scvi.model.base.UnsupervisedTrainingMixin#

class scvi.model.base.UnsupervisedTrainingMixin[source]#

General purpose unsupervised train method.

Methods table#

train([max_epochs, use_gpu, accelerator, ...])

Train the model.

Methods#

UnsupervisedTrainingMixin.train(max_epochs=None, use_gpu=None, accelerator='auto', devices='auto', train_size=0.9, validation_size=None, shuffle_set_split=True, batch_size=128, early_stopping=False, plan_kwargs=None, **trainer_kwargs)[source]#

Train the model.

Parameters:

  • max_epochs (Optional[int] (default: None)) – Number of passes through the dataset. If None, defaults to np.min([round((20000 / n_cells) * 400), 400])

  • use_gpu (Union[str, int, bool, None] (default: None)) – Use default GPU if available (if True), or index of GPU to use (if int), or name of GPU (if str, e.g., ‘cuda:0’), or use CPU (if False). Passing in use_gpu!=None will override accelerator and devices arguments. This argument is deprecated in v1.0 and will be removed in v1.1. Please use accelerator and devices instead.

  • accelerator (str (default: 'auto')) – Supports passing different accelerator types (“cpu”, “gpu”, “tpu”, “ipu”, “hpu”, “mps, “auto”) as well as custom accelerator instances.

  • devices (Union[int, List[int], str] (default: 'auto')) – The devices to use. Can be set to a non-negative index (int or str), a sequence of device indices (list or comma-separated str), the value -1 to indicate all available devices, or “auto” for automatic selection based on the chosen accelerator. If set to “auto” and accelerator is not determined to be “cpu”, then devices will be set to the first available device.

  • train_size (float (default: 0.9)) – Size of training set in the range [0.0, 1.0].

  • validation_size (Optional[float] (default: None)) – Size of the test set. If None, defaults to 1 - train_size. If train_size + validation_size < 1, the remaining cells belong to a test set.

  • shuffle_set_split (bool (default: True)) – Whether to shuffle indices before splitting. If False, the val, train, and test set are split in the sequential order of the data according to validation_size and train_size percentages.

  • batch_size (int (default: 128)) – Minibatch size to use during training.

  • early_stopping (bool (default: False)) – Perform early stopping. Additional arguments can be passed in **kwargs. See Trainer for further options.

  • plan_kwargs (Optional[dict] (default: None)) – Keyword args for TrainingPlan. Keyword arguments passed to train() will overwrite values present in plan_kwargs, when appropriate.

  • **trainer_kwargs – Other keyword args for Trainer.