cellink.ml.DonorMILModel

cellink.ml.DonorMILModel#

class cellink.ml.DonorMILModel(n_input_donor=None, n_input_cell=None, n_hidden=128, n_output=1, lr=0.001)#

A PyTorch Lightning model for multiple instance learning (MIL) using donor-level and cell-level features. This model encodes donor-level features and aggregates variable-length cell-level features using an attention mechanism before concatenating them for final regression or classification.

Parameters:

n_input_donor (int) – Number of input features for the donor-level encoder.
n_input_cell (int) – Number of input features for the cell-level encoder.
n_hidden (int, default=128) – Dimension of the hidden representation for donor and cell encoders.
n_output (int, default=1) – Number of output units (e.g., 1 for regression, >1 for multi-class classification).
lr (float, default=1e-3) – Learning rate for the Adam optimizer.

Attributes table#

`CHECKPOINT_HYPER_PARAMS_KEY`
`CHECKPOINT_HYPER_PARAMS_NAME`
`CHECKPOINT_HYPER_PARAMS_TYPE`
`T_destination`
`automatic_optimization`	If set to `False` you are responsible for calling `.backward()`, `.step()`, `.zero_grad()`.
`call_super_init`
`current_epoch`	The current epoch in the `Trainer`, or 0 if not attached.
`device`
`device_mesh`	Strategies like `ModelParallelStrategy` will create a device mesh that can be accessed in the `configure_model()` hook to parallelize the LightningModule.
`dtype`
`dump_patches`
`example_input_array`	The example input array is a specification of what the module can consume in the `forward()` method.
`fabric`
`global_rank`	The index of the current process across all nodes and devices.
`global_step`	Total training batches seen across all epochs.
`hparams`	The collection of hyperparameters saved with `save_hyperparameters()`.
`hparams_initial`	The collection of hyperparameters saved with `save_hyperparameters()`.
`local_rank`	The index of the current process within a single node.
`logger`	Reference to the logger object in the Trainer.
`loggers`	Reference to the list of loggers in the Trainer.
`on_gpu`	Returns `True` if this model is currently located on a GPU.
`strict_loading`	Determines how Lightning loads this model using `.load_state_dict(..., strict=model.strict_loading)`.
`trainer`
`training`

Methods table#

`add_module`(name, module)	Add a child module to the current module.
`all_gather`(data[, group, sync_grads])	Gather tensors or collections of tensors from multiple processes.
`apply`(fn)	Apply `fn` recursively to every submodule (as returned by `.children()`) as well as self.
`backward`(loss, args, *kwargs)	Called to perform backward on the loss returned in `training_step()`.
`bfloat16`()	Casts all floating point parameters and buffers to `bfloat16` datatype.
`buffers`([recurse])	Return an iterator over module buffers.
`children`()	Return an iterator over immediate children modules.
`clip_gradients`(optimizer[, ...])	Handles gradient clipping internally.
`compile`(args, *kwargs)	Compile this Module's forward using `torch.compile()`.
`configure_callbacks`()	Configure model-specific callbacks.
`configure_gradient_clipping`(optimizer[, ...])	Perform gradient clipping for the optimizer parameters.
`configure_model`()	Hook to create modules in a strategy and precision aware context.
`configure_optimizers`()	Configure the optimizer for training.
`configure_sharded_model`()	Deprecated.
`cpu`()	See `torch.nn.Module.cpu()`.
`cuda`([device])	Moves all model parameters and buffers to the GPU.
`double`()	See `torch.nn.Module.double()`.
`eval`()	Set the module in evaluation mode.
`extra_repr`()	Return the extra representation of the module.
`float`()	See `torch.nn.Module.float()`.
`forward`(batch)	Forward pass of the model.
`freeze`()	Freeze all params for inference.
`get_buffer`(target)	Return the buffer given by `target` if it exists, otherwise throw an error.
`get_extra_state`()	Return any extra state to include in the module's state_dict.
`get_parameter`(target)	Return the parameter given by `target` if it exists, otherwise throw an error.
`get_submodule`(target)	Return the submodule given by `target` if it exists, otherwise throw an error.
`half`()	See `torch.nn.Module.half()`.
`ipu`([device])	Move all model parameters and buffers to the IPU.
`load_from_checkpoint`(cls, checkpoint_path[, ...])	Primary way of loading a model from a checkpoint.
`load_state_dict`(state_dict[, strict, assign])	Copy parameters and buffers from `state_dict` into this module and its descendants.
`log`(name, value[, prog_bar, logger, ...])	Log a key, value pair.
`log_dict`(dictionary[, prog_bar, logger, ...])	Log a dictionary of values at once.
`lr_scheduler_step`(scheduler, metric)	Override this method to adjust the default way the `Trainer` calls each scheduler.
`lr_schedulers`()	Returns the learning rate scheduler(s) that are being used during training.
`manual_backward`(loss, args, *kwargs)	Call this directly from your `training_step()` when doing optimizations manually.
`modules`([remove_duplicate])	Return an iterator over all modules in the network.
`mtia`([device])	Move all model parameters and buffers to the MTIA.
`named_buffers`([prefix, recurse, ...])	Return an iterator over module buffers, yielding both the name of the buffer as well as the buffer itself.
`named_children`()	Return an iterator over immediate children modules, yielding both the name of the module as well as the module itself.
`named_modules`([memo, prefix, remove_duplicate])	Return an iterator over all modules in the network, yielding both the name of the module as well as the module itself.
`named_parameters`([prefix, recurse, ...])	Return an iterator over module parameters, yielding both the name of the parameter as well as the parameter itself.
`on_after_backward`()	Called after `loss.backward()` and before optimizers are stepped.
`on_after_batch_transfer`(batch, dataloader_idx)	Override to alter or apply batch augmentations to your batch after it is transferred to the device.
`on_before_backward`(loss)	Called before `loss.backward()`.
`on_before_batch_transfer`(batch, dataloader_idx)	Override to alter or apply batch augmentations to your batch before it is transferred to the device.
`on_before_optimizer_step`(optimizer)	Called before `optimizer.step()`.
`on_before_zero_grad`(optimizer)	Called after `training_step()` and before `optimizer.zero_grad()`.
`on_fit_end`()	Called at the very end of fit.
`on_fit_start`()	Called at the very beginning of fit.
`on_load_checkpoint`(checkpoint)	Called by Lightning to restore your model.
`on_predict_batch_end`(outputs, batch, batch_idx)	Called in the predict loop after the batch.
`on_predict_batch_start`(batch, batch_idx[, ...])	Called in the predict loop before anything happens for that batch.
`on_predict_end`()	Called at the end of predicting.
`on_predict_epoch_end`()	Called at the end of predicting.
`on_predict_epoch_start`()	Called at the beginning of predicting.
`on_predict_model_eval`()	Called when the predict loop starts.
`on_predict_start`()	Called at the beginning of predicting.
`on_save_checkpoint`(checkpoint)	Called by Lightning when saving a checkpoint to give you a chance to store anything else you might want to save.
`on_test_batch_end`(outputs, batch, batch_idx)	Called in the test loop after the batch.
`on_test_batch_start`(batch, batch_idx[, ...])	Called in the test loop before anything happens for that batch.
`on_test_end`()	Called at the end of testing.
`on_test_epoch_end`()	Called in the test loop at the very end of the epoch.
`on_test_epoch_start`()	Called in the test loop at the very beginning of the epoch.
`on_test_model_eval`()	Called when the test loop starts.
`on_test_model_train`()	Called when the test loop ends.
`on_test_start`()	Called at the beginning of testing.
`on_train_batch_end`(outputs, batch, batch_idx)	Called in the training loop after the batch.
`on_train_batch_start`(batch, batch_idx)	Called in the training loop before anything happens for that batch.
`on_train_end`()	Called at the end of training before logger experiment is closed.
`on_train_epoch_end`()	Called in the training loop at the very end of the epoch.
`on_train_epoch_start`()	Called in the training loop at the very beginning of the epoch.
`on_train_start`()	Called at the beginning of training after sanity check.
`on_validation_batch_end`(outputs, batch, ...)	Called in the validation loop after the batch.
`on_validation_batch_start`(batch, batch_idx)	Called in the validation loop before anything happens for that batch.
`on_validation_end`()	Called at the end of validation.
`on_validation_epoch_end`()	Called in the validation loop at the very end of the epoch.
`on_validation_epoch_start`()	Called in the validation loop at the very beginning of the epoch.
`on_validation_model_eval`()	Called when the validation loop starts.
`on_validation_model_train`()	Called when the validation loop ends.
`on_validation_model_zero_grad`()	Called by the training loop to release gradients before entering the validation loop.
`on_validation_start`()	Called at the beginning of validation.
`optimizer_step`(epoch, batch_idx, optimizer)	Override this method to adjust the default way the `Trainer` calls the optimizer.
`optimizer_zero_grad`(epoch, batch_idx, optimizer)	Override this method to change the default behaviour of `optimizer.zero_grad()`.
`optimizers`([use_pl_optimizer])	Returns the optimizer(s) that are being used during training.
`parameters`([recurse])	Return an iterator over module parameters.
`predict_dataloader`()	An iterable or collection of iterables specifying prediction samples.
`predict_step`(args, *kwargs)	Step function called during `predict()`.
`prepare_data`()	Use this to download and prepare data.
`print`(args, *kwargs)	Prints only from process 0.
`register_backward_hook`(hook)	Register a backward hook on the module.
`register_buffer`(name, tensor[, persistent])	Add a buffer to the module.
`register_forward_hook`(hook, *[, prepend, ...])	Register a forward hook on the module.
`register_forward_pre_hook`(hook, *[, ...])	Register a forward pre-hook on the module.
`register_full_backward_hook`(hook[, prepend])	Register a backward hook on the module.
`register_full_backward_pre_hook`(hook[, prepend])	Register a backward pre-hook on the module.
`register_load_state_dict_post_hook`(hook)	Register a post-hook to be run after module's `load_state_dict()` is called.
`register_load_state_dict_pre_hook`(hook)	Register a pre-hook to be run before module's `load_state_dict()` is called.
`register_module`(name, module)	Alias for `add_module()`.
`register_parameter`(name, param)	Add a parameter to the module.
`register_state_dict_post_hook`(hook)	Register a post-hook for the `state_dict()` method.
`register_state_dict_pre_hook`(hook)	Register a pre-hook for the `state_dict()` method.
`remove_ignored_hparams`(ignore_list)	Remove ignored hyperparameters from the stored state.
`requires_grad_`([requires_grad])	Change if autograd should record operations on parameters in this module.
`save_hyperparameters`(*args[, ignore, frame, ...])	Save arguments to `hparams` attribute.
`set_extra_state`(state)	Set extra state contained in the loaded `state_dict`.
`set_submodule`(target, module[, strict])	Set the submodule given by `target` if it exists, otherwise throw an error.
`setup`(stage)	Called at the beginning of fit (train + validate), validate, test, or predict.
`share_memory`()	See `torch.Tensor.share_memory_()`.
`state_dict`(*args[, destination, prefix, ...])	Return a dictionary containing references to the whole state of the module.
`teardown`(stage)	Called at the end of fit (train + validate), validate, test, or predict.
`test_dataloader`()	An iterable or collection of iterables specifying test samples.
`test_step`(args, *kwargs)	Operates on a single batch of data from the test set.
`to`(args, *kwargs)	See `torch.nn.Module.to()`.
`to_empty`(*, device[, recurse])	Move the parameters and buffers to the specified device without copying storage.
`to_onnx`([file_path, input_sample])	Saves the model in ONNX format.
`to_tensorrt`([file_path, input_sample, ir, ...])	Export the model to ScriptModule or GraphModule using TensorRT compile backend.
`to_torchscript`([file_path, method, ...])	By default compiles the whole model to a `ScriptModule`.
`toggle_optimizer`(optimizer)	Makes sure only the gradients of the current optimizer's parameters are calculated in the training step to prevent dangling gradients in multiple-optimizer setup.
`toggled_optimizer`(optimizer)	Makes sure only the gradients of the current optimizer's parameters are calculated in the training step to prevent dangling gradients in multiple-optimizer setup.
`train`([mode])	Set the module in training mode.
`train_dataloader`()	An iterable or collection of iterables specifying training samples.
`training_step`(batch, batch_idx)	Training step used by PyTorch Lightning.
`transfer_batch_to_device`(batch, device, ...)	Override this hook if your `DataLoader` returns tensors wrapped in a custom data structure.
`type`(dst_type)	See `torch.nn.Module.type()`.
`unfreeze`()	Unfreeze all parameters for training.
`untoggle_optimizer`(optimizer)	Resets the state of required gradients that were toggled with `toggle_optimizer()`.
`val_dataloader`()	An iterable or collection of iterables specifying validation samples.
`validation_step`(batch, batch_idx)	Validation step used by PyTorch Lightning.
`xpu`([device])	Move all model parameters and buffers to the XPU.
`zero_grad`([set_to_none])	Reset gradients of all model parameters.

Attributes#

DonorMILModel.CHECKPOINT_HYPER_PARAMS_KEY = 'hyper_parameters'#

DonorMILModel.CHECKPOINT_HYPER_PARAMS_NAME = 'hparams_name'#

DonorMILModel.CHECKPOINT_HYPER_PARAMS_TYPE = 'hparams_type'#

DonorMILModel.T_destination = ~T_destination#

DonorMILModel.automatic_optimization#: If set to False you are responsible for calling .backward(), .step(), .zero_grad().

DonorMILModel.call_super_init: bool = False#

DonorMILModel.current_epoch#: The current epoch in the Trainer, or 0 if not attached.

DonorMILModel.device#

DonorMILModel.device_mesh#: Strategies like ModelParallelStrategy will create a device mesh that can be accessed in the configure_model() hook to parallelize the LightningModule.

DonorMILModel.dtype#

DonorMILModel.dump_patches: bool = False#

DonorMILModel.example_input_array#

The example input array is a specification of what the module can consume in the forward() method. The return type is interpreted as follows:

Single tensor: It is assumed the model takes a single argument, i.e., model.forward(model.example_input_array)
Tuple: The input array should be interpreted as a sequence of positional arguments, i.e., model.forward(*model.example_input_array)
Dict: The input array represents named keyword arguments, i.e., model.forward(**model.example_input_array)

DonorMILModel.fabric#

DonorMILModel.global_rank#: The index of the current process across all nodes and devices.

DonorMILModel.global_step#

Total training batches seen across all epochs.

If no Trainer is attached, this property is 0.

DonorMILModel.hparams#

The collection of hyperparameters saved with save_hyperparameters(). It is mutable by the user. For the frozen set of initial hyperparameters, use hparams_initial.

Returns:: Mutable hyperparameters dictionary

DonorMILModel.hparams_initial#

The collection of hyperparameters saved with save_hyperparameters(). These contents are read-only. Manual updates to the saved hyperparameters can instead be performed through hparams.

Returns:: AttributeDict: immutable initial hyperparameters

DonorMILModel.local_rank#: The index of the current process within a single node.

DonorMILModel.logger#: Reference to the logger object in the Trainer.

DonorMILModel.loggers#: Reference to the list of loggers in the Trainer.

DonorMILModel.on_gpu#

Returns True if this model is currently located on a GPU.

Useful to set flags around the LightningModule for different CPU vs GPU behavior.

DonorMILModel.strict_loading#: Determines how Lightning loads this model using .load_state_dict(..., strict=model.strict_loading).

DonorMILModel.trainer#

DonorMILModel.training: bool#

Methods#

DonorMILModel.add_module(name, module)#

Add a child module to the current module.

The module can be accessed as an attribute using the given name.

Return type:: None

Args:

name (str): name of the child module. The child module can be: accessed from this module using the given name

module (Module): child module to be added to the module.

DonorMILModel.all_gather(data, group=None, sync_grads=False)#

Gather tensors or collections of tensors from multiple processes.

This method needs to be called on all processes and the tensors need to have the same shape across all processes, otherwise your program will stall forever.

Return type:: Union[Tensor, dict, list, tuple]

Args:: data: int, float, tensor of shape (batch, …), or a (possibly nested) collection thereof. group: the process group to gather results from. Defaults to all processes (world) sync_grads: flag that allows users to synchronize gradients for the all_gather operation
Return:: A tensor of shape (world_size, batch, …), or if the input was a collection the output will also be a collection with tensors of this shape. For the special case where world_size is 1, no additional dimension is added to the tensor(s).

DonorMILModel.apply(fn)#

Apply fn recursively to every submodule (as returned by .children()) as well as self.

Typical use includes initializing the parameters of a model (see also nn-init-doc).

Return type:: Self

Args:: fn (Module -> None): function to be applied to each submodule
Returns:: Module: self

Example:

>>> @torch.no_grad()
>>> def init_weights(m):
>>>     print(m)
>>>     if type(m) is nn.Linear:
>>>         m.weight.fill_(1.0)
>>>         print(m.weight)
>>> net = nn.Sequential(nn.Linear(2, 2), nn.Linear(2, 2))
>>> net.apply(init_weights)
Linear(in_features=2, out_features=2, bias=True)
Parameter containing:
tensor([[1., 1.],
        [1., 1.]], requires_grad=True)
Linear(in_features=2, out_features=2, bias=True)
Parameter containing:
tensor([[1., 1.],
        [1., 1.]], requires_grad=True)
Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
)

DonorMILModel.backward(loss, *args, **kwargs)#

Called to perform backward on the loss returned in training_step(). Override this hook with your own implementation if you need to.

Return type:: None

Args:

loss: The loss tensor returned by training_step(). If gradient accumulation is used, the loss here: holds the normalized value (scaled by 1 / accumulation steps).

Example:

def backward(self, loss):
    loss.backward()

DonorMILModel.bfloat16()#

Casts all floating point parameters and buffers to bfloat16 datatype.

Note

This method modifies the module in-place.

Returns:: Module: self

Return type:: Self

DonorMILModel.buffers(recurse=True)#

Return an iterator over module buffers.

Return type:: Iterator[Tensor]

Args:

recurse (bool): if True, then yields buffers of this module: and all submodules. Otherwise, yields only buffers that are direct members of this module.

Yields:

torch.Tensor: module buffer

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for buf in model.buffers():
>>>     print(type(buf), buf.size())
<class 'torch.Tensor'> (20L,)
<class 'torch.Tensor'> (20L, 1L, 5L, 5L)

DonorMILModel.children()#

Return an iterator over immediate children modules.

Return type:: Iterator[Module]

Yields:: Module: a child module

DonorMILModel.clip_gradients(optimizer, gradient_clip_val=None, gradient_clip_algorithm=None)#

Handles gradient clipping internally.

Return type:: None

Note:

Do not override this method. If you want to customize gradient clipping, consider using configure_gradient_clipping() method.
For manual optimization (self.automatic_optimization = False), if you want to use gradient clipping, consider calling self.clip_gradients(opt, gradient_clip_val=0.5, gradient_clip_algorithm="norm") manually in the training step.

Args:

optimizer: Current optimizer being used. gradient_clip_val: The value at which to clip gradients. gradient_clip_algorithm: The gradient clipping algorithm to use. Pass gradient_clip_algorithm="value"

to clip by value, and gradient_clip_algorithm="norm" to clip by norm.

DonorMILModel.compile(*args, **kwargs)#

Compile this Module’s forward using torch.compile().

This Module’s __call__ method is compiled and all arguments are passed as-is to torch.compile().

See torch.compile() for details on the arguments for this function.

Return type:: None

DonorMILModel.configure_callbacks()#

Configure model-specific callbacks. When the model gets attached, e.g., when .fit() or .test() gets called, the list or a callback returned here will be merged with the list of callbacks passed to the Trainer’s callbacks argument. If a callback returned here has the same type as one or several callbacks already present in the Trainer’s callbacks list, it will take priority and replace them. In addition, Lightning will make sure ModelCheckpoint callbacks run last.

Return type:: Union[Sequence[Callback], Callback]

Return:: A callback or a list of callbacks which will extend the list of callbacks in the Trainer.

Example:

def configure_callbacks(self):
    early_stop = EarlyStopping(monitor="val_acc", mode="max")
    checkpoint = ModelCheckpoint(monitor="val_loss")
    return [early_stop, checkpoint]

DonorMILModel.configure_gradient_clipping(optimizer, gradient_clip_val=None, gradient_clip_algorithm=None)#

Perform gradient clipping for the optimizer parameters. Called before optimizer_step().

Return type:: None

Args:

optimizer: Current optimizer being used. gradient_clip_val: The value at which to clip gradients. By default, value passed in Trainer

will be available here.

gradient_clip_algorithm: The gradient clipping algorithm to use. By default, value: passed in Trainer will be available here.

Example:

def configure_gradient_clipping(self, optimizer, gradient_clip_val, gradient_clip_algorithm):
    # Implement your own custom logic to clip gradients
    # You can call `self.clip_gradients` with your settings:
    self.clip_gradients(
        optimizer,
        gradient_clip_val=gradient_clip_val,
        gradient_clip_algorithm=gradient_clip_algorithm
    )

DonorMILModel.configure_model()#

Hook to create modules in a strategy and precision aware context.

This is particularly useful for when using sharded strategies (FSDP and DeepSpeed), where we’d like to shard the model instantly to save memory and initialization time. For non-sharded strategies, you can choose to override this hook or to initialize your model under the init_module() context manager.

This hook is called during each of fit/val/test/predict stages in the same process, so ensure that implementation of this hook is idempotent, i.e., after the first time the hook is called, subsequent calls to it should be a no-op.

Return type:: None

DonorMILModel.configure_optimizers()#

Configure the optimizer for training.

Returns:: torch.optim.Optimizer Adam optimizer with learning rate specified in self.hparams.lr.

DonorMILModel.configure_sharded_model()#

Deprecated.

Use configure_model() instead.

Return type:: None

DonorMILModel.cpu()#

See torch.nn.Module.cpu().

Return type:: Self

DonorMILModel.cuda(device=None)#

Moves all model parameters and buffers to the GPU. This also makes associated parameters and buffers different objects. So it should be called before constructing optimizer if the module will live on GPU while being optimized.

Return type:: Self

Arguments:

device: If specified, all parameters will be copied to that device. If None, the current CUDA device: index will be used.

Returns:

Module: self

DonorMILModel.double()#

See torch.nn.Module.double().

Return type:: Self

DonorMILModel.eval()#

Set the module in evaluation mode.

This has an effect only on certain modules. See the documentation of particular modules for details of their behaviors in training/evaluation mode, i.e. whether they are affected, e.g. Dropout, BatchNorm, etc.

This is equivalent with self.train(False).

See locally-disable-grad-doc for a comparison between .eval() and several similar mechanisms that may be confused with it.

Return type:: Self

Returns:: Module: self

DonorMILModel.extra_repr()#

Return the extra representation of the module.

To print customized extra information, you should re-implement this method in your own modules. Both single-line and multi-line strings are acceptable.

Return type:: str

DonorMILModel.float()#

See torch.nn.Module.float().

Return type:: Self

DonorMILModel.forward(batch)#

Forward pass of the model.

Parameters:

batch (dict) –

Dictionary containing input features: - “donor_x”: Tensor of shape (B, D_donor) with donor-level features. - “cell_x”: List of tensors [(N_i, D_cell), …] with cell-level features

for each donor in the batch, where N_i is the number of cells for donor i.

Returns:

torch.Tensor Output logits of shape (B, n_output), representing the predicted target for each donor.

DonorMILModel.freeze()#

Freeze all params for inference.

model = MyLightningModule(...)
model.freeze()

Return type:: Self

Returns:: LightningModule with all parameters frozen.

DonorMILModel.get_buffer(target)#

Return the buffer given by target if it exists, otherwise throw an error.

See the docstring for get_submodule for a more detailed explanation of this method’s functionality as well as how to correctly specify target.

Return type:: Tensor

Args:

target: The fully-qualified string name of the buffer: to look for. (See get_submodule for how to specify a fully-qualified string.)

Returns:

torch.Tensor: The buffer referenced by target

Raises:

AttributeError: If the target string references an invalid: path or resolves to something that is not a buffer

DonorMILModel.get_extra_state()#

Return any extra state to include in the module’s state_dict.

Implement this and a corresponding set_extra_state() for your module if you need to store extra state. This function is called when building the module’s state_dict().

Note that extra state should be picklable to ensure working serialization of the state_dict. We only provide backwards compatibility guarantees for serializing Tensors; other objects may break backwards compatibility if their serialized pickled form changes.

Return type:: Any

Returns:: object: Any extra state to store in the module’s state_dict

DonorMILModel.get_parameter(target)#

Return the parameter given by target if it exists, otherwise throw an error.

See the docstring for get_submodule for a more detailed explanation of this method’s functionality as well as how to correctly specify target.

Return type:: Parameter

Args:

target: The fully-qualified string name of the Parameter: to look for. (See get_submodule for how to specify a fully-qualified string.)

Returns:

torch.nn.Parameter: The Parameter referenced by target

Raises:

AttributeError: If the target string references an invalid: path or resolves to something that is not an nn.Parameter

DonorMILModel.get_submodule(target)#

Return the submodule given by target if it exists, otherwise throw an error.

For example, let’s say you have an nn.Module A that looks like this:

A(
    (net_b): Module(
        (net_c): Module(
            (conv): Conv2d(16, 33, kernel_size=(3, 3), stride=(2, 2))
        )
        (linear): Linear(in_features=100, out_features=200, bias=True)
    )
)

(The diagram shows an nn.Module A. A which has a nested submodule net_b, which itself has two submodules net_c and linear. net_c then has a submodule conv.)

To check whether or not we have the linear submodule, we would call get_submodule("net_b.linear"). To check whether we have the conv submodule, we would call get_submodule("net_b.net_c.conv").

The runtime of get_submodule is bounded by the degree of module nesting in target. A query against named_modules achieves the same result, but it is O(N) in the number of transitive modules. So, for a simple check to see if some submodule exists, get_submodule should always be used.

Return type:: Module

Args:

target: The fully-qualified string name of the submodule: to look for. (See above example for how to specify a fully-qualified string.)

Returns:

torch.nn.Module: The submodule referenced by target

Raises:

AttributeError: If at any point along the path resulting from: the target string the (sub)path resolves to a non-existent attribute name or an object that is not an instance of nn.Module.

DonorMILModel.half()#

See torch.nn.Module.half().

Return type:: Self

DonorMILModel.ipu(device=None)#

Move all model parameters and buffers to the IPU.

This also makes associated parameters and buffers different objects. So it should be called before constructing the optimizer if the module will live on IPU while being optimized.

Note

This method modifies the module in-place.

Arguments:

device (int, optional): if specified, all parameters will be: copied to that device

Returns:

Module: self

Return type:: Self

DonorMILModel.load_from_checkpoint(cls, checkpoint_path, map_location=None, hparams_file=None, strict=None, weights_only=None, **kwargs)#

Primary way of loading a model from a checkpoint. When Lightning saves a checkpoint it stores the arguments passed to __init__ in the checkpoint under "hyper_parameters".

Any arguments specified through **kwargs will override args stored in "hyper_parameters".

Return type:: Self

Args:

checkpoint_path: Path to checkpoint. This can also be a URL, or file-like object map_location:

If your checkpoint saved a GPU model and you now load on CPUs or a different number of GPUs, use this to map to the new setup. The behaviour is the same as in torch.load().

hparams_file: Optional path to a .yaml or .csv file with hierarchical structure

as in this example:

drop_prob: 0.2
dataloader:
    batch_size: 32

You most likely won’t need this since Lightning will always save the hyperparameters to the checkpoint. However, if your checkpoint weights don’t have the hyperparameters saved, use this method to pass in a .yaml file with the hparams you’d like to use. These will be converted into a dict and passed into your LightningModule for use.

If your model’s hparams argument is Namespace and .yaml file has hierarchical structure, you need to refactor your model to treat hparams as dict.

strict: Whether to strictly enforce that the keys in checkpoint_path match the keys

returned by this module’s state dict. Defaults to True unless LightningModule.strict_loading is set, in which case it defaults to the value of LightningModule.strict_loading.

weights_only: If True, restricts loading to state_dicts of plain torch.Tensor and other

primitive types. If loading a checkpoint from a trusted source that contains an nn.Module, use weights_only=False. If loading checkpoint from an untrusted source, we recommend using weights_only=True. For more information, please refer to the PyTorch Developer Notes on Serialization Semantics.

**kwargs: Any extra keyword args needed to init the model. Can also be used to override saved

hyperparameter values.

Return:

LightningModule instance with loaded weights and hyperparameters (if available).

Note:

load_from_checkpoint is a class method. You should use your LightningModule class to call it instead of the LightningModule instance, or a TypeError will be raised.

Note:

To ensure all layers can be loaded from the checkpoint, this function will call configure_model() directly after instantiating the model if this hook is overridden in your LightningModule. However, note that load_from_checkpoint does not support loading sharded checkpoints, and you may run out of memory if the model is too large. In this case, consider loading through the Trainer via .fit(ckpt_path=...).

Example:

# load weights without mapping ...
model = MyLightningModule.load_from_checkpoint('path/to/checkpoint.ckpt')

# or load weights mapping all weights from GPU 1 to GPU 0 ...
map_location = {'cuda:1':'cuda:0'}
model = MyLightningModule.load_from_checkpoint(
    'path/to/checkpoint.ckpt',
    map_location=map_location
)

# or load weights and hyperparameters from separate files.
model = MyLightningModule.load_from_checkpoint(
    'path/to/checkpoint.ckpt',
    hparams_file='/path/to/hparams_file.yaml'
)

# override some of the params with new values
model = MyLightningModule.load_from_checkpoint(
    PATH,
    num_layers=128,
    pretrained_ckpt_path=NEW_PATH,
)

# predict
pretrained_model.eval()
pretrained_model.freeze()
y_hat = pretrained_model(x)

DonorMILModel.load_state_dict(state_dict, strict=True, assign=False)#

Copy parameters and buffers from state_dict into this module and its descendants.

If strict is True, then the keys of state_dict must exactly match the keys returned by this module’s state_dict() function.

Warning

If assign is True the optimizer must be created after the call to load_state_dict unless get_swap_module_params_on_conversion() is True.

Args:

state_dict (dict): a dict containing parameters and: persistent buffers.
strict (bool, optional): whether to strictly enforce that the keys: in state_dict match the keys returned by this module’s state_dict() function. Default: True
assign (bool, optional): When set to False, the properties of the tensors: in the current module are preserved whereas setting it to True preserves properties of the Tensors in the state dict. The only exception is the requires_grad field of Parameter for which the value from the module is preserved. Default: False

Returns:

NamedTuple with missing_keys and unexpected_keys fields:

missing_keys is a list of str containing any keys that are expected
by this module but missing from the provided state_dict.
unexpected_keys is a list of str containing the keys that are not
expected by this module but present in the provided state_dict.

Note:

If a parameter or buffer is registered as None and its corresponding key exists in state_dict, load_state_dict() will raise a RuntimeError.

DonorMILModel.log(name, value, prog_bar=False, logger=None, on_step=None, on_epoch=None, reduce_fx='mean', enable_graph=False, sync_dist=False, sync_dist_group=None, add_dataloader_idx=True, batch_size=None, metric_attribute=None, rank_zero_only=False)#

Log a key, value pair.

Example:

self.log('train_loss', loss)

The default behavior per hook is documented here: extensions/logging:Automatic Logging.

Return type:: None

Args:

name: key to log. Must be identical across all processes if using DDP or any other distributed strategy. value: value to log. Can be a float, Tensor, or a Metric. prog_bar: if True logs to the progress bar. logger: if True logs to the logger. on_step: if True logs at this step. The default value is determined by the hook.

See extensions/logging:Automatic Logging for details.

on_epoch: if True logs epoch accumulated metrics. The default value is determined by the hook.: See extensions/logging:Automatic Logging for details.

reduce_fx: reduction function over step values for end of epoch. torch.mean() by default. enable_graph: if True, will not auto detach the graph. sync_dist: if True, reduces the metric across devices. Use with care as this may lead to a significant

communication overhead.

sync_dist_group: the DDP group to sync across. add_dataloader_idx: if True, appends the index of the current dataloader to

the name (when using multiple dataloaders). If False, user needs to give unique names for each dataloader to not mix the values.

batch_size: Current batch_size. This will be directly inferred from the loaded batch,: but for some data structures you might need to explicitly provide it.
metric_attribute: To restore the metric state, Lightning requires the reference of the: torchmetrics.Metric in your model. This is found automatically if it is a model attribute.
rank_zero_only: Tells Lightning if you are calling self.log from every process (default) or only from: rank 0. If True, you won’t be able to use this metric as a monitor in callbacks (e.g., early stopping). Warning: Improper use can lead to deadlocks! See Advanced Logging for more details.

DonorMILModel.log_dict(dictionary, prog_bar=False, logger=None, on_step=None, on_epoch=None, reduce_fx='mean', enable_graph=False, sync_dist=False, sync_dist_group=None, add_dataloader_idx=True, batch_size=None, rank_zero_only=False)#

Log a dictionary of values at once.

Example:

values = {'loss': loss, 'acc': acc, ..., 'metric_n': metric_n}
self.log_dict(values)

Return type:: None

Args:

dictionary: key value pairs.: Keys must be identical across all processes if using DDP or any other distributed strategy. The values can be a float, Tensor, Metric, or MetricCollection.

prog_bar: if True logs to the progress base. logger: if True logs to the logger. on_step: if True logs at this step.

None auto-logs for training_step but not validation/test_step. The default value is determined by the hook. See extensions/logging:Automatic Logging for details.

on_epoch: if True logs epoch accumulated metrics.: None auto-logs for val/test step but not training_step. The default value is determined by the hook. See extensions/logging:Automatic Logging for details.

reduce_fx: reduction function over step values for end of epoch. torch.mean() by default. enable_graph: if True, will not auto-detach the graph sync_dist: if True, reduces the metric across GPUs/TPUs. Use with care as this may lead to a significant

communication overhead.

sync_dist_group: the ddp group to sync across. add_dataloader_idx: if True, appends the index of the current dataloader to

the name (when using multiple). If False, user needs to give unique names for each dataloader to not mix values.

batch_size: Current batch size. This will be directly inferred from the loaded batch,: but some data structures might need to explicitly provide it.
rank_zero_only: Tells Lightning if you are calling self.log from every process (default) or only from: rank 0. If True, you won’t be able to use this metric as a monitor in callbacks (e.g., early stopping). Warning: Improper use can lead to deadlocks! See Advanced Logging for more details.

DonorMILModel.lr_scheduler_step(scheduler, metric)#

Override this method to adjust the default way the Trainer calls each scheduler. By default, Lightning calls step() and as shown in the example for each scheduler based on its interval.

Return type:: None

Args:: scheduler: Learning rate scheduler. metric: Value of the monitor used for schedulers like ReduceLROnPlateau.

Examples:

# DEFAULT
def lr_scheduler_step(self, scheduler, metric):
    if metric is None:
        scheduler.step()
    else:
        scheduler.step(metric)

# Alternative way to update schedulers if it requires an epoch value
def lr_scheduler_step(self, scheduler, metric):
    scheduler.step(epoch=self.current_epoch)

DonorMILModel.lr_schedulers()#

Returns the learning rate scheduler(s) that are being used during training. Useful for manual optimization.

Return type:: Union[None, list[Union[LRScheduler, ReduceLROnPlateau]], LRScheduler, ReduceLROnPlateau]

Returns:: A single scheduler, or a list of schedulers in case multiple ones are present, or None if no schedulers were returned in configure_optimizers().

DonorMILModel.manual_backward(loss, *args, **kwargs)#

Call this directly from your training_step() when doing optimizations manually. By using this, Lightning can ensure that all the proper scaling gets applied when using mixed precision.

See manual optimization for more examples.

Example:

def training_step(...):
    opt = self.optimizers()
    loss = ...
    opt.zero_grad()
    # automatically applies scaling, etc...
    self.manual_backward(loss)
    opt.step()

Return type:: None

Args:: loss: The tensor on which to compute gradients. Must have a graph attached. *args: Additional positional arguments to be forwarded to backward() **kwargs: Additional keyword arguments to be forwarded to backward()

DonorMILModel.modules(remove_duplicate=True)#

Return an iterator over all modules in the network.

Return type:: Iterator[Module]

Args:

remove_duplicate: whether to remove the duplicated module instances in the result: or not.

Yields:

Module: a module in the network

Note:

Duplicate modules are returned only once by default. In the following example, l will be returned only once.

Example:

>>> l = nn.Linear(2, 2)
>>> net = nn.Sequential(l, l)
>>> for idx, m in enumerate(net.modules()):
...     print(idx, '->', m)

0 -> Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
)
1 -> Linear(in_features=2, out_features=2, bias=True)

DonorMILModel.mtia(device=None)#

Move all model parameters and buffers to the MTIA.

This also makes associated parameters and buffers different objects. So it should be called before constructing the optimizer if the module will live on MTIA while being optimized.

Note

This method modifies the module in-place.

Arguments:

device (int, optional): if specified, all parameters will be: copied to that device

Returns:

Module: self

Return type:: Self

DonorMILModel.named_buffers(prefix='', recurse=True, remove_duplicate=True)#

Return an iterator over module buffers, yielding both the name of the buffer as well as the buffer itself.

Return type:: Iterator[tuple[str, Tensor]]

Args:

prefix (str): prefix to prepend to all buffer names. recurse (bool, optional): if True, then yields buffers of this module

and all submodules. Otherwise, yields only buffers that are direct members of this module. Defaults to True.

remove_duplicate (bool, optional): whether to remove the duplicated buffers in the result. Defaults to True.

Yields:

(str, torch.Tensor): Tuple containing the name and buffer

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, buf in self.named_buffers():
>>>     if name in ['running_var']:
>>>         print(buf.size())

DonorMILModel.named_children()#

Return an iterator over immediate children modules, yielding both the name of the module as well as the module itself.

Return type:: Iterator[tuple[str, Module]]

Yields:: (str, Module): Tuple containing a name and child module

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, module in model.named_children():
>>>     if name in ['conv4', 'conv5']:
>>>         print(module)

DonorMILModel.named_modules(memo=None, prefix='', remove_duplicate=True)#

Return an iterator over all modules in the network, yielding both the name of the module as well as the module itself.

Args:: memo: a memo to store the set of modules already added to the result prefix: a prefix that will be added to the name of the module remove_duplicate: whether to remove the duplicated module instances in the result

or not
Yields:: (str, Module): Tuple of name and module
Note:: Duplicate modules are returned only once. In the following example, l will be returned only once.

Example:

>>> l = nn.Linear(2, 2)
>>> net = nn.Sequential(l, l)
>>> for idx, m in enumerate(net.named_modules()):
...     print(idx, '->', m)

0 -> ('', Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
))
1 -> ('0', Linear(in_features=2, out_features=2, bias=True))

DonorMILModel.named_parameters(prefix='', recurse=True, remove_duplicate=True)#

Return an iterator over module parameters, yielding both the name of the parameter as well as the parameter itself.

Return type:: Iterator[tuple[str, Parameter]]

Args:

prefix (str): prefix to prepend to all parameter names. recurse (bool): if True, then yields parameters of this module

and all submodules. Otherwise, yields only parameters that are direct members of this module.

remove_duplicate (bool, optional): whether to remove the duplicated: parameters in the result. Defaults to True.

Yields:

(str, Parameter): Tuple containing the name and parameter

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, param in self.named_parameters():
>>>     if name in ['bias']:
>>>         print(param.size())

DonorMILModel.on_after_backward()#

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

Return type:: None

Note:: If using native AMP, the gradients will not be unscaled at this point. Use the on_before_optimizer_step if you need the unscaled gradients.

DonorMILModel.on_after_batch_transfer(batch, dataloader_idx)#

Override to alter or apply batch augmentations to your batch after it is transferred to the device.

Return type:: Any

Note:: To check the current state of execution of this hook you can use self.trainer.training/testing/validating/predicting so that you can add different logic as per your requirement.
Args:: batch: A batch of data that needs to be altered or augmented. dataloader_idx: The index of the dataloader to which the batch belongs.
Returns:: A batch of data

Example:

def on_after_batch_transfer(self, batch, dataloader_idx):
    batch['x'] = gpu_transforms(batch['x'])
    return batch

See Also:

on_before_batch_transfer()
transfer_batch_to_device()

DonorMILModel.on_before_backward(loss)#

Called before loss.backward().

Return type:: None

Args:: loss: Loss divided by number of batches for gradient accumulation and scaled if using AMP.

DonorMILModel.on_before_batch_transfer(batch, dataloader_idx)#

Override to alter or apply batch augmentations to your batch before it is transferred to the device.

Return type:: Any

Note:: To check the current state of execution of this hook you can use self.trainer.training/testing/validating/predicting so that you can add different logic as per your requirement.
Args:: batch: A batch of data that needs to be altered or augmented. dataloader_idx: The index of the dataloader to which the batch belongs.
Returns:: A batch of data

Example:

def on_before_batch_transfer(self, batch, dataloader_idx):
    batch['x'] = transforms(batch['x'])
    return batch

See Also:

on_after_batch_transfer()
transfer_batch_to_device()

DonorMILModel.on_before_optimizer_step(optimizer)#

Called before optimizer.step().

Return type:: None

If using gradient accumulation, the hook is called once the gradients have been accumulated. See: :paramref:`~pytorch_lightning.trainer.trainer.Trainer.accumulate_grad_batches`.

If using AMP, the loss will be unscaled before calling this hook. See these docs for more information on the scaling of gradients.

If clipping gradients, the gradients will not have been clipped yet.

Args:: optimizer: Current optimizer being used.

Example:

def on_before_optimizer_step(self, optimizer):
    # example to inspect gradient information in tensorboard
    if self.trainer.global_step % 25 == 0:  # don't make the tf file huge
        for k, v in self.named_parameters():
            self.logger.experiment.add_histogram(
                tag=k, values=v.grad, global_step=self.trainer.global_step
            )

DonorMILModel.on_before_zero_grad(optimizer)#

Called after training_step() and before optimizer.zero_grad().

Called in the training loop after taking an optimizer step and before zeroing grads. Good place to inspect weight information with weights updated.

This is where it is called:

for optimizer in optimizers:
    out = training_step(...)

    model.on_before_zero_grad(optimizer) # < ---- called here
    optimizer.zero_grad()

    backward()

Return type:: None

Args:: optimizer: The optimizer for which grads should be zeroed.

DonorMILModel.on_fit_end()#

Called at the very end of fit.

If on DDP it is called on every process

Return type:: None

DonorMILModel.on_fit_start()#

Called at the very beginning of fit.

If on DDP it is called on every process

Return type:: None

DonorMILModel.on_load_checkpoint(checkpoint)#

Called by Lightning to restore your model. If you saved something with on_save_checkpoint() this is your chance to restore this.

Return type:: None

Args:: checkpoint: Loaded checkpoint

Example:

def on_load_checkpoint(self, checkpoint):
    # 99% of the time you don't need to implement this method
    self.something_cool_i_want_to_save = checkpoint['something_cool_i_want_to_save']

Note:: Lightning auto-restores global step, epoch, and train state including amp scaling. There is no need for you to restore anything regarding training.

DonorMILModel.on_predict_batch_end(outputs, batch, batch_idx, dataloader_idx=0)#

Called in the predict loop after the batch.

Return type:: None

Args:: outputs: The outputs of predict_step(x) batch: The batched data as it is returned by the prediction DataLoader. batch_idx: the index of the batch dataloader_idx: the index of the dataloader

DonorMILModel.on_predict_batch_start(batch, batch_idx, dataloader_idx=0)#

Called in the predict loop before anything happens for that batch.

Return type:: None

Args:: batch: The batched data as it is returned by the test DataLoader. batch_idx: the index of the batch dataloader_idx: the index of the dataloader

DonorMILModel.on_predict_end()#

Called at the end of predicting.

Return type:: None

DonorMILModel.on_predict_epoch_end()#

Called at the end of predicting.

Return type:: None

DonorMILModel.on_predict_epoch_start()#

Called at the beginning of predicting.

Return type:: None

DonorMILModel.on_predict_model_eval()#

Called when the predict loop starts.

The predict loop by default calls .eval() on the LightningModule before it starts. Override this hook to change the behavior.

Return type:: None

DonorMILModel.on_predict_start()#

Called at the beginning of predicting.

Return type:: None

DonorMILModel.on_save_checkpoint(checkpoint)#

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

Return type:: None

Args:

checkpoint: The full checkpoint dictionary before it gets dumped to a file.: Implementations of this hook can insert additional data into this dictionary.

Example:

def on_save_checkpoint(self, checkpoint):
    # 99% of use cases you don't need to implement this method
    checkpoint['something_cool_i_want_to_save'] = my_cool_pickable_object

Note:: Lightning saves all aspects of training (epoch, global step, etc…) including amp scaling. There is no need for you to store anything about training.

DonorMILModel.on_test_batch_end(outputs, batch, batch_idx, dataloader_idx=0)#

Called in the test loop after the batch.

Return type:: None

Args:: outputs: The outputs of test_step(x) batch: The batched data as it is returned by the test DataLoader. batch_idx: the index of the batch dataloader_idx: the index of the dataloader

DonorMILModel.on_test_batch_start(batch, batch_idx, dataloader_idx=0)#

Called in the test loop before anything happens for that batch.

Return type:: None

Args:: batch: The batched data as it is returned by the test DataLoader. batch_idx: the index of the batch dataloader_idx: the index of the dataloader

DonorMILModel.on_test_end()#

Called at the end of testing.

Return type:: None

DonorMILModel.on_test_epoch_end()#

Called in the test loop at the very end of the epoch.

Return type:: None

DonorMILModel.on_test_epoch_start()#

Called in the test loop at the very beginning of the epoch.

Return type:: None

DonorMILModel.on_test_model_eval()#

Called when the test loop starts.

The test loop by default calls .eval() on the LightningModule before it starts. Override this hook to change the behavior. See also on_test_model_train().

Return type:: None

DonorMILModel.on_test_model_train()#

Called when the test loop ends.

The test loop by default restores the training mode of the LightningModule to what it was before starting testing. Override this hook to change the behavior. See also on_test_model_eval().

Return type:: None

DonorMILModel.on_test_start()#

Called at the beginning of testing.

Return type:: None

DonorMILModel.on_train_batch_end(outputs, batch, batch_idx)#

Called in the training loop after the batch.

Return type:: None

Args:: outputs: The outputs of training_step(x) batch: The batched data as it is returned by the training DataLoader. batch_idx: the index of the batch
Note:: The value outputs["loss"] here will be the normalized value w.r.t accumulate_grad_batches of the loss returned from training_step.

DonorMILModel.on_train_batch_start(batch, batch_idx)#

Called in the training loop before anything happens for that batch.

If you return -1 here, you will skip training for the rest of the current epoch. Learning rate scheduler will still be stepped at the end of epoch.

Return type:: Optional[int]

Args:: batch: The batched data as it is returned by the training DataLoader. batch_idx: the index of the batch

DonorMILModel.on_train_end()#

Called at the end of training before logger experiment is closed.

Return type:: None

DonorMILModel.on_train_epoch_end()#

Called in the training loop at the very end of the epoch.

To access all batch outputs at the end of the epoch, you can cache step outputs as an attribute of the LightningModule and access them in this hook:

class MyLightningModule(L.LightningModule):
    def __init__(self):
        super().__init__()
        self.training_step_outputs = []

    def training_step(self):
        loss = ...
        self.training_step_outputs.append(loss)
        return loss

    def on_train_epoch_end(self):
        # do something with all training_step outputs, for example:
        epoch_mean = torch.stack(self.training_step_outputs).mean()
        self.log("training_epoch_mean", epoch_mean)
        # free up the memory
        self.training_step_outputs.clear()

Return type:: None

DonorMILModel.on_train_epoch_start()#

Called in the training loop at the very beginning of the epoch.

Return type:: None

DonorMILModel.on_train_start()#

Called at the beginning of training after sanity check.

Return type:: None

DonorMILModel.on_validation_batch_end(outputs, batch, batch_idx, dataloader_idx=0)#

Called in the validation loop after the batch.

Return type:: None

Args:: outputs: The outputs of validation_step(x) batch: The batched data as it is returned by the validation DataLoader. batch_idx: the index of the batch dataloader_idx: the index of the dataloader

DonorMILModel.on_validation_batch_start(batch, batch_idx, dataloader_idx=0)#

Called in the validation loop before anything happens for that batch.

Return type:: None

Args:: batch: The batched data as it is returned by the validation DataLoader. batch_idx: the index of the batch dataloader_idx: the index of the dataloader

DonorMILModel.on_validation_end()#

Called at the end of validation.

Return type:: None

DonorMILModel.on_validation_epoch_end()#

Called in the validation loop at the very end of the epoch.

Return type:: None

DonorMILModel.on_validation_epoch_start()#

Called in the validation loop at the very beginning of the epoch.

Return type:: None

DonorMILModel.on_validation_model_eval()#

Called when the validation loop starts.

The validation loop by default calls .eval() on the LightningModule before it starts. Override this hook to change the behavior. See also on_validation_model_train().

Return type:: None

DonorMILModel.on_validation_model_train()#

Called when the validation loop ends.

The validation loop by default restores the training mode of the LightningModule to what it was before starting validation. Override this hook to change the behavior. See also on_validation_model_eval().

Return type:: None

DonorMILModel.on_validation_model_zero_grad()#

Called by the training loop to release gradients before entering the validation loop.

Return type:: None

DonorMILModel.on_validation_start()#

Called at the beginning of validation.

Return type:: None

DonorMILModel.optimizer_step(epoch, batch_idx, optimizer, optimizer_closure=None)#

Override this method to adjust the default way the Trainer calls the optimizer.

By default, Lightning calls step() and zero_grad() as shown in the example. This method (and zero_grad()) won’t be called during the accumulation phase when Trainer(accumulate_grad_batches != 1). Overriding this hook has no benefit with manual optimization.

Return type:: None

Args:: epoch: Current epoch batch_idx: Index of current batch optimizer: A PyTorch optimizer optimizer_closure: The optimizer closure. This closure must be executed as it includes the

calls to training_step(), optimizer.zero_grad(), and backward().

Examples:

def optimizer_step(self, epoch, batch_idx, optimizer, optimizer_closure):
    # Add your custom logic to run directly before `optimizer.step()`

    optimizer.step(closure=optimizer_closure)

    # Add your custom logic to run directly after `optimizer.step()`

DonorMILModel.optimizer_zero_grad(epoch, batch_idx, optimizer)#

Override this method to change the default behaviour of optimizer.zero_grad().

Return type:: None

Args:: epoch: Current epoch batch_idx: Index of current batch optimizer: A PyTorch optimizer

Examples:

# DEFAULT
def optimizer_zero_grad(self, epoch, batch_idx, optimizer):
    optimizer.zero_grad()

# Set gradients to `None` instead of zero to improve performance (not required on `torch>=2.0.0`).
def optimizer_zero_grad(self, epoch, batch_idx, optimizer):
    optimizer.zero_grad(set_to_none=True)

See torch.optim.Optimizer.zero_grad() for the explanation of the above example.

DonorMILModel.optimizers(use_pl_optimizer=True)#

Returns the optimizer(s) that are being used during training. Useful for manual optimization.

Return type:: Union[Optimizer, LightningOptimizer, _FabricOptimizer, list[Optimizer], list[LightningOptimizer], list[_FabricOptimizer]]

Args:

use_pl_optimizer: If True, will wrap the optimizer(s) in a: LightningOptimizer for automatic handling of precision, profiling, and counting of step calls for proper logging and checkpointing. It specifically wraps the step method and custom optimizers that don’t have this method are not supported.

Returns:

A single optimizer, or a list of optimizers in case multiple ones are present.

DonorMILModel.parameters(recurse=True)#

Return an iterator over module parameters.

This is typically passed to an optimizer.

Return type:: Iterator[Parameter]

Args:

recurse (bool): if True, then yields parameters of this module: and all submodules. Otherwise, yields only parameters that are direct members of this module.

Yields:

Parameter: module parameter

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for param in model.parameters():
>>>     print(type(param), param.size())
<class 'torch.Tensor'> (20L,)
<class 'torch.Tensor'> (20L, 1L, 5L, 5L)

DonorMILModel.predict_dataloader()#

An iterable or collection of iterables specifying prediction samples.

For more information about multiple dataloaders, see this section.

It’s recommended that all data downloads and preparation happen in prepare_data().

predict()
prepare_data()
setup()

Note:: Lightning tries to add the correct sampler for distributed and arbitrary hardware There is no need to set it yourself.
Return:: A torch.utils.data.DataLoader or a sequence of them specifying prediction samples.

Return type:: Any

DonorMILModel.predict_step(*args, **kwargs)#

Step function called during predict(). By default, it calls forward(). Override to add any processing logic.

The predict_step() is used to scale inference on multi-devices.

To prevent an OOM error, it is possible to use BasePredictionWriter callback to write the predictions to disk or database after each batch or on epoch end.

The BasePredictionWriter should be used while using a spawn based accelerator. This happens for Trainer(strategy="ddp_spawn") or training on 8 TPU cores with Trainer(accelerator="tpu", devices=8) as predictions won’t be returned.

Return type:: Any

Args:: batch: The output of your data iterable, normally a DataLoader. batch_idx: The index of this batch. dataloader_idx: The index of the dataloader that produced this batch.

(only if multiple dataloaders used)
Return:: Predicted output (optional).

Example

class MyModel(LightningModule):

    def predict_step(self, batch, batch_idx, dataloader_idx=0):
        return self(batch)

dm = ...
model = MyModel()
trainer = Trainer(accelerator="gpu", devices=2)
predictions = trainer.predict(model, dm)

DonorMILModel.prepare_data()#

Use this to download and prepare data. Downloading and saving data with multiple processes (distributed settings) will result in corrupted data. Lightning ensures this method is called only within a single process, so you can safely add your downloading logic within.

Warning

DO NOT set state to the model (use setup instead) since this is NOT called on every device

Example:

def prepare_data(self):
    # good
    download_data()
    tokenize()
    etc()

    # bad
    self.split = data_split
    self.some_state = some_other_state()

In a distributed environment, prepare_data can be called in two ways (using prepare_data_per_node)

Once per node. This is the default and is only called on LOCAL_RANK=0.
Once in total. Only called on GLOBAL_RANK=0.

Example:

# DEFAULT
# called once per node on LOCAL_RANK=0 of that node
class LitDataModule(LightningDataModule):
    def __init__(self):
        super().__init__()
        self.prepare_data_per_node = True


# call on GLOBAL_RANK=0 (great for shared file systems)
class LitDataModule(LightningDataModule):
    def __init__(self):
        super().__init__()
        self.prepare_data_per_node = False

This is called before requesting the dataloaders:

model.prepare_data()
initialize_distributed()
model.setup(stage)
model.train_dataloader()
model.val_dataloader()
model.test_dataloader()
model.predict_dataloader()

Return type:: None

DonorMILModel.print(*args, **kwargs)#

Prints only from process 0. Use this in any distributed mode to log only once.

Return type:: None

Args:: *args: The thing to print. The same as for Python’s built-in print function. **kwargs: The same as for Python’s built-in print function.

Example:

def forward(self, x):
    self.print(x, 'in forward')

DonorMILModel.register_backward_hook(hook)#

This function is deprecated in favor of register_full_backward_hook() and the behavior of this function will change in future versions.

Return type:: RemovableHandle

Returns:

torch.utils.hooks.RemovableHandle:: a handle that can be used to remove the added hook by calling handle.remove()

DonorMILModel.register_buffer(name, tensor, persistent=True)#

Add a buffer to the module.

This is typically used to register a buffer that should not be considered a model parameter. For example, BatchNorm’s running_mean is not a parameter, but is part of the module’s state. Buffers, by default, are persistent and will be saved alongside parameters. This behavior can be changed by setting persistent to False. The only difference between a persistent buffer and a non-persistent buffer is that the latter will not be a part of this module’s state_dict.

Buffers can be accessed as attributes using given names.

Return type:: None

Args:

name (str): name of the buffer. The buffer can be accessed: from this module using the given name
tensor (Tensor or None): buffer to be registered. If None, then operations: that run on buffers, such as cuda, are ignored. If None, the buffer is not included in the module’s state_dict.
persistent (bool): whether the buffer is part of this module’s: state_dict.

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> self.register_buffer('running_mean', torch.zeros(num_features))

DonorMILModel.register_forward_hook(hook, *, prepend=False, with_kwargs=False, always_call=False)#

The hook will be called every time after forward() has computed an output.

If with_kwargs is False or not specified, the input contains only the positional arguments given to the module. Keyword arguments won’t be passed to the hooks and only to the forward. The hook can modify the output. It can modify the input inplace but it will not have effect on forward since this is called after forward() is called. The hook should have the following signature:

hook(module, args, output) -> None or modified output

If with_kwargs is True, the forward hook will be passed the kwargs given to the forward function and be expected to return the output possibly modified. The hook should have the following signature:

hook(module, args, kwargs, output) -> None or modified output

Return type:: RemovableHandle

Args:

hook (Callable): The user defined hook to be registered. prepend (bool): If True, the provided hook will be fired

before all existing forward hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing forward hooks on this torch.nn.Module. Note that global forward hooks registered with register_module_forward_hook() will fire before all hooks registered by this method. Default: False

with_kwargs (bool): If True, the hook will be passed the: kwargs given to the forward function. Default: False
always_call (bool): If True the hook will be run regardless of: whether an exception is raised while calling the Module. Default: False

Returns:

torch.utils.hooks.RemovableHandle:: a handle that can be used to remove the added hook by calling handle.remove()

DonorMILModel.register_forward_pre_hook(hook, *, prepend=False, with_kwargs=False)#

The hook will be called every time before forward() is invoked.

If with_kwargs is false or not specified, the input contains only the positional arguments given to the module. Keyword arguments won’t be passed to the hooks and only to the forward. The hook can modify the input. User can either return a tuple or a single modified value in the hook. We will wrap the value into a tuple if a single value is returned (unless that value is already a tuple). The hook should have the following signature:

hook(module, args) -> None or modified input

If with_kwargs is true, the forward pre-hook will be passed the kwargs given to the forward function. And if the hook modifies the input, both the args and kwargs should be returned. The hook should have the following signature:

hook(module, args, kwargs) -> None or a tuple of modified input and kwargs

Return type:: RemovableHandle

Args:

hook (Callable): The user defined hook to be registered. prepend (bool): If true, the provided hook will be fired before

all existing forward_pre hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing forward_pre hooks on this torch.nn.Module. Note that global forward_pre hooks registered with register_module_forward_pre_hook() will fire before all hooks registered by this method. Default: False

with_kwargs (bool): If true, the hook will be passed the kwargs: given to the forward function. Default: False

Returns:

torch.utils.hooks.RemovableHandle:: a handle that can be used to remove the added hook by calling handle.remove()

DonorMILModel.register_full_backward_hook(hook, prepend=False)#

The hook will be called every time the gradients with respect to a module are computed, and its firing rules are as follows:

Ordinarily, the hook fires when the gradients are computed with respect to the module inputs.

If none of the module inputs require gradients, the hook will fire when the gradients are computed with respect to module outputs.

If none of the module outputs require gradients, then the hooks will not fire.

The hook should have the following signature:

hook(module, grad_input, grad_output) -> tuple(Tensor) or None

The grad_input and grad_output are tuples that contain the gradients with respect to the inputs and outputs respectively. The hook should not modify its arguments, but it can optionally return a new gradient with respect to the input that will be used in place of grad_input in subsequent computations. grad_input will only correspond to the inputs given as positional arguments and all kwarg arguments are ignored. Entries in grad_input and grad_output will be None for all non-Tensor arguments.

For technical reasons, when this hook is applied to a Module, its forward function will receive a view of each Tensor passed to the Module. Similarly the caller will receive a view of each Tensor returned by the Module’s forward function.

Warning

Modifying inputs or outputs inplace is not allowed when using backward hooks and will raise an error.

Args:

hook (Callable): The user-defined hook to be registered. prepend (bool): If true, the provided hook will be fired before

all existing backward hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing backward hooks on this torch.nn.Module. Note that global backward hooks registered with register_module_full_backward_hook() will fire before all hooks registered by this method.

Returns:

torch.utils.hooks.RemovableHandle:: a handle that can be used to remove the added hook by calling handle.remove()

Return type:: RemovableHandle

DonorMILModel.register_full_backward_pre_hook(hook, prepend=False)#

The hook will be called every time the gradients for the module are computed. The hook should have the following signature:

hook(module, grad_output) -> tuple[Tensor, ...], Tensor or None

The grad_output is a tuple. The hook should not modify its arguments, but it can optionally return a new gradient with respect to the output that will be used in place of grad_output in subsequent computations. Entries in grad_output will be None for all non-Tensor arguments.

Warning

Modifying inputs inplace is not allowed when using backward hooks and will raise an error.

Args:

hook (Callable): The user-defined hook to be registered. prepend (bool): If true, the provided hook will be fired before

all existing backward_pre hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing backward_pre hooks on this torch.nn.Module. Note that global backward_pre hooks registered with register_module_full_backward_pre_hook() will fire before all hooks registered by this method.

Returns:

torch.utils.hooks.RemovableHandle:: a handle that can be used to remove the added hook by calling handle.remove()

Return type:: RemovableHandle

DonorMILModel.register_load_state_dict_post_hook(hook)#

It should have the following signature::: hook(module, incompatible_keys) -> None

The module argument is the current module that this hook is registered on, and the incompatible_keys argument is a NamedTuple consisting of attributes missing_keys and unexpected_keys. missing_keys is a list of str containing the missing keys and unexpected_keys is a list of str containing the unexpected keys.

The given incompatible_keys can be modified inplace if needed.

Note that the checks performed when calling load_state_dict() with strict=True are affected by modifications the hook makes to missing_keys or unexpected_keys, as expected. Additions to either set of keys will result in an error being thrown when strict=True, and clearing out both missing and unexpected keys will avoid an error.

Returns:

torch.utils.hooks.RemovableHandle:: a handle that can be used to remove the added hook by calling handle.remove()

DonorMILModel.register_load_state_dict_pre_hook(hook)#

It should have the following signature::

hook(module, state_dict, prefix, local_metadata, strict, missing_keys, unexpected_keys, error_msgs) -> None # noqa: B950

Arguments:

hook (Callable): Callable hook that will be invoked before: loading the state dict.

DonorMILModel.register_module(name, module)#

Alias for add_module().

Return type:: None

DonorMILModel.register_parameter(name, param)#

Add a parameter to the module.

The parameter can be accessed as an attribute using given name.

Return type:: None

Args:

name (str): name of the parameter. The parameter can be accessed: from this module using the given name
param (Parameter or None): parameter to be added to the module. If: None, then operations that run on parameters, such as cuda, are ignored. If None, the parameter is not included in the module’s state_dict.

DonorMILModel.register_state_dict_post_hook(hook)#

It should have the following signature::: hook(module, state_dict, prefix, local_metadata) -> None

The registered hooks can modify the state_dict inplace.

DonorMILModel.register_state_dict_pre_hook(hook)#

It should have the following signature::: hook(module, prefix, keep_vars) -> None

The registered hooks can be used to perform pre-processing before the state_dict call is made.

DonorMILModel.remove_ignored_hparams(ignore_list)#

Remove ignored hyperparameters from the stored state.

This allows derived classes to drop hyperparameters previously saved by base classes.

Return type:: None

Args:: ignore_list: Names of hyperparameters to remove.

DonorMILModel.requires_grad_(requires_grad=True)#

Change if autograd should record operations on parameters in this module.

This method sets the parameters’ requires_grad attributes in-place.

This method is helpful for freezing part of the module for finetuning or training parts of a model individually (e.g., GAN training).

See locally-disable-grad-doc for a comparison between .requires_grad_() and several similar mechanisms that may be confused with it.

Return type:: Self

Args:

requires_grad (bool): whether autograd should record operations on: parameters in this module. Default: True.

Returns:

Module: self

DonorMILModel.save_hyperparameters(*args, ignore=None, frame=None, logger=True)#

Save arguments to hparams attribute.

Return type:: None

Args:

args: single object of dict, NameSpace or OmegaConf: or string names or arguments from class __init__
ignore: an argument name or a list of argument names from: class __init__ to be ignored

frame: a frame object. Default is None logger: Whether to send the hyperparameters to the logger. Default: True

Example::

>>> from pytorch_lightning.core.mixins import HyperparametersMixin
>>> class ManuallyArgsModel(HyperparametersMixin):
...     def __init__(self, arg1, arg2, arg3):
...         super().__init__()
...         # manually assign arguments
...         self.save_hyperparameters('arg1', 'arg3')
...     def forward(self, *args, **kwargs):
...         ...
>>> model = ManuallyArgsModel(1, 'abc', 3.14)
>>> model.hparams
"arg1": 1
"arg3": 3.14

>>> from pytorch_lightning.core.mixins import HyperparametersMixin
>>> class AutomaticArgsModel(HyperparametersMixin):
...     def __init__(self, arg1, arg2, arg3):
...         super().__init__()
...         # equivalent automatic
...         self.save_hyperparameters()
...     def forward(self, *args, **kwargs):
...         ...
>>> model = AutomaticArgsModel(1, 'abc', 3.14)
>>> model.hparams
"arg1": 1
"arg2": abc
"arg3": 3.14

>>> from pytorch_lightning.core.mixins import HyperparametersMixin
>>> class SingleArgModel(HyperparametersMixin):
...     def __init__(self, params):
...         super().__init__()
...         # manually assign single argument
...         self.save_hyperparameters(params)
...     def forward(self, *args, **kwargs):
...         ...
>>> model = SingleArgModel(Namespace(p1=1, p2='abc', p3=3.14))
>>> model.hparams
"p1": 1
"p2": abc
"p3": 3.14

>>> from pytorch_lightning.core.mixins import HyperparametersMixin
>>> class ManuallyArgsModel(HyperparametersMixin):
...     def __init__(self, arg1, arg2, arg3):
...         super().__init__()
...         # pass argument(s) to ignore as a string or in a list
...         self.save_hyperparameters(ignore='arg2')
...     def forward(self, *args, **kwargs):
...         ...
>>> model = ManuallyArgsModel(1, 'abc', 3.14)
>>> model.hparams
"arg1": 1
"arg3": 3.14

DonorMILModel.set_extra_state(state)#

Set extra state contained in the loaded state_dict.

This function is called from load_state_dict() to handle any extra state found within the state_dict. Implement this function and a corresponding get_extra_state() for your module if you need to store extra state within its state_dict.

Return type:: None

Args:: state (dict): Extra state from the state_dict

DonorMILModel.set_submodule(target, module, strict=False)#

Set the submodule given by target if it exists, otherwise throw an error.

Note

If strict is set to False (default), the method will replace an existing submodule or create a new submodule if the parent module exists. If strict is set to True, the method will only attempt to replace an existing submodule and throw an error if the submodule does not exist.

For example, let’s say you have an nn.Module A that looks like this:

A(
    (net_b): Module(
        (net_c): Module(
            (conv): Conv2d(3, 3, 3)
        )
        (linear): Linear(3, 3)
    )
)

(The diagram shows an nn.Module A. A has a nested submodule net_b, which itself has two submodules net_c and linear. net_c then has a submodule conv.)

To override the Conv2d with a new submodule Linear, you could call set_submodule("net_b.net_c.conv", nn.Linear(1, 1)) where strict could be True or False

To add a new submodule Conv2d to the existing net_b module, you would call set_submodule("net_b.conv", nn.Conv2d(1, 1, 1)).

In the above if you set strict=True and call set_submodule("net_b.conv", nn.Conv2d(1, 1, 1), strict=True), an AttributeError will be raised because net_b does not have a submodule named conv.

Args:

target: The fully-qualified string name of the submodule: to look for. (See above example for how to specify a fully-qualified string.)

module: The module to set the submodule to. strict: If False, the method will replace an existing submodule

or create a new submodule if the parent module exists. If True, the method will only attempt to replace an existing submodule and throw an error if the submodule doesn’t already exist.

Raises:

ValueError: If the target string is empty or if module is not an instance of nn.Module. AttributeError: If at any point along the path resulting from

the target string the (sub)path resolves to a non-existent attribute name or an object that is not an instance of nn.Module.

Return type:: None

DonorMILModel.setup(stage)#

Called at the beginning of fit (train + validate), validate, test, or predict. This is a good hook when you need to build models dynamically or adjust something about them. This hook is called on every process when using DDP.

Return type:: None

Args:: stage: either 'fit', 'validate', 'test', or 'predict'

Example:

class LitModel(...):
    def __init__(self):
        self.l1 = None

    def prepare_data(self):
        download_data()
        tokenize()

        # don't do this
        self.something = else

    def setup(self, stage):
        data = load_data(...)
        self.l1 = nn.Linear(28, data.num_classes)

DonorMILModel.share_memory()#

See torch.Tensor.share_memory_().

Return type:: Self

DonorMILModel.state_dict(*args, destination=None, prefix='', keep_vars=False)#

Return a dictionary containing references to the whole state of the module.

Both parameters and persistent buffers (e.g. running averages) are included. Keys are corresponding parameter and buffer names. Parameters and buffers set to None are not included.

Note

The returned object is a shallow copy. It contains references to the module’s parameters and buffers.

Warning

Currently state_dict() also accepts positional arguments for destination, prefix and keep_vars in order. However, this is being deprecated and keyword arguments will be enforced in future releases.

Warning

Please avoid the use of argument destination as it is not designed for end-users.

Args:

destination (dict, optional): If provided, the state of module will: be updated into the dict and the same object is returned. Otherwise, an OrderedDict will be created and returned. Default: None.
prefix (str, optional): a prefix added to parameter and buffer: names to compose the keys in state_dict. Default: ''.
keep_vars (bool, optional): by default the Tensor s: returned in the state dict are detached from autograd. If it’s set to True, detaching will not be performed. Default: False.

Returns:

dict:: a dictionary containing a whole state of the module

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> module.state_dict().keys()
['bias', 'weight']

DonorMILModel.teardown(stage)#

Called at the end of fit (train + validate), validate, test, or predict.

Return type:: None

Args:: stage: either 'fit', 'validate', 'test', or 'predict'

DonorMILModel.test_dataloader()#

An iterable or collection of iterables specifying test samples.

For more information about multiple dataloaders, see this section.

For data processing use the following pattern:

download in prepare_data()

process and split in setup()

However, the above are only necessary for distributed processing.

Warning

do not assign state in prepare_data

test()
prepare_data()
setup()

Note:: Lightning tries to add the correct sampler for distributed and arbitrary hardware. There is no need to set it yourself.
Note:: If you don’t need a test dataset and a test_step(), you don’t need to implement this method.

Return type:: Any

DonorMILModel.test_step(*args, **kwargs)#

Operates on a single batch of data from the test set. In this step you’d normally generate examples or calculate anything of interest such as accuracy.

Return type:: Union[Tensor, Mapping[str, Any], None]

Args:

batch: The output of your data iterable, normally a DataLoader. batch_idx: The index of this batch. dataloader_idx: The index of the dataloader that produced this batch.

(only if multiple dataloaders used)

Return:

Tensor - The loss tensor
dict - A dictionary. Can include any keys, but must include the key 'loss'.
None - Skip to the next batch.

# if you have one test dataloader:
def test_step(self, batch, batch_idx): ...


# if you have multiple test dataloaders:
def test_step(self, batch, batch_idx, dataloader_idx=0): ...

Examples:

# CASE 1: A single test dataset
def test_step(self, batch, batch_idx):
    x, y = batch

    # implement your own
    out = self(x)
    loss = self.loss(out, y)

    # log 6 example images
    # or generated text... or whatever
    sample_imgs = x[:6]
    grid = torchvision.utils.make_grid(sample_imgs)
    self.logger.experiment.add_image('example_images', grid, 0)

    # calculate acc
    labels_hat = torch.argmax(out, dim=1)
    test_acc = torch.sum(y == labels_hat).item() / (len(y) * 1.0)

    # log the outputs!
    self.log_dict({'test_loss': loss, 'test_acc': test_acc})

If you pass in multiple test dataloaders, test_step() will have an additional argument. We recommend setting the default value of 0 so that you can quickly switch between single and multiple dataloaders.

# CASE 2: multiple test dataloaders
def test_step(self, batch, batch_idx, dataloader_idx=0):
    # dataloader_idx tells you which dataset this is.
    x, y = batch

    # implement your own
    out = self(x)

    if dataloader_idx == 0:
        loss = self.loss0(out, y)
    else:
        loss = self.loss1(out, y)

    # calculate acc
    labels_hat = torch.argmax(out, dim=1)
    acc = torch.sum(y == labels_hat).item() / (len(y) * 1.0)

    # log the outputs separately for each dataloader
    self.log_dict({f"test_loss_{dataloader_idx}": loss, f"test_acc_{dataloader_idx}": acc})

Note:: If you don’t need to test you don’t need to implement this method.
Note:: When the test_step() is called, the model has been put in eval mode and PyTorch gradients have been disabled. At the end of the test epoch, the model goes back to training mode and gradients are enabled.

DonorMILModel.to(*args, **kwargs)#

See torch.nn.Module.to().

Return type:: Self

DonorMILModel.to_empty(*, device, recurse=True)#

Move the parameters and buffers to the specified device without copying storage.

Return type:: Self

Args:

device (torch.device): The desired device of the parameters: and buffers in this module.
recurse (bool): Whether parameters and buffers of submodules should: be recursively moved to the specified device.

Returns:

Module: self

DonorMILModel.to_onnx(file_path=None, input_sample=None, **kwargs)#

Saves the model in ONNX format.

Return type:: Optional[ONNXProgram]

Args:

file_path: The path of the file the onnx model should be saved to. Default: None (no file saved). input_sample: An input for tracing. Default: None (Use self.example_input_array)

**kwargs: Will be passed to torch.onnx.export function.

Example:

class SimpleModel(LightningModule):
    def __init__(self):
        super().__init__()
        self.l1 = torch.nn.Linear(in_features=64, out_features=4)

    def forward(self, x):
        return torch.relu(self.l1(x.view(x.size(0), -1)

model = SimpleModel()
input_sample = torch.randn(1, 64)
model.to_onnx("export.onnx", input_sample, export_params=True)

DonorMILModel.to_tensorrt(file_path=None, input_sample=None, ir='default', output_format='exported_program', retrace=False, default_device='cuda', **compile_kwargs)#

Export the model to ScriptModule or GraphModule using TensorRT compile backend.

Return type:: Union[ScriptModule, GraphModule]

Args:

file_path: Path where to save the tensorrt model. Default: None (no file saved). input_sample: inputs to be used during torch_tensorrt.compile.

Default: None (Use example_input_array).

ir: The IR mode to use for TensorRT compilation. Default: “default”. output_format: The format of the output model. Default: “exported_program”. retrace: Whether to retrace the model. Default: False. default_device: The device to use for the model when the current model is not in CUDA. Default: “cuda”. **compile_kwargs: Additional arguments that will be passed to the TensorRT compile function.

Example:

class SimpleModel(LightningModule):
    def __init__(self):
        super().__init__()
        self.l1 = torch.nn.Linear(in_features=64, out_features=4)

    def forward(self, x):
        return torch.relu(self.l1(x.view(x.size(0), -1)

model = SimpleModel()
input_sample = torch.randn(1, 64)
exported_program = model.to_tensorrt(
    file_path="export.ep",
    inputs=input_sample,
)

DonorMILModel.to_torchscript(file_path=None, method='script', example_inputs=None, **kwargs)#

By default compiles the whole model to a ScriptModule. If you want to use tracing, please provided the argument method='trace' and make sure that either the example_inputs argument is provided, or the model has example_input_array set. If you would like to customize the modules that are scripted you should override this method. In case you want to return multiple modules, we recommend using a dictionary.

Deprecated since version ``LightningModule.to_torchscript``: has been deprecated in v2.7 and will be removed in v2.8. TorchScript is deprecated in PyTorch. Use torch.export.export() for model exporting instead. See https://pytorch.org/docs/stable/export.html for more information.

Args:

file_path: Path where to save the torchscript. Default: None (no file saved). method: Whether to use TorchScript’s script or trace method. Default: ‘script’ example_inputs: An input to be used to do tracing when method is set to ‘trace’.

Default: None (uses example_input_array)

**kwargs: Additional arguments that will be passed to the torch.jit.script() or: torch.jit.trace() function.

Note:

Requires the implementation of the forward() method.
The exported script will be set to evaluation mode.
It is recommended that you install the latest supported version of PyTorch to use this feature without limitations. See also the torch.jit documentation for supported features.

Example:

class SimpleModel(LightningModule):
    def __init__(self):
        super().__init__()
        self.l1 = torch.nn.Linear(in_features=64, out_features=4)

    def forward(self, x):
        return torch.relu(self.l1(x.view(x.size(0), -1)))

model = SimpleModel()
model.to_torchscript(file_path="model.pt")

torch.jit.save(model.to_torchscript(
    file_path="model_trace.pt", method='trace', example_inputs=torch.randn(1, 64))
)

Return:: This LightningModule as a torchscript, regardless of whether file_path is defined or not.

Return type:: Union[ScriptModule, dict[str, ScriptModule]]

DonorMILModel.toggle_optimizer(optimizer)#

Makes sure only the gradients of the current optimizer’s parameters are calculated in the training step to prevent dangling gradients in multiple-optimizer setup.

It works with untoggle_optimizer() to make sure param_requires_grad_state is properly reset.

Return type:: None

Args:: optimizer: The optimizer to toggle.

DonorMILModel.toggled_optimizer(optimizer)#

Makes sure only the gradients of the current optimizer’s parameters are calculated in the training step to prevent dangling gradients in multiple-optimizer setup. Combines toggle_optimizer() and untoggle_optimizer() into context manager.

Return type:: Generator

Args:: optimizer: The optimizer to toggle.

Example:

def training_step(...):
    opt = self.optimizers()
    with self.toggled_optimizer(opt):
        loss = ...
        opt.zero_grad()
        self.manual_backward(loss)
        opt.step()

DonorMILModel.train(mode=True)#

Set the module in training mode.

This has an effect only on certain modules. See the documentation of particular modules for details of their behaviors in training/evaluation mode, i.e., whether they are affected, e.g. Dropout, BatchNorm, etc.

Return type:: Self

Args:

mode (bool): whether to set training mode (True) or evaluation: mode (False). Default: True.

Returns:

Module: self

DonorMILModel.train_dataloader()#

An iterable or collection of iterables specifying training samples.

For more information about multiple dataloaders, see this section.

The dataloader you return will not be reloaded unless you set :paramref:`~pytorch_lightning.trainer.trainer.Trainer.reload_dataloaders_every_n_epochs` to a positive integer.

For data processing use the following pattern:

download in prepare_data()

process and split in setup()

However, the above are only necessary for distributed processing.

Warning

do not assign state in prepare_data

fit()
prepare_data()
setup()

Note:: Lightning tries to add the correct sampler for distributed and arbitrary hardware. There is no need to set it yourself.

Return type:: Any

DonorMILModel.training_step(batch, batch_idx)#

Training step used by PyTorch Lightning.

Parameters:

batch (dict) – Dictionary containing input features and target labels.
batch_idx (int) – Index of the batch (unused).

Returns:

torch.Tensor The computed MSE loss for the batch.

DonorMILModel.transfer_batch_to_device(batch, device, dataloader_idx)#

Override this hook if your DataLoader returns tensors wrapped in a custom data structure.

The data types listed below (and any arbitrary nesting of them) are supported out of the box:

torch.Tensor or anything that implements .to(...)
list
dict
tuple

For anything else, you need to define how the data is moved to the target device (CPU, GPU, TPU, …).

Note:: This hook should only transfer the data and not modify it, nor should it move the data to any other device than the one passed in as argument (unless you know what you are doing). To check the current state of execution of this hook you can use self.trainer.training/testing/validating/predicting so that you can add different logic as per your requirement.
Args:: batch: A batch of data that needs to be transferred to a new device. device: The target device as defined in PyTorch. dataloader_idx: The index of the dataloader to which the batch belongs.
Returns:: A reference to the data on the new device.

Example:

def transfer_batch_to_device(self, batch, device, dataloader_idx):
    if isinstance(batch, CustomBatch):
        # move all tensors in your custom data structure to the device
        batch.samples = batch.samples.to(device)
        batch.targets = batch.targets.to(device)
    elif dataloader_idx == 0:
        # skip device transfer for the first dataloader or anything you wish
        pass
    else:
        batch = super().transfer_batch_to_device(batch, device, dataloader_idx)
    return batch

See Also:

move_data_to_device()
apply_to_collection()

Return type:: Any

DonorMILModel.type(dst_type)#

See torch.nn.Module.type().

Return type:: Self

DonorMILModel.unfreeze()#

Unfreeze all parameters for training.

model = MyLightningModule(...)
model.unfreeze()

Return type:: Self

Returns:: LightningModule self with all parameters unfrozen.

DonorMILModel.untoggle_optimizer(optimizer)#

Resets the state of required gradients that were toggled with toggle_optimizer().

Return type:: None

Args:: optimizer: The optimizer to untoggle.

DonorMILModel.val_dataloader()#

An iterable or collection of iterables specifying validation samples.

For more information about multiple dataloaders, see this section.

The dataloader you return will not be reloaded unless you set :paramref:`~pytorch_lightning.trainer.trainer.Trainer.reload_dataloaders_every_n_epochs` to a positive integer.

It’s recommended that all data downloads and preparation happen in prepare_data().

fit()
validate()
prepare_data()
setup()

Note:: Lightning tries to add the correct sampler for distributed and arbitrary hardware There is no need to set it yourself.
Note:: If you don’t need a validation dataset and a validation_step(), you don’t need to implement this method.

Return type:: Any

DonorMILModel.validation_step(batch, batch_idx)#

Validation step used by PyTorch Lightning.

Parameters:

batch (dict) – Dictionary containing input features and target labels.
batch_idx (int) – Index of the batch (unused).

Returns:

None Logs validation loss to PyTorch Lightning without returning a value.

DonorMILModel.xpu(device=None)#

Move all model parameters and buffers to the XPU.

This also makes associated parameters and buffers different objects. So it should be called before constructing optimizer if the module will live on XPU while being optimized.

Note

This method modifies the module in-place.

Arguments:

device (int, optional): if specified, all parameters will be: copied to that device

Returns:

Module: self

Return type:: Self

DonorMILModel.zero_grad(set_to_none=True)#

Reset gradients of all model parameters.

See similar function under torch.optim.Optimizer for more context.

Return type:: None

Args:

set_to_none (bool): instead of setting to zero, set the grads to None.: See torch.optim.Optimizer.zero_grad() for details.

cellink.ml.DonorMILModel

Contents

cellink.ml.DonorMILModel#

Attributes table#

Methods table#

Attributes#

Methods#