def __init__(self, num_epochs: int = 5, lr: float = 1e-4):
super().__init__()
self.save_hyperparameters()
self.encoder = nn.Sequential(nn.Linear(28 * 28, 64), nn.ReLU(),
nn.Linear(64, 3))
self.decoder = nn.Sequential(nn.Linear(3, 64), nn.ReLU(),
nn.Linear(64, 28 * 28))
self.mse = MeanSquaredError()
def __init__(self):
super().__init__()
setattr(self, "layer_0", nn.Linear(16, 64))
setattr(self, "layer_0a", torch.nn.ReLU())
for i in range(1, 3):
setattr(self, f"layer_{i}", nn.Linear(64, 64))
setattr(self, f"layer_{i}a", torch.nn.ReLU())
setattr(self, "layer_end", nn.Linear(64, 1))
self.train_mse = MeanSquaredError()
self.valid_mse = MeanSquaredError()
self.test_mse = MeanSquaredError()
def test_result_collection_batch_size_extraction():
fx_name = "training_step"
log_val = torch.tensor(7.0)
results = _ResultCollection(training=True, device="cpu")
results.batch = torch.randn(1, 4)
train_mse = MeanSquaredError()
train_mse(torch.randn(4, 5), torch.randn(4, 5))
results.log(fx_name,
"train_logs", {
"mse": train_mse,
"log_val": log_val
},
on_step=False,
on_epoch=True)
assert results.batch_size == 1
assert isinstance(results["training_step.train_logs"]["mse"].value,
MeanSquaredError)
assert results["training_step.train_logs"]["log_val"].value == log_val
results = _ResultCollection(training=True, device="cpu")
results.batch = torch.randn(1, 4)
results.log(fx_name, "train_log", log_val, on_step=False, on_epoch=True)
assert results.batch_size == 1
assert results["training_step.train_log"].value == log_val
assert results["training_step.train_log"].cumulated_batch_size == 1
def __init__(
self,
n_channel: int = 1,
learning_rate: float = 1e-4,
backbone: Union[str, nn.Module] = "simple-cnn",
backbone_output_size: int = 0,
n_hidden: int = 512,
dropout: float = 0.2,
loss_fn: str = "mse",
lr_scheduler: bool = False,
lr_scheduler_warmup_steps: int = 100,
lr_scheduler_total_steps: int = 0,
**kwargs,
):
super().__init__()
self.save_hyperparameters()
if isinstance(backbone, str):
self.backbone, backbone_output_size = get_backbone(
backbone, channels=n_channel, dropout=dropout, **kwargs)
self.regressor = Classifier(backbone_output_size, 1, n_hidden, dropout)
if loss_fn == "mse":
self.loss_fn = nn.MSELoss()
elif loss_fn == "mae":
self.loss_fn = nn.L1Loss() # MAE
else:
raise RuntimeError("Undefined loss function")
self.test_metrics = MetricCollection([
MeanAbsoluteError(),
MeanSquaredError(),
])
def test_result_collection_no_batch_size_extraction():
results = _ResultCollection(training=True, device="cpu")
results.batch = torch.randn(1, 4)
fx_name = "training_step"
batch_size = 10
log_val = torch.tensor(7.0)
train_mae = MeanAbsoluteError()
train_mae(torch.randn(4, 5), torch.randn(4, 5))
train_mse = MeanSquaredError()
train_mse(torch.randn(4, 5), torch.randn(4, 5))
results.log(fx_name, "step_log_val", log_val, on_step=True, on_epoch=False)
results.log(fx_name, "epoch_log_val", log_val, on_step=False, on_epoch=True, batch_size=batch_size)
results.log(fx_name, "epoch_sum_log_val", log_val, on_step=True, on_epoch=True, reduce_fx="sum")
results.log(fx_name, "train_mae", train_mae, on_step=True, on_epoch=False)
results.log(fx_name, "train_mse", {"mse": train_mse}, on_step=True, on_epoch=False)
assert results.batch_size is None
assert isinstance(results["training_step.train_mse"]["mse"].value, MeanSquaredError)
assert isinstance(results["training_step.train_mae"].value, MeanAbsoluteError)
assert results["training_step.step_log_val"].value == log_val
assert results["training_step.step_log_val"].cumulated_batch_size == 0
assert results["training_step.epoch_log_val"].value == log_val * batch_size
assert results["training_step.epoch_log_val"].cumulated_batch_size == batch_size
assert results["training_step.epoch_sum_log_val"].value == log_val
def get_metrics_collections_base(
prefix,
is_regressor: bool = True
# device="cuda" if torch.cuda.is_available() else "cpu",
):
if is_regressor:
metrics = MetricCollection(
{
"MeanAbsoluteError": MeanAbsoluteError(),
"MeanSquaredError": MeanSquaredError(),
"SpearmanCorrcoef": SpearmanCorrcoef(),
"PearsonCorrcoef": PearsonCorrcoef()
},
prefix=prefix)
else:
metrics = MetricCollection(
{
"Accuracy": Accuracy(),
"Top_3": Accuracy(top_k=3),
# "Top_5" :Accuracy(top_k=5),
# "Precision_micro":Precision(num_classes=NUM_CLASS,average="micro"),
# "Precision_macro":Precision(num_classes=NUM_CLASS,average="macro"),
# "Recall_micro":Recall(num_classes=NUM_CLASS,average="micro"),
# "Recall_macro":Recall(num_classes=NUM_CLASS,average="macro"),
# "F1_micro":torchmetrics.F1(NUM_CLASS,average="micro"),
# "F1_macro":torchmetrics.F1(NUM_CLASS,average="micro"),
},
prefix=prefix)
return metrics
class LitAutoEncoder(pl.LightningModule):
def __init__(self, num_epochs: int = 5, lr: float = 1e-4):
super().__init__()
self.save_hyperparameters()
self.encoder = nn.Sequential(nn.Linear(28 * 28, 64), nn.ReLU(),
nn.Linear(64, 3))
self.decoder = nn.Sequential(nn.Linear(3, 64), nn.ReLU(),
nn.Linear(64, 28 * 28))
self.mse = MeanSquaredError()
def forward(self, x):
# in lightning, forward defines the prediction/inference actions
embedding = self.encoder(x)
return embedding
def training_step(self, batch, batch_idx):
x, y = batch
x = x.view(x.size(0), -1)
z = self.encoder(x)
x_hat = self.decoder(z)
loss = self.mse(x_hat, x)
self.log('train_mse', loss, sync_dist=True)
return loss
def training_epoch_end(self, outputs):
self.mse.reset()
# ---------------------
# training setup
# ---------------------
def configure_optimizers(self):
optimizer = torch.optim.Adam(self.parameters(), lr=self.hparams.lr)
scheduler = CosineAnnealingWarmRestarts(optimizer,
self.hparams.num_epochs,
eta_min=1e-4)
metric_to_track = 'train_mse'
return {
'optimizer': optimizer,
'lr_scheduler': scheduler,
'monitor': metric_to_track
}
def test_raises_error_on_wrong_input():
"""Make sure that input type errors are raised on the wrong input."""
with pytest.raises(TypeError, match="Metric arg need to be an instance of a .*"):
MetricTracker([1, 2, 3])
with pytest.raises(ValueError, match="Argument `maximize` should either be a single bool or list of bool"):
MetricTracker(MeanAbsoluteError(), maximize=2)
with pytest.raises(
ValueError, match="The len of argument `maximize` should match the length of the metric collection"
):
MetricTracker(MetricCollection([MeanAbsoluteError(), MeanSquaredError()]), maximize=[False, False, False])
def __init__(self, num_users, num_movies, user_training_tensor,
movie_training_tensor, label_training_tensor, batch_size):
super().__init__()
self.users_tensor = user_training_tensor
self.movies_tensor = movie_training_tensor
self.labels_tensor = label_training_tensor
self.user_embedding = torch.nn.Embedding(num_embeddings=num_users,
embedding_dim=32)
self.movie_embedding = torch.nn.Embedding(num_embeddings=num_movies,
embedding_dim=32)
self.output = torch.nn.Linear(64, 1)
self.batch_size = batch_size
# defining some metrics attributes
self.MSE = MeanSquaredError()
self.MAE = MeanAbsoluteError()
self.epoch_loss = 0
loss_history.clear() ##initiate loss history global variable
v_min = v_min if v_min < val else val
v_max = v_max if v_max > val else val
raw = base_fn(preds, target)
return [raw.cpu().numpy(), v_min, v_max]
@pytest.mark.parametrize(
"preds, target, base_metric",
[
(
torch.rand(NUM_BATCHES, BATCH_SIZE, NUM_CLASSES).softmax(dim=-1),
torch.randint(NUM_CLASSES, (NUM_BATCHES, BATCH_SIZE)),
Accuracy(num_classes=NUM_CLASSES),
),
(torch.randn(NUM_BATCHES, BATCH_SIZE),
torch.randn(NUM_BATCHES, BATCH_SIZE), MeanSquaredError()),
],
)
class TestMinMaxWrapper(MetricTester):
"""Test the MinMaxMetric wrapper works as expected."""
atol = 1e-6
# TODO: fix ddp=True case, difference in how compare function works and wrapper metric
@pytest.mark.parametrize("ddp", [False])
def test_minmax_wrapper(self, preds, target, base_metric, ddp):
self.run_class_metric_test(
ddp,
preds,
target,
TestingMinMaxMetric,
def test_raises_error_if_increment_not_called(method, method_input):
tracker = MetricTracker(Accuracy(num_classes=10))
with pytest.raises(ValueError, match=f"`{method}` cannot be called before .*"):
if method_input is not None:
getattr(tracker, method)(*method_input)
else:
getattr(tracker, method)()
@pytest.mark.parametrize(
"base_metric, metric_input, maximize",
[
(Accuracy(num_classes=10), (torch.randint(10, (50,)), torch.randint(10, (50,))), True),
(Precision(num_classes=10), (torch.randint(10, (50,)), torch.randint(10, (50,))), True),
(Recall(num_classes=10), (torch.randint(10, (50,)), torch.randint(10, (50,))), True),
(MeanSquaredError(), (torch.randn(50), torch.randn(50)), False),
(MeanAbsoluteError(), (torch.randn(50), torch.randn(50)), False),
(
MetricCollection([Accuracy(num_classes=10), Precision(num_classes=10), Recall(num_classes=10)]),
(torch.randint(10, (50,)), torch.randint(10, (50,))),
True,
),
(
MetricCollection([Accuracy(num_classes=10), Precision(num_classes=10), Recall(num_classes=10)]),
(torch.randint(10, (50,)), torch.randint(10, (50,))),
[True, True, True],
),
(MetricCollection([MeanSquaredError(), MeanAbsoluteError()]), (torch.randn(50), torch.randn(50)), False),
(
MetricCollection([MeanSquaredError(), MeanAbsoluteError()]),
(torch.randn(50), torch.randn(50)),
def __init__(self, device = 'cuda:0'):
super(iRMSE, self).__init__()
self.rmse = MeanSquaredError(squared = False).to(device)
"kwargs",
[
{},
dict(train_only=True),
dict(
loss=MultiLoss([QuantileLoss(), MAE()]),
data_loader_kwargs=dict(
time_varying_unknown_reals=["volume", "discount"],
target=["volume", "discount"],
),
),
dict(
loss=CrossEntropy(),
data_loader_kwargs=dict(target="agency", ),
),
dict(loss=MeanSquaredError()),
dict(
loss=MeanSquaredError(),
data_loader_kwargs=dict(min_prediction_length=1,
min_encoder_length=1),
),
],
)
def test_integration(data_with_covariates, tmp_path, gpus, kwargs):
_integration(data_with_covariates.assign(target=lambda x: x.volume),
tmp_path, gpus, **kwargs)
@pytest.fixture
def model(dataloaders_with_covariates):
dataset = dataloaders_with_covariates["train"].dataset
found_zero = _sample_checker(old_samples, new_samples, operator.ne, 0)
assert found_zero, "resampling did not work because all samples were atleast sampled once"
@pytest.mark.parametrize("device", ["cpu", "cuda"])
@pytest.mark.parametrize("sampling_strategy", ["poisson", "multinomial"])
@pytest.mark.parametrize(
"metric, sk_metric",
[
[
Precision(average="micro"),
partial(precision_score, average="micro")
],
[Recall(average="micro"),
partial(recall_score, average="micro")],
[MeanSquaredError(), mean_squared_error],
],
)
def test_bootstrap(device, sampling_strategy, metric, sk_metric):
"""Test that the different bootstraps gets updated as we expected and that the compute method works."""
if device == "cuda" and not torch.cuda.is_available():
pytest.skip("Test with device='cuda' requires gpu")
_kwargs = {
"base_metric": metric,
"mean": True,
"std": True,
"raw": True,
"sampling_strategy": sampling_strategy
}
if _TORCH_GREATER_EQUAL_1_7: