Index

Symbols

**compile_kwargs (spatialvi.train.DeconvolutionTrainingPlan.to_tensorrt parameter) (spatialvi.train.NicheTrainingPlan.to_tensorrt parameter) (spatialvi.train.SpatialTrainingPlan.to_tensorrt parameter) **kwargs (spatialvi.external.DestVI parameter), [1] (spatialvi.external.destvi.DestVI parameter) (spatialvi.external.destvi.DestVI.from_rna_model parameter) (spatialvi.external.destvi.DestVI.setup_anndata parameter) (spatialvi.external.destvi.DestVI.train parameter) (spatialvi.external.DestVI.from_rna_model parameter), [1] (spatialvi.external.DestVI.setup_anndata parameter), [1] (spatialvi.external.DestVI.train parameter), [1] (spatialvi.external.Lambda parameter), [1] (spatialvi.external.Lambda.predict parameter), [1] (spatialvi.external.lambda_model.Lambda parameter) (spatialvi.external.lambda_model.Lambda.predict parameter) (spatialvi.external.nolan.Nolan.predict parameter) (spatialvi.external.Nolan.predict parameter), [1] (spatialvi.external.ResolVI parameter), [1] (spatialvi.external.resolvi.ResolVI parameter) (spatialvi.external.resolvi.ResolVI.setup_anndata parameter) (spatialvi.external.resolvi.ResolVI.train parameter) (spatialvi.external.ResolVI.setup_anndata parameter), [1] (spatialvi.external.ResolVI.train parameter), [1] (spatialvi.external.scVIVA parameter), [1] (spatialvi.external.scVIVA.differential_niche_expression parameter), [1] (spatialvi.external.scviva.scVIVA parameter) (spatialvi.external.scviva.scVIVA.differential_niche_expression parameter) (spatialvi.external.scviva.scVIVA.setup_anndata parameter) (spatialvi.external.scviva.scVIVA.train parameter) (spatialvi.external.scVIVA.setup_anndata parameter), [1] (spatialvi.external.scVIVA.train parameter), [1] (spatialvi.train._training_plans.DeconvolutionTrainingPlan parameter) (spatialvi.train._training_plans.NicheTrainingPlan parameter) (spatialvi.train._training_plans.SpatialTrainingPlan parameter) (spatialvi.train.DeconvolutionTrainingPlan parameter), [1] (spatialvi.train.DeconvolutionTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.DeconvolutionTrainingPlan.manual_backward parameter) (spatialvi.train.DeconvolutionTrainingPlan.print parameter) (spatialvi.train.DeconvolutionTrainingPlan.to_onnx parameter) (spatialvi.train.DeconvolutionTrainingPlan.to_torchscript parameter) (spatialvi.train.NicheTrainingPlan parameter), [1] (spatialvi.train.NicheTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.NicheTrainingPlan.manual_backward parameter) (spatialvi.train.NicheTrainingPlan.print parameter) (spatialvi.train.NicheTrainingPlan.to_onnx parameter) (spatialvi.train.NicheTrainingPlan.to_torchscript parameter) (spatialvi.train.SpatialTrainingPlan parameter), [1] (spatialvi.train.SpatialTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.SpatialTrainingPlan.manual_backward parameter) (spatialvi.train.SpatialTrainingPlan.print parameter) (spatialvi.train.SpatialTrainingPlan.to_onnx parameter) (spatialvi.train.SpatialTrainingPlan.to_torchscript parameter) (spatialvi.utils._visualization.plot_interactions parameter) (spatialvi.utils._visualization.plot_niche_composition parameter) (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_proportions parameter), [1] (spatialvi.utils.plot_spatial parameter), [1]

**model_kwargs (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.Nolan parameter), [1] (spatialvi.external.nolan.Nolan parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] **model_params (spatialvi.external.SPARL parameter), [1] (spatialvi.external.sparl.SPARL parameter) **save_kwargs (spatialvi.external.AMICI.convert_legacy_save parameter) (spatialvi.model.BaseSpatialModel.convert_legacy_save parameter) (spatialvi.model.SpatialVAE.convert_legacy_save parameter) **train_kwargs (spatialvi.external.nolan.Nolan.train parameter) (spatialvi.external.Nolan.train parameter), [1] (spatialvi.external.sparl.SPARL.train parameter) (spatialvi.external.SPARL.train parameter), [1] **trainer_kwargs (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) **vae_kwargs (spatialvi.external.scviva.nicheVAE parameter) *args (spatialvi.train.DeconvolutionTrainingPlan.manual_backward parameter) (spatialvi.train.DeconvolutionTrainingPlan.print parameter) (spatialvi.train.NicheTrainingPlan.manual_backward parameter) (spatialvi.train.NicheTrainingPlan.print parameter) (spatialvi.train.SpatialTrainingPlan.manual_backward parameter) (spatialvi.train.SpatialTrainingPlan.print parameter)

_

__init__() (spatialvi.external.AMICI method) (spatialvi.external.DestVI method) (spatialvi.external.Harreman method) (spatialvi.external.Lambda method) (spatialvi.external.Nolan method) (spatialvi.external.PPIInference method) (spatialvi.external.ResolVI method) (spatialvi.external.scVIVA method) (spatialvi.external.SPARL method) (spatialvi.external.Starfysh method) (spatialvi.external.VIVS method) (spatialvi.model.BaseSpatialModel method) (spatialvi.model.SpatialVAE method) (spatialvi.module.DeconvolutionModule method) (spatialvi.module.NicheModule method) (spatialvi.module.SpatialVAEModule method) (spatialvi.nn.NeighborAttention method) (spatialvi.nn.SpatialAttention method) (spatialvi.nn.SpatialDecoder method) (spatialvi.nn.SpatialEncoder method) (spatialvi.train.DeconvolutionTrainingPlan method) (spatialvi.train.NicheTrainingPlan method) (spatialvi.train.SpatialTrainingPlan method)

A

accelerator (spatialvi.external.AMICI.load parameter) (spatialvi.external.AMICI.train parameter) (spatialvi.external.destvi.DestVI.train parameter) (spatialvi.external.DestVI.train parameter), [1] (spatialvi.external.resolvi.ResolVI.train parameter) (spatialvi.external.ResolVI.train parameter), [1] (spatialvi.external.scviva.scVIVA.train parameter) (spatialvi.external.scVIVA.train parameter), [1] (spatialvi.model.BaseSpatialModel.load parameter) (spatialvi.model.SpatialVAE.load parameter) (spatialvi.model.SpatialVAE.train parameter) adata (spatialvi.data._fields.NeighborDistanceField.validate_field parameter) (spatialvi.data._fields.NeighborIndexField.validate_field parameter) (spatialvi.data._fields.NicheCompositionField.validate_field parameter) (spatialvi.data._fields.SpatialCoordinatesField.validate_field parameter) (spatialvi.data._preprocessing.add_spatial_noise parameter) (spatialvi.data._preprocessing.compute_niche_composition parameter) (spatialvi.data._preprocessing.compute_spatial_neighbors parameter) (spatialvi.data._preprocessing.filter_by_spatial_density parameter) (spatialvi.data._preprocessing.get_neighbor_expression parameter) (spatialvi.data._preprocessing.normalize_spatial parameter) (spatialvi.data.compute_niche_composition parameter), [1] (spatialvi.data.compute_spatial_neighbors parameter), [1] (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICI.get_cell_type_interactions parameter) (spatialvi.external.amici.AMICI.get_interaction_scores parameter) (spatialvi.external.amici.AMICI.get_latent_representation parameter) (spatialvi.external.amici.AMICI.setup_anndata parameter) (spatialvi.external.AMICI.compute_niche_composition parameter) (spatialvi.external.AMICI.compute_spatial_neighbors parameter) (spatialvi.external.AMICI.get_anndata_manager parameter) (spatialvi.external.AMICI.get_cell_type_interactions parameter), [1] (spatialvi.external.AMICI.get_from_registry parameter) (spatialvi.external.AMICI.get_interaction_scores parameter), [1] (spatialvi.external.AMICI.get_latent_representation parameter), [1] (spatialvi.external.AMICI.get_spatial_coordinates parameter) (spatialvi.external.AMICI.get_spatial_neighbors parameter) (spatialvi.external.AMICI.load parameter) (spatialvi.external.AMICI.setup_anndata parameter), [1] (spatialvi.external.AMICI.view_anndata_setup parameter) (spatialvi.external.destvi.DestVI.get_gamma parameter) (spatialvi.external.destvi.DestVI.get_latent_representation parameter) (spatialvi.external.destvi.DestVI.get_proportions parameter) (spatialvi.external.destvi.DestVI.get_scale_for_ct parameter) (spatialvi.external.destvi.DestVI.setup_anndata parameter) (spatialvi.external.DestVI.get_gamma parameter), [1] (spatialvi.external.DestVI.get_latent_representation parameter), [1] (spatialvi.external.DestVI.get_proportions parameter), [1] (spatialvi.external.DestVI.get_scale_for_ct parameter), [1] (spatialvi.external.DestVI.setup_anndata parameter), [1] (spatialvi.external.Harreman parameter), [1] (spatialvi.external.harreman.Harreman parameter) (spatialvi.external.Lambda parameter), [1] (spatialvi.external.lambda_model.Lambda parameter) (spatialvi.external.lambda_model.LambdaAnnotator.extract_marker_genes parameter) (spatialvi.external.Nolan parameter), [1] (spatialvi.external.Nolan.get_niche_assignments parameter), [1] (spatialvi.external.nolan.Nolan parameter) (spatialvi.external.nolan.Nolan.get_niche_assignments parameter) (spatialvi.external.nolan.Nolan.predict parameter) (spatialvi.external.Nolan.predict parameter), [1] (spatialvi.external.ResolVI parameter), [1] (spatialvi.external.ResolVI.get_background_fraction parameter), [1] (spatialvi.external.ResolVI.get_denoised_expression parameter), [1] (spatialvi.external.ResolVI.get_latent_representation parameter), [1] (spatialvi.external.ResolVI.predict parameter), [1] (spatialvi.external.resolvi.ResolVI parameter) (spatialvi.external.resolvi.ResolVI.get_background_fraction parameter) (spatialvi.external.resolvi.ResolVI.get_denoised_expression parameter) (spatialvi.external.resolvi.ResolVI.get_latent_representation parameter) (spatialvi.external.resolvi.ResolVI.predict parameter) (spatialvi.external.resolvi.ResolVI.setup_anndata parameter) (spatialvi.external.ResolVI.setup_anndata parameter), [1] (spatialvi.external.scVIVA parameter), [1] (spatialvi.external.scVIVA.get_latent_representation parameter), [1] (spatialvi.external.scVIVA.get_niche_effects parameter), [1] (spatialvi.external.scviva.scVIVA parameter) (spatialvi.external.scviva.scVIVA.get_latent_representation parameter) (spatialvi.external.scviva.scVIVA.get_niche_effects parameter) (spatialvi.external.scviva.scVIVA.setup_anndata parameter) (spatialvi.external.scVIVA.setup_anndata parameter), [1] (spatialvi.external.SPARL parameter), [1] (spatialvi.external.SPARL.get_latent_representation parameter), [1] (spatialvi.external.SPARL.impute_proteins parameter), [1] (spatialvi.external.SPARL.predict parameter), [1] (spatialvi.external.SPARL.reconstruct parameter), [1] (spatialvi.external.sparl.SPARL parameter) (spatialvi.external.sparl.SPARL.get_latent_representation parameter) (spatialvi.external.sparl.SPARL.impute_proteins parameter) (spatialvi.external.sparl.SPARL.predict parameter) (spatialvi.external.sparl.SPARL.reconstruct parameter) (spatialvi.external.VIVS parameter), [1] (spatialvi.external.vivs.VIVS parameter) (spatialvi.model.BaseSpatialModel parameter), [1] (spatialvi.model.BaseSpatialModel.compute_niche_composition parameter), [1] (spatialvi.model.BaseSpatialModel.compute_spatial_neighbors parameter), [1] (spatialvi.model.BaseSpatialModel.get_anndata_manager parameter) (spatialvi.model.BaseSpatialModel.get_from_registry parameter) (spatialvi.model.BaseSpatialModel.get_latent_representation parameter), [1] (spatialvi.model.BaseSpatialModel.get_normalized_expression parameter), [1] (spatialvi.model.BaseSpatialModel.load parameter) (spatialvi.model.BaseSpatialModel.view_anndata_setup parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.model.SpatialVAE.compute_niche_composition parameter) (spatialvi.model.SpatialVAE.compute_spatial_neighbors parameter) (spatialvi.model.SpatialVAE.get_anndata_manager parameter) (spatialvi.model.SpatialVAE.get_from_registry parameter) (spatialvi.model.SpatialVAE.get_latent_representation parameter) (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2] (spatialvi.model.SpatialVAE.get_spatial_coordinates parameter) (spatialvi.model.SpatialVAE.get_spatial_neighbors parameter) (spatialvi.model.SpatialVAE.get_spatial_representation parameter), [1], [2] (spatialvi.model.SpatialVAE.load parameter) (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] (spatialvi.model.SpatialVAE.view_anndata_setup parameter) (spatialvi.utils._metrics.niche_purity parameter) (spatialvi.utils._metrics.silhouette_spatial parameter) (spatialvi.utils._metrics.spatial_autocorrelation parameter) (spatialvi.utils._metrics.spatial_mixing_score parameter) (spatialvi.utils._visualization.plot_niche_composition parameter) (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_proportions parameter), [1] (spatialvi.utils.plot_spatial parameter), [1] (spatialvi.utils.spatial_autocorrelation parameter), [1]

adata_ref (spatialvi.external.Starfysh parameter), [1] (spatialvi.external.starfysh.Starfysh parameter) adata_spatial (spatialvi.external.Starfysh parameter), [1] (spatialvi.external.starfysh.Starfysh parameter) add_celltypes (spatialvi.external.destvi.MRDeconv parameter) add_dataloader_idx (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) add_spatial_noise() (in module spatialvi.data._preprocessing) aggregate (spatialvi.external.amici.AMICI.get_cell_type_interactions parameter) (spatialvi.external.AMICI.get_cell_type_interactions parameter), [1] aggregate_scores() (spatialvi.external.vivs.MultiScaleVIVS method) aggregation (spatialvi.data._preprocessing.get_neighbor_expression parameter) (spatialvi.external.vivs.MultiScaleVIVS parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn._layers.SpatialConv parameter) (spatialvi.nn.SpatialEncoder parameter), [1] allow_zero_length_dataloader_with_multiple_devices (spatialvi.train._training_plans.DeconvolutionTrainingPlan attribute) (spatialvi.train._training_plans.NicheTrainingPlan attribute) (spatialvi.train._training_plans.SpatialTrainingPlan attribute) allowed_classes_names_list (spatialvi.external.AMICI.load parameter) (spatialvi.model.BaseSpatialModel.load parameter) (spatialvi.model.SpatialVAE.load parameter) alpha (spatialvi.external.ppi.PPIInference.classical_mean_ci parameter) (spatialvi.external.ppi.PPIInference.mean_ci parameter) (spatialvi.external.ppi.PPIInference.ols_ci parameter) (spatialvi.external.PPIInference.classical_mean_ci parameter), [1] (spatialvi.external.PPIInference.mean_ci parameter), [1] (spatialvi.external.PPIInference.ols_ci parameter), [1] (spatialvi.nn.GATLayer parameter) (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_spatial parameter), [1] always_call (spatialvi.module.DeconvolutionModule.register_forward_hook parameter) (spatialvi.module.NicheModule.register_forward_hook parameter) (spatialvi.module.SpatialVAEModule.register_forward_hook parameter) (spatialvi.nn.NeighborAttention.register_forward_hook parameter) (spatialvi.nn.SpatialAttention.register_forward_hook parameter) (spatialvi.nn.SpatialDecoder.register_forward_hook parameter) (spatialvi.nn.SpatialEncoder.register_forward_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_forward_hook parameter) (spatialvi.train.NicheTrainingPlan.register_forward_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_forward_hook parameter) AMICI (class in spatialvi.external) (class in spatialvi.external.amici) AMICIModule (class in spatialvi.external.amici) amortization (spatialvi.external.destvi.MRDeconv parameter) anndata_write_kwargs (spatialvi.external.AMICI.save parameter) (spatialvi.model.BaseSpatialModel.save parameter) (spatialvi.model.SpatialVAE.save parameter) annot (spatialvi.utils._visualization.plot_interactions parameter) args (spatialvi.train.DeconvolutionTrainingPlan.save_hyperparameters parameter) (spatialvi.train.NicheTrainingPlan.save_hyperparameters parameter) (spatialvi.train.SpatialTrainingPlan.save_hyperparameters parameter) assign (spatialvi.module.DeconvolutionModule.load_state_dict parameter) (spatialvi.module.NicheModule.load_state_dict parameter) (spatialvi.module.SpatialVAEModule.load_state_dict parameter) (spatialvi.nn.NeighborAttention.load_state_dict parameter) (spatialvi.nn.SpatialAttention.load_state_dict parameter) (spatialvi.nn.SpatialDecoder.load_state_dict parameter) (spatialvi.nn.SpatialEncoder.load_state_dict parameter) (spatialvi.train.DeconvolutionTrainingPlan.load_state_dict parameter) (spatialvi.train.NicheTrainingPlan.load_state_dict parameter) (spatialvi.train.SpatialTrainingPlan.load_state_dict parameter) AttentionEncoder (class in spatialvi.nn._encoders) attr_key (spatialvi.data._fields.NeighborDistanceField parameter) (spatialvi.data._fields.NeighborIndexField parameter) (spatialvi.data._fields.NicheCompositionField parameter) (spatialvi.data._fields.SpatialCoordinatesField parameter) augmentation (spatialvi.external.destvi.MRDeconv parameter) ax (spatialvi.utils._visualization.plot_interactions parameter) (spatialvi.utils._visualization.plot_niche_composition parameter) (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_spatial parameter), [1]

B

background_ratio (spatialvi.external.resolvi.RESOLVAE parameter) backup_url (spatialvi.external.AMICI.load parameter) (spatialvi.model.BaseSpatialModel.load parameter) (spatialvi.model.SpatialVAE.load parameter) BaseSpatialModel (class in spatialvi.model) batch (spatialvi.train.DeconvolutionTrainingPlan.on_after_batch_transfer parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_before_batch_transfer parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_test_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_test_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_train_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_train_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.predict_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.test_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.transfer_batch_to_device parameter) (spatialvi.train.NicheTrainingPlan.on_after_batch_transfer parameter) (spatialvi.train.NicheTrainingPlan.on_before_batch_transfer parameter) (spatialvi.train.NicheTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.NicheTrainingPlan.on_test_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_test_batch_start parameter) (spatialvi.train.NicheTrainingPlan.on_train_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_train_batch_start parameter) (spatialvi.train.NicheTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.NicheTrainingPlan.predict_step parameter) (spatialvi.train.NicheTrainingPlan.test_step parameter) (spatialvi.train.NicheTrainingPlan.transfer_batch_to_device parameter) (spatialvi.train.SpatialTrainingPlan.on_after_batch_transfer parameter) (spatialvi.train.SpatialTrainingPlan.on_before_batch_transfer parameter) (spatialvi.train.SpatialTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.on_test_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_test_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.on_train_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_train_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.predict_step parameter) (spatialvi.train.SpatialTrainingPlan.test_step parameter) (spatialvi.train.SpatialTrainingPlan.transfer_batch_to_device parameter) batch_embedding_kwargs (spatialvi.external.scviva.nicheVAE parameter) batch_idx (spatialvi.train.DeconvolutionTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_test_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_test_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_train_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_train_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.optimizer_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.optimizer_zero_grad parameter) (spatialvi.train.DeconvolutionTrainingPlan.predict_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.test_step parameter) (spatialvi.train.NicheTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.NicheTrainingPlan.on_test_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_test_batch_start parameter) (spatialvi.train.NicheTrainingPlan.on_train_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_train_batch_start parameter) (spatialvi.train.NicheTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.NicheTrainingPlan.optimizer_step parameter) (spatialvi.train.NicheTrainingPlan.optimizer_zero_grad parameter) (spatialvi.train.NicheTrainingPlan.predict_step parameter) (spatialvi.train.NicheTrainingPlan.test_step parameter) (spatialvi.train.SpatialTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.on_test_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_test_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.on_train_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_train_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.optimizer_step parameter) (spatialvi.train.SpatialTrainingPlan.optimizer_zero_grad parameter) (spatialvi.train.SpatialTrainingPlan.predict_step parameter) (spatialvi.train.SpatialTrainingPlan.test_step parameter)

batch_index (spatialvi.external.amici.AMICIModule.generative parameter) (spatialvi.external.amici.AMICIModule.inference parameter) (spatialvi.external.destvi.MRDeconv.generative parameter) (spatialvi.external.scviva.nicheVAE.generative parameter) (spatialvi.module.DeconvolutionModule.generative parameter), [1] (spatialvi.module.DeconvolutionModule.inference parameter), [1] (spatialvi.module.NicheModule.generative parameter), [1] (spatialvi.module.NicheModule.inference parameter), [1] (spatialvi.module.SpatialVAEModule.generative parameter), [1], [2] (spatialvi.module.SpatialVAEModule.inference parameter), [1], [2] batch_key (spatialvi.external.amici.AMICI.setup_anndata parameter) (spatialvi.external.AMICI.setup_anndata parameter), [1] (spatialvi.external.Nolan parameter), [1] (spatialvi.external.nolan.Nolan parameter) (spatialvi.external.resolvi.ResolVI.setup_anndata parameter) (spatialvi.external.ResolVI.setup_anndata parameter), [1] (spatialvi.external.scviva.scVIVA.setup_anndata parameter) (spatialvi.external.scVIVA.setup_anndata parameter), [1] (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] (spatialvi.utils._metrics.spatial_mixing_score parameter) batch_representation (spatialvi.external.scviva.nicheVAE parameter) batch_size (spatialvi.external.amici.AMICI.get_interaction_scores parameter) (spatialvi.external.amici.AMICI.get_latent_representation parameter) (spatialvi.external.AMICI.get_interaction_scores parameter), [1] (spatialvi.external.AMICI.get_latent_representation parameter), [1] (spatialvi.external.AMICI.train parameter) (spatialvi.external.destvi.DestVI.get_gamma parameter) (spatialvi.external.destvi.DestVI.get_latent_representation parameter) (spatialvi.external.destvi.DestVI.get_proportions parameter) (spatialvi.external.destvi.DestVI.get_scale_for_ct parameter) (spatialvi.external.DestVI.get_gamma parameter), [1] (spatialvi.external.DestVI.get_latent_representation parameter), [1] (spatialvi.external.DestVI.get_proportions parameter), [1] (spatialvi.external.DestVI.get_scale_for_ct parameter), [1] (spatialvi.external.nolan.Nolan.predict parameter) (spatialvi.external.Nolan.predict parameter), [1] (spatialvi.external.ResolVI.get_background_fraction parameter), [1] (spatialvi.external.ResolVI.get_denoised_expression parameter), [1] (spatialvi.external.ResolVI.get_latent_representation parameter), [1] (spatialvi.external.ResolVI.predict parameter), [1] (spatialvi.external.resolvi.ResolVI.get_background_fraction parameter) (spatialvi.external.resolvi.ResolVI.get_denoised_expression parameter) (spatialvi.external.resolvi.ResolVI.get_latent_representation parameter) (spatialvi.external.resolvi.ResolVI.predict parameter) (spatialvi.external.scVIVA.get_latent_representation parameter), [1] (spatialvi.external.scVIVA.get_niche_effects parameter), [1] (spatialvi.external.scviva.scVIVA.get_latent_representation parameter) (spatialvi.external.scviva.scVIVA.get_niche_effects parameter) (spatialvi.external.SPARL.get_latent_representation parameter), [1] (spatialvi.external.SPARL.reconstruct parameter), [1] (spatialvi.external.sparl.SPARL.get_latent_representation parameter) (spatialvi.external.sparl.SPARL.reconstruct parameter) (spatialvi.external.sparl.SPARL.train parameter) (spatialvi.external.SPARL.train parameter), [1] (spatialvi.external.Starfysh.fit parameter), [1] (spatialvi.external.starfysh.Starfysh.fit parameter) (spatialvi.external.VIVS.fit parameter), [1] (spatialvi.external.vivs.VIVS.fit parameter) (spatialvi.model.BaseSpatialModel.get_latent_representation parameter), [1] (spatialvi.model.BaseSpatialModel.get_normalized_expression parameter), [1] (spatialvi.model.SpatialVAE.get_latent_representation parameter) (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2] (spatialvi.model.SpatialVAE.get_spatial_representation parameter), [1], [2] (spatialvi.model.SpatialVAE.train parameter) (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) bias (spatialvi.nn._layers.GraphConv parameter) (spatialvi.nn._layers.MixedLinear parameter)

C

cat_covs (spatialvi.external.scviva.nicheVAE.generative parameter) (spatialvi.module.SpatialVAEModule.generative parameter), [1], [2] (spatialvi.module.SpatialVAEModule.inference parameter), [1], [2] cat_list (spatialvi.nn._decoders.SpatialDecoder.forward parameter) (spatialvi.nn._encoders.SpatialEncoder.forward parameter) (spatialvi.nn._encoders.SpatialEncoder.forward_spatial parameter) (spatialvi.nn.SpatialDecoder.forward parameter), [1] (spatialvi.nn.SpatialEncoder.forward parameter), [1] (spatialvi.nn.SpatialEncoder.forward_spatial parameter), [1] categorical_covariate_keys (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] cell_rec_weight (spatialvi.external.scviva.nicheVAE parameter) cell_type (spatialvi.external.destvi.DestVI.get_scale_for_ct parameter) (spatialvi.external.DestVI.get_scale_for_ct parameter), [1] cell_type_key (spatialvi.external.Starfysh parameter), [1] (spatialvi.external.starfysh.Starfysh parameter) cell_types (spatialvi.utils._visualization.plot_interactions parameter) (spatialvi.utils._visualization.plot_niche_composition parameter) (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils.plot_proportions parameter), [1] cells_per_spot_mean (spatialvi.data._datasets.synthetic_visium parameter) cells_per_spot_std (spatialvi.data._datasets.synthetic_visium parameter) check_val_every_n_epoch (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) checkpoint (spatialvi.train.DeconvolutionTrainingPlan.on_load_checkpoint parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_save_checkpoint parameter) (spatialvi.train.NicheTrainingPlan.on_load_checkpoint parameter) (spatialvi.train.NicheTrainingPlan.on_save_checkpoint parameter) (spatialvi.train.SpatialTrainingPlan.on_load_checkpoint parameter) (spatialvi.train.SpatialTrainingPlan.on_save_checkpoint parameter) checkpoint_path (spatialvi.train.DeconvolutionTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.NicheTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.SpatialTrainingPlan.load_from_checkpoint parameter) ckpt_dir (spatialvi.external.nolan.Nolan.train parameter) (spatialvi.external.Nolan.train parameter), [1] classical_mean_ci() (spatialvi.external.ppi.PPIInference static method) (spatialvi.external.PPIInference static method) classification_ratio (spatialvi.external.scviva.nicheVAE.loss parameter) classification_weight (spatialvi.train._training_plans.NicheTrainingPlan parameter) (spatialvi.train.NicheTrainingPlan parameter), [1] classifier_parameters (spatialvi.external.resolvi.RESOLVAE parameter) cluster_id (spatialvi.external.lambda_model.LambdaAnnotator.extract_marker_genes parameter) cluster_key (spatialvi.external.lambda_model.LambdaAnnotator.extract_marker_genes parameter) cmap (spatialvi.utils._visualization.plot_interactions parameter) (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_proportions parameter), [1] (spatialvi.utils.plot_spatial parameter), [1] color (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_spatial parameter), [1] composition_key (spatialvi.data._preprocessing.compute_niche_composition parameter) (spatialvi.data.compute_niche_composition parameter), [1] (spatialvi.external.AMICI.compute_niche_composition parameter) (spatialvi.model.BaseSpatialModel.compute_niche_composition parameter), [1] (spatialvi.model.SpatialVAE.compute_niche_composition parameter) (spatialvi.utils._visualization.plot_niche_composition parameter)

compute_every_n_epochs (spatialvi.train._callbacks.SpatialMetricsCallback parameter) compute_gearys_c() (in module spatialvi.utils._metrics) compute_local_variance() (spatialvi.external.vivs.VIVSModule method) compute_loss (spatialvi.module.DeconvolutionModule.forward parameter) (spatialvi.module.NicheModule.forward parameter) (spatialvi.module.SpatialVAEModule.forward parameter) compute_morans_i() (in module spatialvi.utils._metrics) compute_neighbor_expression() (spatialvi.external.harreman.HarremanModule method) compute_niche_composition() (in module spatialvi.data) (in module spatialvi.data._preprocessing) (spatialvi.model.BaseSpatialModel static method) compute_null_distribution() (spatialvi.external.vivs.VIVSModule method) compute_spatial_correlation() (spatialvi.external.harreman.HarremanModule method) compute_spatial_neighbors() (in module spatialvi.data) (in module spatialvi.data._preprocessing) (spatialvi.model.BaseSpatialModel static method) concat (spatialvi.nn.GATLayer parameter) condition (spatialvi.nn._decoders.ConditionalDecoder.forward parameter) (spatialvi.nn._layers.FiLMLayer.forward parameter) condition_dim (spatialvi.nn._layers.FiLMLayer parameter) ConditionalDecoder (class in spatialvi.nn._decoders) config (spatialvi.external.lambda_model.LambdaAnnotator parameter) (spatialvi.external.ppi.MeanEstimator parameter) (spatialvi.external.ppi.OLSEstimator parameter) configure_optimizers() (spatialvi.train._training_plans.DeconvolutionTrainingPlan method) (spatialvi.train.DeconvolutionTrainingPlan method) cont_covs (spatialvi.external.scviva.nicheVAE.generative parameter) (spatialvi.module.SpatialVAEModule.generative parameter), [1], [2] (spatialvi.module.SpatialVAEModule.inference parameter), [1], [2] context (spatialvi.nn.CrossAttention.forward parameter) context_mask (spatialvi.nn.CrossAttention.forward parameter) continuous_covariate_keys (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] contrastive_loss() (spatialvi.external.nolan.NolanModule method) coords (spatialvi.nn._layers.PositionalEncoding.forward parameter) copy (spatialvi.data._preprocessing.add_spatial_noise parameter) (spatialvi.data._preprocessing.compute_niche_composition parameter) (spatialvi.data._preprocessing.compute_spatial_neighbors parameter) (spatialvi.data._preprocessing.filter_by_spatial_density parameter) (spatialvi.data._preprocessing.normalize_spatial parameter) (spatialvi.data.compute_niche_composition parameter), [1] (spatialvi.data.compute_spatial_neighbors parameter), [1] correlation_method (spatialvi.external.Harreman.fit parameter), [1] (spatialvi.external.harreman.Harreman.fit parameter) (spatialvi.external.harreman.HarremanModule parameter) CrossAttention (class in spatialvi.nn)

D

d_model (spatialvi.nn._layers.PositionalEncoding parameter) data (spatialvi.train.DeconvolutionTrainingPlan.all_gather parameter) (spatialvi.train.NicheTrainingPlan.all_gather parameter) (spatialvi.train.SpatialTrainingPlan.all_gather parameter) dataloader_idx (spatialvi.train.DeconvolutionTrainingPlan.on_after_batch_transfer parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_before_batch_transfer parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_test_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_test_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.DeconvolutionTrainingPlan.predict_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.test_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.transfer_batch_to_device parameter) (spatialvi.train.NicheTrainingPlan.on_after_batch_transfer parameter) (spatialvi.train.NicheTrainingPlan.on_before_batch_transfer parameter) (spatialvi.train.NicheTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.NicheTrainingPlan.on_test_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_test_batch_start parameter) (spatialvi.train.NicheTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.NicheTrainingPlan.predict_step parameter) (spatialvi.train.NicheTrainingPlan.test_step parameter) (spatialvi.train.NicheTrainingPlan.transfer_batch_to_device parameter) (spatialvi.train.SpatialTrainingPlan.on_after_batch_transfer parameter) (spatialvi.train.SpatialTrainingPlan.on_before_batch_transfer parameter) (spatialvi.train.SpatialTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_predict_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.on_test_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_test_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_validation_batch_start parameter) (spatialvi.train.SpatialTrainingPlan.predict_step parameter) (spatialvi.train.SpatialTrainingPlan.test_step parameter) (spatialvi.train.SpatialTrainingPlan.transfer_batch_to_device parameter) datamodule (spatialvi.external.AMICI.load parameter) (spatialvi.external.AMICI.save parameter) (spatialvi.model.BaseSpatialModel.load parameter) (spatialvi.model.BaseSpatialModel.save parameter) (spatialvi.model.SpatialVAE.load parameter) (spatialvi.model.SpatialVAE.save parameter) datasplitter_kwargs (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) decoder_state_dict (spatialvi.external.destvi.MRDeconv parameter) DeconvolutionModule (class in spatialvi.module) DeconvolutionTrainingPlan (class in spatialvi.train) (class in spatialvi.train._training_plans) deeply_inject_covariates (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) default_device (spatialvi.train.DeconvolutionTrainingPlan.to_tensorrt parameter) (spatialvi.train.NicheTrainingPlan.to_tensorrt parameter) (spatialvi.train.SpatialTrainingPlan.to_tensorrt parameter) destination (spatialvi.module.DeconvolutionModule.state_dict parameter) (spatialvi.module.NicheModule.state_dict parameter) (spatialvi.module.SpatialVAEModule.state_dict parameter) (spatialvi.nn.NeighborAttention.state_dict parameter) (spatialvi.nn.SpatialAttention.state_dict parameter) (spatialvi.nn.SpatialDecoder.state_dict parameter) (spatialvi.nn.SpatialEncoder.state_dict parameter) (spatialvi.train.DeconvolutionTrainingPlan.state_dict parameter) (spatialvi.train.NicheTrainingPlan.state_dict parameter) (spatialvi.train.SpatialTrainingPlan.state_dict parameter) DestVI (class in spatialvi.external) (class in spatialvi.external.destvi) device (spatialvi.external.AMICI.load parameter) (spatialvi.external.AMICI.to_device parameter) (spatialvi.external.Starfysh.fit parameter), [1] (spatialvi.external.starfysh.Starfysh.fit parameter) (spatialvi.model.BaseSpatialModel.load parameter) (spatialvi.model.BaseSpatialModel.to_device parameter) (spatialvi.model.SpatialVAE.load parameter) (spatialvi.model.SpatialVAE.to_device parameter) (spatialvi.module.DeconvolutionModule.cuda parameter) (spatialvi.module.DeconvolutionModule.ipu parameter) (spatialvi.module.DeconvolutionModule.mtia parameter) (spatialvi.module.DeconvolutionModule.to parameter) (spatialvi.module.DeconvolutionModule.to_empty parameter) (spatialvi.module.DeconvolutionModule.xpu parameter) (spatialvi.module.NicheModule.cuda parameter) (spatialvi.module.NicheModule.ipu parameter) (spatialvi.module.NicheModule.mtia parameter) (spatialvi.module.NicheModule.to parameter) (spatialvi.module.NicheModule.to_empty parameter) (spatialvi.module.NicheModule.xpu parameter) (spatialvi.module.SpatialVAEModule.cuda parameter) (spatialvi.module.SpatialVAEModule.ipu parameter) (spatialvi.module.SpatialVAEModule.mtia parameter) (spatialvi.module.SpatialVAEModule.to parameter) (spatialvi.module.SpatialVAEModule.to_empty parameter) (spatialvi.module.SpatialVAEModule.xpu parameter) (spatialvi.nn.NeighborAttention.cuda parameter) (spatialvi.nn.NeighborAttention.ipu parameter) (spatialvi.nn.NeighborAttention.mtia parameter) (spatialvi.nn.NeighborAttention.to parameter) (spatialvi.nn.NeighborAttention.to_empty parameter) (spatialvi.nn.NeighborAttention.xpu parameter) (spatialvi.nn.SpatialAttention.cuda parameter) (spatialvi.nn.SpatialAttention.ipu parameter) (spatialvi.nn.SpatialAttention.mtia parameter) (spatialvi.nn.SpatialAttention.to parameter) (spatialvi.nn.SpatialAttention.to_empty parameter) (spatialvi.nn.SpatialAttention.xpu parameter) (spatialvi.nn.SpatialDecoder.cuda parameter) (spatialvi.nn.SpatialDecoder.ipu parameter) (spatialvi.nn.SpatialDecoder.mtia parameter) (spatialvi.nn.SpatialDecoder.to parameter) (spatialvi.nn.SpatialDecoder.to_empty parameter) (spatialvi.nn.SpatialDecoder.xpu parameter) (spatialvi.nn.SpatialEncoder.cuda parameter) (spatialvi.nn.SpatialEncoder.ipu parameter) (spatialvi.nn.SpatialEncoder.mtia parameter) (spatialvi.nn.SpatialEncoder.to parameter) (spatialvi.nn.SpatialEncoder.to_empty parameter) (spatialvi.nn.SpatialEncoder.xpu parameter) (spatialvi.train.DeconvolutionTrainingPlan.cuda parameter) (spatialvi.train.DeconvolutionTrainingPlan.ipu parameter) (spatialvi.train.DeconvolutionTrainingPlan.mtia parameter) (spatialvi.train.DeconvolutionTrainingPlan.to_empty parameter) (spatialvi.train.DeconvolutionTrainingPlan.transfer_batch_to_device parameter) (spatialvi.train.DeconvolutionTrainingPlan.xpu parameter) (spatialvi.train.NicheTrainingPlan.cuda parameter) (spatialvi.train.NicheTrainingPlan.ipu parameter) (spatialvi.train.NicheTrainingPlan.mtia parameter) (spatialvi.train.NicheTrainingPlan.to_empty parameter) (spatialvi.train.NicheTrainingPlan.transfer_batch_to_device parameter) (spatialvi.train.NicheTrainingPlan.xpu parameter) (spatialvi.train.SpatialTrainingPlan.cuda parameter) (spatialvi.train.SpatialTrainingPlan.ipu parameter) (spatialvi.train.SpatialTrainingPlan.mtia parameter) (spatialvi.train.SpatialTrainingPlan.to_empty parameter) (spatialvi.train.SpatialTrainingPlan.transfer_batch_to_device parameter) (spatialvi.train.SpatialTrainingPlan.xpu parameter)

devices (spatialvi.external.AMICI.train parameter) (spatialvi.external.destvi.DestVI.train parameter) (spatialvi.external.DestVI.train parameter), [1] (spatialvi.external.resolvi.ResolVI.train parameter) (spatialvi.external.ResolVI.train parameter), [1] (spatialvi.external.scviva.scVIVA.train parameter) (spatialvi.external.scVIVA.train parameter), [1] (spatialvi.model.SpatialVAE.train parameter) dictionary (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) differential_niche_expression() (spatialvi.external.scVIVA method) (spatialvi.external.scviva.scVIVA method) diffusion_eps (spatialvi.external.resolvi.RESOLVAE parameter) dir_path (spatialvi.external.AMICI.convert_legacy_save parameter) (spatialvi.external.AMICI.load parameter) (spatialvi.external.AMICI.load_registry parameter) (spatialvi.external.AMICI.save parameter) (spatialvi.external.AMICI.view_setup_args parameter) (spatialvi.model.BaseSpatialModel.convert_legacy_save parameter) (spatialvi.model.BaseSpatialModel.load parameter) (spatialvi.model.BaseSpatialModel.load_registry parameter) (spatialvi.model.BaseSpatialModel.save parameter) (spatialvi.model.BaseSpatialModel.view_setup_args parameter) (spatialvi.model.SpatialVAE.convert_legacy_save parameter) (spatialvi.model.SpatialVAE.load parameter) (spatialvi.model.SpatialVAE.load_registry parameter) (spatialvi.model.SpatialVAE.save parameter) (spatialvi.model.SpatialVAE.view_setup_args parameter) dispersion (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.SpatialVAEModule parameter), [1], [2] dist_key (spatialvi.data._preprocessing.compute_spatial_neighbors parameter) (spatialvi.data.compute_spatial_neighbors parameter), [1] (spatialvi.external.AMICI.compute_spatial_neighbors parameter) (spatialvi.model.BaseSpatialModel.compute_spatial_neighbors parameter), [1] (spatialvi.model.SpatialVAE.compute_spatial_neighbors parameter) distance_decay (spatialvi.nn.SpatialAttention parameter), [1], [2] distances (spatialvi.nn.SpatialAttention.forward parameter), [1], [2] downsample_counts_mean (spatialvi.external.resolvi.RESOLVAE parameter) downsample_counts_std (spatialvi.external.resolvi.RESOLVAE parameter) dropout (spatialvi.nn.CrossAttention parameter) (spatialvi.nn.GATLayer parameter) (spatialvi.nn.NeighborAttention parameter), [1], [2] (spatialvi.nn.SpatialAttention parameter), [1], [2] dropout_amortization (spatialvi.external.destvi.MRDeconv parameter) dropout_decoder (spatialvi.external.destvi.MRDeconv parameter) dropout_rate (spatialvi.data._datasets.synthetic_scrna parameter) (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data.synthetic_scrna parameter), [1] (spatialvi.data.synthetic_spatial parameter), [1] (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICIModule parameter) (spatialvi.external.nolan.NolanModule parameter) (spatialvi.external.ResolVI parameter), [1] (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.resolvi.ResolVI parameter) (spatialvi.external.scVIVA parameter), [1] (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.external.scviva.scVIVA parameter) (spatialvi.external.sparl.SPARLModule parameter) (spatialvi.external.starfysh.StarfyshModule parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.DeconvolutionModule parameter), [1] (spatialvi.module.NicheModule parameter), [1] (spatialvi.module.SpatialVAEModule parameter), [1], [2] (spatialvi.nn._decoders.ConditionalDecoder parameter) (spatialvi.nn._decoders.FactorizedDecoder parameter) (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn._encoders.AttentionEncoder parameter) (spatialvi.nn._encoders.GraphEncoder parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] (spatialvi.nn.SpatialEncoder parameter), [1] dst_type (spatialvi.module.DeconvolutionModule.type parameter) (spatialvi.module.NicheModule.type parameter) (spatialvi.module.SpatialVAEModule.type parameter) (spatialvi.nn.NeighborAttention.type parameter) (spatialvi.nn.SpatialAttention.type parameter) (spatialvi.nn.SpatialDecoder.type parameter) (spatialvi.nn.SpatialEncoder.type parameter) dtype (spatialvi.module.DeconvolutionModule.to parameter) (spatialvi.module.NicheModule.to parameter) (spatialvi.module.SpatialVAEModule.to parameter) (spatialvi.nn.NeighborAttention.to parameter) (spatialvi.nn.SpatialAttention.to parameter) (spatialvi.nn.SpatialDecoder.to parameter) (spatialvi.nn.SpatialEncoder.to parameter)

E

early_stopping (spatialvi.external.AMICI.train parameter) (spatialvi.external.Starfysh.fit parameter), [1] (spatialvi.external.starfysh.Starfysh.fit parameter) (spatialvi.model.SpatialVAE.train parameter) early_stopping_min_delta (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) early_stopping_patience (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) EarlyStoppingOnSpatialLoss (class in spatialvi.train._callbacks) edge_index (spatialvi.nn._encoders.GraphEncoder.forward parameter) (spatialvi.nn._layers.GraphConv.forward parameter) (spatialvi.nn.GATLayer.forward parameter) edge_weight (spatialvi.nn._layers.GraphConv.forward parameter) emb_key (spatialvi.external.Nolan parameter), [1] (spatialvi.external.nolan.Nolan parameter) embed_dim (spatialvi.nn.CrossAttention parameter) (spatialvi.nn.SpatialAttention parameter), [1], [2] enable_graph (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter)

encode() (spatialvi.external.nolan.NolanModule method) encode_covariates (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) encoding_type (spatialvi.nn._layers.PositionalEncoding parameter) epoch (spatialvi.train.DeconvolutionTrainingPlan.optimizer_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.optimizer_zero_grad parameter) (spatialvi.train.NicheTrainingPlan.optimizer_step parameter) (spatialvi.train.NicheTrainingPlan.optimizer_zero_grad parameter) (spatialvi.train.SpatialTrainingPlan.optimizer_step parameter) (spatialvi.train.SpatialTrainingPlan.optimizer_zero_grad parameter) eps_v (spatialvi.external.destvi.MRDeconv parameter) epsilon (spatialvi.external.scviva.nicheVAE.loss parameter) example_inputs (spatialvi.train.DeconvolutionTrainingPlan.to_torchscript parameter) (spatialvi.train.NicheTrainingPlan.to_torchscript parameter) (spatialvi.train.SpatialTrainingPlan.to_torchscript parameter) expression_anntorchdata (spatialvi.external.resolvi.RESOLVAE parameter) extra_decoder_kwargs (spatialvi.external.destvi.MRDeconv parameter) (spatialvi.external.scviva.nicheVAE parameter) extra_encoder_kwargs (spatialvi.external.destvi.MRDeconv parameter) (spatialvi.external.scviva.nicheVAE parameter) extract_marker_genes() (spatialvi.external.lambda_model.LambdaAnnotator method)

F

factor_weights (spatialvi.external.starfysh.StarfyshModule.generative parameter) FactorizedDecoder (class in spatialvi.nn._decoders) fdr_threshold (spatialvi.external.Harreman.get_metabolic_exchanges parameter), [1] (spatialvi.external.harreman.Harreman.get_metabolic_exchanges parameter) (spatialvi.external.VIVS.get_spatially_variable_genes parameter), [1] (spatialvi.external.vivs.VIVS.get_spatially_variable_genes parameter) feature_dim (spatialvi.nn._layers.FiLMLayer parameter) file_path (spatialvi.train.DeconvolutionTrainingPlan.to_onnx parameter) (spatialvi.train.DeconvolutionTrainingPlan.to_tensorrt parameter) (spatialvi.train.DeconvolutionTrainingPlan.to_torchscript parameter) (spatialvi.train.NicheTrainingPlan.to_onnx parameter) (spatialvi.train.NicheTrainingPlan.to_tensorrt parameter) (spatialvi.train.NicheTrainingPlan.to_torchscript parameter) (spatialvi.train.SpatialTrainingPlan.to_onnx parameter) (spatialvi.train.SpatialTrainingPlan.to_tensorrt parameter) (spatialvi.train.SpatialTrainingPlan.to_torchscript parameter) FiLMLayer (class in spatialvi.nn._layers) filter_by_spatial_density() (in module spatialvi.data._preprocessing) final_weight (spatialvi.train._callbacks.SpatialRegularizationScheduler parameter) fit() (spatialvi.external.Harreman method) (spatialvi.external.harreman.Harreman method) (spatialvi.external.ppi.MeanEstimator method) (spatialvi.external.ppi.OLSEstimator method) (spatialvi.external.Starfysh method) (spatialvi.external.starfysh.Starfysh method) (spatialvi.external.VIVS method) (spatialvi.external.vivs.VIVS method) fn (spatialvi.module.DeconvolutionModule.apply parameter) (spatialvi.module.NicheModule.apply parameter) (spatialvi.module.SpatialVAEModule.apply parameter) (spatialvi.nn.NeighborAttention.apply parameter) (spatialvi.nn.SpatialAttention.apply parameter) (spatialvi.nn.SpatialDecoder.apply parameter) (spatialvi.nn.SpatialEncoder.apply parameter) (spatialvi.train.DeconvolutionTrainingPlan.apply parameter) (spatialvi.train.NicheTrainingPlan.apply parameter) (spatialvi.train.SpatialTrainingPlan.apply parameter)

forward() (spatialvi.external.amici.AMICIModule method) (spatialvi.external.harreman.HarremanModule method) (spatialvi.external.harreman.MetabolicExchangeScorer method) (spatialvi.external.nolan.NicheClusteringHead method) (spatialvi.external.nolan.NolanModule method) (spatialvi.external.sparl.SPARLModule method) (spatialvi.external.starfysh.StarfyshModule method) (spatialvi.external.vivs.MultiScaleVIVS method) (spatialvi.external.vivs.VIVSModule method) (spatialvi.nn._decoders.ConditionalDecoder method) (spatialvi.nn._decoders.FactorizedDecoder method) (spatialvi.nn._decoders.SpatialDecoder method) (spatialvi.nn._encoders.AttentionEncoder method) (spatialvi.nn._encoders.GraphConvLayer method) (spatialvi.nn._encoders.GraphEncoder method) (spatialvi.nn._encoders.SpatialEncoder method) (spatialvi.nn._layers.FiLMLayer method) (spatialvi.nn._layers.GraphConv method) (spatialvi.nn._layers.MixedLinear method) (spatialvi.nn._layers.PositionalEncoding method) (spatialvi.nn._layers.SpatialConv method) (spatialvi.nn.CrossAttention method) (spatialvi.nn.GATLayer method) (spatialvi.nn.NeighborAttention method), [1] (spatialvi.nn.SpatialAttention method), [1] (spatialvi.nn.SpatialDecoder method) (spatialvi.nn.SpatialEncoder method) forward_spatial() (spatialvi.nn._encoders.SpatialEncoder method) (spatialvi.nn.SpatialEncoder method) frame (spatialvi.train.DeconvolutionTrainingPlan.save_hyperparameters parameter) (spatialvi.train.NicheTrainingPlan.save_hyperparameters parameter) (spatialvi.train.SpatialTrainingPlan.save_hyperparameters parameter) from_rna_model() (spatialvi.external.DestVI class method) (spatialvi.external.destvi.DestVI class method)

G

GATLayer (class in spatialvi.nn) gene_likelihood (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICIModule parameter) (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.SpatialVAEModule parameter), [1], [2] gene_list (spatialvi.model.BaseSpatialModel.get_normalized_expression parameter), [1] (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2] gene_names (spatialvi.external.VIVS.get_scale_contributions parameter), [1] (spatialvi.external.vivs.VIVS.get_scale_contributions parameter) generative() (spatialvi.external.amici.AMICIModule method) (spatialvi.external.destvi.MRDeconv method) (spatialvi.external.scviva.nicheVAE method) (spatialvi.external.sparl.SPARLModule method) (spatialvi.external.starfysh.StarfyshModule method) (spatialvi.module.DeconvolutionModule method) (spatialvi.module.NicheModule method) (spatialvi.module.SpatialVAEModule method), [1] generative_kwargs (spatialvi.module.DeconvolutionModule.forward parameter) (spatialvi.module.NicheModule.forward parameter) (spatialvi.module.SpatialVAEModule.forward parameter) generative_outputs (spatialvi.external.amici.AMICIModule.loss parameter) (spatialvi.external.destvi.MRDeconv.loss parameter) (spatialvi.external.scviva.nicheVAE.loss parameter) (spatialvi.external.sparl.SPARLModule.loss parameter) (spatialvi.external.starfysh.StarfyshModule.loss parameter) (spatialvi.module.DeconvolutionModule.loss parameter), [1] (spatialvi.module.NicheModule.loss parameter), [1] (spatialvi.module.SpatialVAEModule.loss parameter), [1], [2] get_annotations() (spatialvi.external.Lambda method) (spatialvi.external.lambda_model.Lambda method) get_background_fraction() (spatialvi.external.ResolVI method) (spatialvi.external.resolvi.ResolVI method) get_cell_type_exchanges() (spatialvi.external.Harreman method) (spatialvi.external.harreman.Harreman method) get_cell_type_expression() (spatialvi.module.DeconvolutionModule method) get_cell_type_interactions() (spatialvi.external.AMICI method) (spatialvi.external.amici.AMICI method) get_denoised_expression() (spatialvi.external.ResolVI method) (spatialvi.external.resolvi.ResolVI method) get_gamma() (spatialvi.external.DestVI method) (spatialvi.external.destvi.DestVI method) get_generative_input_kwargs (spatialvi.module.DeconvolutionModule.forward parameter) (spatialvi.module.NicheModule.forward parameter) (spatialvi.module.SpatialVAEModule.forward parameter) get_inference_input_kwargs (spatialvi.module.DeconvolutionModule.forward parameter) (spatialvi.module.NicheModule.forward parameter) (spatialvi.module.SpatialVAEModule.forward parameter) get_interaction_scores() (spatialvi.external.AMICI method) (spatialvi.external.amici.AMICI method) get_latent_representation() (spatialvi.external.AMICI method) (spatialvi.external.amici.AMICI method) (spatialvi.external.DestVI method) (spatialvi.external.destvi.DestVI method) (spatialvi.external.ResolVI method) (spatialvi.external.resolvi.ResolVI method) (spatialvi.external.scVIVA method) (spatialvi.external.scviva.scVIVA method) (spatialvi.external.SPARL method) (spatialvi.external.sparl.SPARL method) (spatialvi.model.BaseSpatialModel method) get_metabolic_exchanges() (spatialvi.external.Harreman method) (spatialvi.external.harreman.Harreman method)

get_mixed_output() (spatialvi.nn._decoders.FactorizedDecoder method) get_neighbor_expression() (in module spatialvi.data._preprocessing) get_niche_assignments() (spatialvi.external.Nolan method) (spatialvi.external.nolan.Nolan method) get_niche_effects() (spatialvi.external.scVIVA method) (spatialvi.external.scviva.scVIVA method) get_normalized_expression() (spatialvi.external.AMICI method) (spatialvi.external.amici.AMICI method) (spatialvi.model.BaseSpatialModel method) (spatialvi.model.SpatialVAE method), [1] get_proportions() (spatialvi.external.DestVI method) (spatialvi.external.destvi.DestVI method) (spatialvi.external.destvi.MRDeconv method) (spatialvi.external.Starfysh method) (spatialvi.external.starfysh.Starfysh method) get_reconstruction() (spatialvi.external.Starfysh method) (spatialvi.external.starfysh.Starfysh method) get_scale_contributions() (spatialvi.external.VIVS method) (spatialvi.external.vivs.VIVS method) get_scale_for_ct() (spatialvi.external.DestVI method) (spatialvi.external.destvi.DestVI method) get_spatial_representation() (spatialvi.model.SpatialVAE method), [1] get_spatially_variable_genes() (spatialvi.external.VIVS method) (spatialvi.external.vivs.VIVS method) give_mean (spatialvi.external.amici.AMICI.get_latent_representation parameter) (spatialvi.external.AMICI.get_latent_representation parameter), [1] (spatialvi.external.ResolVI.get_latent_representation parameter), [1] (spatialvi.external.resolvi.ResolVI.get_latent_representation parameter) (spatialvi.external.scVIVA.get_latent_representation parameter), [1] (spatialvi.external.scviva.scVIVA.get_latent_representation parameter) (spatialvi.model.BaseSpatialModel.get_latent_representation parameter), [1] (spatialvi.model.SpatialVAE.get_latent_representation parameter) gradient_clip_algorithm (spatialvi.train.DeconvolutionTrainingPlan.clip_gradients parameter) (spatialvi.train.DeconvolutionTrainingPlan.configure_gradient_clipping parameter) (spatialvi.train.NicheTrainingPlan.clip_gradients parameter) (spatialvi.train.NicheTrainingPlan.configure_gradient_clipping parameter) (spatialvi.train.SpatialTrainingPlan.clip_gradients parameter) (spatialvi.train.SpatialTrainingPlan.configure_gradient_clipping parameter) gradient_clip_val (spatialvi.train.DeconvolutionTrainingPlan.clip_gradients parameter) (spatialvi.train.DeconvolutionTrainingPlan.configure_gradient_clipping parameter) (spatialvi.train.NicheTrainingPlan.clip_gradients parameter) (spatialvi.train.NicheTrainingPlan.configure_gradient_clipping parameter) (spatialvi.train.SpatialTrainingPlan.clip_gradients parameter) (spatialvi.train.SpatialTrainingPlan.configure_gradient_clipping parameter) GraphConv (class in spatialvi.nn._layers) GraphConvLayer (class in spatialvi.nn._encoders) GraphEncoder (class in spatialvi.nn._encoders) grid_cols (spatialvi.data._datasets.synthetic_visium parameter) grid_rows (spatialvi.data._datasets.synthetic_visium parameter) group (spatialvi.train.DeconvolutionTrainingPlan.all_gather parameter) (spatialvi.train.NicheTrainingPlan.all_gather parameter) (spatialvi.train.SpatialTrainingPlan.all_gather parameter) group1 (spatialvi.external.scVIVA.differential_niche_expression parameter), [1] (spatialvi.external.scviva.scVIVA.differential_niche_expression parameter) group2 (spatialvi.external.scVIVA.differential_niche_expression parameter), [1] (spatialvi.external.scviva.scVIVA.differential_niche_expression parameter) group_key (spatialvi.external.Lambda.predict parameter), [1] (spatialvi.external.lambda_model.Lambda.predict parameter) groupby (spatialvi.external.scVIVA.differential_niche_expression parameter), [1] (spatialvi.external.scviva.scVIVA.differential_niche_expression parameter) groups (spatialvi.external.Lambda.predict parameter), [1] (spatialvi.external.lambda_model.Lambda.predict parameter) guide (spatialvi.external.resolvi.RESOLVAE property)

H

h (spatialvi.external.nolan.NolanModule.project parameter) Harreman (class in spatialvi.external) (class in spatialvi.external.harreman) HarremanModule (class in spatialvi.external.harreman) hidden_dim (spatialvi.external.nolan.NolanModule parameter) (spatialvi.nn._layers.FiLMLayer parameter) (spatialvi.nn.NeighborAttention parameter), [1], [2] hide_state_registries (spatialvi.external.AMICI.view_anndata_setup parameter) (spatialvi.external.AMICI.view_registry parameter) (spatialvi.model.BaseSpatialModel.view_anndata_setup parameter) (spatialvi.model.BaseSpatialModel.view_registry parameter) (spatialvi.model.SpatialVAE.view_anndata_setup parameter) (spatialvi.model.SpatialVAE.view_registry parameter) histology (spatialvi.external.starfysh.StarfyshModule.inference parameter) histology_dim (spatialvi.external.starfysh.StarfyshModule parameter) hook (spatialvi.module.DeconvolutionModule.register_forward_hook parameter) (spatialvi.module.DeconvolutionModule.register_forward_pre_hook parameter) (spatialvi.module.DeconvolutionModule.register_full_backward_hook parameter) (spatialvi.module.DeconvolutionModule.register_full_backward_pre_hook parameter) (spatialvi.module.DeconvolutionModule.register_load_state_dict_pre_hook parameter) (spatialvi.module.NicheModule.register_forward_hook parameter) (spatialvi.module.NicheModule.register_forward_pre_hook parameter) (spatialvi.module.NicheModule.register_full_backward_hook parameter) (spatialvi.module.NicheModule.register_full_backward_pre_hook parameter) (spatialvi.module.NicheModule.register_load_state_dict_pre_hook parameter) (spatialvi.module.SpatialVAEModule.register_forward_hook parameter) (spatialvi.module.SpatialVAEModule.register_forward_pre_hook parameter) (spatialvi.module.SpatialVAEModule.register_full_backward_hook parameter) (spatialvi.module.SpatialVAEModule.register_full_backward_pre_hook parameter) (spatialvi.module.SpatialVAEModule.register_load_state_dict_pre_hook parameter) (spatialvi.nn.NeighborAttention.register_forward_hook parameter) (spatialvi.nn.NeighborAttention.register_forward_pre_hook parameter) (spatialvi.nn.NeighborAttention.register_full_backward_hook parameter) (spatialvi.nn.NeighborAttention.register_full_backward_pre_hook parameter) (spatialvi.nn.NeighborAttention.register_load_state_dict_pre_hook parameter) (spatialvi.nn.SpatialAttention.register_forward_hook parameter) (spatialvi.nn.SpatialAttention.register_forward_pre_hook parameter) (spatialvi.nn.SpatialAttention.register_full_backward_hook parameter) (spatialvi.nn.SpatialAttention.register_full_backward_pre_hook parameter) (spatialvi.nn.SpatialAttention.register_load_state_dict_pre_hook parameter) (spatialvi.nn.SpatialDecoder.register_forward_hook parameter) (spatialvi.nn.SpatialDecoder.register_forward_pre_hook parameter) (spatialvi.nn.SpatialDecoder.register_full_backward_hook parameter) (spatialvi.nn.SpatialDecoder.register_full_backward_pre_hook parameter) (spatialvi.nn.SpatialDecoder.register_load_state_dict_pre_hook parameter) (spatialvi.nn.SpatialEncoder.register_forward_hook parameter) (spatialvi.nn.SpatialEncoder.register_forward_pre_hook parameter) (spatialvi.nn.SpatialEncoder.register_full_backward_hook parameter) (spatialvi.nn.SpatialEncoder.register_full_backward_pre_hook parameter) (spatialvi.nn.SpatialEncoder.register_load_state_dict_pre_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_forward_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_forward_pre_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_full_backward_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_full_backward_pre_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_load_state_dict_pre_hook parameter) (spatialvi.train.NicheTrainingPlan.register_forward_hook parameter) (spatialvi.train.NicheTrainingPlan.register_forward_pre_hook parameter) (spatialvi.train.NicheTrainingPlan.register_full_backward_hook parameter) (spatialvi.train.NicheTrainingPlan.register_full_backward_pre_hook parameter) (spatialvi.train.NicheTrainingPlan.register_load_state_dict_pre_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_forward_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_forward_pre_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_full_backward_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_full_backward_pre_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_load_state_dict_pre_hook parameter)

hparams_file (spatialvi.train.DeconvolutionTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.NicheTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.SpatialTrainingPlan.load_from_checkpoint parameter)

I

ignore (spatialvi.train.DeconvolutionTrainingPlan.save_hyperparameters parameter) (spatialvi.train.NicheTrainingPlan.save_hyperparameters parameter) (spatialvi.train.SpatialTrainingPlan.save_hyperparameters parameter) impute_proteins() (spatialvi.external.SPARL method) (spatialvi.external.sparl.SPARL method) in_channels (spatialvi.nn._layers.GraphConv parameter) (spatialvi.nn._layers.SpatialConv parameter) in_features (spatialvi.nn._layers.MixedLinear parameter) (spatialvi.nn.GATLayer parameter) include_neighbor_expr (spatialvi.train._callbacks.NeighborSamplingCallback parameter) ind_x (spatialvi.external.destvi.MRDeconv.generative parameter) (spatialvi.external.destvi.MRDeconv.get_proportions parameter) (spatialvi.external.destvi.MRDeconv.inference parameter) index_key (spatialvi.data._preprocessing.compute_niche_composition parameter) (spatialvi.data._preprocessing.compute_spatial_neighbors parameter) (spatialvi.data._preprocessing.get_neighbor_expression parameter) (spatialvi.data.compute_niche_composition parameter), [1] (spatialvi.data.compute_spatial_neighbors parameter), [1] (spatialvi.external.AMICI.compute_niche_composition parameter) (spatialvi.external.AMICI.compute_spatial_neighbors parameter) (spatialvi.model.BaseSpatialModel.compute_niche_composition parameter), [1] (spatialvi.model.BaseSpatialModel.compute_spatial_neighbors parameter), [1] (spatialvi.model.SpatialVAE.compute_niche_composition parameter) (spatialvi.model.SpatialVAE.compute_spatial_neighbors parameter) indices (spatialvi.external.amici.AMICI.get_interaction_scores parameter) (spatialvi.external.amici.AMICI.get_latent_representation parameter) (spatialvi.external.AMICI.get_interaction_scores parameter), [1] (spatialvi.external.AMICI.get_latent_representation parameter), [1] (spatialvi.external.AMICI.get_spatial_coordinates parameter) (spatialvi.external.AMICI.get_spatial_neighbors parameter) (spatialvi.external.destvi.DestVI.get_gamma parameter) (spatialvi.external.destvi.DestVI.get_latent_representation parameter) (spatialvi.external.destvi.DestVI.get_proportions parameter) (spatialvi.external.destvi.DestVI.get_scale_for_ct parameter) (spatialvi.external.DestVI.get_gamma parameter), [1] (spatialvi.external.DestVI.get_latent_representation parameter), [1] (spatialvi.external.DestVI.get_proportions parameter), [1] (spatialvi.external.DestVI.get_scale_for_ct parameter), [1] (spatialvi.external.ResolVI.get_background_fraction parameter), [1] (spatialvi.external.ResolVI.get_denoised_expression parameter), [1] (spatialvi.external.ResolVI.get_latent_representation parameter), [1] (spatialvi.external.ResolVI.predict parameter), [1] (spatialvi.external.resolvi.ResolVI.get_background_fraction parameter) (spatialvi.external.resolvi.ResolVI.get_denoised_expression parameter) (spatialvi.external.resolvi.ResolVI.get_latent_representation parameter) (spatialvi.external.resolvi.ResolVI.predict parameter) (spatialvi.external.scVIVA.get_latent_representation parameter), [1] (spatialvi.external.scVIVA.get_niche_effects parameter), [1] (spatialvi.external.scviva.scVIVA.get_latent_representation parameter) (spatialvi.external.scviva.scVIVA.get_niche_effects parameter) (spatialvi.model.BaseSpatialModel.get_latent_representation parameter), [1] (spatialvi.model.BaseSpatialModel.get_normalized_expression parameter), [1] (spatialvi.model.SpatialVAE.get_latent_representation parameter) (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2] (spatialvi.model.SpatialVAE.get_spatial_coordinates parameter) (spatialvi.model.SpatialVAE.get_spatial_neighbors parameter) (spatialvi.model.SpatialVAE.get_spatial_representation parameter), [1], [2]

inference() (spatialvi.external.amici.AMICIModule method) (spatialvi.external.destvi.MRDeconv method) (spatialvi.external.sparl.SPARLModule method) (spatialvi.external.starfysh.StarfyshModule method) (spatialvi.module.DeconvolutionModule method) (spatialvi.module.NicheModule method) (spatialvi.module.SpatialVAEModule method), [1] inference_kwargs (spatialvi.module.DeconvolutionModule.forward parameter) (spatialvi.module.NicheModule.forward parameter) (spatialvi.module.SpatialVAEModule.forward parameter) inference_outputs (spatialvi.external.amici.AMICIModule.loss parameter) (spatialvi.external.destvi.MRDeconv.loss parameter) (spatialvi.external.scviva.nicheVAE.loss parameter) (spatialvi.external.sparl.SPARLModule.loss parameter) (spatialvi.external.starfysh.StarfyshModule.loss parameter) (spatialvi.module.DeconvolutionModule.loss parameter), [1] (spatialvi.module.NicheModule.loss parameter), [1] (spatialvi.module.SpatialVAEModule.loss parameter), [1], [2] initial_weight (spatialvi.train._callbacks.SpatialRegularizationScheduler parameter) input_dim (spatialvi.external.nolan.NicheClusteringHead parameter) (spatialvi.external.nolan.NolanModule parameter) (spatialvi.nn.NeighborAttention parameter), [1], [2] input_sample (spatialvi.train.DeconvolutionTrainingPlan.to_onnx parameter) (spatialvi.train.DeconvolutionTrainingPlan.to_tensorrt parameter) (spatialvi.train.NicheTrainingPlan.to_onnx parameter) (spatialvi.train.NicheTrainingPlan.to_tensorrt parameter) (spatialvi.train.SpatialTrainingPlan.to_onnx parameter) (spatialvi.train.SpatialTrainingPlan.to_tensorrt parameter) inpute_covariates_niche_decoder (spatialvi.external.scviva.nicheVAE parameter) interaction_context (spatialvi.external.amici.AMICIModule.generative parameter) interaction_layers (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICIModule parameter) interaction_matrix (spatialvi.utils._visualization.plot_interactions parameter) ir (spatialvi.train.DeconvolutionTrainingPlan.to_tensorrt parameter) (spatialvi.train.NicheTrainingPlan.to_tensorrt parameter) (spatialvi.train.SpatialTrainingPlan.to_tensorrt parameter)

K

keep_vars (spatialvi.module.DeconvolutionModule.state_dict parameter) (spatialvi.module.NicheModule.state_dict parameter) (spatialvi.module.SpatialVAEModule.state_dict parameter) (spatialvi.nn.NeighborAttention.state_dict parameter) (spatialvi.nn.SpatialAttention.state_dict parameter) (spatialvi.nn.SpatialDecoder.state_dict parameter) (spatialvi.nn.SpatialEncoder.state_dict parameter) (spatialvi.train.DeconvolutionTrainingPlan.state_dict parameter) (spatialvi.train.NicheTrainingPlan.state_dict parameter) (spatialvi.train.SpatialTrainingPlan.state_dict parameter)

key (spatialvi.nn.SpatialAttention.forward parameter), [1], [2] key_is_hierarchical (spatialvi.external.Lambda.predict parameter), [1] (spatialvi.external.lambda_model.Lambda.predict parameter) kl_weight (spatialvi.external.amici.AMICIModule.loss parameter) (spatialvi.external.destvi.MRDeconv.loss parameter) (spatialvi.external.scviva.nicheVAE.loss parameter) (spatialvi.external.sparl.SPARLModule.loss parameter) (spatialvi.external.starfysh.StarfyshModule.loss parameter) (spatialvi.module.DeconvolutionModule.loss parameter), [1] (spatialvi.module.NicheModule.loss parameter), [1] (spatialvi.module.SpatialVAEModule.loss parameter), [1], [2]

L

labels (spatialvi.external.amici.AMICIModule.inference parameter) labels_key (spatialvi.data._preprocessing.compute_niche_composition parameter) (spatialvi.data.compute_niche_composition parameter), [1] (spatialvi.external.amici.AMICI.setup_anndata parameter) (spatialvi.external.AMICI.compute_niche_composition parameter) (spatialvi.external.AMICI.setup_anndata parameter), [1] (spatialvi.external.destvi.DestVI.setup_anndata parameter) (spatialvi.external.DestVI.setup_anndata parameter), [1] (spatialvi.external.Harreman parameter), [1] (spatialvi.external.harreman.Harreman parameter) (spatialvi.external.resolvi.ResolVI.setup_anndata parameter) (spatialvi.external.ResolVI.setup_anndata parameter), [1] (spatialvi.external.scviva.scVIVA.setup_anndata parameter) (spatialvi.external.scVIVA.setup_anndata parameter), [1] (spatialvi.model.BaseSpatialModel.compute_niche_composition parameter), [1] (spatialvi.model.SpatialVAE.compute_niche_composition parameter) (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] (spatialvi.utils._metrics.niche_purity parameter) (spatialvi.utils._metrics.silhouette_spatial parameter) Lambda (class in spatialvi.external) (class in spatialvi.external.lambda_model) LambdaAnnotator (class in spatialvi.external.lambda_model) latent_distribution (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.SpatialVAEModule parameter), [1], [2] latent_kl_weight (spatialvi.external.scviva.nicheVAE parameter) layer (spatialvi.data._preprocessing.get_neighbor_expression parameter) (spatialvi.external.amici.AMICI.setup_anndata parameter) (spatialvi.external.AMICI.setup_anndata parameter), [1] (spatialvi.external.destvi.DestVI.setup_anndata parameter) (spatialvi.external.DestVI.setup_anndata parameter), [1] (spatialvi.external.resolvi.ResolVI.setup_anndata parameter) (spatialvi.external.ResolVI.setup_anndata parameter), [1] (spatialvi.external.scviva.scVIVA.setup_anndata parameter) (spatialvi.external.scVIVA.setup_anndata parameter), [1] (spatialvi.external.SPARL parameter), [1] (spatialvi.external.sparl.SPARL parameter) (spatialvi.external.VIVS parameter), [1] (spatialvi.external.vivs.VIVS parameter) (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] (spatialvi.utils._metrics.spatial_autocorrelation parameter) (spatialvi.utils.spatial_autocorrelation parameter), [1] legacy_mudata_format (spatialvi.external.AMICI.save parameter) (spatialvi.model.BaseSpatialModel.save parameter) (spatialvi.model.SpatialVAE.save parameter) level (spatialvi.external.Lambda.get_annotations parameter), [1] (spatialvi.external.Lambda.predict parameter), [1] (spatialvi.external.lambda_model.Lambda.get_annotations parameter) (spatialvi.external.lambda_model.Lambda.predict parameter) library (spatialvi.external.amici.AMICIModule.generative parameter) (spatialvi.external.scviva.nicheVAE.generative parameter) (spatialvi.external.starfysh.StarfyshModule.generative parameter) (spatialvi.module.DeconvolutionModule.generative parameter), [1] (spatialvi.module.NicheModule.generative parameter), [1] (spatialvi.module.SpatialVAEModule.generative parameter), [1], [2] (spatialvi.nn._decoders.SpatialDecoder.forward parameter) (spatialvi.nn.SpatialDecoder.forward parameter), [1] library_log_means (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.SpatialVAEModule parameter), [1], [2] library_log_vars (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.SpatialVAEModule parameter), [1], [2] library_size (spatialvi.model.BaseSpatialModel.get_normalized_expression parameter), [1] (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2] library_size_mean (spatialvi.data._datasets.synthetic_scrna parameter) (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data.synthetic_scrna parameter), [1] (spatialvi.data.synthetic_spatial parameter), [1]

library_size_std (spatialvi.data._datasets.synthetic_scrna parameter) (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data.synthetic_scrna parameter), [1] (spatialvi.data.synthetic_spatial parameter), [1] linear_classifier (spatialvi.external.scviva.nicheVAE parameter) list_obs_plate_vars (spatialvi.external.resolvi.RESOLVAE property) load() (spatialvi.external.DestVI class method) (spatialvi.external.destvi.DestVI class method) (spatialvi.external.ResolVI class method) (spatialvi.external.resolvi.ResolVI class method) (spatialvi.external.scVIVA class method) (spatialvi.external.scviva.scVIVA class method) load_sparse_tensor (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) location (spatialvi.external.Lambda parameter), [1] (spatialvi.external.lambda_model.Lambda parameter) log_variational (spatialvi.external.scviva.nicheVAE parameter) logger (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.DeconvolutionTrainingPlan.save_hyperparameters parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.save_hyperparameters parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.save_hyperparameters parameter) loss (spatialvi.train.DeconvolutionTrainingPlan.backward parameter) (spatialvi.train.DeconvolutionTrainingPlan.manual_backward parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_before_backward parameter) (spatialvi.train.NicheTrainingPlan.backward parameter) (spatialvi.train.NicheTrainingPlan.manual_backward parameter) (spatialvi.train.NicheTrainingPlan.on_before_backward parameter) (spatialvi.train.SpatialTrainingPlan.backward parameter) (spatialvi.train.SpatialTrainingPlan.manual_backward parameter) (spatialvi.train.SpatialTrainingPlan.on_before_backward parameter) loss() (spatialvi.external.amici.AMICIModule method) (spatialvi.external.destvi.MRDeconv method) (spatialvi.external.scviva.nicheVAE method) (spatialvi.external.sparl.SPARLModule method) (spatialvi.external.starfysh.StarfyshModule method) (spatialvi.module.DeconvolutionModule method) (spatialvi.module.NicheModule method) (spatialvi.module.SpatialVAEModule method), [1] loss_kwargs (spatialvi.module.DeconvolutionModule.forward parameter) (spatialvi.module.NicheModule.forward parameter) (spatialvi.module.SpatialVAEModule.forward parameter) loss_output (spatialvi.train.DeconvolutionTrainingPlan.compute_and_log_metrics parameter) (spatialvi.train.NicheTrainingPlan.compute_and_log_metrics parameter) (spatialvi.train.SpatialTrainingPlan.compute_and_log_metrics parameter) lr (spatialvi.external.destvi.DestVI.train parameter) (spatialvi.external.DestVI.train parameter), [1] (spatialvi.external.resolvi.ResolVI.train parameter) (spatialvi.external.ResolVI.train parameter), [1] (spatialvi.external.scviva.scVIVA.train parameter) (spatialvi.external.scVIVA.train parameter), [1] (spatialvi.external.sparl.SPARL.train parameter) (spatialvi.external.SPARL.train parameter), [1] (spatialvi.external.Starfysh.fit parameter), [1] (spatialvi.external.starfysh.Starfysh.fit parameter) (spatialvi.train._training_plans.DeconvolutionTrainingPlan parameter) (spatialvi.train._training_plans.NicheTrainingPlan parameter) (spatialvi.train._training_plans.SpatialTrainingPlan parameter) (spatialvi.train.DeconvolutionTrainingPlan parameter), [1] (spatialvi.train.NicheTrainingPlan parameter), [1] (spatialvi.train.SpatialTrainingPlan parameter), [1]

M

map_location (spatialvi.train.DeconvolutionTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.NicheTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.SpatialTrainingPlan.load_from_checkpoint parameter) mask (spatialvi.nn._encoders.AttentionEncoder.forward parameter) (spatialvi.nn.SpatialAttention.forward parameter), [1], [2] max_density (spatialvi.data._preprocessing.filter_by_spatial_density parameter) max_epochs (spatialvi.external.AMICI.train parameter) (spatialvi.external.destvi.DestVI.train parameter) (spatialvi.external.DestVI.train parameter), [1] (spatialvi.external.resolvi.ResolVI.train parameter) (spatialvi.external.ResolVI.train parameter), [1] (spatialvi.external.scviva.scVIVA.train parameter) (spatialvi.external.scVIVA.train parameter), [1] (spatialvi.external.sparl.SPARL.train parameter) (spatialvi.external.SPARL.train parameter), [1] (spatialvi.external.Starfysh.fit parameter), [1] (spatialvi.external.starfysh.Starfysh.fit parameter) (spatialvi.model.SpatialVAE.train parameter) max_len (spatialvi.nn._layers.PositionalEncoding parameter) mean_ci() (spatialvi.external.ppi.PPIInference static method) (spatialvi.external.PPIInference static method) mean_pointestimate() (spatialvi.external.ppi.PPIInference static method) (spatialvi.external.PPIInference static method) mean_vprior (spatialvi.external.destvi.MRDeconv parameter) MeanEstimator (class in spatialvi.external.ppi) median_distance (spatialvi.external.resolvi.RESOLVAE parameter) memo (spatialvi.module.DeconvolutionModule.named_modules parameter) (spatialvi.module.NicheModule.named_modules parameter) (spatialvi.module.SpatialVAEModule.named_modules parameter) (spatialvi.nn.NeighborAttention.named_modules parameter) (spatialvi.nn.SpatialAttention.named_modules parameter) (spatialvi.nn.SpatialDecoder.named_modules parameter) (spatialvi.nn.SpatialEncoder.named_modules parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_modules parameter) (spatialvi.train.NicheTrainingPlan.named_modules parameter) (spatialvi.train.SpatialTrainingPlan.named_modules parameter) memory_format (spatialvi.module.DeconvolutionModule.to parameter) (spatialvi.module.NicheModule.to parameter) (spatialvi.module.SpatialVAEModule.to parameter) (spatialvi.nn.NeighborAttention.to parameter) (spatialvi.nn.SpatialAttention.to parameter) (spatialvi.nn.SpatialDecoder.to parameter) (spatialvi.nn.SpatialEncoder.to parameter) metabolic_genes (spatialvi.external.Harreman parameter), [1] (spatialvi.external.harreman.Harreman parameter) MetabolicExchangeScorer (class in spatialvi.external.harreman) method (spatialvi.data._preprocessing.normalize_spatial parameter) (spatialvi.train.DeconvolutionTrainingPlan.to_torchscript parameter) (spatialvi.train.NicheTrainingPlan.to_torchscript parameter) (spatialvi.train.SpatialTrainingPlan.to_torchscript parameter) (spatialvi.utils._metrics.spatial_autocorrelation parameter) (spatialvi.utils._visualization.plot_niche_composition parameter) (spatialvi.utils.spatial_autocorrelation parameter), [1] metric (spatialvi.data._preprocessing.compute_spatial_neighbors parameter) (spatialvi.data.compute_spatial_neighbors parameter), [1] (spatialvi.external.AMICI.compute_spatial_neighbors parameter) (spatialvi.model.BaseSpatialModel.compute_spatial_neighbors parameter), [1] (spatialvi.model.SpatialVAE.compute_spatial_neighbors parameter) (spatialvi.train.DeconvolutionTrainingPlan.lr_scheduler_step parameter) (spatialvi.train.NicheTrainingPlan.lr_scheduler_step parameter) (spatialvi.train.SpatialTrainingPlan.lr_scheduler_step parameter) metric_attribute (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) metrics (spatialvi.train._callbacks.SpatialMetricsCallback parameter) (spatialvi.train.DeconvolutionTrainingPlan.compute_and_log_metrics parameter) (spatialvi.train.NicheTrainingPlan.compute_and_log_metrics parameter) (spatialvi.train.SpatialTrainingPlan.compute_and_log_metrics parameter)

min_cells (spatialvi.external.Harreman.get_cell_type_exchanges parameter), [1] (spatialvi.external.harreman.Harreman.get_cell_type_exchanges parameter) min_delta (spatialvi.train._callbacks.EarlyStoppingOnSpatialLoss parameter) min_density (spatialvi.data._preprocessing.filter_by_spatial_density parameter) MixedLinear (class in spatialvi.nn._layers) mixture_k (spatialvi.external.resolvi.RESOLVAE parameter) mode (spatialvi.module.DeconvolutionModule.train parameter) (spatialvi.module.NicheModule.train parameter) (spatialvi.module.SpatialVAEModule.train parameter) (spatialvi.nn.NeighborAttention.train parameter) (spatialvi.nn.SpatialAttention.train parameter) (spatialvi.nn.SpatialDecoder.train parameter) (spatialvi.nn.SpatialEncoder.train parameter) (spatialvi.train.DeconvolutionTrainingPlan.compute_and_log_metrics parameter) (spatialvi.train.DeconvolutionTrainingPlan.train parameter) (spatialvi.train.NicheTrainingPlan.compute_and_log_metrics parameter) (spatialvi.train.NicheTrainingPlan.train parameter) (spatialvi.train.SpatialTrainingPlan.compute_and_log_metrics parameter) (spatialvi.train.SpatialTrainingPlan.train parameter) model (spatialvi.external.resolvi.RESOLVAE property) model_corrected (spatialvi.external.resolvi.RESOLVAE property) model_unconditioned (spatialvi.external.resolvi.RESOLVAE property) module spatialvi.data._datasets spatialvi.data._fields spatialvi.data._preprocessing spatialvi.nn._decoders spatialvi.nn._encoders spatialvi.nn._layers spatialvi.train._callbacks spatialvi.train._training_plans spatialvi.utils._metrics spatialvi.utils._visualization module (spatialvi.module.DeconvolutionModule.add_module parameter) (spatialvi.module.DeconvolutionModule.set_submodule parameter) (spatialvi.module.NicheModule.add_module parameter) (spatialvi.module.NicheModule.set_submodule parameter) (spatialvi.module.SpatialVAEModule.add_module parameter) (spatialvi.module.SpatialVAEModule.set_submodule parameter) (spatialvi.nn.NeighborAttention.add_module parameter) (spatialvi.nn.NeighborAttention.set_submodule parameter) (spatialvi.nn.SpatialAttention.add_module parameter) (spatialvi.nn.SpatialAttention.set_submodule parameter) (spatialvi.nn.SpatialDecoder.add_module parameter) (spatialvi.nn.SpatialDecoder.set_submodule parameter) (spatialvi.nn.SpatialEncoder.add_module parameter) (spatialvi.nn.SpatialEncoder.set_submodule parameter) (spatialvi.train._training_plans.DeconvolutionTrainingPlan parameter) (spatialvi.train._training_plans.NicheTrainingPlan parameter) (spatialvi.train._training_plans.SpatialTrainingPlan parameter) (spatialvi.train.DeconvolutionTrainingPlan parameter), [1] (spatialvi.train.DeconvolutionTrainingPlan.add_module parameter) (spatialvi.train.DeconvolutionTrainingPlan.set_submodule parameter) (spatialvi.train.NicheTrainingPlan parameter), [1] (spatialvi.train.NicheTrainingPlan.add_module parameter) (spatialvi.train.NicheTrainingPlan.set_submodule parameter) (spatialvi.train.SpatialTrainingPlan parameter), [1] (spatialvi.train.SpatialTrainingPlan.add_module parameter) (spatialvi.train.SpatialTrainingPlan.set_submodule parameter) monitor (spatialvi.train._callbacks.EarlyStoppingOnSpatialLoss parameter) mp_vprior (spatialvi.external.destvi.MRDeconv parameter) MRDeconv (class in spatialvi.external.destvi) MultiScaleVIVS (class in spatialvi.external.vivs)

N

n_attention_heads (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICIModule parameter) n_batch (spatialvi.external.amici.AMICIModule parameter) (spatialvi.external.destvi.MRDeconv parameter) (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.DeconvolutionModule parameter), [1] (spatialvi.module.NicheModule parameter), [1] (spatialvi.module.SpatialVAEModule parameter), [1], [2] n_batches (spatialvi.data._datasets.synthetic_scrna parameter) (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data.synthetic_scrna parameter), [1] (spatialvi.data.synthetic_spatial parameter), [1] n_cat_list (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] (spatialvi.nn.SpatialEncoder parameter), [1] n_cats_per_cov (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.SpatialVAEModule parameter), [1], [2] n_cell_types (spatialvi.data._datasets.synthetic_scrna parameter) (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data._datasets.synthetic_visium parameter) (spatialvi.data._fields.NicheCompositionField parameter) (spatialvi.data.synthetic_scrna parameter), [1] (spatialvi.data.synthetic_spatial parameter), [1] (spatialvi.external.harreman.MetabolicExchangeScorer parameter) (spatialvi.external.starfysh.StarfyshModule parameter) (spatialvi.module.DeconvolutionModule parameter), [1] n_cells (spatialvi.data._datasets.synthetic_scrna parameter) (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data.synthetic_scrna parameter), [1] (spatialvi.data.synthetic_spatial parameter), [1] n_clusters (spatialvi.external.Nolan.get_niche_assignments parameter), [1] (spatialvi.external.nolan.NicheClusteringHead parameter) (spatialvi.external.nolan.Nolan.get_niche_assignments parameter) n_conditions (spatialvi.nn._decoders.ConditionalDecoder parameter) n_continuous_cov (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.SpatialVAEModule parameter), [1], [2] n_dims (spatialvi.nn._layers.PositionalEncoding parameter) n_epochs_kl_warmup (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) n_experts (spatialvi.nn._layers.MixedLinear parameter) n_factors (spatialvi.external.Starfysh parameter), [1] (spatialvi.external.starfysh.Starfysh parameter) (spatialvi.external.starfysh.StarfyshModule parameter) (spatialvi.nn._decoders.FactorizedDecoder parameter) n_genes (spatialvi.data._datasets.synthetic_scrna parameter) (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data._datasets.synthetic_visium parameter) (spatialvi.data.synthetic_scrna parameter), [1] (spatialvi.data.synthetic_spatial parameter), [1] (spatialvi.external.destvi.MRDeconv parameter) (spatialvi.external.harreman.HarremanModule parameter) (spatialvi.external.harreman.MetabolicExchangeScorer parameter) (spatialvi.external.starfysh.StarfyshModule parameter) (spatialvi.external.vivs.MultiScaleVIVS parameter) (spatialvi.external.vivs.VIVSModule parameter) n_heads (spatialvi.nn._encoders.AttentionEncoder parameter) (spatialvi.nn.CrossAttention parameter) (spatialvi.nn.GATLayer parameter) (spatialvi.nn.NeighborAttention parameter), [1], [2] (spatialvi.nn.SpatialAttention parameter), [1], [2] n_hidden (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICIModule parameter) (spatialvi.external.destvi.MRDeconv parameter) (spatialvi.external.harreman.MetabolicExchangeScorer parameter) (spatialvi.external.ResolVI parameter), [1] (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.resolvi.ResolVI parameter) (spatialvi.external.scVIVA parameter), [1] (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.external.scviva.scVIVA parameter) (spatialvi.external.sparl.SPARLModule parameter) (spatialvi.external.Starfysh parameter), [1] (spatialvi.external.starfysh.Starfysh parameter) (spatialvi.external.starfysh.StarfyshModule parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.DeconvolutionModule parameter), [1] (spatialvi.module.NicheModule parameter), [1] (spatialvi.module.SpatialVAEModule parameter), [1], [2] (spatialvi.nn._decoders.ConditionalDecoder parameter) (spatialvi.nn._decoders.FactorizedDecoder parameter) (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn._encoders.AttentionEncoder parameter) (spatialvi.nn._encoders.GraphEncoder parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] (spatialvi.nn.SpatialEncoder parameter), [1] n_hidden_compo (spatialvi.external.scviva.nicheVAE parameter) n_hidden_encoder (spatialvi.external.resolvi.RESOLVAE parameter) n_hidden_niche (spatialvi.external.scviva.nicheVAE parameter) n_input (spatialvi.external.amici.AMICIModule parameter) (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.DeconvolutionModule parameter), [1] (spatialvi.module.NicheModule parameter), [1] (spatialvi.module.SpatialVAEModule parameter), [1], [2] (spatialvi.nn._decoders.ConditionalDecoder parameter) (spatialvi.nn._decoders.FactorizedDecoder parameter) (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn._encoders.AttentionEncoder parameter) (spatialvi.nn._encoders.GraphEncoder parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] (spatialvi.nn.SpatialEncoder parameter), [1] n_labels (spatialvi.external.amici.AMICIModule parameter) (spatialvi.external.destvi.MRDeconv parameter) (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.NicheModule parameter), [1] n_latent (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICIModule parameter) (spatialvi.external.destvi.MRDeconv parameter) (spatialvi.external.ResolVI parameter), [1] (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.resolvi.ResolVI parameter) (spatialvi.external.scVIVA parameter), [1] (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.external.scviva.scVIVA parameter) (spatialvi.external.SPARL parameter), [1] (spatialvi.external.sparl.SPARL parameter) (spatialvi.external.sparl.SPARLModule parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.DeconvolutionModule parameter), [1] (spatialvi.module.NicheModule parameter), [1] (spatialvi.module.SpatialVAEModule parameter), [1], [2] n_latent_amortization (spatialvi.external.destvi.MRDeconv parameter) n_layers (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICIModule parameter) (spatialvi.external.destvi.MRDeconv parameter) (spatialvi.external.nolan.NolanModule parameter) (spatialvi.external.ResolVI parameter), [1] (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.resolvi.ResolVI parameter) (spatialvi.external.scVIVA parameter), [1] (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.external.scviva.scVIVA parameter) (spatialvi.external.sparl.SPARLModule parameter) (spatialvi.external.starfysh.StarfyshModule parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.DeconvolutionModule parameter), [1] (spatialvi.module.NicheModule parameter), [1] (spatialvi.module.SpatialVAEModule parameter), [1], [2] (spatialvi.nn._decoders.ConditionalDecoder parameter) (spatialvi.nn._decoders.FactorizedDecoder parameter) (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn._encoders.AttentionEncoder parameter) (spatialvi.nn._encoders.GraphEncoder parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] (spatialvi.nn.SpatialEncoder parameter), [1] n_layers_compo (spatialvi.external.scviva.nicheVAE parameter)

n_layers_niche (spatialvi.external.scviva.nicheVAE parameter) n_neighbors (spatialvi.data._fields.NeighborIndexField parameter) (spatialvi.data._preprocessing.compute_spatial_neighbors parameter) (spatialvi.data._preprocessing.filter_by_spatial_density parameter) (spatialvi.data.compute_spatial_neighbors parameter), [1] (spatialvi.external.AMICI.compute_spatial_neighbors parameter) (spatialvi.external.Harreman parameter), [1] (spatialvi.external.harreman.Harreman parameter) (spatialvi.external.harreman.HarremanModule parameter) (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.VIVS parameter), [1] (spatialvi.external.vivs.VIVS parameter) (spatialvi.model.BaseSpatialModel property) (spatialvi.model.BaseSpatialModel.compute_spatial_neighbors parameter), [1] (spatialvi.model.SpatialVAE.compute_spatial_neighbors parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn._layers.SpatialConv parameter) (spatialvi.nn.SpatialEncoder parameter), [1] (spatialvi.utils._metrics.spatial_autocorrelation parameter) (spatialvi.utils.spatial_autocorrelation parameter), [1] n_neighbors_base (spatialvi.external.vivs.VIVSModule parameter) n_niche_factors (spatialvi.module.NicheModule parameter), [1] n_obs (spatialvi.external.resolvi.RESOLVAE parameter) n_output (spatialvi.nn._decoders.ConditionalDecoder parameter) (spatialvi.nn._decoders.FactorizedDecoder parameter) (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn._encoders.AttentionEncoder parameter) (spatialvi.nn._encoders.GraphEncoder parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] (spatialvi.nn.SpatialEncoder parameter), [1] n_output_niche (spatialvi.external.scviva.nicheVAE parameter) n_permutations (spatialvi.external.Harreman.fit parameter), [1] (spatialvi.external.harreman.Harreman.fit parameter) (spatialvi.external.VIVS.fit parameter), [1] (spatialvi.external.vivs.MultiScaleVIVS.forward parameter) (spatialvi.external.vivs.VIVS.fit parameter) (spatialvi.external.vivs.VIVSModule.compute_null_distribution parameter) (spatialvi.external.vivs.VIVSModule.forward parameter) n_proteins (spatialvi.external.sparl.SPARLModule parameter) n_samples (spatialvi.external.ResolVI.get_denoised_expression parameter), [1] (spatialvi.external.resolvi.ResolVI.get_denoised_expression parameter) (spatialvi.model.BaseSpatialModel.get_normalized_expression parameter), [1] (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2] (spatialvi.module.SpatialVAEModule.inference parameter), [1], [2] (spatialvi.module.SpatialVAEModule.sample parameter), [1], [2] n_samples_augmentation (spatialvi.external.destvi.MRDeconv parameter) n_samples_mixture (spatialvi.external.scviva.nicheVAE.loss parameter) n_samples_overall (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2] n_scales (spatialvi.external.VIVS parameter), [1] (spatialvi.external.vivs.VIVS parameter) (spatialvi.external.vivs.VIVSModule parameter) n_spots (spatialvi.data._datasets.synthetic_visium parameter) (spatialvi.external.destvi.MRDeconv parameter) n_states_per_label (spatialvi.external.destvi.MRDeconv parameter) n_steps_kl_warmup (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) n_subcell_factors (spatialvi.module.DeconvolutionModule parameter), [1] n_top (spatialvi.external.VIVS.get_spatially_variable_genes parameter), [1] (spatialvi.external.vivs.VIVS.get_spatially_variable_genes parameter) n_top_genes (spatialvi.external.Lambda parameter), [1] (spatialvi.external.lambda_model.Lambda parameter) name (spatialvi.module.DeconvolutionModule.add_module parameter) (spatialvi.module.DeconvolutionModule.register_buffer parameter) (spatialvi.module.DeconvolutionModule.register_parameter parameter) (spatialvi.module.NicheModule.add_module parameter) (spatialvi.module.NicheModule.register_buffer parameter) (spatialvi.module.NicheModule.register_parameter parameter) (spatialvi.module.SpatialVAEModule.add_module parameter) (spatialvi.module.SpatialVAEModule.register_buffer parameter) (spatialvi.module.SpatialVAEModule.register_parameter parameter) (spatialvi.nn.NeighborAttention.add_module parameter) (spatialvi.nn.NeighborAttention.register_buffer parameter) (spatialvi.nn.NeighborAttention.register_parameter parameter) (spatialvi.nn.SpatialAttention.add_module parameter) (spatialvi.nn.SpatialAttention.register_buffer parameter) (spatialvi.nn.SpatialAttention.register_parameter parameter) (spatialvi.nn.SpatialDecoder.add_module parameter) (spatialvi.nn.SpatialDecoder.register_buffer parameter) (spatialvi.nn.SpatialDecoder.register_parameter parameter) (spatialvi.nn.SpatialEncoder.add_module parameter) (spatialvi.nn.SpatialEncoder.register_buffer parameter) (spatialvi.nn.SpatialEncoder.register_parameter parameter) (spatialvi.train.DeconvolutionTrainingPlan.add_module parameter) (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_buffer parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_parameter parameter) (spatialvi.train.NicheTrainingPlan.add_module parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.register_buffer parameter) (spatialvi.train.NicheTrainingPlan.register_parameter parameter) (spatialvi.train.SpatialTrainingPlan.add_module parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.register_buffer parameter) (spatialvi.train.SpatialTrainingPlan.register_parameter parameter) ncols (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils.plot_proportions parameter), [1] neighbor_dist_key (spatialvi.external.amici.AMICI.setup_anndata parameter) (spatialvi.external.AMICI.setup_anndata parameter), [1] (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] neighbor_distances (spatialvi.nn._layers.SpatialConv.forward parameter) (spatialvi.nn.NeighborAttention.forward parameter), [1], [2] neighbor_expr (spatialvi.external.amici.AMICIModule.inference parameter) (spatialvi.module.NicheModule.inference parameter), [1] (spatialvi.nn._encoders.SpatialEncoder.forward_spatial parameter) (spatialvi.nn.SpatialEncoder.forward_spatial parameter), [1] neighbor_index_key (spatialvi.external.amici.AMICI.setup_anndata parameter) (spatialvi.external.AMICI.setup_anndata parameter), [1] (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] neighbor_indices (spatialvi.external.amici.AMICIModule.inference parameter) (spatialvi.external.harreman.HarremanModule.compute_neighbor_expression parameter) (spatialvi.external.harreman.HarremanModule.forward parameter) (spatialvi.external.vivs.VIVSModule.compute_local_variance parameter) (spatialvi.external.vivs.VIVSModule.compute_null_distribution parameter) (spatialvi.external.vivs.VIVSModule.forward parameter) (spatialvi.module.NicheModule.inference parameter), [1] (spatialvi.module.SpatialVAEModule.inference parameter), [1], [2] (spatialvi.nn._encoders.SpatialEncoder.forward_spatial parameter) (spatialvi.nn._layers.SpatialConv.forward parameter) (spatialvi.nn.SpatialEncoder.forward_spatial parameter), [1] neighbor_indices_list (spatialvi.external.vivs.MultiScaleVIVS.forward parameter) neighbor_key (spatialvi.train._callbacks.NeighborSamplingCallback parameter) (spatialvi.utils._metrics.niche_purity parameter) (spatialvi.utils._metrics.spatial_mixing_score parameter) neighbor_mean (spatialvi.external.harreman.HarremanModule.compute_spatial_correlation parameter) neighbor_x (spatialvi.nn.NeighborAttention.forward parameter), [1], [2] neighbor_z (spatialvi.nn._decoders.SpatialDecoder.forward parameter) (spatialvi.nn.SpatialDecoder.forward parameter), [1] NeighborAttention (class in spatialvi.nn), [1] NeighborDistanceField (class in spatialvi.data._fields) NeighborIndexField (class in spatialvi.data._fields) NeighborSamplingCallback (class in spatialvi.train._callbacks) niche_composition (spatialvi.module.NicheModule.inference parameter), [1] niche_likelihood (spatialvi.external.scviva.nicheVAE parameter) niche_purity() (in module spatialvi.utils._metrics) niche_weight (spatialvi.train._training_plans.NicheTrainingPlan parameter) (spatialvi.train.NicheTrainingPlan parameter), [1] niche_z (spatialvi.module.NicheModule.generative parameter), [1] NicheClusteringHead (class in spatialvi.external.nolan) NicheCompositionField (class in spatialvi.data._fields) NicheModule (class in spatialvi.module) NicheTrainingPlan (class in spatialvi.train) (class in spatialvi.train._training_plans) nicheVAE (class in spatialvi.external.scviva) noise_scale (spatialvi.data._preprocessing.add_spatial_noise parameter) Nolan (class in spatialvi.external) (class in spatialvi.external.nolan) NolanModule (class in spatialvi.external.nolan) normalize (spatialvi.nn._layers.GraphConv parameter) (spatialvi.nn._layers.PositionalEncoding.forward parameter) normalize_spatial() (in module spatialvi.data._preprocessing) num_epochs (spatialvi.external.nolan.Nolan.train parameter) (spatialvi.external.Nolan.train parameter), [1] num_niches (spatialvi.external.Nolan parameter), [1] (spatialvi.external.nolan.Nolan parameter) num_parallel (spatialvi.external.Lambda parameter), [1] (spatialvi.external.lambda_model.Lambda parameter)

O

ols_ci() (spatialvi.external.ppi.PPIInference static method) (spatialvi.external.PPIInference static method) ols_pointestimate() (spatialvi.external.ppi.PPIInference static method) (spatialvi.external.PPIInference static method) OLSEstimator (class in spatialvi.external.ppi) on_epoch (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) on_step (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) on_train_batch_start() (spatialvi.train._callbacks.NeighborSamplingCallback method) on_train_epoch_end() (spatialvi.train._callbacks.SpatialMetricsCallback method) on_train_epoch_start() (spatialvi.train._callbacks.SpatialRegularizationScheduler method) (spatialvi.train._training_plans.SpatialTrainingPlan method) (spatialvi.train.SpatialTrainingPlan method) on_validation_epoch_end() (spatialvi.train._callbacks.EarlyStoppingOnSpatialLoss method) optimizer (spatialvi.train.DeconvolutionTrainingPlan.clip_gradients parameter) (spatialvi.train.DeconvolutionTrainingPlan.configure_gradient_clipping parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_before_optimizer_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_before_zero_grad parameter) (spatialvi.train.DeconvolutionTrainingPlan.optimizer_step parameter) (spatialvi.train.DeconvolutionTrainingPlan.optimizer_zero_grad parameter) (spatialvi.train.DeconvolutionTrainingPlan.toggle_optimizer parameter) (spatialvi.train.DeconvolutionTrainingPlan.toggled_optimizer parameter) (spatialvi.train.DeconvolutionTrainingPlan.untoggle_optimizer parameter) (spatialvi.train.NicheTrainingPlan.clip_gradients parameter) (spatialvi.train.NicheTrainingPlan.configure_gradient_clipping parameter) (spatialvi.train.NicheTrainingPlan.on_before_optimizer_step parameter) (spatialvi.train.NicheTrainingPlan.on_before_zero_grad parameter) (spatialvi.train.NicheTrainingPlan.optimizer_step parameter) (spatialvi.train.NicheTrainingPlan.optimizer_zero_grad parameter) (spatialvi.train.NicheTrainingPlan.toggle_optimizer parameter) (spatialvi.train.NicheTrainingPlan.toggled_optimizer parameter) (spatialvi.train.NicheTrainingPlan.untoggle_optimizer parameter) (spatialvi.train.SpatialTrainingPlan.clip_gradients parameter) (spatialvi.train.SpatialTrainingPlan.configure_gradient_clipping parameter) (spatialvi.train.SpatialTrainingPlan.on_before_optimizer_step parameter) (spatialvi.train.SpatialTrainingPlan.on_before_zero_grad parameter) (spatialvi.train.SpatialTrainingPlan.optimizer_step parameter) (spatialvi.train.SpatialTrainingPlan.optimizer_zero_grad parameter) (spatialvi.train.SpatialTrainingPlan.toggle_optimizer parameter) (spatialvi.train.SpatialTrainingPlan.toggled_optimizer parameter) (spatialvi.train.SpatialTrainingPlan.untoggle_optimizer parameter)

optimizer_closure (spatialvi.train.DeconvolutionTrainingPlan.optimizer_step parameter) (spatialvi.train.NicheTrainingPlan.optimizer_step parameter) (spatialvi.train.SpatialTrainingPlan.optimizer_step parameter) organism (spatialvi.external.Lambda parameter), [1] (spatialvi.external.lambda_model.Lambda parameter) out_channels (spatialvi.nn._layers.GraphConv parameter) (spatialvi.nn._layers.SpatialConv parameter) out_features (spatialvi.nn._layers.MixedLinear parameter) (spatialvi.nn.GATLayer parameter) output_dim (spatialvi.external.nolan.NolanModule parameter) output_dir_path (spatialvi.external.AMICI.convert_legacy_save parameter) (spatialvi.model.BaseSpatialModel.convert_legacy_save parameter) (spatialvi.model.SpatialVAE.convert_legacy_save parameter) output_format (spatialvi.train.DeconvolutionTrainingPlan.to_tensorrt parameter) (spatialvi.train.NicheTrainingPlan.to_tensorrt parameter) (spatialvi.train.SpatialTrainingPlan.to_tensorrt parameter) outputs (spatialvi.train.DeconvolutionTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_test_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_train_batch_end parameter) (spatialvi.train.DeconvolutionTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_test_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_train_batch_end parameter) (spatialvi.train.NicheTrainingPlan.on_validation_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_predict_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_test_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_train_batch_end parameter) (spatialvi.train.SpatialTrainingPlan.on_validation_batch_end parameter) overwrite (spatialvi.external.AMICI.convert_legacy_save parameter) (spatialvi.external.AMICI.save parameter) (spatialvi.model.BaseSpatialModel.convert_legacy_save parameter) (spatialvi.model.BaseSpatialModel.save parameter) (spatialvi.model.SpatialVAE.convert_legacy_save parameter) (spatialvi.model.SpatialVAE.save parameter)

P

param (spatialvi.module.DeconvolutionModule.register_parameter parameter) (spatialvi.module.NicheModule.register_parameter parameter) (spatialvi.module.SpatialVAEModule.register_parameter parameter) (spatialvi.nn.NeighborAttention.register_parameter parameter) (spatialvi.nn.SpatialAttention.register_parameter parameter) (spatialvi.nn.SpatialDecoder.register_parameter parameter) (spatialvi.nn.SpatialEncoder.register_parameter parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_parameter parameter) (spatialvi.train.NicheTrainingPlan.register_parameter parameter) (spatialvi.train.SpatialTrainingPlan.register_parameter parameter) parse_llm_response() (spatialvi.external.lambda_model.LambdaAnnotator method) patience (spatialvi.external.Starfysh.fit parameter), [1] (spatialvi.external.starfysh.Starfysh.fit parameter) (spatialvi.train._callbacks.EarlyStoppingOnSpatialLoss parameter) per_ct_bias (spatialvi.external.destvi.MRDeconv parameter) persistent (spatialvi.module.DeconvolutionModule.register_buffer parameter) (spatialvi.module.NicheModule.register_buffer parameter) (spatialvi.module.SpatialVAEModule.register_buffer parameter) (spatialvi.nn.NeighborAttention.register_buffer parameter) (spatialvi.nn.SpatialAttention.register_buffer parameter) (spatialvi.nn.SpatialDecoder.register_buffer parameter) (spatialvi.nn.SpatialEncoder.register_buffer parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_buffer parameter) (spatialvi.train.NicheTrainingPlan.register_buffer parameter) (spatialvi.train.SpatialTrainingPlan.register_buffer parameter) plan_kwargs (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) plot_interactions() (in module spatialvi.utils._visualization) plot_niche_composition() (in module spatialvi.utils._visualization) plot_proportions() (in module spatialvi.utils) (in module spatialvi.utils._visualization) plot_spatial() (in module spatialvi.utils) (in module spatialvi.utils._visualization) PositionalEncoding (class in spatialvi.nn._layers) PPIInference (class in spatialvi.external) (class in spatialvi.external.ppi) predict() (spatialvi.external.Lambda method) (spatialvi.external.lambda_model.Lambda method) (spatialvi.external.Nolan method) (spatialvi.external.nolan.Nolan method) (spatialvi.external.ResolVI method) (spatialvi.external.resolvi.ResolVI method) (spatialvi.external.SPARL method) (spatialvi.external.sparl.SPARL method) prefix (spatialvi.external.AMICI.convert_legacy_save parameter) (spatialvi.external.AMICI.load parameter) (spatialvi.external.AMICI.load_registry parameter) (spatialvi.external.AMICI.save parameter) (spatialvi.external.AMICI.view_setup_args parameter) (spatialvi.model.BaseSpatialModel.convert_legacy_save parameter) (spatialvi.model.BaseSpatialModel.load parameter) (spatialvi.model.BaseSpatialModel.load_registry parameter) (spatialvi.model.BaseSpatialModel.save parameter) (spatialvi.model.BaseSpatialModel.view_setup_args parameter) (spatialvi.model.SpatialVAE.convert_legacy_save parameter) (spatialvi.model.SpatialVAE.load parameter) (spatialvi.model.SpatialVAE.load_registry parameter) (spatialvi.model.SpatialVAE.save parameter) (spatialvi.model.SpatialVAE.view_setup_args parameter) (spatialvi.module.DeconvolutionModule.named_buffers parameter) (spatialvi.module.DeconvolutionModule.named_modules parameter) (spatialvi.module.DeconvolutionModule.named_parameters parameter) (spatialvi.module.DeconvolutionModule.state_dict parameter) (spatialvi.module.NicheModule.named_buffers parameter) (spatialvi.module.NicheModule.named_modules parameter) (spatialvi.module.NicheModule.named_parameters parameter) (spatialvi.module.NicheModule.state_dict parameter) (spatialvi.module.SpatialVAEModule.named_buffers parameter) (spatialvi.module.SpatialVAEModule.named_modules parameter) (spatialvi.module.SpatialVAEModule.named_parameters parameter) (spatialvi.module.SpatialVAEModule.state_dict parameter) (spatialvi.nn.NeighborAttention.named_buffers parameter) (spatialvi.nn.NeighborAttention.named_modules parameter) (spatialvi.nn.NeighborAttention.named_parameters parameter) (spatialvi.nn.NeighborAttention.state_dict parameter) (spatialvi.nn.SpatialAttention.named_buffers parameter) (spatialvi.nn.SpatialAttention.named_modules parameter) (spatialvi.nn.SpatialAttention.named_parameters parameter) (spatialvi.nn.SpatialAttention.state_dict parameter) (spatialvi.nn.SpatialDecoder.named_buffers parameter) (spatialvi.nn.SpatialDecoder.named_modules parameter) (spatialvi.nn.SpatialDecoder.named_parameters parameter) (spatialvi.nn.SpatialDecoder.state_dict parameter) (spatialvi.nn.SpatialEncoder.named_buffers parameter) (spatialvi.nn.SpatialEncoder.named_modules parameter) (spatialvi.nn.SpatialEncoder.named_parameters parameter) (spatialvi.nn.SpatialEncoder.state_dict parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_buffers parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_modules parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_parameters parameter) (spatialvi.train.DeconvolutionTrainingPlan.state_dict parameter) (spatialvi.train.NicheTrainingPlan.named_buffers parameter) (spatialvi.train.NicheTrainingPlan.named_modules parameter) (spatialvi.train.NicheTrainingPlan.named_parameters parameter) (spatialvi.train.NicheTrainingPlan.state_dict parameter) (spatialvi.train.SpatialTrainingPlan.named_buffers parameter) (spatialvi.train.SpatialTrainingPlan.named_modules parameter) (spatialvi.train.SpatialTrainingPlan.named_parameters parameter) (spatialvi.train.SpatialTrainingPlan.state_dict parameter)

prepare_data_per_node (spatialvi.train._training_plans.DeconvolutionTrainingPlan attribute) (spatialvi.train._training_plans.NicheTrainingPlan attribute) (spatialvi.train._training_plans.SpatialTrainingPlan attribute) prepend (spatialvi.module.DeconvolutionModule.register_forward_hook parameter) (spatialvi.module.DeconvolutionModule.register_forward_pre_hook parameter) (spatialvi.module.DeconvolutionModule.register_full_backward_hook parameter) (spatialvi.module.DeconvolutionModule.register_full_backward_pre_hook parameter) (spatialvi.module.NicheModule.register_forward_hook parameter) (spatialvi.module.NicheModule.register_forward_pre_hook parameter) (spatialvi.module.NicheModule.register_full_backward_hook parameter) (spatialvi.module.NicheModule.register_full_backward_pre_hook parameter) (spatialvi.module.SpatialVAEModule.register_forward_hook parameter) (spatialvi.module.SpatialVAEModule.register_forward_pre_hook parameter) (spatialvi.module.SpatialVAEModule.register_full_backward_hook parameter) (spatialvi.module.SpatialVAEModule.register_full_backward_pre_hook parameter) (spatialvi.nn.NeighborAttention.register_forward_hook parameter) (spatialvi.nn.NeighborAttention.register_forward_pre_hook parameter) (spatialvi.nn.NeighborAttention.register_full_backward_hook parameter) (spatialvi.nn.NeighborAttention.register_full_backward_pre_hook parameter) (spatialvi.nn.SpatialAttention.register_forward_hook parameter) (spatialvi.nn.SpatialAttention.register_forward_pre_hook parameter) (spatialvi.nn.SpatialAttention.register_full_backward_hook parameter) (spatialvi.nn.SpatialAttention.register_full_backward_pre_hook parameter) (spatialvi.nn.SpatialDecoder.register_forward_hook parameter) (spatialvi.nn.SpatialDecoder.register_forward_pre_hook parameter) (spatialvi.nn.SpatialDecoder.register_full_backward_hook parameter) (spatialvi.nn.SpatialDecoder.register_full_backward_pre_hook parameter) (spatialvi.nn.SpatialEncoder.register_forward_hook parameter) (spatialvi.nn.SpatialEncoder.register_forward_pre_hook parameter) (spatialvi.nn.SpatialEncoder.register_full_backward_hook parameter) (spatialvi.nn.SpatialEncoder.register_full_backward_pre_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_forward_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_forward_pre_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_full_backward_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_full_backward_pre_hook parameter) (spatialvi.train.NicheTrainingPlan.register_forward_hook parameter) (spatialvi.train.NicheTrainingPlan.register_forward_pre_hook parameter) (spatialvi.train.NicheTrainingPlan.register_full_backward_hook parameter) (spatialvi.train.NicheTrainingPlan.register_full_backward_pre_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_forward_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_forward_pre_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_full_backward_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_full_backward_pre_hook parameter) prior_diffusion_amount (spatialvi.external.resolvi.RESOLVAE parameter) prior_mixture (spatialvi.external.scviva.nicheVAE parameter) prior_mixture_k (spatialvi.external.scviva.nicheVAE parameter) prior_mode (spatialvi.external.destvi.MRDeconv parameter) prior_proportions_rate (spatialvi.external.resolvi.RESOLVAE parameter) prior_true_amount (spatialvi.external.resolvi.RESOLVAE parameter) prog_bar (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) project() (spatialvi.external.nolan.NolanModule method) proportions (spatialvi.external.starfysh.StarfyshModule.generative parameter) (spatialvi.module.DeconvolutionModule.generative parameter), [1] proportions_key (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils.plot_proportions parameter), [1] provider (spatialvi.external.Lambda parameter), [1] (spatialvi.external.lambda_model.Lambda parameter) px_decoder_state_dict (spatialvi.external.destvi.MRDeconv parameter) px_r (spatialvi.external.destvi.MRDeconv parameter)

Q

query (spatialvi.nn.CrossAttention.forward parameter) (spatialvi.nn.SpatialAttention.forward parameter), [1], [2]

R

rank_zero_only (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) receiver_expr (spatialvi.external.harreman.MetabolicExchangeScorer.forward parameter) receiver_type (spatialvi.external.harreman.MetabolicExchangeScorer.forward parameter) reconstruct() (spatialvi.external.SPARL method) (spatialvi.external.sparl.SPARL method) recurse (spatialvi.module.DeconvolutionModule.buffers parameter) (spatialvi.module.DeconvolutionModule.named_buffers parameter) (spatialvi.module.DeconvolutionModule.named_parameters parameter) (spatialvi.module.DeconvolutionModule.parameters parameter) (spatialvi.module.DeconvolutionModule.to_empty parameter) (spatialvi.module.NicheModule.buffers parameter) (spatialvi.module.NicheModule.named_buffers parameter) (spatialvi.module.NicheModule.named_parameters parameter) (spatialvi.module.NicheModule.parameters parameter) (spatialvi.module.NicheModule.to_empty parameter) (spatialvi.module.SpatialVAEModule.buffers parameter) (spatialvi.module.SpatialVAEModule.named_buffers parameter) (spatialvi.module.SpatialVAEModule.named_parameters parameter) (spatialvi.module.SpatialVAEModule.parameters parameter) (spatialvi.module.SpatialVAEModule.to_empty parameter) (spatialvi.nn.NeighborAttention.buffers parameter) (spatialvi.nn.NeighborAttention.named_buffers parameter) (spatialvi.nn.NeighborAttention.named_parameters parameter) (spatialvi.nn.NeighborAttention.parameters parameter) (spatialvi.nn.NeighborAttention.to_empty parameter) (spatialvi.nn.SpatialAttention.buffers parameter) (spatialvi.nn.SpatialAttention.named_buffers parameter) (spatialvi.nn.SpatialAttention.named_parameters parameter) (spatialvi.nn.SpatialAttention.parameters parameter) (spatialvi.nn.SpatialAttention.to_empty parameter) (spatialvi.nn.SpatialDecoder.buffers parameter) (spatialvi.nn.SpatialDecoder.named_buffers parameter) (spatialvi.nn.SpatialDecoder.named_parameters parameter) (spatialvi.nn.SpatialDecoder.parameters parameter) (spatialvi.nn.SpatialDecoder.to_empty parameter) (spatialvi.nn.SpatialEncoder.buffers parameter) (spatialvi.nn.SpatialEncoder.named_buffers parameter) (spatialvi.nn.SpatialEncoder.named_parameters parameter) (spatialvi.nn.SpatialEncoder.parameters parameter) (spatialvi.nn.SpatialEncoder.to_empty parameter) (spatialvi.train.DeconvolutionTrainingPlan.buffers parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_buffers parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_parameters parameter) (spatialvi.train.DeconvolutionTrainingPlan.parameters parameter) (spatialvi.train.DeconvolutionTrainingPlan.to_empty parameter) (spatialvi.train.NicheTrainingPlan.buffers parameter) (spatialvi.train.NicheTrainingPlan.named_buffers parameter) (spatialvi.train.NicheTrainingPlan.named_parameters parameter) (spatialvi.train.NicheTrainingPlan.parameters parameter) (spatialvi.train.NicheTrainingPlan.to_empty parameter) (spatialvi.train.SpatialTrainingPlan.buffers parameter) (spatialvi.train.SpatialTrainingPlan.named_buffers parameter) (spatialvi.train.SpatialTrainingPlan.named_parameters parameter) (spatialvi.train.SpatialTrainingPlan.parameters parameter) (spatialvi.train.SpatialTrainingPlan.to_empty parameter) reduce_fx (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) reference_weight (spatialvi.train._training_plans.DeconvolutionTrainingPlan parameter) (spatialvi.train.DeconvolutionTrainingPlan parameter), [1] registry (spatialvi.external.AMICI.view_setup_method_args parameter) (spatialvi.model.BaseSpatialModel.view_setup_method_args parameter) (spatialvi.model.SpatialVAE.view_setup_method_args parameter) registry_key (spatialvi.data._fields.NeighborDistanceField parameter) (spatialvi.data._fields.NeighborIndexField parameter) (spatialvi.data._fields.NicheCompositionField parameter) (spatialvi.data._fields.SpatialCoordinatesField parameter) (spatialvi.external.AMICI.data_registry parameter) (spatialvi.external.AMICI.get_from_registry parameter) (spatialvi.model.BaseSpatialModel.data_registry parameter) (spatialvi.model.BaseSpatialModel.get_from_registry parameter) (spatialvi.model.SpatialVAE.data_registry parameter) (spatialvi.model.SpatialVAE.get_from_registry parameter)

remove_duplicate (spatialvi.module.DeconvolutionModule.named_buffers parameter) (spatialvi.module.DeconvolutionModule.named_modules parameter) (spatialvi.module.DeconvolutionModule.named_parameters parameter) (spatialvi.module.NicheModule.named_buffers parameter) (spatialvi.module.NicheModule.named_modules parameter) (spatialvi.module.NicheModule.named_parameters parameter) (spatialvi.module.SpatialVAEModule.named_buffers parameter) (spatialvi.module.SpatialVAEModule.named_modules parameter) (spatialvi.module.SpatialVAEModule.named_parameters parameter) (spatialvi.nn.NeighborAttention.named_buffers parameter) (spatialvi.nn.NeighborAttention.named_modules parameter) (spatialvi.nn.NeighborAttention.named_parameters parameter) (spatialvi.nn.SpatialAttention.named_buffers parameter) (spatialvi.nn.SpatialAttention.named_modules parameter) (spatialvi.nn.SpatialAttention.named_parameters parameter) (spatialvi.nn.SpatialDecoder.named_buffers parameter) (spatialvi.nn.SpatialDecoder.named_modules parameter) (spatialvi.nn.SpatialDecoder.named_parameters parameter) (spatialvi.nn.SpatialEncoder.named_buffers parameter) (spatialvi.nn.SpatialEncoder.named_modules parameter) (spatialvi.nn.SpatialEncoder.named_parameters parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_buffers parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_modules parameter) (spatialvi.train.DeconvolutionTrainingPlan.named_parameters parameter) (spatialvi.train.NicheTrainingPlan.named_buffers parameter) (spatialvi.train.NicheTrainingPlan.named_modules parameter) (spatialvi.train.NicheTrainingPlan.named_parameters parameter) (spatialvi.train.SpatialTrainingPlan.named_buffers parameter) (spatialvi.train.SpatialTrainingPlan.named_modules parameter) (spatialvi.train.SpatialTrainingPlan.named_parameters parameter) required (spatialvi.external.AMICI.get_anndata_manager parameter) (spatialvi.model.BaseSpatialModel.get_anndata_manager parameter) (spatialvi.model.SpatialVAE.get_anndata_manager parameter) requires_grad (spatialvi.module.DeconvolutionModule.requires_grad_ parameter) (spatialvi.module.NicheModule.requires_grad_ parameter) (spatialvi.module.SpatialVAEModule.requires_grad_ parameter) (spatialvi.nn.NeighborAttention.requires_grad_ parameter) (spatialvi.nn.SpatialAttention.requires_grad_ parameter) (spatialvi.nn.SpatialDecoder.requires_grad_ parameter) (spatialvi.nn.SpatialEncoder.requires_grad_ parameter) (spatialvi.train.DeconvolutionTrainingPlan.requires_grad_ parameter) (spatialvi.train.NicheTrainingPlan.requires_grad_ parameter) (spatialvi.train.SpatialTrainingPlan.requires_grad_ parameter) reset_parameters() (spatialvi.nn._layers.GraphConv method) (spatialvi.nn._layers.MixedLinear method) resolution (spatialvi.external.Lambda parameter), [1] (spatialvi.external.lambda_model.Lambda parameter) (spatialvi.external.Nolan.get_niche_assignments parameter), [1] (spatialvi.external.nolan.Nolan.get_niche_assignments parameter) RESOLVAE (class in spatialvi.external.resolvi) ResolVI (class in spatialvi.external) (class in spatialvi.external.resolvi) response (spatialvi.external.lambda_model.LambdaAnnotator.parse_llm_response parameter) results (spatialvi.external.lambda_model.LambdaAnnotator property) retrace (spatialvi.train.DeconvolutionTrainingPlan.to_tensorrt parameter) (spatialvi.train.NicheTrainingPlan.to_tensorrt parameter) (spatialvi.train.SpatialTrainingPlan.to_tensorrt parameter) return_attention_weights (spatialvi.external.amici.AMICI.get_interaction_scores parameter) (spatialvi.external.AMICI.get_interaction_scores parameter), [1] return_dataframe (spatialvi.external.destvi.DestVI.get_proportions parameter) (spatialvi.external.DestVI.get_proportions parameter), [1] (spatialvi.external.Starfysh.get_proportions parameter), [1] (spatialvi.external.starfysh.Starfysh.get_proportions parameter) return_mean (spatialvi.model.BaseSpatialModel.get_normalized_expression parameter), [1] (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2] return_numpy (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2]

S

sample() (spatialvi.module.SpatialVAEModule method), [1] save() (spatialvi.external.DestVI method) (spatialvi.external.destvi.DestVI method) (spatialvi.external.ResolVI method) (spatialvi.external.resolvi.ResolVI method) (spatialvi.external.scVIVA method) (spatialvi.external.scviva.scVIVA method) save_anndata (spatialvi.external.AMICI.save parameter) (spatialvi.model.BaseSpatialModel.save parameter) (spatialvi.model.SpatialVAE.save parameter) save_kwargs (spatialvi.external.AMICI.save parameter) (spatialvi.model.BaseSpatialModel.save parameter) (spatialvi.model.SpatialVAE.save parameter) sc_model (spatialvi.external.DestVI parameter), [1] (spatialvi.external.destvi.DestVI parameter) (spatialvi.external.destvi.DestVI.from_rna_model parameter) (spatialvi.external.DestVI.from_rna_model parameter), [1] scale_scores (spatialvi.external.vivs.MultiScaleVIVS.aggregate_scores parameter) scales (spatialvi.external.vivs.MultiScaleVIVS parameter) schedule (spatialvi.train._callbacks.SpatialRegularizationScheduler parameter) scheduler (spatialvi.train.DeconvolutionTrainingPlan.lr_scheduler_step parameter) (spatialvi.train.NicheTrainingPlan.lr_scheduler_step parameter) (spatialvi.train.SpatialTrainingPlan.lr_scheduler_step parameter) scVIVA (class in spatialvi.external) (class in spatialvi.external.scviva) seed (spatialvi.data._datasets.synthetic_scrna parameter) (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data._datasets.synthetic_visium parameter) (spatialvi.data._preprocessing.add_spatial_noise parameter) (spatialvi.data.synthetic_scrna parameter), [1] (spatialvi.data.synthetic_spatial parameter), [1] semisupervised (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) sender_expr (spatialvi.external.harreman.MetabolicExchangeScorer.forward parameter) sender_type (spatialvi.external.harreman.MetabolicExchangeScorer.forward parameter) set_to_none (spatialvi.module.DeconvolutionModule.zero_grad parameter) (spatialvi.module.NicheModule.zero_grad parameter) (spatialvi.module.SpatialVAEModule.zero_grad parameter) (spatialvi.nn.NeighborAttention.zero_grad parameter) (spatialvi.nn.SpatialAttention.zero_grad parameter) (spatialvi.nn.SpatialDecoder.zero_grad parameter) (spatialvi.nn.SpatialEncoder.zero_grad parameter) (spatialvi.train.DeconvolutionTrainingPlan.zero_grad parameter) (spatialvi.train.NicheTrainingPlan.zero_grad parameter) (spatialvi.train.SpatialTrainingPlan.zero_grad parameter) setup_anndata() (spatialvi.external.AMICI class method) (spatialvi.external.amici.AMICI class method) (spatialvi.external.DestVI class method) (spatialvi.external.destvi.DestVI class method) (spatialvi.external.ResolVI class method) (spatialvi.external.resolvi.ResolVI class method) (spatialvi.external.scVIVA class method) (spatialvi.external.scviva.scVIVA class method) (spatialvi.model.SpatialVAE class method), [1] setup_method_args (spatialvi.external.AMICI.update_setup_method_args parameter) (spatialvi.model.BaseSpatialModel.update_setup_method_args parameter) (spatialvi.model.SpatialVAE.update_setup_method_args parameter) show (spatialvi.utils._visualization.plot_interactions parameter) (spatialvi.utils._visualization.plot_niche_composition parameter) (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_proportions parameter), [1] (spatialvi.utils.plot_spatial parameter), [1] shuffle_set_split (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) silhouette_spatial() (in module spatialvi.utils._metrics) size (spatialvi.utils._visualization.plot_niche_composition parameter) (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_proportions parameter), [1] (spatialvi.utils.plot_spatial parameter), [1] size_factor (spatialvi.external.scviva.nicheVAE.generative parameter) size_factor_key (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] soft_assignment (spatialvi.external.nolan.NicheClusteringHead parameter) SPARL (class in spatialvi.external) (class in spatialvi.external.sparl) SPARLModule (class in spatialvi.external.sparl) sparsity_diffusion (spatialvi.external.resolvi.RESOLVAE parameter) sparsity_weight (spatialvi.train._training_plans.DeconvolutionTrainingPlan parameter) (spatialvi.train.DeconvolutionTrainingPlan parameter), [1] spatial (spatialvi.external.sparl.SPARLModule.inference parameter) spatial_autocorrelation() (in module spatialvi.utils) (in module spatialvi.utils._metrics) spatial_coords (spatialvi.module.SpatialVAEModule.inference parameter), [1], [2] (spatialvi.nn._encoders.SpatialEncoder.forward_spatial parameter) (spatialvi.nn.SpatialEncoder.forward_spatial parameter), [1] spatial_dim (spatialvi.external.sparl.SPARLModule parameter) spatial_dims (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data.synthetic_spatial parameter), [1] spatial_hidden (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialEncoder parameter), [1] spatial_key (spatialvi.data._preprocessing.add_spatial_noise parameter) (spatialvi.data._preprocessing.compute_spatial_neighbors parameter) (spatialvi.data._preprocessing.filter_by_spatial_density parameter) (spatialvi.data._preprocessing.normalize_spatial parameter) (spatialvi.data.compute_spatial_neighbors parameter), [1] (spatialvi.external.amici.AMICI.setup_anndata parameter) (spatialvi.external.AMICI.compute_spatial_neighbors parameter) (spatialvi.external.AMICI.get_spatial_coordinates parameter) (spatialvi.external.AMICI.setup_anndata parameter), [1] (spatialvi.external.Harreman parameter), [1] (spatialvi.external.harreman.Harreman parameter) (spatialvi.external.Nolan parameter), [1] (spatialvi.external.nolan.Nolan parameter) (spatialvi.external.resolvi.ResolVI.setup_anndata parameter) (spatialvi.external.ResolVI.setup_anndata parameter), [1] (spatialvi.external.scviva.scVIVA.setup_anndata parameter) (spatialvi.external.scVIVA.setup_anndata parameter), [1] (spatialvi.external.SPARL parameter), [1] (spatialvi.external.sparl.SPARL parameter) (spatialvi.external.Starfysh parameter), [1] (spatialvi.external.starfysh.Starfysh parameter) (spatialvi.external.VIVS parameter), [1] (spatialvi.external.vivs.VIVS parameter) (spatialvi.model.BaseSpatialModel property) (spatialvi.model.BaseSpatialModel.compute_spatial_neighbors parameter), [1] (spatialvi.model.SpatialVAE.compute_spatial_neighbors parameter) (spatialvi.model.SpatialVAE.get_spatial_coordinates parameter) (spatialvi.model.SpatialVAE.setup_anndata parameter), [1], [2] (spatialvi.utils._metrics.silhouette_spatial parameter) (spatialvi.utils._metrics.spatial_autocorrelation parameter) (spatialvi.utils._visualization.plot_niche_composition parameter) (spatialvi.utils._visualization.plot_proportions parameter) (spatialvi.utils._visualization.plot_spatial parameter) (spatialvi.utils.plot_proportions parameter), [1] (spatialvi.utils.plot_spatial parameter), [1] (spatialvi.utils.spatial_autocorrelation parameter), [1] spatial_mixing_score() (in module spatialvi.utils._metrics)

spatial_scale (spatialvi.data._datasets.synthetic_spatial parameter) (spatialvi.data.synthetic_spatial parameter), [1] spatial_warmup_epochs (spatialvi.train._training_plans.SpatialTrainingPlan parameter) (spatialvi.train.SpatialTrainingPlan parameter), [1] spatial_weight (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.SpatialVAEModule parameter), [1], [2] (spatialvi.train._training_plans.SpatialTrainingPlan parameter) (spatialvi.train.SpatialTrainingPlan parameter), [1] SpatialAttention (class in spatialvi.nn), [1] SpatialConv (class in spatialvi.nn._layers) SpatialCoordinatesField (class in spatialvi.data._fields) SpatialDecoder (class in spatialvi.nn) (class in spatialvi.nn._decoders) SpatialEncoder (class in spatialvi.nn) (class in spatialvi.nn._encoders) SpatialMetricsCallback (class in spatialvi.train._callbacks) SpatialRegularizationScheduler (class in spatialvi.train._callbacks) SpatialTrainingPlan (class in spatialvi.train) (class in spatialvi.train._training_plans) SpatialVAE (class in spatialvi.model), [1] SpatialVAEModule (class in spatialvi.module), [1] spatialvi.data._datasets module spatialvi.data._fields module spatialvi.data._preprocessing module spatialvi.nn._decoders module spatialvi.nn._encoders module spatialvi.nn._layers module spatialvi.train._callbacks module spatialvi.train._training_plans module spatialvi.utils._metrics module spatialvi.utils._visualization module st_adata (spatialvi.external.DestVI parameter), [1] (spatialvi.external.destvi.DestVI parameter) (spatialvi.external.destvi.DestVI.from_rna_model parameter) (spatialvi.external.DestVI.from_rna_model parameter), [1] stage (spatialvi.train.DeconvolutionTrainingPlan.setup parameter) (spatialvi.train.DeconvolutionTrainingPlan.teardown parameter) (spatialvi.train.NicheTrainingPlan.setup parameter) (spatialvi.train.NicheTrainingPlan.teardown parameter) (spatialvi.train.SpatialTrainingPlan.setup parameter) (spatialvi.train.SpatialTrainingPlan.teardown parameter) Starfysh (class in spatialvi.external) (class in spatialvi.external.starfysh) StarfyshModule (class in spatialvi.external.starfysh) state (spatialvi.module.DeconvolutionModule.set_extra_state parameter) (spatialvi.module.NicheModule.set_extra_state parameter) (spatialvi.module.SpatialVAEModule.set_extra_state parameter) (spatialvi.nn.NeighborAttention.set_extra_state parameter) (spatialvi.nn.SpatialAttention.set_extra_state parameter) (spatialvi.nn.SpatialDecoder.set_extra_state parameter) (spatialvi.nn.SpatialEncoder.set_extra_state parameter) (spatialvi.train.DeconvolutionTrainingPlan.set_extra_state parameter) (spatialvi.train.NicheTrainingPlan.set_extra_state parameter) (spatialvi.train.SpatialTrainingPlan.set_extra_state parameter) state_dict (spatialvi.module.DeconvolutionModule.load_state_dict parameter) (spatialvi.module.NicheModule.load_state_dict parameter) (spatialvi.module.SpatialVAEModule.load_state_dict parameter) (spatialvi.nn.NeighborAttention.load_state_dict parameter) (spatialvi.nn.SpatialAttention.load_state_dict parameter) (spatialvi.nn.SpatialDecoder.load_state_dict parameter) (spatialvi.nn.SpatialEncoder.load_state_dict parameter) (spatialvi.train.DeconvolutionTrainingPlan.load_state_dict parameter) (spatialvi.train.NicheTrainingPlan.load_state_dict parameter) (spatialvi.train.SpatialTrainingPlan.load_state_dict parameter) store_key (spatialvi.external.Nolan.get_niche_assignments parameter), [1] (spatialvi.external.nolan.Nolan.get_niche_assignments parameter) (spatialvi.external.nolan.Nolan.predict parameter) (spatialvi.external.Nolan.predict parameter), [1] (spatialvi.external.SPARL.predict parameter), [1] (spatialvi.external.sparl.SPARL.predict parameter) store_key_prefix (spatialvi.external.Lambda.predict parameter), [1] (spatialvi.external.lambda_model.Lambda.predict parameter) store_layer (spatialvi.external.SPARL.impute_proteins parameter), [1] (spatialvi.external.sparl.SPARL.impute_proteins parameter) strict (spatialvi.module.DeconvolutionModule.load_state_dict parameter) (spatialvi.module.DeconvolutionModule.set_submodule parameter) (spatialvi.module.NicheModule.load_state_dict parameter) (spatialvi.module.NicheModule.set_submodule parameter) (spatialvi.module.SpatialVAEModule.load_state_dict parameter) (spatialvi.module.SpatialVAEModule.set_submodule parameter) (spatialvi.nn.NeighborAttention.load_state_dict parameter) (spatialvi.nn.NeighborAttention.set_submodule parameter) (spatialvi.nn.SpatialAttention.load_state_dict parameter) (spatialvi.nn.SpatialAttention.set_submodule parameter) (spatialvi.nn.SpatialDecoder.load_state_dict parameter) (spatialvi.nn.SpatialDecoder.set_submodule parameter) (spatialvi.nn.SpatialEncoder.load_state_dict parameter) (spatialvi.nn.SpatialEncoder.set_submodule parameter) (spatialvi.train.DeconvolutionTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.DeconvolutionTrainingPlan.load_state_dict parameter) (spatialvi.train.DeconvolutionTrainingPlan.set_submodule parameter) (spatialvi.train.NicheTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.NicheTrainingPlan.load_state_dict parameter) (spatialvi.train.NicheTrainingPlan.set_submodule parameter) (spatialvi.train.SpatialTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.SpatialTrainingPlan.load_state_dict parameter) (spatialvi.train.SpatialTrainingPlan.set_submodule parameter) subcell_factors (spatialvi.module.DeconvolutionModule.generative parameter), [1] sync_dist (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) sync_dist_group (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.DeconvolutionTrainingPlan.log_dict parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log_dict parameter) (spatialvi.train.SpatialTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log_dict parameter) sync_grads (spatialvi.train.DeconvolutionTrainingPlan.all_gather parameter) (spatialvi.train.NicheTrainingPlan.all_gather parameter) (spatialvi.train.SpatialTrainingPlan.all_gather parameter) synthetic_scrna() (in module spatialvi.data) (in module spatialvi.data._datasets) synthetic_spatial() (in module spatialvi.data) (in module spatialvi.data._datasets) synthetic_visium() (in module spatialvi.data._datasets)

T

target (spatialvi.module.DeconvolutionModule.get_buffer parameter) (spatialvi.module.DeconvolutionModule.get_parameter parameter) (spatialvi.module.DeconvolutionModule.get_submodule parameter) (spatialvi.module.DeconvolutionModule.set_submodule parameter) (spatialvi.module.NicheModule.get_buffer parameter) (spatialvi.module.NicheModule.get_parameter parameter) (spatialvi.module.NicheModule.get_submodule parameter) (spatialvi.module.NicheModule.set_submodule parameter) (spatialvi.module.SpatialVAEModule.get_buffer parameter) (spatialvi.module.SpatialVAEModule.get_parameter parameter) (spatialvi.module.SpatialVAEModule.get_submodule parameter) (spatialvi.module.SpatialVAEModule.set_submodule parameter) (spatialvi.nn.NeighborAttention.get_buffer parameter) (spatialvi.nn.NeighborAttention.get_parameter parameter) (spatialvi.nn.NeighborAttention.get_submodule parameter) (spatialvi.nn.NeighborAttention.set_submodule parameter) (spatialvi.nn.SpatialAttention.get_buffer parameter) (spatialvi.nn.SpatialAttention.get_parameter parameter) (spatialvi.nn.SpatialAttention.get_submodule parameter) (spatialvi.nn.SpatialAttention.set_submodule parameter) (spatialvi.nn.SpatialDecoder.get_buffer parameter) (spatialvi.nn.SpatialDecoder.get_parameter parameter) (spatialvi.nn.SpatialDecoder.get_submodule parameter) (spatialvi.nn.SpatialDecoder.set_submodule parameter) (spatialvi.nn.SpatialEncoder.get_buffer parameter) (spatialvi.nn.SpatialEncoder.get_parameter parameter) (spatialvi.nn.SpatialEncoder.get_submodule parameter) (spatialvi.nn.SpatialEncoder.set_submodule parameter) (spatialvi.train.DeconvolutionTrainingPlan.get_buffer parameter) (spatialvi.train.DeconvolutionTrainingPlan.get_parameter parameter) (spatialvi.train.DeconvolutionTrainingPlan.get_submodule parameter) (spatialvi.train.DeconvolutionTrainingPlan.set_submodule parameter) (spatialvi.train.NicheTrainingPlan.get_buffer parameter) (spatialvi.train.NicheTrainingPlan.get_parameter parameter) (spatialvi.train.NicheTrainingPlan.get_submodule parameter) (spatialvi.train.NicheTrainingPlan.set_submodule parameter) (spatialvi.train.SpatialTrainingPlan.get_buffer parameter) (spatialvi.train.SpatialTrainingPlan.get_parameter parameter) (spatialvi.train.SpatialTrainingPlan.get_submodule parameter) (spatialvi.train.SpatialTrainingPlan.set_submodule parameter) temperature (spatialvi.external.nolan.NolanModule parameter) tensor (spatialvi.module.DeconvolutionModule.register_buffer parameter) (spatialvi.module.DeconvolutionModule.to parameter) (spatialvi.module.NicheModule.register_buffer parameter) (spatialvi.module.NicheModule.to parameter) (spatialvi.module.SpatialVAEModule.register_buffer parameter) (spatialvi.module.SpatialVAEModule.to parameter) (spatialvi.nn.NeighborAttention.register_buffer parameter) (spatialvi.nn.NeighborAttention.to parameter) (spatialvi.nn.SpatialAttention.register_buffer parameter) (spatialvi.nn.SpatialAttention.to parameter) (spatialvi.nn.SpatialDecoder.register_buffer parameter) (spatialvi.nn.SpatialDecoder.to parameter) (spatialvi.nn.SpatialEncoder.register_buffer parameter) (spatialvi.nn.SpatialEncoder.to parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_buffer parameter) (spatialvi.train.NicheTrainingPlan.register_buffer parameter) (spatialvi.train.SpatialTrainingPlan.register_buffer parameter)

tensors (spatialvi.external.amici.AMICIModule.loss parameter) (spatialvi.external.destvi.MRDeconv.loss parameter) (spatialvi.external.scviva.nicheVAE.loss parameter) (spatialvi.external.sparl.SPARLModule.loss parameter) (spatialvi.external.starfysh.StarfyshModule.loss parameter) (spatialvi.module.DeconvolutionModule.forward parameter) (spatialvi.module.DeconvolutionModule.get_cell_type_expression parameter), [1] (spatialvi.module.DeconvolutionModule.loss parameter), [1] (spatialvi.module.NicheModule.forward parameter) (spatialvi.module.NicheModule.loss parameter), [1] (spatialvi.module.SpatialVAEModule.forward parameter) (spatialvi.module.SpatialVAEModule.loss parameter), [1], [2] (spatialvi.module.SpatialVAEModule.sample parameter), [1], [2] to_adata() (spatialvi.external.Harreman method) (spatialvi.external.harreman.Harreman method) (spatialvi.external.Starfysh method) (spatialvi.external.starfysh.Starfysh method) (spatialvi.external.VIVS method) (spatialvi.external.vivs.VIVS method) train() (spatialvi.external.DestVI method) (spatialvi.external.destvi.DestVI method) (spatialvi.external.Lambda method) (spatialvi.external.lambda_model.Lambda method) (spatialvi.external.Nolan method) (spatialvi.external.nolan.Nolan method) (spatialvi.external.ResolVI method) (spatialvi.external.resolvi.ResolVI method) (spatialvi.external.scVIVA method) (spatialvi.external.scviva.scVIVA method) (spatialvi.external.SPARL method) (spatialvi.external.sparl.SPARL method) train_size (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) training (spatialvi.module.SpatialVAEModule attribute) (spatialvi.nn._decoders.SpatialDecoder attribute) (spatialvi.nn._encoders.SpatialEncoder attribute) (spatialvi.nn.NeighborAttention attribute) (spatialvi.nn.SpatialAttention attribute) (spatialvi.train._training_plans.DeconvolutionTrainingPlan attribute) (spatialvi.train._training_plans.NicheTrainingPlan attribute) (spatialvi.train._training_plans.SpatialTrainingPlan attribute) training_step() (spatialvi.train._training_plans.DeconvolutionTrainingPlan method) (spatialvi.train._training_plans.NicheTrainingPlan method) (spatialvi.train._training_plans.SpatialTrainingPlan method) (spatialvi.train.DeconvolutionTrainingPlan method) (spatialvi.train.NicheTrainingPlan method) (spatialvi.train.SpatialTrainingPlan method) transform_batch (spatialvi.external.scviva.nicheVAE.generative parameter) (spatialvi.model.BaseSpatialModel.get_normalized_expression parameter), [1] (spatialvi.model.SpatialVAE.get_normalized_expression parameter), [1], [2]

U

use_attention (spatialvi.module.NicheModule parameter), [1] use_batch_norm (spatialvi.external.nolan.NolanModule parameter) (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.SpatialVAEModule parameter), [1], [2] (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] (spatialvi.nn.SpatialEncoder parameter), [1] use_cell_type_attention (spatialvi.external.AMICI parameter), [1] (spatialvi.external.amici.AMICI parameter) (spatialvi.external.amici.AMICIModule parameter) use_distance_weights (spatialvi.nn.NeighborAttention parameter), [1], [2] use_edge_features (spatialvi.nn._layers.SpatialConv parameter) use_gpu (spatialvi.external.VIVS.fit parameter), [1] (spatialvi.external.vivs.VIVS.fit parameter) (spatialvi.external.vivs.VIVSModule parameter) use_histology (spatialvi.external.Starfysh parameter), [1] (spatialvi.external.starfysh.Starfysh parameter) (spatialvi.external.starfysh.StarfyshModule parameter)

use_layer_norm (spatialvi.external.resolvi.RESOLVAE parameter) (spatialvi.external.scviva.nicheVAE parameter) (spatialvi.module.SpatialVAEModule parameter), [1], [2] (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn._encoders.SpatialEncoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] (spatialvi.nn.SpatialEncoder parameter), [1] use_observed_lib_size (spatialvi.external.scviva.nicheVAE parameter) use_pl_optimizer (spatialvi.train.DeconvolutionTrainingPlan.optimizers parameter) (spatialvi.train.NicheTrainingPlan.optimizers parameter) (spatialvi.train.SpatialTrainingPlan.optimizers parameter) use_size_factor_key (spatialvi.external.scviva.nicheVAE parameter) use_spatial (spatialvi.external.sparl.SPARLModule parameter) (spatialvi.model.SpatialVAE parameter), [1], [2] (spatialvi.module.SpatialVAEModule parameter), [1], [2] use_spatial_context (spatialvi.nn._decoders.SpatialDecoder parameter) (spatialvi.nn.SpatialDecoder parameter), [1] use_subcell_variation (spatialvi.module.DeconvolutionModule parameter), [1]

V

v (spatialvi.external.destvi.MRDeconv.generative parameter) validate_field() (spatialvi.data._fields.NeighborDistanceField method) (spatialvi.data._fields.NeighborIndexField method) (spatialvi.data._fields.NicheCompositionField method) (spatialvi.data._fields.SpatialCoordinatesField method) validation_size (spatialvi.external.AMICI.train parameter) (spatialvi.model.SpatialVAE.train parameter) value (spatialvi.nn.SpatialAttention.forward parameter), [1], [2] (spatialvi.train.DeconvolutionTrainingPlan.log parameter) (spatialvi.train.NicheTrainingPlan.log parameter) (spatialvi.train.SpatialTrainingPlan.log parameter)

values (spatialvi.utils._metrics.compute_gearys_c parameter) (spatialvi.utils._metrics.compute_morans_i parameter) var_activation (spatialvi.external.resolvi.RESOLVAE parameter) var_names (spatialvi.utils._metrics.spatial_autocorrelation parameter) (spatialvi.utils.spatial_autocorrelation parameter), [1] var_vprior (spatialvi.external.destvi.MRDeconv parameter) VIVS (class in spatialvi.external) (class in spatialvi.external.vivs) VIVSModule (class in spatialvi.external.vivs) vmax (spatialvi.utils._visualization.plot_interactions parameter) vmin (spatialvi.utils._visualization.plot_interactions parameter)

W

warmup_epochs (spatialvi.train._callbacks.SpatialRegularizationScheduler parameter) weight_decay (spatialvi.train._training_plans.SpatialTrainingPlan parameter) (spatialvi.train.SpatialTrainingPlan parameter), [1] weights (spatialvi.utils._metrics.compute_gearys_c parameter) (spatialvi.utils._metrics.compute_morans_i parameter) weights_only (spatialvi.train.DeconvolutionTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.NicheTrainingPlan.load_from_checkpoint parameter) (spatialvi.train.SpatialTrainingPlan.load_from_checkpoint parameter) with_kwargs (spatialvi.module.DeconvolutionModule.register_forward_hook parameter) (spatialvi.module.DeconvolutionModule.register_forward_pre_hook parameter) (spatialvi.module.NicheModule.register_forward_hook parameter) (spatialvi.module.NicheModule.register_forward_pre_hook parameter) (spatialvi.module.SpatialVAEModule.register_forward_hook parameter) (spatialvi.module.SpatialVAEModule.register_forward_pre_hook parameter) (spatialvi.nn.NeighborAttention.register_forward_hook parameter) (spatialvi.nn.NeighborAttention.register_forward_pre_hook parameter) (spatialvi.nn.SpatialAttention.register_forward_hook parameter) (spatialvi.nn.SpatialAttention.register_forward_pre_hook parameter) (spatialvi.nn.SpatialDecoder.register_forward_hook parameter) (spatialvi.nn.SpatialDecoder.register_forward_pre_hook parameter) (spatialvi.nn.SpatialEncoder.register_forward_hook parameter) (spatialvi.nn.SpatialEncoder.register_forward_pre_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_forward_hook parameter) (spatialvi.train.DeconvolutionTrainingPlan.register_forward_pre_hook parameter) (spatialvi.train.NicheTrainingPlan.register_forward_hook parameter) (spatialvi.train.NicheTrainingPlan.register_forward_pre_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_forward_hook parameter) (spatialvi.train.SpatialTrainingPlan.register_forward_pre_hook parameter)

X

x (spatialvi.external.amici.AMICIModule.inference parameter) (spatialvi.external.destvi.MRDeconv.generative parameter) (spatialvi.external.destvi.MRDeconv.get_proportions parameter) (spatialvi.external.destvi.MRDeconv.inference parameter) X (spatialvi.external.harreman.HarremanModule.compute_neighbor_expression parameter) (spatialvi.external.harreman.HarremanModule.compute_spatial_correlation parameter) (spatialvi.external.harreman.HarremanModule.forward parameter) x (spatialvi.external.nolan.NolanModule.encode parameter) (spatialvi.external.nolan.NolanModule.forward parameter) X (spatialvi.external.ppi.PPIInference.ols_ci parameter) (spatialvi.external.ppi.PPIInference.ols_pointestimate parameter) (spatialvi.external.PPIInference.ols_ci parameter), [1] (spatialvi.external.PPIInference.ols_pointestimate parameter), [1] x (spatialvi.external.sparl.SPARLModule.inference parameter) (spatialvi.external.starfysh.StarfyshModule.inference parameter) X (spatialvi.external.vivs.MultiScaleVIVS.forward parameter) (spatialvi.external.vivs.VIVSModule.compute_local_variance parameter) (spatialvi.external.vivs.VIVSModule.compute_null_distribution parameter) (spatialvi.external.vivs.VIVSModule.forward parameter) x (spatialvi.module.DeconvolutionModule.inference parameter), [1] (spatialvi.module.NicheModule.inference parameter), [1] (spatialvi.module.SpatialVAEModule.inference parameter), [1], [2] (spatialvi.nn._encoders.AttentionEncoder.forward parameter) (spatialvi.nn._encoders.GraphEncoder.forward parameter) (spatialvi.nn._encoders.SpatialEncoder.forward parameter) (spatialvi.nn._encoders.SpatialEncoder.forward_spatial parameter) (spatialvi.nn._layers.FiLMLayer.forward parameter) (spatialvi.nn._layers.GraphConv.forward parameter) (spatialvi.nn._layers.MixedLinear.forward parameter) (spatialvi.nn._layers.SpatialConv.forward parameter) (spatialvi.nn.GATLayer.forward parameter) (spatialvi.nn.NeighborAttention.forward parameter), [1], [2] (spatialvi.nn.SpatialEncoder.forward parameter), [1] (spatialvi.nn.SpatialEncoder.forward_spatial parameter), [1]

X_labeled (spatialvi.external.ppi.OLSEstimator.fit parameter) x_neighbor (spatialvi.external.nolan.NolanModule.forward parameter) X_unlabeled (spatialvi.external.ppi.OLSEstimator.fit parameter) (spatialvi.external.ppi.PPIInference.ols_ci parameter) (spatialvi.external.ppi.PPIInference.ols_pointestimate parameter) (spatialvi.external.PPIInference.ols_ci parameter), [1] (spatialvi.external.PPIInference.ols_pointestimate parameter), [1]

Y

y (spatialvi.external.ppi.PPIInference.classical_mean_ci parameter) (spatialvi.external.ppi.PPIInference.mean_ci parameter) (spatialvi.external.ppi.PPIInference.mean_pointestimate parameter) (spatialvi.external.ppi.PPIInference.ols_ci parameter) (spatialvi.external.ppi.PPIInference.ols_pointestimate parameter) (spatialvi.external.PPIInference.classical_mean_ci parameter), [1] (spatialvi.external.PPIInference.mean_ci parameter), [1] (spatialvi.external.PPIInference.mean_pointestimate parameter), [1] (spatialvi.external.PPIInference.ols_ci parameter), [1] (spatialvi.external.PPIInference.ols_pointestimate parameter), [1] (spatialvi.external.scviva.nicheVAE.generative parameter) y_labeled (spatialvi.external.ppi.MeanEstimator.fit parameter) (spatialvi.external.ppi.OLSEstimator.fit parameter) yhat (spatialvi.external.ppi.PPIInference.mean_ci parameter) (spatialvi.external.ppi.PPIInference.mean_pointestimate parameter) (spatialvi.external.ppi.PPIInference.ols_ci parameter) (spatialvi.external.ppi.PPIInference.ols_pointestimate parameter) (spatialvi.external.PPIInference.mean_ci parameter), [1] (spatialvi.external.PPIInference.mean_pointestimate parameter), [1] (spatialvi.external.PPIInference.ols_ci parameter), [1] (spatialvi.external.PPIInference.ols_pointestimate parameter), [1]

yhat_labeled (spatialvi.external.ppi.MeanEstimator.fit parameter) (spatialvi.external.ppi.OLSEstimator.fit parameter) yhat_unlabeled (spatialvi.external.ppi.MeanEstimator.fit parameter) (spatialvi.external.ppi.OLSEstimator.fit parameter) (spatialvi.external.ppi.PPIInference.mean_ci parameter) (spatialvi.external.ppi.PPIInference.mean_pointestimate parameter) (spatialvi.external.ppi.PPIInference.ols_ci parameter) (spatialvi.external.ppi.PPIInference.ols_pointestimate parameter) (spatialvi.external.PPIInference.mean_ci parameter), [1] (spatialvi.external.PPIInference.mean_pointestimate parameter), [1] (spatialvi.external.PPIInference.ols_ci parameter), [1] (spatialvi.external.PPIInference.ols_pointestimate parameter), [1]

Z

z (spatialvi.external.amici.AMICIModule.generative parameter) (spatialvi.external.destvi.MRDeconv.generative parameter) (spatialvi.external.nolan.NicheClusteringHead.forward parameter) (spatialvi.external.nolan.NolanModule.contrastive_loss parameter) (spatialvi.external.scviva.nicheVAE.generative parameter) (spatialvi.external.sparl.SPARLModule.generative parameter) (spatialvi.module.NicheModule.generative parameter), [1] (spatialvi.module.SpatialVAEModule.generative parameter), [1], [2] (spatialvi.nn._decoders.ConditionalDecoder.forward parameter) (spatialvi.nn._decoders.FactorizedDecoder.forward parameter) (spatialvi.nn._decoders.FactorizedDecoder.get_mixed_output parameter) (spatialvi.nn._decoders.SpatialDecoder.forward parameter) (spatialvi.nn.SpatialDecoder.forward parameter), [1]

z_neg (spatialvi.external.nolan.NolanModule.contrastive_loss parameter) z_pos (spatialvi.external.nolan.NolanModule.contrastive_loss parameter)