scvi.model.base.BaseModelClass#

class scvi.model.base.BaseModelClass(adata=None)[source]#: Abstract class for scvi-tools models.

Attributes table#

`adata`	Data attached to model instance.
`adata_manager`	Manager instance associated with self.adata.
`device`	The current device that the module's params are on.
`history`	Returns computed metrics during training.
`is_trained`	Whether the model has been trained.
`test_indices`	Observations that are in test set.
`train_indices`	Observations that are in train set.
`validation_indices`	Observations that are in validation set.

Methods table#

`convert_legacy_save`(dir_path, output_dir_path)	Converts a legacy saved model (<v0.15.0) to the updated save format.
`get_anndata_manager`(adata[, required])	Retrieves the `AnnDataManager` for a given AnnData object specific to this model instance.
`get_from_registry`(adata, registry_key)	Returns the object in AnnData associated with the key in the data registry.
`load`(dir_path[, adata, use_gpu, prefix, ...])	Instantiate a model from the saved output.
`load_registry`(dir_path[, prefix])	Return the full registry saved with the model.
`register_manager`(adata_manager)	Registers an `AnnDataManager` instance with this model class.
`save`(dir_path[, prefix, overwrite, save_anndata])	Save the state of the model.
`setup_anndata`(adata, args, *kwargs)	Sets up the `AnnData` object for this model.
`to_device`(device)	Move model to device.
`train`()	Trains the model.
`view_anndata_setup`([adata, ...])	Print summary of the setup for the initial AnnData or a given AnnData object.
`view_setup_args`(dir_path[, prefix])	Print args used to setup a saved model.

Attributes#

adata#

BaseModelClass.adata[source]#

Data attached to model instance.

Return type:: AnnData | MuDataUnion[AnnData, MuData]

adata_manager#

BaseModelClass.adata_manager[source]#

Manager instance associated with self.adata.

Return type:: AnnDataManager

device#

BaseModelClass.device[source]#

The current device that the module’s params are on.

Return type:: str

history#

BaseModelClass.history[source]#: Returns computed metrics during training.

is_trained#

BaseModelClass.is_trained[source]#

Whether the model has been trained.

Return type:: bool

test_indices#

BaseModelClass.test_indices[source]#

Observations that are in test set.

Return type:: ndarray

train_indices#

BaseModelClass.train_indices[source]#

Observations that are in train set.

Return type:: ndarray

validation_indices#

BaseModelClass.validation_indices[source]#

Observations that are in validation set.

Return type:: ndarray

Methods#

convert_legacy_save#

classmethod BaseModelClass.convert_legacy_save(dir_path, output_dir_path, overwrite=False, prefix=None)[source]#

Converts a legacy saved model (<v0.15.0) to the updated save format.

Parameters:

dir_path : str: Path to directory where legacy model is saved.
output_dir_path : str: Path to save converted save files.
overwrite : bool (default: False): Overwrite existing data or not. If False and directory already exists at output_dir_path, error will be raised.
prefix : str | NoneOptional[str] (default: None): Prefix of saved file names.

Return type:

None

get_anndata_manager#

BaseModelClass.get_anndata_manager(adata, required=False)[source]#

Retrieves the AnnDataManager for a given AnnData object specific to this model instance.

Requires self.id has been set. Checks for an AnnDataManager specific to this model instance.

Parameters:

adata : AnnData | MuDataUnion[AnnData, MuData]: AnnData object to find manager instance for.
required : bool (default: False): If True, errors on missing manager. Otherwise, returns None when manager is missing.

Return type:

AnnDataManager | NoneOptional[AnnDataManager]

get_from_registry#

BaseModelClass.get_from_registry(adata, registry_key)[source]#

Returns the object in AnnData associated with the key in the data registry.

AnnData object should be registered with the model prior to calling this function via the self._validate_anndata method.

Parameters:

registry_key : str: key of object to get from data registry.
adata : AnnData | MuDataUnion[AnnData, MuData]: AnnData to pull data from.

Return type:

ndarray

Returns:

The requested data as a NumPy array.

load#

classmethod BaseModelClass.load(dir_path, adata=None, use_gpu=None, prefix=None, backup_url=None)[source]#

Instantiate a model from the saved output.

Parameters:

dir_path : str: Path to saved outputs.
adata : AnnData | MuData | NoneUnion[AnnData, MuData, None] (default: None): AnnData organized in the same way as data used to train model. It is not necessary to run setup_anndata, as AnnData is validated against the saved scvi setup dictionary. If None, will check for and load anndata saved with the model.
use_gpu : str | int | bool | NoneUnion[str, int, bool, None] (default: None): Load model on default GPU if available (if None or True), or index of GPU to use (if int), or name of GPU (if str), or use CPU (if False).
prefix : str | NoneOptional[str] (default: None): Prefix of saved file names.
backup_url : str | NoneOptional[str] (default: None): URL to retrieve saved outputs from if not present on disk.

Returns:

Model with loaded state dictionaries.

Examples

>>> model = ModelClass.load(save_path, adata) # use the name of the model class used to save
>>> model.get_....

load_registry#

static BaseModelClass.load_registry(dir_path, prefix=None)[source]#

Return the full registry saved with the model.

Parameters:

dir_path : str: Path to saved outputs.
prefix : str | NoneOptional[str] (default: None): Prefix of saved file names.

Return type:

dict

Returns:

The full registry saved with the model

register_manager#

classmethod BaseModelClass.register_manager(adata_manager)[source]#

Registers an AnnDataManager instance with this model class.

Stores the AnnDataManager reference in a class-specific manager store. Intended for use in the setup_anndata() class method followed up by retrieval of the AnnDataManager via the _get_most_recent_anndata_manager() method in the model init method.

Notes

Subsequent calls to this method with an AnnDataManager instance referring to the same underlying AnnData object will overwrite the reference to previous AnnDataManager.

save#

BaseModelClass.save(dir_path, prefix=None, overwrite=False, save_anndata=False, **anndata_write_kwargs)[source]#

Save the state of the model.

Neither the trainer optimizer state nor the trainer history are saved. Model files are not expected to be reproducibly saved and loaded across versions until we reach version 1.0.

Parameters:

dir_path : str: Path to a directory.
prefix : str | NoneOptional[str] (default: None): Prefix to prepend to saved file names.
overwrite : bool (default: False): Overwrite existing data or not. If False and directory already exists at dir_path, error will be raised.
save_anndata : bool (default: False): If True, also saves the anndata
anndata_write_kwargs: Kwargs for write()

setup_anndata#

abstract classmethod BaseModelClass.setup_anndata(adata, *args, **kwargs)[source]#

Sets up the AnnData object for this model.

A mapping will be created between data fields used by this model to their respective locations in adata.

None of the data in adata are modified. Only adds fields to adata.

Each model class deriving from this class provides parameters to this method according to its needs. To operate correctly with the model initialization, the implementation must call register_manager() on a model-specific instance of AnnDataManager.

to_device#

BaseModelClass.to_device(device)[source]#

Move model to device.

Parameters:

device : str | intUnion[str, int]: Device to move model to. Options: ‘cpu’ for CPU, integer GPU index (eg. 0), or ‘cuda:X’ where X is the GPU index (eg. ‘cuda:0’). See torch.device for more info.

Examples

>>> adata = scvi.data.synthetic_iid()
>>> model = scvi.model.SCVI(adata)
>>> model.to_device('cpu')      # moves model to CPU
>>> model.to_device('cuda:0')   # moves model to GPU 0
>>> model.to_device(0)          # also moves model to GPU 0

train#

abstract BaseModelClass.train()[source]#: Trains the model.

view_anndata_setup#

BaseModelClass.view_anndata_setup(adata=None, hide_state_registries=False)[source]#

Print summary of the setup for the initial AnnData or a given AnnData object.

Parameters:

adata : AnnData | MuData | NoneUnion[AnnData, MuData, None] (default: None): AnnData object setup with setup_anndata or transfer_fields().
hide_state_registries : bool (default: False): If True, prints a shortened summary without details of each state registry.

Return type:

None

view_setup_args#

static BaseModelClass.view_setup_args(dir_path, prefix=None)[source]#

Print args used to setup a saved model.

Parameters:

dir_path : str: Path to saved outputs.
prefix : str | NoneOptional[str] (default: None): Prefix of saved file names.

Return type:

None