drvi.model.DRVIModule

drvi.model.DRVIModule#

class drvi.model.DRVIModule(n_input, n_latent=32, n_labels=1, n_split_latent=-1, split_aggregation='logsumexp', split_method='split_map', decoder_reuse_weights='everywhere', encoder_dims=(128, 128), decoder_dims=(128, 128), n_cats_per_cov=(), n_continuous_cov=0, encode_covariates=False, deeply_inject_covariates=False, categorical_covariate_dims=(), covariate_modeling_strategy='one_hot', use_batch_norm='none', affine_batch_norm='both', use_layer_norm='both', fill_in_the_blanks_ratio=0.0, reconstruction_strategy='dense', input_dropout_rate=0.0, encoder_dropout_rate=0.1, decoder_dropout_rate=0.0, gene_likelihood='pnb', dispersion='gene', prior='normal', var_activation='exp', mean_activation='identity', encoder_layer_factory=None, decoder_layer_factory=None, last_layer_gradient_scale=1.0, extra_encoder_kwargs=None, extra_decoder_kwargs=None)[source]#

DRVI (Disentangled Representation Variational Inference) pytorch module.

Parameters:

n_input (int) – Number of input genes.
n_latent (int (default: 32)) – Dimensionality of the latent space.
n_labels (int (default: 1)) – Number of ground-truth labels. Only used for calculation of metrics during training.
n_split_latent (int | None (default: -1)) – Number of splits in the latent space. -1 means split all dimensions (n_split_latent=n_latent).
split_aggregation (Literal['sum', 'logsumexp', 'max'] (default: 'logsumexp')) – How to aggregate splits in the last layer of the decoder.
split_method (Literal['split', 'power', 'split_map', 'split_diag'] | str (default: 'split_map')) – How to make splits: - “split” : Split the latent space - “power” : Transform the latent space to n_split vectors of size n_latent - “power@Z” : Transform the latent space to n_split vectors of size n_latent Z - “split_map” : Split the latent space then map each to latent space using unique transformations - “split_map@Z” : Split the latent space then map each to vector of size Z using unique transformations - “split_diag” : Simple diagonal splitting
decoder_reuse_weights (Literal['everywhere', 'last', 'intermediate', 'nowhere', 'not_first'] (default: 'everywhere')) – Where to reuse the weights of the decoder layers when using splitting. Possible values are ‘everywhere’, ‘last’, ‘intermediate’, ‘nowhere’, ‘not_first’. Defaults to “everywhere”.
encoder_dims (Sequence[int] (default: (128, 128))) – Number of nodes in hidden layers of the encoder.
decoder_dims (Sequence[int] (default: (128, 128))) – Number of nodes in hidden layers of the decoder.
n_cats_per_cov (Iterable[int] | None (default: ())) – Number of categories for each categorical covariate.
n_continuous_cov (int (default: 0)) – Number of continuous covariates.
encode_covariates (bool (default: False)) – Whether to concatenate covariates to expression in encoder.
deeply_inject_covariates (bool (default: False)) – Whether to concatenate covariates into output of hidden layers in encoder/decoder. This option only applies when n_layers >= 1. The covariates are concatenated to the input of subsequent hidden layers.
categorical_covariate_dims (Sequence[int] (default: ())) – Embedding dimension of covariate keys if applicable.
covariate_modeling_strategy (Literal['one_hot', 'emb', 'emb_shared', 'one_hot_linear', 'emb_linear', 'emb_shared_linear'] (default: 'one_hot')) – The strategy model takes to remove covariates.
use_batch_norm (Literal['encoder', 'decoder', 'none', 'both'] (default: 'none')) – Whether to use batch norm in layers.
affine_batch_norm (Literal['encoder', 'decoder', 'none', 'both'] (default: 'both')) – Whether to use affine batch norm in layers.
use_layer_norm (Literal['encoder', 'decoder', 'none', 'both'] (default: 'both')) – Whether to use layer norm in layers.
fill_in_the_blanks_ratio (float (default: 0.0)) – Ratio for fill-in-the-blanks training.
reconstruction_strategy (str (default: 'dense')) – Strategy for reconstruction. - “dense” : Reconstruct all features. - “random_batch@M” : Reconstruct M random features for each batch.
input_dropout_rate (float (default: 0.0)) – Dropout rate to apply to the input.
encoder_dropout_rate (float (default: 0.1)) – Dropout rate to apply to each of the encoder hidden layers.
decoder_dropout_rate (float (default: 0.0)) – Dropout rate to apply to each of the decoder hidden layers.
gene_likelihood (Literal['pnb', 'nb', 'poisson', 'normal', 'normal_unit_var'] (default: 'pnb')) – Gene likelihood model. Options include: - “poisson” : Poisson distributions - “nb” : Negative binomial distributions - “pnb”: Log negative binomial distributions - “normal” : Normal distributions - “normal_unit_var” : Normal distributions with unit variance
dispersion (Literal['gene', 'gene-batch', 'gene-cell'] (default: 'gene')) – Dispersion parameter modeling strategy for negative binomial distributions. Options: - “gene” (default): Dispersion parameter is constant per gene across all cells - “gene-batch”: Dispersion can differ between different batches - “gene-cell”: Dispersion can differ for every gene in every cell Only used when relevant to the gene likelihood model.
prior (Literal['normal'] (default: 'normal')) – Prior model.
var_activation (Callable | Literal['exp', 'pow2', '2sig'] (default: 'exp')) – The activation function to ensure positivity of the variational distribution. Options include “exp”, “pow2”, “2sig” or a custom callable.
mean_activation (Callable | str (default: 'identity')) – The activation function at the end of mean encoder. Options include “identity”, “relu”, “leaky_relu”, “leaky_relu_{slope}”, “elu”, “elu_{min_value}” or a custom callable.
encoder_layer_factory (LayerFactory | None (default: None)) – A layer Factory instance for building encoder layers.
decoder_layer_factory (LayerFactory | None (default: None)) – A layer Factory instance for building decoder layers.
last_layer_gradient_scale (float (default: 1.0)) – Gradient scale for the last layer of the decoder.
extra_encoder_kwargs (dict[str, Any] | None (default: None)) – Extra keyword arguments passed into encoder.
extra_decoder_kwargs (dict[str, Any] | None (default: None)) – Extra keyword arguments passed into decoder.

Attributes table#

`T_destination`
`call_super_init`
`device`
`dump_patches`
`fully_deterministic`
`training`

Methods table#

`add_module`(name, module)	Add a child module to the current module.
`apply`(fn)	Apply `fn` recursively to every submodule (as returned by `.children()`) as well as self.
`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.
`compile`(args, *kwargs)	Compile this Module's forward using `torch.compile()`.
`cpu`()	Move all model parameters and buffers to the CPU.
`cuda`([device])	Move all model parameters and buffers to the GPU.
`double`()	Casts all floating point parameters and buffers to `double` datatype.
`eval`()	Set the module in evaluation mode.
`extra_repr`()	Return the extra representation of the module.
`float`()	Casts all floating point parameters and buffers to `float` datatype.
`forward`(tensors[, ...])	Forward pass through the network.
`generative`(z, library[, cat_covs, ...])	Runs the generative model.
`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`()	Casts all floating point parameters and buffers to `half` datatype.
`inference`(x[, cont_covs, cat_covs, n_samples])	High level inference method.
`ipu`([device])	Move all model parameters and buffers to the IPU.
`load_state_dict`(state_dict[, strict, assign])	Copy parameters and buffers from `state_dict` into this module and its descendants.
`loss`(tensors, inference_outputs, ...[, ...])	Loss function.
`marginal_ll`(tensors, n_mc_samples)	Compute marginal log-likelihood.
`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_load`(model, **kwargs)	Callback function run in `load()`.
`parameters`([recurse])	Return an iterator over module parameters.
`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.
`requires_grad_`([requires_grad])	Change if autograd should record operations on parameters in this module.
`sample`(tensors[, n_samples, library_size, ...])	Generate observation samples from the posterior predictive distribution.
`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.
`share_memory`()	See `torch.Tensor.share_memory_()`.
`state_dict`(*args[, destination, prefix, ...])
`to`(args, *kwargs)
`to_empty`(*, device[, recurse])	Move the parameters and buffers to the specified device without copying storage.
`train`([mode])	Set the module in training mode.
`type`(dst_type)	Casts all parameters and buffers to `dst_type`.
`xpu`([device])	Move all model parameters and buffers to the XPU.
`zero_grad`([set_to_none])	Reset gradients of all model parameters.

Attributes#

DRVIModule.T_destination = ~T_destination#

DRVIModule.call_super_init: bool = False#

DRVIModule.device#

DRVIModule.dump_patches: bool = False#

DRVIModule.fully_deterministic#

DRVIModule.training: bool#

Methods#

DRVIModule.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.

DRVIModule.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 torch.nn.init).

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)
)

DRVIModule.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

DRVIModule.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)

DRVIModule.children()#

Return an iterator over immediate children modules.

Return type:: Iterator[Module]

Yields:: Module: a child module

DRVIModule.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

DRVIModule.cpu()#

Move all model parameters and buffers to the CPU.

Note

This method modifies the module in-place.

Returns:: Module: self

Return type:: Self

DRVIModule.cuda(device=None)#

Move all model parameters and buffers to the GPU.

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

Note

This method modifies the module in-place.

Args:

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

Returns:

Module: self

Return type:: Self

DRVIModule.double()#

Casts all floating point parameters and buffers to double datatype.

Note

This method modifies the module in-place.

Returns:: Module: self

Return type:: Self

DRVIModule.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 disabling gradient computation for a comparison between .eval() and several similar mechanisms that may be confused with it.

Return type:: Self

Returns:: Module: self

DRVIModule.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

DRVIModule.float()#

Casts all floating point parameters and buffers to float datatype.

Note

This method modifies the module in-place.

Returns:: Module: self

Return type:: Self

DRVIModule.forward(tensors, get_inference_input_kwargs=None, get_generative_input_kwargs=None, inference_kwargs=None, generative_kwargs=None, loss_kwargs=None, compute_loss=True)#

Forward pass through the network.

Parameters:

tensors – tensors to pass through
get_inference_input_kwargs (dict | None (default: None)) – Keyword args for _get_inference_input()
get_generative_input_kwargs (dict | None (default: None)) – Keyword args for _get_generative_input()
inference_kwargs (dict | None (default: None)) – Keyword args for inference()
generative_kwargs (dict | None (default: None)) – Keyword args for generative()
loss_kwargs (dict | None (default: None)) – Keyword args for loss()
compute_loss (default: True) – Whether to compute loss on forward pass. This adds another return value.

Return type:

tuple[Tensor, Tensor] | tuple[Tensor, Tensor, LossOutput]

DRVIModule.generative(z, library, cat_covs=None, cont_covs=None, transform_batch=None, reconstruction_indices=None, n_samples=1)[source]#

Runs the generative model.

Parameters:

z (Tensor) – Latent variables.
library (Tensor) – Library size information.
cont_covs (Tensor | None (default: None)) – Continuous covariates.
cat_covs (Tensor | None (default: None)) – Categorical covariates.
transform_batch (Tensor | None (default: None)) – Batch to condition on. Currently not used but required for RNASeqMixin compatibility.
reconstruction_indices (Tensor | None (default: None)) – Indices of features to reconstruct.

Return type:

dict[str, Any]

Returns:

dict Dictionary containing generative model outputs.

DRVIModule.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

DRVIModule.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

DRVIModule.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

DRVIModule.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.

DRVIModule.half()#

Casts all floating point parameters and buffers to half datatype.

Note

This method modifies the module in-place.

Returns:: Module: self

Return type:: Self

DRVIModule.inference(x, cont_covs=None, cat_covs=None, n_samples=1)[source]#

High level inference method.

Runs the inference (encoder) model.

Parameters:

x (Tensor) – Input tensor data.
cont_covs (Tensor | None (default: None)) – Continuous covariates.
cat_covs (Tensor | None (default: None)) – Categorical covariates.
n_samples (int (default: 1)) – Number of samples to generate.

Return type:

dict[str, Any]

Returns:

dict Dictionary containing inference outputs including latent variables.

DRVIModule.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

DRVIModule.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.

DRVIModule.loss(tensors, inference_outputs, generative_outputs, kl_weight=1.0)[source]#

Loss function.

Parameters:

tensors (dict[str, Tensor]) – Dictionary containing tensor data.
inference_outputs (dict[str, Any]) – Outputs from the inference step.
generative_outputs (dict[str, Any]) – Outputs from the generative step.
kl_weight (float (default: 1.0)) – Weight for KL divergence term.

Return type:

LossOutput

Returns:

LossOutput Loss output object containing various loss components.

DRVIModule.marginal_ll(tensors, n_mc_samples)[source]#

Compute marginal log-likelihood.

Parameters:

tensors (dict[str, Tensor]) – Dictionary containing tensor data.
n_mc_samples (int) – Number of Monte Carlo samples for estimation.

Return type:

float

Returns:

float Marginal log-likelihood value.

DRVIModule.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)

DRVIModule.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

DRVIModule.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())

DRVIModule.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)

DRVIModule.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))

DRVIModule.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())

DRVIModule.on_load(model, **kwargs)#: Callback function run in load().

DRVIModule.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)

DRVIModule.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()

DRVIModule.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))

DRVIModule.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()

DRVIModule.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()

DRVIModule.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

DRVIModule.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

DRVIModule.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()

DRVIModule.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.

DRVIModule.register_module(name, module)#

Alias for add_module().

Return type:: None

DRVIModule.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.

DRVIModule.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.

DRVIModule.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.

DRVIModule.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 disabling gradient computation 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

DRVIModule.sample(tensors, n_samples=1, library_size=1, generative_kwargs=None)[source]#

Generate observation samples from the posterior predictive distribution.

The posterior predictive distribution is written as $p(\hat{x} \mid x)$ .

Parameters:

tensors (dict[str, Tensor]) – Dictionary containing tensor data.
n_samples (int (default: 1)) – Number of required samples for each cell.
library_size (int (default: 1)) – Library size to scale samples to.
generative_kwargs (dict | None (default: None)) – Keyword args for generative() in fwd pass

Return type:

Tensor

Returns:

torch.Tensor Tensor with shape (n_cells, n_genes, n_samples).

DRVIModule.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

DRVIModule.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

DRVIModule.share_memory()#

See torch.Tensor.share_memory_().

Return type:: Self

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

Overloads:

self, destination (T_destination), prefix (str), keep_vars (bool) → T_destination
self, prefix (str), keep_vars (bool) → dict[str, Any]

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']

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

Overloads:

self, device (DeviceLikeType | None), dtype (dtype | None), non_blocking (bool) → Self
self, dtype (dtype), non_blocking (bool) → Self
self, tensor (Tensor), non_blocking (bool) → Self

Move and/or cast the parameters and buffers.

This can be called as

to(device=None, dtype=None, non_blocking=False)

drvi.model.to(dtype, non_blocking=False)

drvi.model.to(tensor, non_blocking=False)

drvi.model.to(memory_format=torch.channels_last)

Its signature is similar to torch.Tensor.to(), but only accepts floating point or complex dtypes. In addition, this method will only cast the floating point or complex parameters and buffers to dtype (if given). The integral parameters and buffers will be moved device, if that is given, but with dtypes unchanged. When non_blocking is set, it tries to convert/move asynchronously with respect to the host if possible, e.g., moving CPU Tensors with pinned memory to CUDA devices.

See below for examples.

Note

This method modifies the module in-place.

Args:

device (torch.device): the desired device of the parameters: and buffers in this module
dtype (torch.dtype): the desired floating point or complex dtype of: the parameters and buffers in this module
tensor (torch.Tensor): Tensor whose dtype and device are the desired: dtype and device for all parameters and buffers in this module
memory_format (torch.memory_format): the desired memory: format for 4D parameters and buffers in this module (keyword only argument)

Returns:

Module: self

Examples:

>>> # xdoctest: +IGNORE_WANT("non-deterministic")
>>> linear = nn.Linear(2, 2)
>>> linear.weight
Parameter containing:
tensor([[ 0.1913, -0.3420],
        [-0.5113, -0.2325]])
>>> linear.to(torch.double)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1913, -0.3420],
        [-0.5113, -0.2325]], dtype=torch.float64)
>>> # xdoctest: +REQUIRES(env:TORCH_DOCTEST_CUDA1)
>>> gpu1 = torch.device("cuda:1")
>>> linear.to(gpu1, dtype=torch.half, non_blocking=True)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1914, -0.3420],
        [-0.5112, -0.2324]], dtype=torch.float16, device='cuda:1')
>>> cpu = torch.device("cpu")
>>> linear.to(cpu)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1914, -0.3420],
        [-0.5112, -0.2324]], dtype=torch.float16)

>>> linear = nn.Linear(2, 2, bias=None).to(torch.cdouble)
>>> linear.weight
Parameter containing:
tensor([[ 0.3741+0.j,  0.2382+0.j],
        [ 0.5593+0.j, -0.4443+0.j]], dtype=torch.complex128)
>>> linear(torch.ones(3, 2, dtype=torch.cdouble))
tensor([[0.6122+0.j, 0.1150+0.j],
        [0.6122+0.j, 0.1150+0.j],
        [0.6122+0.j, 0.1150+0.j]], dtype=torch.complex128)

DRVIModule.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

DRVIModule.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

DRVIModule.type(dst_type)#

Casts all parameters and buffers to dst_type.

Note

This method modifies the module in-place.

Args:: dst_type (type or string): the desired type
Returns:: Module: self

Return type:: Self

DRVIModule.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

DRVIModule.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.

drvi.model.DRVIModule

Contents

drvi.model.DRVIModule#

Attributes table#

Methods table#

Attributes#

Methods#