scvi.model.base.PyroJitGuideWarmup#

class scvi.model.base.PyroJitGuideWarmup(dataloader=None)[source]#

A callback to warmup a Pyro guide.

This helps initialize all the relevant parameters by running one minibatch through the Pyro model.

Attributes table#

state_key

Identifier for the state of the callback.

Methods table#

load_state_dict(state_dict)

Called when loading a checkpoint, implement to reload callback state given callback's state_dict.

on_after_backward(trainer, pl_module)

Called after loss.backward() and before optimizers are stepped.

on_before_backward(trainer, pl_module, loss)

Called before loss.backward().

on_before_optimizer_step(trainer, pl_module, ...)

Called before optimizer.step().

on_before_zero_grad(trainer, pl_module, ...)

Called before optimizer.zero_grad().

on_exception(trainer, pl_module, exception)

Called when any trainer execution is interrupted by an exception.

on_fit_end(trainer, pl_module)

Called when fit ends.

on_fit_start(trainer, pl_module)

Called when fit begins.

on_load_checkpoint(trainer, pl_module, ...)

Called when loading a model checkpoint, use to reload state.

on_predict_batch_end(trainer, pl_module, ...)

Called when the predict batch ends.

on_predict_batch_start(trainer, pl_module, ...)

Called when the predict batch begins.

on_predict_end(trainer, pl_module)

Called when predict ends.

on_predict_epoch_end(trainer, pl_module, outputs)

Called when the predict epoch ends.

on_predict_epoch_start(trainer, pl_module)

Called when the predict epoch begins.

on_predict_start(trainer, pl_module)

Called when the predict begins.

on_sanity_check_end(trainer, pl_module)

Called when the validation sanity check ends.

on_sanity_check_start(trainer, pl_module)

Called when the validation sanity check starts.

on_save_checkpoint(trainer, pl_module, ...)

Called when saving a checkpoint to give you a chance to store anything else you might want to save.

on_test_batch_end(trainer, pl_module, ...)

Called when the test batch ends.

on_test_batch_start(trainer, pl_module, ...)

Called when the test batch begins.

on_test_end(trainer, pl_module)

Called when the test ends.

on_test_epoch_end(trainer, pl_module)

Called when the test epoch ends.

on_test_epoch_start(trainer, pl_module)

Called when the test epoch begins.

on_test_start(trainer, pl_module)

Called when the test begins.

on_train_batch_end(trainer, pl_module, ...)

Called when the train batch ends.

on_train_batch_start(trainer, pl_module, ...)

Called when the train batch begins.

on_train_end(trainer, pl_module)

Called when the train ends.

on_train_epoch_end(trainer, pl_module)

Called when the train epoch ends.

on_train_epoch_start(trainer, pl_module)

Called when the train epoch begins.

on_train_start(trainer, pl_module)

Way to warmup Pyro Guide in an automated way.

on_validation_batch_end(trainer, pl_module, ...)

Called when the validation batch ends.

on_validation_batch_start(trainer, ...)

Called when the validation batch begins.

on_validation_end(trainer, pl_module)

Called when the validation loop ends.

on_validation_epoch_end(trainer, pl_module)

Called when the val epoch ends.

on_validation_epoch_start(trainer, pl_module)

Called when the val epoch begins.

on_validation_start(trainer, pl_module)

Called when the validation loop begins.

setup(trainer, pl_module, stage)

Called when fit, validate, test, predict, or tune begins.

state_dict()

Called when saving a checkpoint, implement to generate callback's state_dict.

teardown(trainer, pl_module, stage)

Called when fit, validate, test, predict, or tune ends.

Attributes#

state_key

PyroJitGuideWarmup.state_key[source]#

Identifier for the state of the callback.

Used to store and retrieve a callback’s state from the checkpoint dictionary by checkpoint["callbacks"][state_key]. Implementations of a callback need to provide a unique state key if 1) the callback has state and 2) it is desired to maintain the state of multiple instances of that callback.

Methods#

load_state_dict

PyroJitGuideWarmup.load_state_dict(state_dict)[source]#

Called when loading a checkpoint, implement to reload callback state given callback’s state_dict.

Parameters:

state_dict (Dict[str, Any]) – the callback state returned by state_dict.

Return type:

None

on_after_backward

PyroJitGuideWarmup.on_after_backward(trainer, pl_module)[source]#

Called after loss.backward() and before optimizers are stepped.

Return type:

None

on_before_backward

PyroJitGuideWarmup.on_before_backward(trainer, pl_module, loss)[source]#

Called before loss.backward().

Return type:

None

on_before_optimizer_step

PyroJitGuideWarmup.on_before_optimizer_step(trainer, pl_module, optimizer, opt_idx)[source]#

Called before optimizer.step().

Return type:

None

on_before_zero_grad

PyroJitGuideWarmup.on_before_zero_grad(trainer, pl_module, optimizer)[source]#

Called before optimizer.zero_grad().

Return type:

None

on_exception

PyroJitGuideWarmup.on_exception(trainer, pl_module, exception)[source]#

Called when any trainer execution is interrupted by an exception.

Return type:

None

on_fit_end

PyroJitGuideWarmup.on_fit_end(trainer, pl_module)[source]#

Called when fit ends.

Return type:

None

on_fit_start

PyroJitGuideWarmup.on_fit_start(trainer, pl_module)[source]#

Called when fit begins.

Return type:

None

on_load_checkpoint

PyroJitGuideWarmup.on_load_checkpoint(trainer, pl_module, checkpoint)[source]#

Called when loading a model checkpoint, use to reload state.

Parameters:
Return type:

None

on_predict_batch_end

PyroJitGuideWarmup.on_predict_batch_end(trainer, pl_module, outputs, batch, batch_idx, dataloader_idx)[source]#

Called when the predict batch ends.

Return type:

None

on_predict_batch_start

PyroJitGuideWarmup.on_predict_batch_start(trainer, pl_module, batch, batch_idx, dataloader_idx)[source]#

Called when the predict batch begins.

Return type:

None

on_predict_end

PyroJitGuideWarmup.on_predict_end(trainer, pl_module)[source]#

Called when predict ends.

Return type:

None

on_predict_epoch_end

PyroJitGuideWarmup.on_predict_epoch_end(trainer, pl_module, outputs)[source]#

Called when the predict epoch ends.

Return type:

None

on_predict_epoch_start

PyroJitGuideWarmup.on_predict_epoch_start(trainer, pl_module)[source]#

Called when the predict epoch begins.

Return type:

None

on_predict_start

PyroJitGuideWarmup.on_predict_start(trainer, pl_module)[source]#

Called when the predict begins.

Return type:

None

on_sanity_check_end

PyroJitGuideWarmup.on_sanity_check_end(trainer, pl_module)[source]#

Called when the validation sanity check ends.

Return type:

None

on_sanity_check_start

PyroJitGuideWarmup.on_sanity_check_start(trainer, pl_module)[source]#

Called when the validation sanity check starts.

Return type:

None

on_save_checkpoint

PyroJitGuideWarmup.on_save_checkpoint(trainer, pl_module, checkpoint)[source]#

Called when saving a checkpoint to give you a chance to store anything else you might want to save.

Parameters:
Return type:

None

on_test_batch_end

PyroJitGuideWarmup.on_test_batch_end(trainer, pl_module, outputs, batch, batch_idx, dataloader_idx)[source]#

Called when the test batch ends.

Return type:

None

on_test_batch_start

PyroJitGuideWarmup.on_test_batch_start(trainer, pl_module, batch, batch_idx, dataloader_idx)[source]#

Called when the test batch begins.

Return type:

None

on_test_end

PyroJitGuideWarmup.on_test_end(trainer, pl_module)[source]#

Called when the test ends.

Return type:

None

on_test_epoch_end

PyroJitGuideWarmup.on_test_epoch_end(trainer, pl_module)[source]#

Called when the test epoch ends.

Return type:

None

on_test_epoch_start

PyroJitGuideWarmup.on_test_epoch_start(trainer, pl_module)[source]#

Called when the test epoch begins.

Return type:

None

on_test_start

PyroJitGuideWarmup.on_test_start(trainer, pl_module)[source]#

Called when the test begins.

Return type:

None

on_train_batch_end

PyroJitGuideWarmup.on_train_batch_end(trainer, pl_module, outputs, batch, batch_idx)[source]#

Called when the train batch ends.

Return type:

None

Note

The value outputs["loss"] here will be the normalized value w.r.t accumulate_grad_batches of the loss returned from training_step.

on_train_batch_start

PyroJitGuideWarmup.on_train_batch_start(trainer, pl_module, batch, batch_idx)[source]#

Called when the train batch begins.

Return type:

None

on_train_end

PyroJitGuideWarmup.on_train_end(trainer, pl_module)[source]#

Called when the train ends.

Return type:

None

on_train_epoch_end

PyroJitGuideWarmup.on_train_epoch_end(trainer, pl_module)[source]#

Called when the train epoch ends.

To access all batch outputs at the end of the epoch, either:

  1. Implement training_epoch_end in the LightningModule and access outputs via the module OR

  2. Cache data across train batch hooks inside the callback implementation to post-process in this hook.

Return type:

None

on_train_epoch_start

PyroJitGuideWarmup.on_train_epoch_start(trainer, pl_module)[source]#

Called when the train epoch begins.

Return type:

None

on_train_start

PyroJitGuideWarmup.on_train_start(trainer, pl_module)[source]#

Way to warmup Pyro Guide in an automated way.

Also device agnostic.

on_validation_batch_end

PyroJitGuideWarmup.on_validation_batch_end(trainer, pl_module, outputs, batch, batch_idx, dataloader_idx)[source]#

Called when the validation batch ends.

Return type:

None

on_validation_batch_start

PyroJitGuideWarmup.on_validation_batch_start(trainer, pl_module, batch, batch_idx, dataloader_idx)[source]#

Called when the validation batch begins.

Return type:

None

on_validation_end

PyroJitGuideWarmup.on_validation_end(trainer, pl_module)[source]#

Called when the validation loop ends.

Return type:

None

on_validation_epoch_end

PyroJitGuideWarmup.on_validation_epoch_end(trainer, pl_module)[source]#

Called when the val epoch ends.

Return type:

None

on_validation_epoch_start

PyroJitGuideWarmup.on_validation_epoch_start(trainer, pl_module)[source]#

Called when the val epoch begins.

Return type:

None

on_validation_start

PyroJitGuideWarmup.on_validation_start(trainer, pl_module)[source]#

Called when the validation loop begins.

Return type:

None

setup

PyroJitGuideWarmup.setup(trainer, pl_module, stage)[source]#

Called when fit, validate, test, predict, or tune begins.

Return type:

None

state_dict

PyroJitGuideWarmup.state_dict()[source]#

Called when saving a checkpoint, implement to generate callback’s state_dict.

Return type:

Dict[str, Any]

Returns:

A dictionary containing callback state.

teardown

PyroJitGuideWarmup.teardown(trainer, pl_module, stage)[source]#

Called when fit, validate, test, predict, or tune ends.

Return type:

None