Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | Z _ __init__() (scxpand.autoencoders.ae_losses.MSELoss method) (scxpand.autoencoders.ae_losses.NB method) (scxpand.autoencoders.ae_losses.ZINBLoss method) (scxpand.autoencoders.ae_model_output.DecoderOutput method) (scxpand.autoencoders.ae_model_output.ModelOutput method) (scxpand.autoencoders.ae_models.AutoencoderModel method) (scxpand.autoencoders.ae_models.ForkAutoencoder method) (scxpand.autoencoders.ae_modules.BaseAutoencoder method) (scxpand.autoencoders.ae_modules.CategoricalHead method) (scxpand.autoencoders.ae_modules.ClassificationHead method) (scxpand.autoencoders.ae_modules.Decoder method) (scxpand.autoencoders.ae_modules.Encoder method) (scxpand.autoencoders.ae_params.AutoEncoderParams method) (scxpand.core.inference_results.InferenceResults method) (scxpand.core.inference_results.ModelInfo method) (scxpand.core.model_types.ModelSpec method) (scxpand.data_util.dataloaders.BalancedLabelsBatchSampler method) (scxpand.data_util.dataloaders.BalancedTypesBatchSampler method) (scxpand.data_util.dataset.CellsDataset method) (scxpand.data_util.prepare_data_for_train.TrainingDataBundle method) (scxpand.hyperopt.hyperopt_optimizer.HyperparameterOptimizer method), [1] (scxpand.lightgbm.lightgbm_params.LightGBMParams method) (scxpand.linear.linear_params.LinearClassifierParam method) (scxpand.linear.linear_trainer.LinearBatchPredictor method) (scxpand.linear.linear_trainer.LinearTrainer method) (scxpand.linear.linear_trainer.LinearTrainLogger method) (scxpand.linear.linear_trainer.TrainingSession method) (scxpand.mlp.mlp_model.CategoricalHead method) (scxpand.mlp.mlp_model.FC_Net method) (scxpand.mlp.mlp_model.MLPModel method) (scxpand.mlp.mlp_model.ModelOutput method) (scxpand.mlp.mlp_params.MLPParam method) (scxpand.pretrained.model_registry.PretrainedModelInfo method) (scxpand.util.classes.DataAugmentParams method) (scxpand.util.classes.DataLoaderParams method) (scxpand.util.classes.LRSchedulerParams method) (scxpand.util.classes.OptimizerParams method) (scxpand.util.io.IOSettings method) (scxpand.util.train_logger.TrainLogger method) A ADAM (scxpand.util.classes.OptimizerType attribute) adam_betas (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.OptimizerParams attribute) ADAMW (scxpand.util.classes.OptimizerType attribute) adata (scxpand.data_util.prepare_data_for_train.TrainingDataBundle attribute) add_scalars() (scxpand.util.train_logger.TrainLogger method) alpha (scxpand.linear.linear_params.LinearClassifierParam attribute) apply_inverse_log_transform() (in module scxpand.data_util.transforms) apply_inverse_transforms_to_mean() (in module scxpand.autoencoders.ae_modules) apply_inverse_zscore_normalization() (in module scxpand.data_util.transforms) apply_log_transform() (in module scxpand.data_util.transforms) apply_post_normalization_augmentations() (in module scxpand.data_util.dataset) apply_pre_normalization_augmentations() (in module scxpand.data_util.dataset) apply_row_normalization() (in module scxpand.data_util.transforms) apply_zscore_normalization() (in module scxpand.data_util.transforms) AUC (scxpand.lightgbm.lightgbm_params.MetricType attribute) AUTOENCODER (scxpand.ModelType attribute) (scxpand.util.classes.ModelType attribute) AutoencoderModel (class in scxpand.autoencoders.ae_models) AutoEncoderParams (class in scxpand.autoencoders.ae_params) aux_categorical_mappings (scxpand.data_util.data_format.DataFormat attribute) aux_categorical_types (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.data_util.data_format.DataFormat attribute) (scxpand.mlp.mlp_params.MLPParam attribute) average (scxpand.linear.linear_params.LinearClassifierParam attribute) B bagging_fraction (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) BALANCED_LABELS (scxpand.util.classes.SamplerType attribute) BALANCED_TYPES (scxpand.util.classes.SamplerType attribute) BalancedLabelsBatchSampler (class in scxpand.data_util.dataloaders) BalancedTypesBatchSampler (class in scxpand.data_util.dataloaders) BaseAutoencoder (class in scxpand.autoencoders.ae_modules) BaseParams (class in scxpand.util.classes) batch_size (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.util.classes.DataLoaderParams attribute) BINARY (scxpand.lightgbm.lightgbm_params.ObjectiveType attribute) BINARY_LOGLOSS (scxpand.lightgbm.lightgbm_params.MetricType attribute) boosting_type (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) BoostingType (class in scxpand.lightgbm.lightgbm_params) C calculate_and_log_cancer_distribution() (in module scxpand.data_util.data_splitter) calculate_and_log_category_distributions() (in module scxpand.data_util.data_splitter) calculate_metrics() (in module scxpand.util.metrics) calculate_training_metrics() (in module scxpand.autoencoders.ae_trainer) call_training_function() (in module scxpand.util.training_utils) cat_loss_weight (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) categorical_logits (scxpand.autoencoders.ae_model_output.ModelOutput attribute) (scxpand.mlp.mlp_model.ModelOutput attribute) CategoricalHead (class in scxpand.autoencoders.ae_modules) (class in scxpand.mlp.mlp_model) cells_collate_fn() (in module scxpand.data_util.dataset) CellsDataset (class in scxpand.data_util.dataset) check_early_stopping() (in module scxpand.util.train_util) (scxpand.linear.linear_trainer.TrainingSession method) class_logit (scxpand.autoencoders.ae_model_output.ModelOutput attribute) class_weight (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) ClassificationHead (class in scxpand.autoencoders.ae_modules) classifier_hidden_dims (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) cleanup_failed_trial() (in module scxpand.hyperopt.hyperopt_utils) cleanup_incomplete_trials() (in module scxpand.hyperopt.hyperopt_utils) close_adata_file_safely() (in module scxpand.util.io) cls_loss_weight (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) compute_basic_metrics() (in module scxpand.util.metrics) compute_batch_loss() (in module scxpand.mlp.mlp_losses) compute_categorical_targets_from_batch_obs() (in module scxpand.data_util.dataset) compute_error_rate() (in module scxpand.util.general_util) compute_false_negative_rate() (in module scxpand.util.general_util) compute_false_positive_rate() (in module scxpand.util.general_util) compute_preprocessed_genes_means_stds() (in module scxpand.data_util.statistics) compute_row_sums() (in module scxpand.util.general_util) compute_sample_weights() (in module scxpand.lightgbm.run_lightgbm_) compute_scaling_factors() (in module scxpand.util.general_util) compute_soft_labels() (in module scxpand.data_util.dataset) compute_total_autoencoder_loss() (in module scxpand.autoencoders.ae_losses) compute_total_nn_loss() (in module scxpand.mlp.mlp_losses) config_func (scxpand.core.model_types.ModelSpec attribute) configure_ae_trial_params() (in module scxpand.hyperopt.param_grids) configure_lightgbm_trial_params() (in module scxpand.hyperopt.param_grids) configure_logging() (in module scxpand.util.logger) configure_logistic_trial_params() (in module scxpand.hyperopt.param_grids) configure_mlp_trial_params() (in module scxpand.hyperopt.param_grids) configure_svm_trial_params() (in module scxpand.hyperopt.param_grids) CONSTANT_LR (scxpand.util.classes.LRSchedulerType attribute) convert_enums_to_values() (in module scxpand.util.general_util) convert_genes_expression_matrix() (scxpand.data_util.data_format.DataFormat method) copy_array_like() (in module scxpand.util.general_util) COSINE_ANNEALING_LR (scxpand.util.classes.LRSchedulerType attribute) cpu() (scxpand.autoencoders.ae_model_output.ModelOutput method) create_ae_model() (in module scxpand.autoencoders.ae_models) create_autoencoder_recon_loss_function() (in module scxpand.autoencoders.ae_losses) create_data_format() (scxpand.data_util.data_format.DataFormat method) create_eval_dataloader() (in module scxpand.data_util.dataloaders) create_loss_function() (in module scxpand.mlp.mlp_losses) create_optimized_lr_scheduler_config() (in module scxpand.hyperopt.param_grids) create_study() (scxpand.hyperopt.hyperopt_optimizer.HyperparameterOptimizer method), [1] create_train_dataloader() (in module scxpand.data_util.dataloaders) D DART (scxpand.lightgbm.lightgbm_params.BoostingType attribute) data_format (scxpand.data_util.prepare_data_for_train.TrainingDataBundle attribute) DataAugmentParams (class in scxpand.util.classes) DataFormat (class in scxpand.data_util.data_format) DataLoaderParams (class in scxpand.util.classes) decisions_to_probabilities() (in module scxpand.util.general_util) decode() (scxpand.autoencoders.ae_models.AutoencoderModel method) (scxpand.autoencoders.ae_models.ForkAutoencoder method) (scxpand.autoencoders.ae_modules.BaseAutoencoder method) Decoder (class in scxpand.autoencoders.ae_modules) decoder_hidden_dims (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) DecoderOutput (class in scxpand.autoencoders.ae_model_output) default_save_dir (scxpand.core.model_types.ModelSpec attribute) detach() (scxpand.autoencoders.ae_model_output.DecoderOutput method) (scxpand.autoencoders.ae_model_output.ModelOutput method) deterministic (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) device (scxpand.autoencoders.ae_model_output.DecoderOutput property) (scxpand.autoencoders.ae_model_output.ModelOutput property) download_model() (in module scxpand.pretrained.download_manager), [1] download_pretrained_model() (in module scxpand) (in module scxpand.pretrained) (in module scxpand.pretrained.download_manager), [1] dropout_activation() (in module scxpand.autoencoders.ae_modules) dropout_rate (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) E early_stopping_patience (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) encode() (scxpand.autoencoders.ae_models.AutoencoderModel method) (scxpand.autoencoders.ae_models.ForkAutoencoder method) (scxpand.autoencoders.ae_modules.BaseAutoencoder method) encode_categorical_features_batch() (in module scxpand.data_util.dataset) encode_categorical_value() (in module scxpand.data_util.dataset) Encoder (class in scxpand.autoencoders.ae_modules) encoder_hidden_dims (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) ensure_directory_exists() (in module scxpand.util.io) ensure_model_type() (in module scxpand.util.classes) ensure_numpy_array() (in module scxpand.util.general_util) eta0 (scxpand.linear.linear_params.LinearClassifierParam attribute) eval_interval (scxpand.linear.linear_params.LinearClassifierParam attribute) evaluate_and_save() (in module scxpand.util.metrics) evaluate_model() (scxpand.linear.linear_trainer.LinearTrainer method) evaluate_predictions_and_save() (in module scxpand.core.evaluation) exponential_backoff_delay() (in module scxpand.util.io) extract_is_expanded() (in module scxpand.data_util.transforms) F FC_Net (class in scxpand.mlp.mlp_model) feature_fraction (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) fetch_model_and_run_inference() (in module scxpand.pretrained) (in module scxpand.pretrained.inference_api) finalize_training() (scxpand.linear.linear_trainer.LinearTrainer method) fit_intercept (scxpand.linear.linear_params.LinearClassifierParam attribute) flatten_dict() (in module scxpand.util.general_util) flatten_nested_dict() (in module scxpand.util.general_util) floats_to_str() (in module scxpand.util.general_util) flush() (scxpand.util.train_logger.TrainLogger method) force_col_wise (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) ForkAutoencoder (class in scxpand.autoencoders.ae_models) format_float() (in module scxpand.util.general_util) forward() (scxpand.autoencoders.ae_modules.BaseAutoencoder method) (scxpand.autoencoders.ae_modules.CategoricalHead method) (scxpand.autoencoders.ae_modules.ClassificationHead method) (scxpand.autoencoders.ae_modules.Decoder method) (scxpand.autoencoders.ae_modules.Encoder method) (scxpand.mlp.mlp_model.CategoricalHead method) (scxpand.mlp.mlp_model.FC_Net method) (scxpand.mlp.mlp_model.MLPModel method) G GBDT (scxpand.lightgbm.lightgbm_params.BoostingType attribute) gene_names (scxpand.data_util.data_format.DataFormat attribute) genes_mu (scxpand.data_util.data_format.DataFormat attribute) genes_sigma (scxpand.data_util.data_format.DataFormat attribute) get_auroc() (scxpand.core.inference_results.InferenceResults method) get_available_model_types() (in module scxpand.util.model_type) get_binary_predictions() (scxpand.autoencoders.ae_model_output.ModelOutput method) get_data_loader_params() (scxpand.autoencoders.ae_params.AutoEncoderParams method) (scxpand.mlp.mlp_params.MLPParam method) get_dataloader_kwargs() (in module scxpand.data_util.dataset) get_dataset_params() (scxpand.autoencoders.ae_params.AutoEncoderParams method) (scxpand.linear.linear_params.LinearClassifierParam method) (scxpand.mlp.mlp_params.MLPParam method) get_device() (in module scxpand.util.general_util) get_elapsed_time_in_seconds() (scxpand.util.train_logger.TrainLogger method) get_elapsed_time_str() (in module scxpand.util.general_util) get_harmonic_avg_auroc() (scxpand.core.inference_results.InferenceResults method) get_last_git_commit_link() (in module scxpand.util.general_util) get_local_time() (in module scxpand.util.general_util) get_logger() (in module scxpand.util.logger) get_lr_scheduler() (in module scxpand.util.train_util) get_lr_scheduler_params() (scxpand.autoencoders.ae_params.AutoEncoderParams method) (scxpand.linear.linear_params.LinearClassifierParam method) (scxpand.mlp.mlp_params.MLPParam method) get_model_type() (scxpand.autoencoders.ae_params.AutoEncoderParams class method) (scxpand.lightgbm.lightgbm_params.LightGBMParams class method) (scxpand.linear.linear_params.LinearClassifierParam class method) (scxpand.mlp.mlp_params.MLPParam class method) (scxpand.util.classes.BaseParams class method) get_new_version_path() (in module scxpand.util.general_util) get_optimizer() (in module scxpand.util.train_util) get_optimizer_params() (scxpand.autoencoders.ae_params.AutoEncoderParams method) (scxpand.linear.linear_params.LinearClassifierParam method) (scxpand.mlp.mlp_params.MLPParam method) get_patient_identifiers() (in module scxpand.data_util.data_splitter) get_pretrained_model_info() (in module scxpand) (in module scxpand.pretrained) (in module scxpand.pretrained.model_registry) get_score_from_nested_dict() (in module scxpand.util.metrics) get_utc_time() (in module scxpand.util.general_util) GOSS (scxpand.lightgbm.lightgbm_params.BoostingType attribute) H has_checkpoint() (in module scxpand.util.train_logger) has_metrics (scxpand.core.inference_results.InferenceResults property) has_model_info (scxpand.core.inference_results.InferenceResults property) HyperparameterOptimizer (class in scxpand.hyperopt.hyperopt_optimizer), [1] I infer_model_type_from_parameters() (in module scxpand.util.model_type) inference() (in module scxpand.main), [1] inference_batch_size (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) InferenceResults (class in scxpand.core.inference_results) init_learning_rate (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.OptimizerParams attribute) init_linear_training() (scxpand.linear.linear_trainer.LinearTrainLogger method) init_writer() (scxpand.util.train_logger.TrainLogger method) initialize_model() (scxpand.linear.model_manager.ModelManager static method) IOSettings (class in scxpand.util.io) is_hdf5_error() (in module scxpand.util.io) L l1_lambda (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) l1_ratio (scxpand.linear.linear_params.LinearClassifierParam attribute) LAMBDARANK (scxpand.lightgbm.lightgbm_params.ObjectiveType attribute) latent_dim (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) latent_vec (scxpand.autoencoders.ae_model_output.ModelOutput attribute) layer_units (scxpand.mlp.mlp_params.MLPParam attribute) learning_rate (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) LIGHTGBM (scxpand.ModelType attribute) (scxpand.util.classes.ModelType attribute) LightGBMParams (class in scxpand.lightgbm.lightgbm_params) LinearBatchPredictor (class in scxpand.linear.linear_trainer) LinearClassifierParam (class in scxpand.linear.linear_params) LinearTrainer (class in scxpand.linear.linear_trainer) LinearTrainLogger (class in scxpand.linear.linear_trainer) list_pretrained_models() (in module scxpand) (in module scxpand.util.model_registry), [1] load_ae_model() (in module scxpand.autoencoders.ae_models) load_and_override_params() (in module scxpand.util.general_util) load_and_preprocess_data_numpy() (in module scxpand.data_util.transforms) load_and_validate_model() (in module scxpand.util.model_loading) load_best_model() (scxpand.util.train_logger.TrainLogger method) load_data_format() (in module scxpand.data_util.data_format) load_eval_indices() (in module scxpand.util.io) load_model() (in module scxpand.util.inference_utils) load_model_parameters() (in module scxpand.util.model_loading) load_model_state() (scxpand.linear.model_manager.ModelManager static method) load_model_state_dict() (in module scxpand.util.model_loading) load_model_type() (in module scxpand.util.model_type) load_nn_model() (in module scxpand.mlp.mlp_model) load_params() (in module scxpand.util.general_util) load_sklearn_model() (in module scxpand.linear.sklearn_utils) log_dataset_overview() (in module scxpand.data_util.data_splitter) log_epoch_end() (scxpand.linear.linear_trainer.LinearTrainLogger method) log_inference_progress() (in module scxpand.util.general_util) log_nested_metrics() (in module scxpand.util.general_util) log_split_results() (in module scxpand.data_util.data_splitter) log_training_summary() (scxpand.linear.linear_trainer.LinearTrainLogger method) log_trial_progress() (in module scxpand.hyperopt.hyperopt_utils) log_validation_metrics() (scxpand.linear.linear_trainer.LinearTrainLogger method) LOGISTIC (scxpand.ModelType attribute) (scxpand.util.classes.ModelType attribute) loss() (scxpand.autoencoders.ae_losses.NB method) loss_type (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) lr_scheduler_config (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.LRSchedulerParams attribute) lr_scheduler_type (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.LRSchedulerParams attribute) LRSchedulerParams (class in scxpand.util.classes) LRSchedulerType (class in scxpand.util.classes) M MAE (scxpand.lightgbm.lightgbm_params.MetricType attribute) main() (in module scxpand.main) main_logit (scxpand.mlp.mlp_model.ModelOutput attribute) mask_rate (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.DataAugmentParams attribute) max_depth (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) max_grad_norm (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.OptimizerParams attribute) max_iter (scxpand.linear.linear_params.LinearClassifierParam attribute) metric (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) metrics (scxpand.core.inference_results.InferenceResults attribute) metrics_dict_to_dataframes() (in module scxpand.util.general_util) metrics_dict_to_table() (in module scxpand.util.general_util) MetricType (class in scxpand.lightgbm.lightgbm_params) min_child_samples (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) min_child_weight (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) min_split_gain (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) MLP (scxpand.ModelType attribute) (scxpand.util.classes.ModelType attribute) MLPModel (class in scxpand.mlp.mlp_model) MLPParam (class in scxpand.mlp.mlp_params) model_config (scxpand.data_util.data_format.DataFormat attribute) model_info (scxpand.core.inference_results.InferenceResults attribute) model_name (scxpand.core.inference_results.ModelInfo attribute) model_type (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.core.inference_results.ModelInfo attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) ModelInfo (class in scxpand.core.inference_results) ModelLoadingError ModelManager (class in scxpand.linear.model_manager) ModelOutput (class in scxpand.autoencoders.ae_model_output) (class in scxpand.mlp.mlp_model) ModelSpec (class in scxpand.core.model_types) ModelType (class in scxpand) (class in scxpand.util.classes) module scxpand scxpand.autoencoders scxpand.autoencoders.ae_losses scxpand.autoencoders.ae_model_output scxpand.autoencoders.ae_models scxpand.autoencoders.ae_modules scxpand.autoencoders.ae_params scxpand.autoencoders.ae_trainer scxpand.autoencoders.run_ae_train scxpand.core scxpand.core.evaluation scxpand.core.inference, [1] scxpand.core.inference_results scxpand.core.model_types scxpand.core.prediction scxpand.data_util scxpand.data_util.constants scxpand.data_util.data_format scxpand.data_util.data_splitter scxpand.data_util.dataloaders scxpand.data_util.dataset scxpand.data_util.prepare_data_for_train scxpand.data_util.statistics scxpand.data_util.transforms scxpand.hyperopt scxpand.hyperopt.hyperopt_optimizer, [1] scxpand.hyperopt.hyperopt_utils scxpand.hyperopt.param_grids scxpand.lightgbm scxpand.lightgbm.lightgbm_params scxpand.lightgbm.run_lightgbm_ scxpand.linear scxpand.linear.linear_params scxpand.linear.linear_trainer scxpand.linear.model_manager scxpand.linear.sklearn_utils scxpand.main scxpand.mlp scxpand.mlp.mlp_losses scxpand.mlp.mlp_model scxpand.mlp.mlp_params scxpand.mlp.mlp_trainer scxpand.mlp.run_mlp_train scxpand.pretrained scxpand.pretrained.download_manager, [1] scxpand.pretrained.inference_api scxpand.pretrained.model_registry scxpand.util scxpand.util.classes scxpand.util.general_util scxpand.util.inference_utils scxpand.util.io scxpand.util.logger scxpand.util.metrics scxpand.util.model_constants scxpand.util.model_loading scxpand.util.model_registry, [1] scxpand.util.model_type scxpand.util.plots scxpand.util.train_logger scxpand.util.train_util scxpand.util.training_utils mse_loss() (scxpand.autoencoders.ae_losses.MSELoss method) MSELoss (class in scxpand.autoencoders.ae_losses) mu (scxpand.autoencoders.ae_model_output.DecoderOutput attribute) (scxpand.autoencoders.ae_model_output.ModelOutput attribute) MULTICLASS (scxpand.lightgbm.lightgbm_params.ObjectiveType attribute) MULTICLASS_LOGLOSS (scxpand.lightgbm.lightgbm_params.MetricType attribute) N n_epochs (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) n_estimators (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) n_genes (scxpand.data_util.data_format.DataFormat attribute) n_iter_no_change (scxpand.linear.linear_params.LinearClassifierParam attribute) n_jobs (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) n_predictions (scxpand.core.inference_results.InferenceResults property) name (scxpand.pretrained.model_registry.PretrainedModelInfo attribute) NB (class in scxpand.autoencoders.ae_losses) nb_loss() (scxpand.autoencoders.ae_losses.ZINBLoss method) NDCG (scxpand.lightgbm.lightgbm_params.MetricType attribute) needs_pi_head() (scxpand.autoencoders.ae_params.AutoEncoderParams method) needs_theta_head() (scxpand.autoencoders.ae_params.AutoEncoderParams method) nested_dict_to_flat_str() (in module scxpand.util.general_util) nested_dict_to_multiline_str() (in module scxpand.util.general_util) NO_SCHEDULER (scxpand.util.classes.LRSchedulerType attribute) noise_std (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.DataAugmentParams attribute) num2str() (in module scxpand.util.general_util) num_leaves (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) O objective (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) objective() (scxpand.hyperopt.hyperopt_optimizer.HyperparameterOptimizer method), [1] ObjectiveType (class in scxpand.lightgbm.lightgbm_params) ONE_CYCLE_LR (scxpand.util.classes.LRSchedulerType attribute) open_adata() (scxpand.data_util.dataset.CellsDataset method) open_adata_file_with_retry() (in module scxpand.util.io) open_adata_multiprocessing_safe() (in module scxpand.util.io) optimize() (in module scxpand.main), [1] optimize_all() (in module scxpand.main), [1] optimizer_type (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.OptimizerParams attribute) OptimizerParams (class in scxpand.util.classes) OptimizerType (class in scxpand.util.classes) P param_class (scxpand.core.model_types.ModelSpec attribute) penalty (scxpand.linear.linear_params.LinearClassifierParam attribute) pi (scxpand.autoencoders.ae_model_output.DecoderOutput attribute) (scxpand.autoencoders.ae_model_output.ModelOutput attribute) plot_roc_curve() (in module scxpand.util.plots) plot_roc_curves_per_strata() (in module scxpand.util.plots) positives_weight (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) power_t (scxpand.linear.linear_params.LinearClassifierParam attribute) predict_all() (scxpand.linear.linear_trainer.LinearBatchPredictor method) predict_batch() (scxpand.linear.linear_trainer.LinearBatchPredictor method) predictions (scxpand.core.inference_results.InferenceResults attribute) prepare_adata_for_training() (scxpand.data_util.data_format.DataFormat method) prepare_data_and_model() (scxpand.linear.linear_trainer.LinearTrainer method) prepare_data_for_training() (in module scxpand.data_util.prepare_data_for_train) preprocess_expression_data() (in module scxpand.data_util.transforms) PretrainedModelInfo (class in scxpand.pretrained.model_registry) print_results() (scxpand.hyperopt.hyperopt_optimizer.HyperparameterOptimizer method), [1] R RANDOM (scxpand.util.classes.SamplerType attribute) random_seed (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) read_adata_slice_chunked() (in module scxpand.util.io) read_adata_slice_direct() (in module scxpand.util.io) read_adata_slice_sequential() (in module scxpand.util.io) recon_loss_weight (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) REDUCE_LR_ON_PLATEAU (scxpand.util.classes.LRSchedulerType attribute) reg_alpha (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) reg_lambda (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) REGRESSION (scxpand.lightgbm.lightgbm_params.ObjectiveType attribute) reorder_genes_to_match_format() (scxpand.data_util.data_format.DataFormat method) report_optuna_trial_result() (in module scxpand.hyperopt.hyperopt_utils) report_to_optuna_and_handle_pruning() (in module scxpand.util.train_util) resume_from_checkpoint() (scxpand.util.train_logger.TrainLogger method) retry_hdf5_operation() (in module scxpand.util.io) RF (scxpand.lightgbm.lightgbm_params.BoostingType attribute) ridge_lambda (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) RMSE (scxpand.lightgbm.lightgbm_params.MetricType attribute) row_inds_dev (scxpand.data_util.prepare_data_for_train.TrainingDataBundle attribute) row_inds_train (scxpand.data_util.prepare_data_for_train.TrainingDataBundle attribute) run_ae_inference() (in module scxpand.autoencoders.ae_trainer) run_ae_trainer() (in module scxpand.autoencoders.ae_trainer) run_ae_training() (in module scxpand.autoencoders.run_ae_train) run_inference() (in module scxpand) (in module scxpand.core.inference), [1] run_lightgbm_inference() (in module scxpand.lightgbm.run_lightgbm_) run_lightgbm_training() (in module scxpand.lightgbm.run_lightgbm_) run_linear_inference() (in module scxpand.linear.sklearn_utils) run_linear_training() (in module scxpand.linear.linear_trainer) run_mlp_inference() (in module scxpand.mlp.mlp_trainer) run_mlp_training() (in module scxpand.mlp.run_mlp_train) run_model_inference() (in module scxpand.util.inference_utils) run_optimization() (scxpand.hyperopt.hyperopt_optimizer.HyperparameterOptimizer method), [1] run_prediction_pipeline() (in module scxpand) (in module scxpand.core.prediction) run_trainer() (in module scxpand.mlp.mlp_trainer) run_training() (scxpand.linear.linear_trainer.LinearTrainer method) runner (scxpand.core.model_types.ModelSpec attribute) S safe_hmean() (in module scxpand.util.metrics) safe_read_adata_slice() (in module scxpand.util.io) sampler_type (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.DataLoaderParams attribute) SamplerType (class in scxpand.util.classes) save() (scxpand.data_util.data_format.DataFormat method) save_checkpoint() (scxpand.util.train_logger.TrainLogger method) save_final_summary() (scxpand.util.train_logger.TrainLogger method) save_json_data() (in module scxpand.util.general_util) save_model_state() (scxpand.linear.model_manager.ModelManager static method) save_model_type() (in module scxpand.util.model_type) save_params() (in module scxpand.util.general_util) save_path (scxpand.data_util.prepare_data_for_train.TrainingDataBundle attribute) save_patient_ids() (in module scxpand.data_util.data_splitter) save_predictions_to_csv() (in module scxpand.util.io) save_study_info() (in module scxpand.hyperopt.hyperopt_utils) scxpand module scxpand.autoencoders module scxpand.autoencoders.ae_losses module scxpand.autoencoders.ae_model_output module scxpand.autoencoders.ae_models module scxpand.autoencoders.ae_modules module scxpand.autoencoders.ae_params module scxpand.autoencoders.ae_trainer module scxpand.autoencoders.run_ae_train module scxpand.core module scxpand.core.evaluation module scxpand.core.inference module, [1] scxpand.core.inference_results module scxpand.core.model_types module scxpand.core.prediction module scxpand.data_util module scxpand.data_util.constants module scxpand.data_util.data_format module scxpand.data_util.data_splitter module scxpand.data_util.dataloaders module scxpand.data_util.dataset module scxpand.data_util.prepare_data_for_train module scxpand.data_util.statistics module scxpand.data_util.transforms module scxpand.hyperopt module scxpand.hyperopt.hyperopt_optimizer module, [1] scxpand.hyperopt.hyperopt_utils module scxpand.hyperopt.param_grids module scxpand.lightgbm module scxpand.lightgbm.lightgbm_params module scxpand.lightgbm.run_lightgbm_ module scxpand.linear module scxpand.linear.linear_params module scxpand.linear.linear_trainer module scxpand.linear.model_manager module scxpand.linear.sklearn_utils module scxpand.main module scxpand.mlp module scxpand.mlp.mlp_losses module scxpand.mlp.mlp_model module scxpand.mlp.mlp_params module scxpand.mlp.mlp_trainer module scxpand.mlp.run_mlp_train module scxpand.pretrained module scxpand.pretrained.download_manager module, [1] scxpand.pretrained.inference_api module scxpand.pretrained.model_registry module scxpand.util module scxpand.util.classes module scxpand.util.general_util module scxpand.util.inference_utils module scxpand.util.io module scxpand.util.logger module scxpand.util.metrics module scxpand.util.model_constants module scxpand.util.model_loading module scxpand.util.model_registry module, [1] scxpand.util.model_type module scxpand.util.plots module scxpand.util.train_logger module scxpand.util.train_util module scxpand.util.training_utils module set_seed() (in module scxpand.util.general_util) setup_inference_environment() (in module scxpand.util.inference_utils) SGD (scxpand.util.classes.OptimizerType attribute) should_use_soft_loss() (in module scxpand.autoencoders.ae_losses) (in module scxpand.mlp.mlp_losses) shuffle (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.util.classes.DataLoaderParams attribute) sigmoid() (in module scxpand.util.general_util) soft_loss_beta (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.DataAugmentParams attribute) soft_loss_start_epoch (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) source (scxpand.core.inference_results.ModelInfo attribute) split_data() (in module scxpand.data_util.data_splitter) STEP_LR (scxpand.util.classes.LRSchedulerType attribute) SVM (scxpand.ModelType attribute) (scxpand.util.classes.ModelType attribute) T target_sum (scxpand.data_util.data_format.DataFormat attribute) theta (scxpand.autoencoders.ae_model_output.DecoderOutput attribute) (scxpand.autoencoders.ae_model_output.ModelOutput attribute) theta_activation() (in module scxpand.autoencoders.ae_modules) time_seconds_to_str() (in module scxpand.util.general_util) time_to_str() (in module scxpand.util.general_util) to() (scxpand.autoencoders.ae_model_output.DecoderOutput method) (scxpand.autoencoders.ae_model_output.ModelOutput method) to_dict() (scxpand.core.inference_results.InferenceResults method) to_np() (in module scxpand.util.general_util) tol (scxpand.linear.linear_params.LinearClassifierParam attribute) train() (in module scxpand.main), [1] train_batch_size (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) train_epoch() (scxpand.linear.linear_trainer.LinearTrainer method) train_log_interval (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) TrainingDataBundle (class in scxpand.data_util.prepare_data_for_train) TrainingSession (class in scxpand.linear.linear_trainer) TrainLogger (class in scxpand.util.train_logger) transform_batch_data() (scxpand.data_util.dataset.CellsDataset method) trial_callback() (in module scxpand.hyperopt.hyperopt_utils) U update_best_model() (scxpand.linear.linear_trainer.TrainingSession method) update_best_score() (scxpand.linear.linear_trainer.LinearTrainLogger method) update_lr_scheduler() (in module scxpand.util.train_util) url (scxpand.core.inference_results.ModelInfo attribute) (scxpand.pretrained.model_registry.PretrainedModelInfo attribute) use_log_transform (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.data_util.data_format.DataFormat attribute) (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) (scxpand.linear.linear_params.LinearClassifierParam attribute) (scxpand.mlp.mlp_params.MLPParam attribute) use_zscore_norm (scxpand.data_util.data_format.DataFormat attribute) (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) V validate_and_setup_common() (in module scxpand.util.training_utils) validate_model_directory() (in module scxpand.util.model_loading) validate_patient_cancer_types() (in module scxpand.data_util.data_splitter) validation_fraction (scxpand.linear.linear_params.LinearClassifierParam attribute) verbose (scxpand.lightgbm.lightgbm_params.LightGBMParams attribute) version (scxpand.core.inference_results.ModelInfo attribute) (scxpand.pretrained.model_registry.PretrainedModelInfo attribute) W warm_start (scxpand.linear.linear_params.LinearClassifierParam attribute) weight_decay (scxpand.autoencoders.ae_params.AutoEncoderParams attribute) (scxpand.mlp.mlp_params.MLPParam attribute) (scxpand.util.classes.OptimizerParams attribute) Z zinb_loss() (scxpand.autoencoders.ae_losses.ZINBLoss method) ZINBLoss (class in scxpand.autoencoders.ae_losses)
