def __init__(
self,
module: BaseModuleClass,
n_obs_training,
lr=1e-3,
weight_decay=1e-6,
n_steps_kl_warmup: Union[int, None] = None,
n_epochs_kl_warmup: Union[int, None] = 400,
reduce_lr_on_plateau: bool = False,
lr_factor: float = 0.6,
lr_patience: int = 30,
lr_threshold: float = 0.0,
lr_scheduler_metric: Literal[
"elbo_validation", "reconstruction_loss_validation",
"kl_local_validation"] = "elbo_validation",
lr_min: float = 0,
adversarial_classifier: Union[bool, Classifier] = False,
scale_adversarial_loss: Union[float, Literal["auto"]] = "auto",
**loss_kwargs,
):
super().__init__(
module=module,
n_obs_training=n_obs_training,
lr=lr,
weight_decay=weight_decay,
n_steps_kl_warmup=n_steps_kl_warmup,
n_epochs_kl_warmup=n_epochs_kl_warmup,
reduce_lr_on_plateau=reduce_lr_on_plateau,
lr_factor=lr_factor,
lr_patience=lr_patience,
lr_threshold=lr_threshold,
lr_scheduler_metric=lr_scheduler_metric,
lr_min=lr_min,
)
if adversarial_classifier is True:
self.n_output_classifier = self.module.n_batch
self.adversarial_classifier = Classifier(
n_input=self.module.n_latent,
n_hidden=32,
n_labels=self.n_output_classifier,
n_layers=2,
logits=True,
)
else:
self.adversarial_classifier = adversarial_classifier
self.scale_adversarial_loss = scale_adversarial_loss
def __init__(
self,
n_input,
n_batch,
n_labels,
n_hidden=128,
n_latent=10,
n_layers=1,
dropout_rate=0.1,
y_prior=None,
dispersion="gene",
log_variational=True,
gene_likelihood="zinb",
):
super().__init__(
n_input,
n_batch,
n_labels,
n_hidden=n_hidden,
n_latent=n_latent,
n_layers=n_layers,
dropout_rate=dropout_rate,
dispersion=dispersion,
log_variational=log_variational,
gene_likelihood=gene_likelihood,
use_observed_lib_size=False,
)
self.z_encoder = Encoder(
n_input,
n_latent,
n_cat_list=[n_batch, n_labels],
n_hidden=n_hidden,
n_layers=n_layers,
dropout_rate=dropout_rate,
)
self.decoder = DecoderSCVI(
n_latent,
n_input,
n_cat_list=[n_batch, n_labels],
n_layers=n_layers,
n_hidden=n_hidden,
)
self.y_prior = torch.nn.Parameter(
y_prior if y_prior is not None else
(1 / n_labels) * torch.ones(1, n_labels),
requires_grad=False,
)
self.classifier = Classifier(n_input,
n_hidden,
n_labels,
n_layers=n_layers,
dropout_rate=dropout_rate)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
if kwargs["adversarial_classifier"] is True:
self.n_output_classifier = 2
self.adversarial_classifier = Classifier(
n_input=self.module.n_latent,
n_hidden=32,
n_labels=self.n_output_classifier,
n_layers=3,
logits=True,
)
else:
self.adversarial_classifier = kwargs["adversarial_classifier"]
def __init__(
self,
adata: AnnData,
**classifier_kwargs,
):
# TODO, catch user warning here and logger warning
# about non count data
super().__init__(adata)
self.module = Classifier(
n_input=self.summary_stats.n_vars,
n_labels=2,
logits=True,
**classifier_kwargs,
)
self._model_summary_string = "Solo model"
self.init_params_ = self._get_init_params(locals())
class AdversarialTrainingPlan(TrainingPlan):
"""
Train vaes with adversarial loss option to encourage latent space mixing.
Parameters
----------
module
A module instance from class ``BaseModuleClass``.
lr
Learning rate used for optimization :class:`~torch.optim.Adam`.
weight_decay
Weight decay used in :class:`~torch.optim.Adam`.
n_steps_kl_warmup
Number of training steps (minibatches) to scale weight on KL divergences from 0 to 1.
Only activated when `n_epochs_kl_warmup` is set to None.
n_epochs_kl_warmup
Number of epochs to scale weight on KL divergences from 0 to 1.
Overrides `n_steps_kl_warmup` when both are not `None`.
reduce_lr_on_plateau
Whether to monitor validation loss and reduce learning rate when validation set
`lr_scheduler_metric` plateaus.
lr_factor
Factor to reduce learning rate.
lr_patience
Number of epochs with no improvement after which learning rate will be reduced.
lr_threshold
Threshold for measuring the new optimum.
lr_scheduler_metric
Which metric to track for learning rate reduction.
lr_min
Minimum learning rate allowed
adversarial_classifier
Whether to use adversarial classifier in the latent space
scale_adversarial_loss
Scaling factor on the adversarial components of the loss.
By default, adversarial loss is scaled from 1 to 0 following opposite of
kl warmup.
**loss_kwargs
Keyword args to pass to the loss method of the `module`.
`kl_weight` should not be passed here and is handled automatically.
"""
def __init__(
self,
module: BaseModuleClass,
lr=1e-3,
weight_decay=1e-6,
n_steps_kl_warmup: Union[int, None] = None,
n_epochs_kl_warmup: Union[int, None] = 400,
reduce_lr_on_plateau: bool = False,
lr_factor: float = 0.6,
lr_patience: int = 30,
lr_threshold: float = 0.0,
lr_scheduler_metric: Literal[
"elbo_validation", "reconstruction_loss_validation",
"kl_local_validation"] = "elbo_validation",
lr_min: float = 0,
adversarial_classifier: Union[bool, Classifier] = False,
scale_adversarial_loss: Union[float, Literal["auto"]] = "auto",
**loss_kwargs,
):
super().__init__(
module=module,
lr=lr,
weight_decay=weight_decay,
n_steps_kl_warmup=n_steps_kl_warmup,
n_epochs_kl_warmup=n_epochs_kl_warmup,
reduce_lr_on_plateau=reduce_lr_on_plateau,
lr_factor=lr_factor,
lr_patience=lr_patience,
lr_threshold=lr_threshold,
lr_scheduler_metric=lr_scheduler_metric,
lr_min=lr_min,
)
if adversarial_classifier is True:
self.n_output_classifier = self.module.n_batch
self.adversarial_classifier = Classifier(
n_input=self.module.n_latent,
n_hidden=32,
n_labels=self.n_output_classifier,
n_layers=2,
logits=True,
)
else:
self.adversarial_classifier = adversarial_classifier
self.scale_adversarial_loss = scale_adversarial_loss
def loss_adversarial_classifier(self,
z,
batch_index,
predict_true_class=True):
n_classes = self.n_output_classifier
cls_logits = torch.nn.LogSoftmax(dim=1)(self.adversarial_classifier(z))
if predict_true_class:
cls_target = one_hot(batch_index, n_classes)
else:
one_hot_batch = one_hot(batch_index, n_classes)
cls_target = torch.zeros_like(one_hot_batch)
# place zeroes where true label is
cls_target.masked_scatter_(
~one_hot_batch.bool(),
torch.ones_like(one_hot_batch) / (n_classes - 1))
l_soft = cls_logits * cls_target
loss = -l_soft.sum(dim=1).mean()
return loss
def training_step(self, batch, batch_idx, optimizer_idx=0):
kappa = (1 - self.kl_weight if self.scale_adversarial_loss == "auto"
else self.scale_adversarial_loss)
batch_tensor = batch[_CONSTANTS.BATCH_KEY]
if optimizer_idx == 0:
loss_kwargs = dict(kl_weight=self.kl_weight)
inference_outputs, _, scvi_loss = self.forward(
batch, loss_kwargs=loss_kwargs)
loss = scvi_loss.loss
# fool classifier if doing adversarial training
if kappa > 0 and self.adversarial_classifier is not False:
z = inference_outputs["z"]
fool_loss = self.loss_adversarial_classifier(
z, batch_tensor, False)
loss += fool_loss * kappa
reconstruction_loss = scvi_loss.reconstruction_loss
self.log("train_loss", loss, on_epoch=True)
return {
"loss": loss,
"reconstruction_loss_sum": reconstruction_loss.sum(),
"kl_local_sum": scvi_loss.kl_local.sum(),
"kl_global": scvi_loss.kl_global,
"n_obs": reconstruction_loss.shape[0],
}
# train adversarial classifier
# this condition will not be met unless self.adversarial_classifier is not False
if optimizer_idx == 1:
inference_inputs = self.module._get_inference_input(batch)
outputs = self.module.inference(**inference_inputs)
z = outputs["z"]
loss = self.loss_adversarial_classifier(z.detach(), batch_tensor,
True)
loss *= kappa
return loss
def training_epoch_end(self, outputs):
# only report from optimizer one loss signature
if self.adversarial_classifier:
super().training_epoch_end(outputs[0])
else:
super().training_epoch_end(outputs)
def configure_optimizers(self):
params1 = filter(lambda p: p.requires_grad, self.module.parameters())
optimizer1 = torch.optim.Adam(params1,
lr=self.lr,
eps=0.01,
weight_decay=self.weight_decay)
config1 = {"optimizer": optimizer1}
if self.reduce_lr_on_plateau:
scheduler1 = ReduceLROnPlateau(
optimizer1,
patience=self.lr_patience,
factor=self.lr_factor,
threshold=self.lr_threshold,
min_lr=self.lr_min,
threshold_mode="abs",
verbose=True,
)
config1.update(
{
"lr_scheduler": scheduler1,
"monitor": self.lr_scheduler_metric,
}, )
if self.adversarial_classifier is not False:
params2 = filter(lambda p: p.requires_grad,
self.adversarial_classifier.parameters())
optimizer2 = torch.optim.Adam(params2,
lr=1e-3,
eps=0.01,
weight_decay=self.weight_decay)
config2 = {"optimizer": optimizer2}
# bug in pytorch lightning requires this way to return
opts = [config1.pop("optimizer"), config2["optimizer"]]
if "lr_scheduler" in config1:
config1["scheduler"] = config1.pop("lr_scheduler")
scheds = [config1]
return opts, scheds
else:
return opts
return config1