scvi.model.SCVI

scvi.model.SCVI#

class scvi.model.SCVI(adata=None, n_hidden=128, n_latent=10, n_layers=1, dropout_rate=0.1, dispersion='gene', gene_likelihood='zinb', latent_distribution='normal', **kwargs)[source]#

single-cell Variational Inference [Lopez et al., 2018].

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object that has been registered via setup_anndata(). If None, then the underlying module will not be initialized until training, and a LightningDataModule must be passed in during training (EXPERIMENTAL).

  • n_hidden (int (default: 128)) – Number of nodes per hidden layer.

  • n_latent (int (default: 10)) – Dimensionality of the latent space.

  • n_layers (int (default: 1)) – Number of hidden layers used for encoder and decoder NNs.

  • dropout_rate (float (default: 0.1)) – Dropout rate for neural networks.

  • dispersion (Literal['gene', 'gene-batch', 'gene-label', 'gene-cell'] (default: 'gene')) –

    One of the following:

    • 'gene' - dispersion parameter of NB is constant per gene across cells

    • 'gene-batch' - dispersion can differ between different batches

    • 'gene-label' - dispersion can differ between different labels

    • 'gene-cell' - dispersion can differ for every gene in every cell

  • gene_likelihood (Literal['zinb', 'nb', 'poisson', 'normal'] (default: 'zinb')) –

    One of:

    • 'nb' - Negative binomial distribution

    • 'zinb' - Zero-inflated negative binomial distribution

    • 'poisson' - Poisson distribution

    • 'normal' - EXPERIMENTAL Normal distribution

  • latent_distribution (Literal['normal', 'ln'] (default: 'normal')) –

    One of:

    • 'normal' - Normal distribution

    • 'ln' - Logistic normal distribution (Normal(0, I) transformed by softmax)

  • **kwargs – Additional keyword arguments for VAE.

Examples

>>> adata = anndata.read_h5ad(path_to_anndata)
>>> scvi.model.SCVI.setup_anndata(adata, batch_key="batch")
>>> vae = scvi.model.SCVI(adata)
>>> vae.train()
>>> adata.obsm["X_scVI"] = vae.get_latent_representation()
>>> adata.obsm["X_normalized_scVI"] = vae.get_normalized_expression()

Notes

See further usage examples in the following tutorials:

  1. Introduction to scvi-tools

  2. Atlas-level integration of lung data

  3. Reference mapping with scvi-tools

  4. Integrating datasets with scVI in R

See also

VAE

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.

minified_data_type

The type of minified data associated with this model, if applicable.

summary_string

Summary string of the model.

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.

deregister_manager([adata])

Deregisters the AnnDataManager instance associated with adata.

differential_expression([adata, groupby, ...])

A unified method for differential expression analysis.

get_anndata_manager(adata[, required])

Retrieves the AnnDataManager for a given AnnData object.

get_batch_representation([adata, indices, ...])

Get the batch representation for a given set of indices.

get_elbo([adata, indices, batch_size, ...])

Compute the evidence lower bound (ELBO) on the data.

get_feature_correlation_matrix([adata, ...])

Generate gene-gene correlation matrix using scvi uncertainty and expression.

get_from_registry(adata, registry_key)

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

get_latent_library_size([adata, indices, ...])

Returns the latent library size for each cell.

get_latent_representation([adata, indices, ...])

Compute the latent representation of the data.

get_likelihood_parameters([adata, indices, ...])

Estimates for the parameters of the likelihood \(p(x \mid z)\).

get_marginal_ll([adata, indices, ...])

Compute the marginal log-likehood of the data.

get_normalized_expression([adata, indices, ...])

Returns the normalized (decoded) gene expression.

get_reconstruction_error([adata, indices, ...])

Compute the reconstruction error on the data.

load(dir_path[, adata, accelerator, device, ...])

Instantiate a model from the saved output.

load_query_data(adata, reference_model[, ...])

Online update of a reference model with scArches algorithm [Lotfollahi et al., 2021].

load_registry(dir_path[, prefix])

Return the full registry saved with the model.

minify_adata([minified_data_type, ...])

Minifies the model's adata.

posterior_predictive_sample([adata, ...])

Generate predictive samples from the posterior predictive distribution.

prepare_query_anndata(adata, reference_model)

Prepare data for query integration.

prepare_query_mudata(mdata, reference_model)

Prepare multimodal dataset for query integration.

register_manager(adata_manager)

Registers an AnnDataManager instance with this model class.

save(dir_path[, prefix, overwrite, ...])

Save the state of the model.

setup_anndata(adata[, layer, batch_key, ...])

Sets up the AnnData object for this model.

to_device(device)

Move model to device.

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

Train 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#

SCVI.adata[source]#

Data attached to model instance.

SCVI.adata_manager[source]#

Manager instance associated with self.adata.

SCVI.device[source]#

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

SCVI.history[source]#

Returns computed metrics during training.

SCVI.is_trained[source]#

Whether the model has been trained.

SCVI.minified_data_type[source]#

The type of minified data associated with this model, if applicable.

SCVI.summary_string[source]#

Summary string of the model.

SCVI.test_indices[source]#

Observations that are in test set.

SCVI.train_indices[source]#

Observations that are in train set.

SCVI.validation_indices[source]#

Observations that are in validation set.

Methods#

classmethod SCVI.convert_legacy_save(dir_path, output_dir_path, overwrite=False, prefix=None, **save_kwargs)[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 | None (default: None)) – Prefix of saved file names.

  • **save_kwargs – Keyword arguments passed into save().

Return type:

None

SCVI.deregister_manager(adata=None)[source]#

Deregisters the AnnDataManager instance associated with adata.

If adata is None, deregisters all AnnDataManager instances in both the class and instance-specific manager stores, except for the one associated with this model instance.

SCVI.differential_expression(adata=None, groupby=None, group1=None, group2=None, idx1=None, idx2=None, mode='change', delta=0.25, batch_size=None, all_stats=True, batch_correction=False, batchid1=None, batchid2=None, fdr_target=0.05, silent=False, weights='uniform', filter_outlier_cells=False, importance_weighting_kwargs=None, **kwargs)[source]#

A unified method for differential expression analysis.

Implements 'vanilla' DE [Lopez et al., 2018] and 'change' mode DE [Boyeau et al., 2019].

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with equivalent structure to initial AnnData. If None, defaults to the AnnData object used to initialize the model.

  • groupby (str | None (default: None)) – The key of the observations grouping to consider.

  • group1 (list[str] | None (default: None)) – Subset of groups, e.g. [‘g1’, ‘g2’, ‘g3’], to which comparison shall be restricted, or all groups in groupby (default).

  • group2 (str | None (default: None)) – If None, compare each group in group1 to the union of the rest of the groups in groupby. If a group identifier, compare with respect to this group.

  • idx1 (list[int] | list[bool] | str | None (default: None)) – idx1 and idx2 can be used as an alternative to the AnnData keys. Custom identifier for group1 that can be of three sorts: (1) a boolean mask, (2) indices, or (3) a string. If it is a string, then it will query indices that verifies conditions on adata.obs, as described in pandas.DataFrame.query() If idx1 is not None, this option overrides group1 and group2.

  • idx2 (list[int] | list[bool] | str | None (default: None)) – Custom identifier for group2 that has the same properties as idx1. By default, includes all cells not specified in idx1.

  • mode (Literal['vanilla', 'change'] (default: 'change')) – Method for differential expression. See user guide for full explanation.

  • delta (float (default: 0.25)) – specific case of region inducing differential expression. In this case, we suppose that \(R \setminus [-\delta, \delta]\) does not induce differential expression (change model default case).

  • batch_size (int | None (default: None)) – Minibatch size for data loading into model. Defaults to scvi.settings.batch_size.

  • all_stats (bool (default: True)) – Concatenate count statistics (e.g., mean expression group 1) to DE results.

  • batch_correction (bool (default: False)) – Whether to correct for batch effects in DE inference.

  • batchid1 (list[str] | None (default: None)) – Subset of categories from batch_key registered in setup_anndata, e.g. [‘batch1’, ‘batch2’, ‘batch3’], for group1. Only used if batch_correction is True, and by default all categories are used.

  • batchid2 (list[str] | None (default: None)) – Same as batchid1 for group2. batchid2 must either have null intersection with batchid1, or be exactly equal to batchid1. When the two sets are exactly equal, cells are compared by decoding on the same batch. When sets have null intersection, cells from group1 and group2 are decoded on each group in group1 and group2, respectively.

  • fdr_target (float (default: 0.05)) – Tag features as DE based on posterior expected false discovery rate.

  • silent (bool (default: False)) – If True, disables the progress bar. Default: False.

  • weights (Optional[Literal['uniform', 'importance']] (default: 'uniform')) – Weights to use for sampling. If None, defaults to “uniform”.

  • filter_outlier_cells (bool (default: False)) – Whether to filter outlier cells with filter_outlier_cells().

  • importance_weighting_kwargs (dict | None (default: None)) – Keyword arguments passed into _get_importance_weights().

  • **kwargs – Keyword args for scvi.model.base.DifferentialComputation.get_bayes_factors()

Return type:

DataFrame

Returns:

Differential expression DataFrame.

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

Retrieves the AnnDataManager for a given AnnData object.

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

Parameters:

  • adata (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 | None

SCVI.get_batch_representation(adata=None, indices=None, batch_size=None)[source]#

Get the batch representation for a given set of indices.

Return type:

ndarray

SCVI.get_elbo(adata=None, indices=None, batch_size=None, dataloader=None, return_mean=True, **kwargs)[source]#

Compute the evidence lower bound (ELBO) on the data.

The ELBO is the reconstruction error plus the Kullback-Leibler (KL) divergences between the variational distributions and the priors. It is different from the marginal log-likelihood; specifically, it is a lower bound on the marginal log-likelihood plus a term that is constant with respect to the variational distribution. It still gives good insights on the modeling of the data and is fast to compute.

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with var_names in the same order as the ones used to train the model. If None and dataloader is also None, it defaults to the object used to initialize the model.

  • indices (Sequence[int] | None (default: None)) – Indices of observations in adata to use. If None, defaults to all observations. Ignored if dataloader is not None.

  • batch_size (int | None (default: None)) – Minibatch size for the forward pass. If None, defaults to scvi.settings.batch_size. Ignored if dataloader is not None.

  • dataloader (Iterator[dict[str, Tensor | None]] (default: None)) – An iterator over minibatches of data on which to compute the metric. The minibatches should be formatted as a dictionary of Tensor with keys as expected by the model. If None, a dataloader is created from adata.

  • return_mean (bool (default: True)) – Whether to return the mean of the ELBO or the ELBO for each observation.

  • **kwargs – Additional keyword arguments to pass into the forward method of the module.

Return type:

float

Returns:

Evidence lower bound (ELBO) of the data.

Notes

This is not the negative ELBO, so higher is better.

SCVI.get_feature_correlation_matrix(adata=None, indices=None, n_samples=10, batch_size=64, rna_size_factor=1000, transform_batch=None, correlation_type='spearman')[source]#

Generate gene-gene correlation matrix using scvi uncertainty and expression.

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with equivalent structure to initial AnnData. If None, defaults to the AnnData object used to initialize the model.

  • indices (list[int] | None (default: None)) – Indices of cells in adata to use. If None, all cells are used.

  • n_samples (int (default: 10)) – Number of posterior samples to use for estimation.

  • batch_size (int (default: 64)) – Minibatch size for data loading into model. Defaults to scvi.settings.batch_size.

  • rna_size_factor (int (default: 1000)) – size factor for RNA prior to sampling gamma distribution.

  • transform_batch (list[int | float | str] | None (default: None)) –

    Batches to condition on. If transform_batch is:

    • None, then real observed batch is used.

    • int, then batch transform_batch is used.

    • list of int, then values are averaged over provided batches.

  • correlation_type (Literal['spearman', 'pearson'] (default: 'spearman')) – One of “pearson”, “spearman”.

Return type:

DataFrame

Returns:

Gene-gene correlation matrix

SCVI.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 | MuData) – AnnData to pull data from.

Return type:

ndarray

Returns:

The requested data as a NumPy array.

SCVI.get_latent_library_size(adata=None, indices=None, give_mean=True, batch_size=None)[source]#

Returns the latent library size for each cell.

This is denoted as \(\ell_n\) in the scVI paper.

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with equivalent structure to initial AnnData. If None, defaults to the AnnData object used to initialize the model.

  • indices (list[int] | None (default: None)) – Indices of cells in adata to use. If None, all cells are used.

  • give_mean (bool (default: True)) – Return the mean or a sample from the posterior distribution.

  • batch_size (int | None (default: None)) – Minibatch size for data loading into model. Defaults to scvi.settings.batch_size.

Return type:

ndarray

SCVI.get_latent_representation(adata=None, indices=None, give_mean=True, mc_samples=5000, batch_size=None, return_dist=False, dataloader=None)[source]#

Compute the latent representation of the data.

This is typically denoted as \(z_n\).

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with var_names in the same order as the ones used to train the model. If None and dataloader is also None, it defaults to the object used to initialize the model.

  • indices (Sequence[int] | None (default: None)) – Indices of observations in adata to use. If None, defaults to all observations. Ignored if dataloader is not None

  • give_mean (bool (default: True)) – If True, returns the mean of the latent distribution. If False, returns an estimate of the mean using mc_samples Monte Carlo samples.

  • mc_samples (int (default: 5000)) – Number of Monte Carlo samples to use for the estimator for distributions with no closed-form mean (e.g., the logistic normal distribution). Not used if give_mean is True or if return_dist is True.

  • batch_size (int | None (default: None)) – Minibatch size for the forward pass. If None, defaults to scvi.settings.batch_size. Ignored if dataloader is not None

  • return_dist (bool (default: False)) – If True, returns the mean and variance of the latent distribution. Otherwise, returns the mean of the latent distribution.

  • dataloader (Iterator[dict[str, Tensor | None]] (default: None)) – An iterator over minibatches of data on which to compute the metric. The minibatches should be formatted as a dictionary of Tensor with keys as expected by the model. If None, a dataloader is created from adata.

Return type:

ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]] | tuple[ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]], ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]]

Returns:

An array of shape (n_obs, n_latent) if return_dist is False. Otherwise, returns a tuple of arrays (n_obs, n_latent) with the mean and variance of the latent distribution.

SCVI.get_likelihood_parameters(adata=None, indices=None, n_samples=1, give_mean=False, batch_size=None)[source]#

Estimates for the parameters of the likelihood \(p(x \mid z)\).

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with equivalent structure to initial AnnData. If None, defaults to the AnnData object used to initialize the model.

  • indices (list[int] | None (default: None)) – Indices of cells in adata to use. If None, all cells are used.

  • n_samples (int | None (default: 1)) – Number of posterior samples to use for estimation.

  • give_mean (bool | None (default: False)) – Return expected value of parameters or a samples

  • batch_size (int | None (default: None)) – Minibatch size for data loading into model. Defaults to scvi.settings.batch_size.

Return type:

dict[str, ndarray]

SCVI.get_marginal_ll(adata=None, indices=None, n_mc_samples=1000, batch_size=None, return_mean=True, dataloader=None, **kwargs)[source]#

Compute the marginal log-likehood of the data.

The computation here is a biased estimator of the marginal log-likelihood of the data.

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with var_names in the same order as the ones used to train the model. If None and dataloader is also None, it defaults to the object used to initialize the model.

  • indices (Sequence[int] | None (default: None)) – Indices of observations in adata to use. If None, defaults to all observations. Ignored if dataloader is not None.

  • n_mc_samples (int (default: 1000)) – Number of Monte Carlo samples to use for the estimator. Passed into the module’s marginal_ll method.

  • batch_size (int | None (default: None)) – Minibatch size for the forward pass. If None, defaults to scvi.settings.batch_size. Ignored if dataloader is not None.

  • return_mean (bool (default: True)) – Whether to return the mean of the marginal log-likelihood or the marginal-log likelihood for each observation.

  • dataloader (Iterator[dict[str, Tensor | None]] (default: None)) – An iterator over minibatches of data on which to compute the metric. The minibatches should be formatted as a dictionary of Tensor with keys as expected by the model. If None, a dataloader is created from adata.

  • **kwargs – Additional keyword arguments to pass into the module’s marginal_ll method.

Return type:

float | Tensor

Returns:

If True, returns the mean marginal log-likelihood. Otherwise returns a tensor of shape (n_obs,) with the marginal log-likelihood for each observation.

Notes

This is not the negative log-likelihood, so higher is better.

SCVI.get_normalized_expression(adata=None, indices=None, transform_batch=None, gene_list=None, library_size=1, n_samples=1, n_samples_overall=None, weights=None, batch_size=None, return_mean=True, return_numpy=None, **importance_weighting_kwargs)[source]#

Returns the normalized (decoded) gene expression.

This is denoted as \(\rho_n\) in the scVI paper.

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with equivalent structure to initial AnnData. If None, defaults to the AnnData object used to initialize the model.

  • indices (list[int] | None (default: None)) – Indices of cells in adata to use. If None, all cells are used.

  • transform_batch (list[int | float | str] | None (default: None)) –

    Batch to condition on. If transform_batch is:

    • None, then real observed batch is used.

    • int, then batch transform_batch is used.

  • gene_list (list[str] | None (default: None)) – Return frequencies of expression for a subset of genes. This can save memory when working with large datasets and few genes are of interest.

  • library_size (Union[float, Literal['latent']] (default: 1)) – Scale the expression frequencies to a common library size. This allows gene expression levels to be interpreted on a common scale of relevant magnitude. If set to “latent”, use the latent library size.

  • n_samples (int (default: 1)) – Number of posterior samples to use for estimation.

  • n_samples_overall (int (default: None)) – Number of posterior samples to use for estimation. Overrides n_samples.

  • weights (Optional[Literal['uniform', 'importance']] (default: None)) – Weights to use for sampling. If None, defaults to “uniform”.

  • batch_size (int | None (default: None)) – Minibatch size for data loading into model. Defaults to scvi.settings.batch_size.

  • return_mean (bool (default: True)) – Whether to return the mean of the samples.

  • return_numpy (bool | None (default: None)) – Return a ndarray instead of a DataFrame. DataFrame includes gene names as columns. If either n_samples=1 or return_mean=True, defaults to False. Otherwise, it defaults to True.

  • importance_weighting_kwargs – Keyword arguments passed into _get_importance_weights().

Return type:

ndarray | DataFrame

Returns:

If n_samples is provided and return_mean is False, this method returns a 3d tensor of shape (n_samples, n_cells, n_genes). If n_samples is provided and return_mean is True, it returns a 2d tensor of shape (n_cells, n_genes). In this case, return type is DataFrame unless return_numpy is True. Otherwise, the method expects n_samples_overall to be provided and returns a 2d tensor of shape (n_samples_overall, n_genes).

SCVI.get_reconstruction_error(adata=None, indices=None, batch_size=None, dataloader=None, return_mean=True, **kwargs)[source]#

Compute the reconstruction error on the data.

The reconstruction error is the negative log likelihood of the data given the latent variables. It is different from the marginal log-likelihood, but still gives good insights on the modeling of the data and is fast to compute. This is typically written as \(p(x \mid z)\), the likelihood term given one posterior sample.

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with var_names in the same order as the ones used to train the model. If None and dataloader is also None, it defaults to the object used to initialize the model.

  • indices (Sequence[int] | None (default: None)) – Indices of observations in adata to use. If None, defaults to all observations. Ignored if dataloader is not None

  • batch_size (int | None (default: None)) – Minibatch size for the forward pass. If None, defaults to scvi.settings.batch_size. Ignored if dataloader is not None

  • dataloader (Iterator[dict[str, Tensor | None]] (default: None)) – An iterator over minibatches of data on which to compute the metric. The minibatches should be formatted as a dictionary of Tensor with keys as expected by the model. If None, a dataloader is created from adata.

  • return_mean (bool (default: True)) – Whether to return the mean reconstruction loss or the reconstruction loss for each observation.

  • **kwargs – Additional keyword arguments to pass into the forward method of the module.

Return type:

dict[str, float]

Returns:

Reconstruction error for the data.

Notes

This is not the negative reconstruction error, so higher is better.

classmethod SCVI.load(dir_path, adata=None, accelerator='auto', device='auto', prefix=None, backup_url=None)[source]#

Instantiate a model from the saved output.

Parameters:

  • dir_path (str) – Path to saved outputs.

  • adata (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.

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

  • device (int | str (default: 'auto')) – The device to use. Can be set to a non-negative index (int or str) or “auto” for automatic selection based on the chosen accelerator. If set to “auto” and accelerator is not determined to be “cpu”, then device will be set to the first available device.

  • prefix (str | None (default: None)) – Prefix of saved file names.

  • backup_url (str | None (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)
>>> model.get_....
classmethod SCVI.load_query_data(adata, reference_model, inplace_subset_query_vars=False, accelerator='auto', device='auto', unfrozen=False, freeze_dropout=False, freeze_expression=True, freeze_decoder_first_layer=True, freeze_batchnorm_encoder=True, freeze_batchnorm_decoder=False, freeze_classifier=True)[source]#

Online update of a reference model with scArches algorithm [Lotfollahi et al., 2021].

Parameters:

  • adata (AnnData | MuData) – 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 registry.

  • reference_model (str | BaseModelClass) – Either an already instantiated model of the same class, or a path to saved outputs for reference model.

  • inplace_subset_query_vars (bool (default: False)) – Whether to subset and rearrange query vars inplace based on vars used to train reference model.

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

  • device (int | str (default: 'auto')) – The device to use. Can be set to a non-negative index (int or str) or “auto” for automatic selection based on the chosen accelerator. If set to “auto” and accelerator is not determined to be “cpu”, then device will be set to the first available device.

  • unfrozen (bool (default: False)) – Override all other freeze options for a fully unfrozen model

  • freeze_dropout (bool (default: False)) – Whether to freeze dropout during training

  • freeze_expression (bool (default: True)) – Freeze neurons corersponding to expression in first layer

  • freeze_decoder_first_layer (bool (default: True)) – Freeze neurons corersponding to first layer in decoder

  • freeze_batchnorm_encoder (bool (default: True)) – Whether to freeze batchnorm weight and bias during training for encoder

  • freeze_batchnorm_decoder (bool (default: False)) – Whether to freeze batchnorm weight and bias during training for decoder

  • freeze_classifier (bool (default: True)) – Whether to freeze classifier completely. Only applies to SCANVI.

static SCVI.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 | None (default: None)) – Prefix of saved file names.

Return type:

dict

Returns:

The full registry saved with the model

SCVI.minify_adata(minified_data_type='latent_posterior_parameters', use_latent_qzm_key='X_latent_qzm', use_latent_qzv_key='X_latent_qzv')[source]#

Minifies the model’s adata.

Minifies the adata, and registers new anndata fields: latent qzm, latent qzv, adata uns containing minified-adata type, and library size. This also sets the appropriate property on the module to indicate that the adata is minified.

Parameters:

  • minified_data_type (Literal['latent_posterior_parameters'] (default: 'latent_posterior_parameters')) –

    How to minify the data. Currently only supports latent_posterior_parameters. If minified_data_type == latent_posterior_parameters:

    • the original count data is removed (adata.X, adata.raw, and any layers)

    • the parameters of the latent representation of the original data is stored

    • everything else is left untouched

  • use_latent_qzm_key (str (default: 'X_latent_qzm')) – Key to use in adata.obsm where the latent qzm params are stored

  • use_latent_qzv_key (str (default: 'X_latent_qzv')) – Key to use in adata.obsm where the latent qzv params are stored

Return type:

None

Notes

The modification is not done inplace – instead the model is assigned a new (minified) version of the adata.

SCVI.posterior_predictive_sample(adata=None, indices=None, n_samples=1, gene_list=None, batch_size=None)[source]#

Generate predictive samples from the posterior predictive distribution.

The posterior predictive distribution is denoted as \(p(\hat{x} \mid x)\), where \(x\) is the input data and \(\hat{x}\) is the sampled data.

We sample from this distribution by first sampling n_samples times from the posterior distribution \(q(z \mid x)\) for a given observation, and then sampling from the likelihood \(p(\hat{x} \mid z)\) for each of these.

Parameters:

  • adata (AnnData | None (default: None)) – AnnData object with an equivalent structure to the model’s dataset. If None, defaults to the AnnData object used to initialize the model.

  • indices (list[int] | None (default: None)) – Indices of the observations in adata to use. If None, defaults to all the observations.

  • n_samples (int (default: 1)) – Number of Monte Carlo samples to draw from the posterior predictive distribution for each observation.

  • gene_list (list[str] | None (default: None)) – Names of the genes to which to subset. If None, defaults to all genes.

  • batch_size (int | None (default: None)) – Minibatch size to use for data loading and model inference. Defaults to scvi.settings.batch_size. Passed into _make_data_loader().

Return type:

GCXS

Returns:

Sparse multidimensional array of shape (n_obs, n_vars) if n_samples == 1, else (n_obs, n_vars, n_samples).

static SCVI.prepare_query_anndata(adata, reference_model, return_reference_var_names=False, inplace=True)[source]#

Prepare data for query integration.

This function will return a new AnnData object with padded zeros for missing features, as well as correctly sorted features.

Parameters:

  • adata (AnnData) – 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 registry.

  • reference_model (str | BaseModelClass) – Either an already instantiated model of the same class, or a path to saved outputs for reference model.

  • return_reference_var_names (bool (default: False)) – Only load and return reference var names if True.

  • inplace (bool (default: True)) – Whether to subset and rearrange query vars inplace or return new AnnData.

Return type:

AnnData | Index | None

Returns:

Query adata ready to use in load_query_data unless return_reference_var_names in which case a pd.Index of reference var names is returned.

static SCVI.prepare_query_mudata(mdata, reference_model, return_reference_var_names=False, inplace=True)[source]#

Prepare multimodal dataset for query integration.

This function will return a new MuData object such that the AnnData objects for individual modalities are given padded zeros for missing features, as well as correctly sorted features.

Parameters:

  • mdata (MuData) – MuData organized in the same way as data used to train model. It is not necessary to run setup_mudata, as MuData is validated against the registry.

  • reference_model (str | BaseModelClass) – Either an already instantiated model of the same class, or a path to saved outputs for reference model.

  • return_reference_var_names (bool (default: False)) – Only load and return reference var names if True.

  • inplace (bool (default: True)) – Whether to subset and rearrange query vars inplace or return new MuData.

Return type:

MuData | dict[str, Index] | None

Returns:

Query mudata ready to use in load_query_data unless return_reference_var_names in which case a dictionary of pd.Index of reference var names is returned.

classmethod SCVI.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.

SCVI.save(dir_path, prefix=None, overwrite=False, save_anndata=False, save_kwargs=None, legacy_mudata_format=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 (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

  • save_kwargs (dict | None (default: None)) – Keyword arguments passed into save().

  • legacy_mudata_format (bool (default: False)) – If True, saves the model var_names in the legacy format if the model was trained with a MuData object. The legacy format is a flat array with variable names across all modalities concatenated, while the new format is a dictionary with keys corresponding to the modality names and values corresponding to the variable names for each modality.

  • anndata_write_kwargs – Kwargs for write()

classmethod SCVI.setup_anndata(adata, layer=None, batch_key=None, labels_key=None, size_factor_key=None, categorical_covariate_keys=None, continuous_covariate_keys=None, **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.

Parameters:

  • adata (AnnData) – AnnData object. Rows represent cells, columns represent features.

  • layer (str | None (default: None)) – if not None, uses this as the key in adata.layers for raw count data.

  • batch_key (str | None (default: None)) – key in adata.obs for batch information. Categories will automatically be converted into integer categories and saved to adata.obs[‘_scvi_batch’]. If None, assigns the same batch to all the data.

  • labels_key (str | None (default: None)) – key in adata.obs for label information. Categories will automatically be converted into integer categories and saved to adata.obs[‘_scvi_labels’]. If None, assigns the same label to all the data.

  • size_factor_key (str | None (default: None)) – key in adata.obs for size factor information. Instead of using library size as a size factor, the provided size factor column will be used as offset in the mean of the likelihood. Assumed to be on linear scale.

  • categorical_covariate_keys (list[str] | None (default: None)) – keys in adata.obs that correspond to categorical data. These covariates can be added in addition to the batch covariate and are also treated as nuisance factors (i.e., the model tries to minimize their effects on the latent space). Thus, these should not be used for biologically-relevant factors that you do _not_ want to correct for.

  • continuous_covariate_keys (list[str] | None (default: None)) – keys in adata.obs that correspond to continuous data. These covariates can be added in addition to the batch covariate and are also treated as nuisance factors (i.e., the model tries to minimize their effects on the latent space). Thus, these should not be used for biologically-relevant factors that you do _not_ want to correct for.

SCVI.to_device(device)[source]#

Move model to device.

Parameters:

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

Train the model.

Parameters:

  • max_epochs (int | None (default: None)) – The maximum number of epochs to train the model. The actual number of epochs may be less if early stopping is enabled. If None, defaults to a heuristic based on get_max_epochs_heuristic(). Must be passed in if datamodule is passed in, and it does not have an n_obs attribute.

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

  • devices (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]. Passed into DataSplitter. Not used if datamodule is passed in.

  • validation_size (float | None (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. Passed into DataSplitter. Not used if datamodule is passed in.

  • 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. Passed into DataSplitter. Not used if datamodule is passed in.

  • load_sparse_tensor (bool (default: False)) – EXPERIMENTAL If True, loads data with sparse CSR or CSC layout as a Tensor with the same layout. Can lead to speedups in data transfers to GPUs, depending on the sparsity of the data. Passed into DataSplitter. Not used if datamodule is passed in.

  • batch_size (int (default: 128)) – Minibatch size to use during training. Passed into DataSplitter. Not used if datamodule is passed in.

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

  • datasplitter_kwargs (dict | None (default: None)) – Additional keyword arguments passed into DataSplitter. Values in this argument can be overwritten by arguments directly passed into this method, when appropriate. Not used if datamodule is passed in.

  • plan_kwargs (dict | None (default: None)) – Additional keyword arguments passed into TrainingPlan. Values in this argument can be overwritten by arguments directly passed into this method, when appropriate.

  • datamodule (LightningDataModule | None (default: None)) – EXPERIMENTAL A LightningDataModule instance to use for training in place of the default DataSplitter. Can only be passed in if the model was not initialized with AnnData.

  • **kwargs – Additional keyword arguments passed into Trainer.

SCVI.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 | 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

static SCVI.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 | None (default: None)) – Prefix of saved file names.

Return type:

None

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