scvi.model.base.BaseModelClass#
Attributes table#
Data attached to model instance. |
|
Manager instance associated with self.adata. |
|
The current device that the module's params are on. |
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Returns computed metrics during training. |
|
Whether the model has been trained. |
|
Observations that are in test set. |
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Observations that are in train set. |
|
Observations that are in validation set. |
Methods table#
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Converts a legacy saved model (<v0.15.0) to the updated save format. |
|
Retrieves the |
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Returns the object in AnnData associated with the key in the data registry. |
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Instantiate a model from the saved output. |
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Registers an |
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Save the state of the model. |
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Sets up the |
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Move model to device. |
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Trains the model. |
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Print summary of the setup for the initial AnnData or a given AnnData object. |
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Print args used to setup a saved model. |
Attributes#
adata#
adata_manager#
- BaseModelClass.adata_manager#
Manager instance associated with self.adata.
- Return type
device#
history#
- BaseModelClass.history#
Returns computed metrics during training.
is_trained#
test_indices#
train_indices#
validation_indices#
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 atoutput_dir_path
, error will be raised.- prefix :
str
|None
Optional
[str
] (default:None
) Prefix of saved file names.
- dir_path :
- Return type
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 anAnnDataManager
specific to this model instance.- Parameters
- Return type
get_from_registry#
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
|None
Optional
[AnnData
] (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
|None
Union
[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
|None
Optional
[str
] (default:None
) Prefix of saved file names.
- backup_url :
str
|None
Optional
[str
] (default:None
) URL to retrieve saved outputs from if not present on disk.
- dir_path :
- 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_....
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 thesetup_anndata()
class method followed up by retrieval of theAnnDataManager
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 previousAnnDataManager
.
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
|None
Optional
[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()
- dir_path :
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 ofAnnDataManager
.- Sets up the
to_device#
- BaseModelClass.to_device(device)[source]#
Move model to device.
- Parameters
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