Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | X | Z A adata (sccoral.model.SCCORAL attribute) adata_manager (sccoral.model.SCCORAL attribute) add_module() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) all_gather() (sccoral.train.ScCoralTrainingPlan method) apply() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) automatic_optimization (sccoral.train.ScCoralTrainingPlan attribute) B backward() (sccoral.train.ScCoralTrainingPlan method) bfloat16() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) buffers() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) C call_super_init (sccoral.module.MODULE attribute) (sccoral.train.ScCoralTrainingPlan attribute) CHECKPOINT_HYPER_PARAMS_KEY (sccoral.train.ScCoralTrainingPlan attribute) CHECKPOINT_HYPER_PARAMS_NAME (sccoral.train.ScCoralTrainingPlan attribute) CHECKPOINT_HYPER_PARAMS_TYPE (sccoral.train.ScCoralTrainingPlan attribute) children() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) clip_gradients() (sccoral.train.ScCoralTrainingPlan method) compile() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) compute_and_log_metrics() (sccoral.train.ScCoralTrainingPlan method) configure_callbacks() (sccoral.train.ScCoralTrainingPlan method) configure_gradient_clipping() (sccoral.train.ScCoralTrainingPlan method) configure_model() (sccoral.train.ScCoralTrainingPlan method) configure_optimizers() (sccoral.train.ScCoralTrainingPlan method) configure_sharded_model() (sccoral.train.ScCoralTrainingPlan method) convert_legacy_save() (sccoral.model.SCCORAL class method) cpu() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) cuda() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) current_epoch (sccoral.train.ScCoralTrainingPlan attribute) D deregister_manager() (sccoral.model.SCCORAL method) device (sccoral.model.SCCORAL attribute) (sccoral.module.MODULE attribute) (sccoral.train.ScCoralTrainingPlan attribute) device_mesh (sccoral.train.ScCoralTrainingPlan attribute) double() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) dtype (sccoral.train.ScCoralTrainingPlan attribute) dump_patches (sccoral.module.MODULE attribute) (sccoral.train.ScCoralTrainingPlan attribute) E eval() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) example_input_array (sccoral.train.ScCoralTrainingPlan attribute) extra_repr() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) F fabric (sccoral.train.ScCoralTrainingPlan attribute) float() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) forward() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) freeze() (sccoral.train.ScCoralTrainingPlan method) G generative() (sccoral.module.MODULE method) get_anndata_manager() (sccoral.model.SCCORAL method) get_buffer() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) get_elbo() (sccoral.model.SCCORAL method) get_explained_variance_per_factor() (sccoral.model.SCCORAL method) get_extra_state() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) get_from_registry() (sccoral.model.SCCORAL method) get_latent_representation() (sccoral.model.SCCORAL method) get_loadings() (sccoral.model.SCCORAL method) (sccoral.module.MODULE method) get_marginal_ll() (sccoral.model.SCCORAL method) get_optimizer_creator() (sccoral.train.ScCoralTrainingPlan method) get_parameter() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) get_reconstruction_error() (sccoral.model.SCCORAL method) get_submodule() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) global_rank (sccoral.train.ScCoralTrainingPlan attribute) global_step (sccoral.train.ScCoralTrainingPlan attribute) H half() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) history (sccoral.model.SCCORAL attribute) hparams (sccoral.train.ScCoralTrainingPlan attribute) hparams_initial (sccoral.train.ScCoralTrainingPlan attribute) I inference() (sccoral.module.MODULE method) initialize_train_metrics() (sccoral.train.ScCoralTrainingPlan method) initialize_val_metrics() (sccoral.train.ScCoralTrainingPlan method) ipu() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) is_pretrained (sccoral.train.ScCoralTrainingPlan attribute) is_trained (sccoral.model.SCCORAL attribute) K kl_weight (sccoral.train.ScCoralTrainingPlan attribute) L load() (sccoral.model.SCCORAL class method) load_from_checkpoint() (sccoral.train.ScCoralTrainingPlan method) load_registry() (sccoral.model.SCCORAL static method) load_state_dict() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) local_rank (sccoral.train.ScCoralTrainingPlan attribute) log() (sccoral.train.ScCoralTrainingPlan method) log_dict() (sccoral.train.ScCoralTrainingPlan method) logger (sccoral.train.ScCoralTrainingPlan attribute) loggers (sccoral.train.ScCoralTrainingPlan attribute) loss() (sccoral.module.MODULE method) lr_scheduler_step() (sccoral.train.ScCoralTrainingPlan method) lr_schedulers() (sccoral.train.ScCoralTrainingPlan method) M manual_backward() (sccoral.train.ScCoralTrainingPlan method) marginal_ll() (sccoral.module.MODULE method) module sccoral.data sccoral.model sccoral.module sccoral.train MODULE (class in sccoral.module) modules() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) mtia() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) N n_obs_training (sccoral.train.ScCoralTrainingPlan attribute) n_obs_validation (sccoral.train.ScCoralTrainingPlan attribute) named_buffers() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) named_children() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) named_modules() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) named_parameters() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) O on_after_backward() (sccoral.train.ScCoralTrainingPlan method) on_after_batch_transfer() (sccoral.train.ScCoralTrainingPlan method) on_before_backward() (sccoral.train.ScCoralTrainingPlan method) on_before_batch_transfer() (sccoral.train.ScCoralTrainingPlan method) on_before_optimizer_step() (sccoral.train.ScCoralTrainingPlan method) on_before_zero_grad() (sccoral.train.ScCoralTrainingPlan method) on_fit_end() (sccoral.train.ScCoralTrainingPlan method) on_fit_start() (sccoral.train.ScCoralTrainingPlan method) on_gpu (sccoral.train.ScCoralTrainingPlan attribute) on_load() (sccoral.module.MODULE method) on_load_checkpoint() (sccoral.train.ScCoralTrainingPlan method) on_predict_batch_end() (sccoral.train.ScCoralTrainingPlan method) on_predict_batch_start() (sccoral.train.ScCoralTrainingPlan method) on_predict_end() (sccoral.train.ScCoralTrainingPlan method) on_predict_epoch_end() (sccoral.train.ScCoralTrainingPlan method) on_predict_epoch_start() (sccoral.train.ScCoralTrainingPlan method) on_predict_model_eval() (sccoral.train.ScCoralTrainingPlan method) on_predict_start() (sccoral.train.ScCoralTrainingPlan method) on_save_checkpoint() (sccoral.train.ScCoralTrainingPlan method) on_test_batch_end() (sccoral.train.ScCoralTrainingPlan method) on_test_batch_start() (sccoral.train.ScCoralTrainingPlan method) on_test_end() (sccoral.train.ScCoralTrainingPlan method) on_test_epoch_end() (sccoral.train.ScCoralTrainingPlan method) on_test_epoch_start() (sccoral.train.ScCoralTrainingPlan method) on_test_model_eval() (sccoral.train.ScCoralTrainingPlan method) on_test_model_train() (sccoral.train.ScCoralTrainingPlan method) on_test_start() (sccoral.train.ScCoralTrainingPlan method) on_train_batch_end() (sccoral.train.ScCoralTrainingPlan method) on_train_batch_start() (sccoral.train.ScCoralTrainingPlan method) on_train_end() (sccoral.train.ScCoralTrainingPlan method) on_train_epoch_end() (sccoral.train.ScCoralTrainingPlan method) on_train_epoch_start() (sccoral.train.ScCoralTrainingPlan method) on_train_start() (sccoral.train.ScCoralTrainingPlan method) on_validation_batch_end() (sccoral.train.ScCoralTrainingPlan method) on_validation_batch_start() (sccoral.train.ScCoralTrainingPlan method) on_validation_end() (sccoral.train.ScCoralTrainingPlan method) on_validation_epoch_end() (sccoral.train.ScCoralTrainingPlan method) on_validation_epoch_start() (sccoral.train.ScCoralTrainingPlan method) on_validation_model_eval() (sccoral.train.ScCoralTrainingPlan method) on_validation_model_train() (sccoral.train.ScCoralTrainingPlan method) on_validation_model_zero_grad() (sccoral.train.ScCoralTrainingPlan method) on_validation_start() (sccoral.train.ScCoralTrainingPlan method) optimizer_step() (sccoral.train.ScCoralTrainingPlan method) optimizer_zero_grad() (sccoral.train.ScCoralTrainingPlan method) optimizers() (sccoral.train.ScCoralTrainingPlan method) P parameters() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) predict_dataloader() (sccoral.train.ScCoralTrainingPlan method) predict_step() (sccoral.train.ScCoralTrainingPlan method) prepare_data() (sccoral.train.ScCoralTrainingPlan method) pretraining_early_stopping_condition (sccoral.train.ScCoralTrainingPlan attribute) print() (sccoral.train.ScCoralTrainingPlan method) R register_backward_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_buffer() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_forward_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_forward_pre_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_full_backward_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_full_backward_pre_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_load_state_dict_post_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_load_state_dict_pre_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_manager() (sccoral.model.SCCORAL class method) register_module() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_parameter() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_state_dict_post_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) register_state_dict_pre_hook() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) requires_grad_() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) S sample() (sccoral.module.MODULE method) save() (sccoral.model.SCCORAL method) save_hyperparameters() (sccoral.train.ScCoralTrainingPlan method) SCCORAL (class in sccoral.model) sccoral.data module sccoral.model module sccoral.module module sccoral.train module ScCoralTrainingPlan (class in sccoral.train) set_extra_state() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) set_submodule() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) setup() (sccoral.train.ScCoralTrainingPlan method) setup_anndata() (sccoral.model.SCCORAL class method) share_memory() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) splatter_simulation() (in module sccoral.data) state_dict() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) strict_loading (sccoral.train.ScCoralTrainingPlan attribute) summary_string (sccoral.model.SCCORAL attribute) T T_destination (sccoral.module.MODULE attribute) (sccoral.train.ScCoralTrainingPlan attribute) teardown() (sccoral.train.ScCoralTrainingPlan method) test_dataloader() (sccoral.train.ScCoralTrainingPlan method) test_indices (sccoral.model.SCCORAL attribute) test_step() (sccoral.train.ScCoralTrainingPlan method) to() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) to_device() (sccoral.model.SCCORAL method) to_empty() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) to_onnx() (sccoral.train.ScCoralTrainingPlan method) to_torchscript() (sccoral.train.ScCoralTrainingPlan method) toggle_optimizer() (sccoral.train.ScCoralTrainingPlan method) toggled_optimizer() (sccoral.train.ScCoralTrainingPlan method) train() (sccoral.model.SCCORAL method) (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) train_dataloader() (sccoral.train.ScCoralTrainingPlan method) train_indices (sccoral.model.SCCORAL attribute) trainer (sccoral.train.ScCoralTrainingPlan attribute) training (sccoral.module.MODULE attribute) (sccoral.train.ScCoralTrainingPlan attribute) training_step() (sccoral.train.ScCoralTrainingPlan method) transfer_batch_to_device() (sccoral.train.ScCoralTrainingPlan method) type() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) U unfreeze() (sccoral.train.ScCoralTrainingPlan method) untoggle_optimizer() (sccoral.train.ScCoralTrainingPlan method) use_sync_dist (sccoral.train.ScCoralTrainingPlan attribute) V val_dataloader() (sccoral.train.ScCoralTrainingPlan method) validation_indices (sccoral.model.SCCORAL attribute) validation_step() (sccoral.train.ScCoralTrainingPlan method) view_anndata_setup() (sccoral.model.SCCORAL method) view_setup_args() (sccoral.model.SCCORAL static method) X xpu() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method) Z zero_grad() (sccoral.module.MODULE method) (sccoral.train.ScCoralTrainingPlan method)
