CODES,HIDDEN_UNIT1,BATCH_SIZE,LR,EPS,EPOCHS,FREEZE_BERT=False):
super(CorefClassifier, self).__init__()
#self.save_hyperparameters()
self.BEST_THRESHOLD = 0
self.train_data = TRAIN_DATA
self.train_codes = TRAIN_CODES
self.dev_data = DEV_DATA
self.dev_codes = DEV_CODES
self.test_data = TEST_DATA
self.test_codes = TEST_CODES
self.model = AutoModel.from_pretrained(MODEL)
self.hidden_unit1 = HIDDEN_UNIT1
if self.hidden_unit1:
self.hidden_layer1 = nn.Linear(768, self.hidden_unit1)
self.hidden_layer2 = nn.Linear(self.hidden_unit1, 1)
else:
self.hidden_layer1 = nn.Linear(768, 1)
self.lossfn = nn.BCELoss()
self.batch_size = BATCH_SIZE
self.lr = LR
self.eps = EPS
self.epochs = EPOCHS
if FREEZE_BERT:
for param in self.model.parameters():
param.requires_grad = False
#Metrics
self.valid_metrics = MetricCollection([Accuracy(),
Precision(num_classes=1, average='macro'),
Recall(num_classes=1, average='macro'),
F1(num_classes=1, average='macro')
])
self.test_metrics = MetricCollection([Accuracy(),
Precision(num_classes=1, average='macro'),
Recall(num_classes=1, average='macro'),
F1(num_classes=1, average='macro')
])
def __init__(self, hparams):
super(EdgeCompleteModel, self).__init__()
self.save_hyperparameters()
# Hyperparameters
self.hparams = hparams
self.lr = hparams.lr
# Modules
self.mask_refine_net = MaskRefineNet(hparams.mask_refine_weights)
self.mask_refine_net.freeze()
self.net = load_network(hparams)
self.tv_loss = TverskyLoss(hparams.tversky_alpha, hparams.tversky_beta)
# Metrics
self.train_metrics = MetricCollection([Precision(), Recall(), F1(2)])
self.val_metrics = MetricCollection([Precision(), Recall(), F1(2)])
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.model = nn.Module()
self.criterion = F.cross_entropy
self.metrics = nn.ModuleDict({
'accuracy': Accuracy(),
'precision': Precision(),
'recall': Recall(),
})
def __init__(self, params):
super().__init__()
self.hparams = params
self.lr = self.hparams.lr
self.save_hyperparameters()
self.model = Net(name=self.hparams.model)
self.criterion = torch.nn.BCEWithLogitsLoss()
self.train_accuracy = Accuracy(subset_accuracy=True)
self.val_accuracy = Accuracy(subset_accuracy=True)
self.train_recall = Recall()
self.val_recall = Recall()
self.train_df = pd.read_csv(
f'data_preprocessing/train_fold_{self.hparams.fold}.csv')
self.valid_df = pd.read_csv(
f'data_preprocessing/valid_fold_{self.hparams.fold}.csv')
self.train_transforms = A.Compose([
A.Rotate(),
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.Resize(width=self.hparams.img_size,
height=self.hparams.img_size),
A.Normalize(),
ToTensorV2(),
])
self.valid_transforms = A.Compose([
A.Resize(width=self.hparams.img_size,
height=self.hparams.img_size),
A.Normalize(),
ToTensorV2(),
])
self.train_dataset = CellDataset(data_dir=self.hparams.data_dir,
csv_file=self.train_df,
transform=self.train_transforms)
self.val_dataset = CellDataset(data_dir=self.hparams.data_dir,
csv_file=self.valid_df,
transform=self.valid_transforms)
def __init__(self):
super().__init__()
self.cnn = ConvNet()
self.criterion = FocalLoss(alpha=0.5, gamma=2.0, reduction='mean')
self.config = load_classifier_config()
self.learning_rate = self.config['training']['learning_rates']
self.batch_size = self.config['training']['batch_sizes']
self.accuracy = Accuracy(num_classes=2)
self.f1 = F1()
self.recall = Recall()
self.precision = Precision()
def validation_epoch_end(self, outputs):
avg_loss = torch.stack([x['val_loss'] for x in outputs]).mean()
gap_epoch = self.gap[self.val_mode].compute_final()
acc_metric = Accuracy()
recall_metric = Recall()
precision_metric = Precision()
val_acc = acc_metric.forward(
pred=torch.stack([batch['preds'] for batch in outputs]),
target=torch.stack([batch['targets'] for batch in outputs]))
val_recall = recall_metric.forward(
pred=torch.stack([batch['preds'] for batch in outputs]),
target=torch.stack([batch['targets'] for batch in outputs]))
val_precision = precision_metric.forward(
pred=torch.stack([batch['preds'] for batch in outputs]),
target=torch.stack([batch['targets'] for batch in outputs]))
val_logs = {
'val_loss': avg_loss,
'val_gap': gap_epoch,
'val_acc': val_acc,
'val_recall': val_recall,
'val_precision': val_precision
}
# reset metrics every epoch
self.gap[self.val_mode].reset_stats()
return {
'val_loss': avg_loss,
'val_acc': val_acc,
'val_recall': val_recall,
'val_precision': val_precision,
'log': val_logs,
'progress_bar': {
'val_acc': val_acc,
'gap': gap_epoch
}
}
def __init__(self):
super().__init__()
num_classes = len(emotion_dict)
num_classes = 9
weight = torch.tensor([
0.01030928,
0.00552486,
0.00344828,
0.01388889,
0.02222222,
0.01204819,
0.02272727,
0.00307692,
0.00055249,
])
rnn_hidden_size = 256
self.rnn = nn.GRU(768,
rnn_hidden_size,
2,
batch_first=True,
bidirectional=False,
dropout=0.3)
self.criterion = nn.CrossEntropyLoss(weight=weight)
# self.criterion = nn.CrossEntropyLoss()
self.metrics = {
"accuracy": Accuracy(),
"recall_macro": Recall(num_classes=num_classes, average="macro"),
"precision_macro": Precision(num_classes=num_classes,
average="macro"),
}
self.classifier = nn.Sequential(
nn.ReLU(),
nn.Linear(rnn_hidden_size * 1, 128),
nn.Dropout(0.3),
nn.ReLU(),
nn.Linear(128, 64),
nn.Dropout(0.3),
nn.ReLU(),
nn.Linear(64, num_classes),
)
def test_v1_5_metric_precision_recall():
AveragePrecision.__init__.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
AveragePrecision()
Precision.__init__.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
Precision()
Recall.__init__.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
Recall()
PrecisionRecallCurve.__init__.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
PrecisionRecallCurve()
pred = torch.tensor([0, 1, 2, 3])
target = torch.tensor([0, 1, 1, 1])
average_precision.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
assert average_precision(pred, target) == torch.tensor(1.)
precision.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
assert precision(pred, target) == torch.tensor(0.5)
recall.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
assert recall(pred, target) == torch.tensor(0.5)
precision_recall.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
prec, rc = precision_recall(pred, target)
assert prec == torch.tensor(0.5)
assert rc == torch.tensor(0.5)
precision_recall_curve.warned = False
with pytest.deprecated_call(match='It will be removed in v1.5.0'):
prec, rc, thrs = precision_recall_curve(pred, target)
assert torch.equal(prec, torch.tensor([1., 1., 1., 1.]))
assert torch.allclose(rc,
torch.tensor([1., 0.6667, 0.3333, 0.]),
atol=1e-4)
assert torch.equal(thrs, torch.tensor([1, 2, 3]))
def __init__(self, num_classes):
super().__init__()
self.criterion = nn.CrossEntropyLoss()
self.metrics = {
"accuracy": Accuracy(),
"recall_macro": Recall(num_classes=num_classes, average="macro"),
"precision_macro": Precision(num_classes=num_classes,
average="macro"),
}
self.model = models.resnet50(pretrained=True)
## Only the last layer is trained
# for p in self.model.parameters():
# p.requires_grad = False
self.num_ftrs = self.model.fc.in_features
self.num_classes = num_classes
self.model.fc = nn.Linear(self.num_ftrs, self.num_classes)
def __init__(self, hparams:dict):
super().__init__()
# self.model = models.resnet50(pretrained=True)
self.model = models.wide_resnet50_2(pretrained=True)
# self.model = models.densenet201(pretrained=True)
self.model.fc = torch.nn.Linear(self.model.fc.in_features, 2)
# self.model.classifier = torch.nn.Linear(self.model.classifier.in_features, 2)
self.criterion = torch.nn.CrossEntropyLoss()
# self.softmax = torch.nn.Softmax()
# hyper param setting
self.hparmas = hparams
self.init_lr = hparams['optimizer_lr']
print(hparams)
self.accuracy = Accuracy()
self.prec = Precision(num_classes=1, is_multiclass=False)
self.rc = Recall(num_classes=1, is_multiclass=False)
self.f1 = F1(num_classes=1, multilabel=False)
# self.confmat = ConfusionMatrix(num_classes=1)
self.preds = []
self.gts = []
def __init__(self,
*,
d_model,
hidden_dim=2048,
num_heads,
dropout,
num_layers,
activation='relu',
kernel_size,
num_emb,
emb_dim,
learning_rate):
super().__init__()
encoder_layer = nn.TransformerEncoderLayer(d_model,
num_heads,
dim_feedforward=hidden_dim,
dropout=dropout,
activation=activation)
self.dataset = DataModule()
self.learning_rate = learning_rate
train_size = 185452
test_size = 39740
val_size = 39740
self.train_set, self.test_set, self.val_set = random_split(
self.dataset, [train_size, test_size, val_size],
generator=torch.Generator().manual_seed(42))
self.train_loader = DataLoader(self.train_set,
batch_size=4,
num_workers=4,
pin_memory=True)
self.val_loader = DataLoader(self.val_set,
batch_size=4,
num_workers=4,
pin_memory=True)
self.emb = nn.Embedding(num_emb, emb_dim, padding_idx=0)
self.task_list = [
'eco', 'result', 'black', 'white', 'whiteelo', 'blackelo', 'decade'
]
task_labels = {
'eco': eco_dict,
'result': result_dict,
'black': names_dict,
'white': names_dict,
'whiteelo': elo_dict,
'blackelo': elo_dict,
'decade': year_dict
}
self.train_metrics_list = []
self.train_loss_metrics_list = []
self.classifiers = nn.ModuleDict()
self.train_metrics = nn.ModuleDict()
self.val_metrics = nn.ModuleDict()
self.loss = nn.ModuleDict()
for task in self.task_list:
labels = task_labels[task]
xmetrics = pl.metrics.MetricCollection([
Accuracy(),
Precision(num_classes=len(labels), average='macro'),
Recall(num_classes=len(labels), average='macro')
])
self.train_metrics[task] = xmetrics.clone()
self.val_metrics[task] = xmetrics.clone()
self.classifiers[task] = nn.Linear(emb_dim, len(labels))
self.loss[task] = nn.CrossEntropyLoss()
self.encoder = nn.TransformerEncoder(encoder_layer, num_layers)
self.smax = torch.nn.Softmax(dim=1)
def __init__(self,
*,
d_model,
hidden_dim=2048,
num_heads,
dropout,
num_layers,
activation='relu',
kernel_size,
num_emb,
emb_dim,
learning_rate,
label_encoder,
hparams):
super().__init__()
self.losses_weight = {
'ECO': hparams.eco_loss_wt,
'Result': hparams.result_loss_wt,
'Black': hparams.black_loss_wt,
'White': hparams.white_loss_wt,
'WhiteElo2': hparams.whiteelo_loss_wt,
'BlackElo2': hparams.blackelo_loss_wt,
'Decade': hparams.decade_loss_wt
}
self.learning_rate = learning_rate
self.task_list = [
'ECO', 'Result', 'Black', 'White', 'WhiteElo2', 'BlackElo2',
'Decade'
]
self.train_metrics_list = []
self.train_loss_metrics_list = []
self.wt_loss_metrics_list = []
self.classifiers = nn.ModuleDict()
self.train_metrics = nn.ModuleDict()
self.val_metrics = nn.ModuleDict()
self.loss = nn.ModuleDict()
for task in self.task_list:
xmetrics = pl.metrics.MetricCollection([
Accuracy(),
Precision(num_classes=label_encoder[task].vocab_size,
average='macro'),
Recall(num_classes=label_encoder[task].vocab_size,
average='macro')
])
self.train_metrics[task] = xmetrics.clone()
self.val_metrics[task] = xmetrics.clone()
self.classifiers[task] = nn.Linear(emb_dim,
label_encoder[task].vocab_size)
self.loss[task] = nn.CrossEntropyLoss()
self.emb = nn.Embedding(num_emb, emb_dim, padding_idx=0)
encoder_layer = nn.TransformerEncoderLayer(d_model,
num_heads,
dim_feedforward=hidden_dim,
dropout=dropout,
activation=activation)
self.encoder = nn.TransformerEncoder(encoder_layer, num_layers)
self.smax = torch.nn.Softmax(dim=1)
def run_epoch(model,
dataloader,
criterion,
optimizer=None,
epoch=0,
scheduler=None,
device='cpu'):
import pytorch_lightning.metrics.functional.classification as clmetrics
from pytorch_lightning.metrics import Precision, Accuracy, Recall
from sklearn.metrics import roc_auc_score, average_precision_score
metrics = Accumulator()
cnt = 0
total_steps = len(dataloader)
steps = 0
running_corrects = 0
accuracy = Accuracy()
precision = Precision(num_classes=2)
recall = Recall(num_classes=2)
preds_epoch = []
labels_epoch = []
for inputs, labels in dataloader:
steps += 1
inputs = inputs.to(device) # torch.Size([2, 1, 224, 224])
labels = labels.to(device).unsqueeze(1).float() ## torch.Size([2, 1])
outputs = model(inputs) # [batch_size, nb_classes]
loss = criterion(outputs, labels)
if optimizer:
loss.backward()
optimizer.step()
optimizer.zero_grad()
preds_epoch.extend(torch.sigmoid(outputs).tolist())
labels_epoch.extend(labels.tolist())
threshold = 0.5
prob = (torch.sigmoid(outputs) > threshold).long()
conf = torch.flatten(
clmetrics.confusion_matrix(prob, labels, num_classes=2))
tn, fp, fn, tp = conf
metrics.add_dict({
'data_count': len(inputs),
'loss': loss.item() * len(inputs),
'tp': tp.item(),
'tn': tn.item(),
'fp': fp.item(),
'fn': fn.item(),
})
cnt += len(inputs)
if scheduler:
scheduler.step()
del outputs, loss, inputs, labels, prob
logger.info(f'cnt = {cnt}')
metrics['loss'] /= cnt
def safe_div(x, y):
if y == 0:
return 0
return x / y
_TP, _TN, _FP, _FN = metrics['tp'], metrics['tn'], metrics['fp'], metrics[
'fn']
acc = (_TP + _TN) / cnt
sen = safe_div(_TP, (_TP + _FN))
spe = safe_div(_TN, (_FP + _TN))
prec = safe_div(_TP, (_TP + _FP))
metrics.add('accuracy', acc)
metrics.add('sensitivity', sen)
metrics.add('specificity', spe)
metrics.add('precision', prec)
auc = roc_auc_score(labels_epoch, preds_epoch)
aupr = average_precision_score(labels_epoch, preds_epoch)
metrics.add('auroc', auc)
metrics.add('aupr', aupr)
logger.info(metrics)
return metrics, preds_epoch, labels_epoch
class HPALit(pl.LightningModule):
def __init__(self, params):
super().__init__()
self.hparams = params
self.lr = self.hparams.lr
self.save_hyperparameters()
self.model = Net(name=self.hparams.model)
self.criterion = torch.nn.BCEWithLogitsLoss()
self.train_accuracy = Accuracy(subset_accuracy=True)
self.val_accuracy = Accuracy(subset_accuracy=True)
self.train_recall = Recall()
self.val_recall = Recall()
self.train_df = pd.read_csv(
f'data_preprocessing/train_fold_{self.hparams.fold}.csv')
self.valid_df = pd.read_csv(
f'data_preprocessing/valid_fold_{self.hparams.fold}.csv')
self.train_transforms = A.Compose([
A.Rotate(),
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.Resize(width=self.hparams.img_size,
height=self.hparams.img_size),
A.Normalize(),
ToTensorV2(),
])
self.valid_transforms = A.Compose([
A.Resize(width=self.hparams.img_size,
height=self.hparams.img_size),
A.Normalize(),
ToTensorV2(),
])
self.train_dataset = CellDataset(data_dir=self.hparams.data_dir,
csv_file=self.train_df,
transform=self.train_transforms)
self.val_dataset = CellDataset(data_dir=self.hparams.data_dir,
csv_file=self.valid_df,
transform=self.valid_transforms)
def train_dataloader(self):
return DataLoader(
self.train_dataset,
batch_size=self.hparams.batch_size,
shuffle=True,
num_workers=self.hparams.n_workers,
pin_memory=True,
)
def val_dataloader(self):
return DataLoader(
self.val_dataset,
batch_size=self.hparams.batch_size,
shuffle=False,
num_workers=self.hparams.n_workers,
pin_memory=True,
)
def configure_optimizers(self):
optimizer = torch.optim.Adam(self.model.parameters(), lr=self.lr)
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer,
'min',
factor=0.5,
patience=2,
eps=1e-6)
lr_scheduler = {
'scheduler': scheduler,
'interval': 'epoch',
'monitor': 'valid_loss_epoch'
}
return [optimizer], [lr_scheduler]
def training_step(self, batch, batch_idx):
x, y = batch
pred = self.model(x)
train_loss = self.criterion(pred, y)
self.train_accuracy(torch.sigmoid(pred), y.type(torch.int))
self.train_recall(torch.sigmoid(pred), y.type(torch.int))
return {'loss': train_loss}
def training_epoch_end(self, outputs):
train_loss_epoch = torch.stack([x['loss'] for x in outputs]).mean()
self.log('train_loss_epoch', train_loss_epoch)
self.log('train_acc_epoch', self.train_accuracy.compute())
self.log('train_recall_epoch', self.train_recall.compute())
self.train_accuracy.reset()
self.train_recall.reset()
def validation_step(self, batch, batch_idx):
x, y = batch
pred = self.model(x)
val_loss = self.criterion(pred, y)
self.val_accuracy(torch.sigmoid(pred), y.type(torch.int))
self.val_recall(torch.sigmoid(pred), y.type(torch.int))
return {'valid_loss': val_loss}
def validation_epoch_end(self, outputs):
val_loss_epoch = torch.stack([x['valid_loss'] for x in outputs]).mean()
self.log('valid_loss_epoch', val_loss_epoch)
self.log('valid_acc_epoch', self.val_accuracy.compute())
self.log('valid_recall_epoch', self.val_recall.compute())
self.val_accuracy.reset()
self.val_recall.reset()
def __init__(self, num_classes, average='macro', **kwargs):
super(L_Recall, self).__init__()
self.measure = Recall(num_classes=num_classes, average=average)
return