Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | W A allboost() (in module structboost) AllboostHistory (class in structboost) apply_encoder() (structboost.BAE method) avg_selected (structboost.StabilitySelectionResult attribute) B BAE (class in structboost) BAEConfig (class in structboost) batch_labels (structboost.SimulationResult attribute) batch_size (structboost.BAEConfig attribute) beta_path (structboost.AllboostHistory attribute) boosting_csf (structboost.BAEConfig attribute) boosting_independent (structboost.BAEConfig attribute) boosting_nu (structboost.BAEConfig attribute) boosting_precompute_covcache (structboost.BAEConfig attribute) boosting_r2 (structboost.TrainingReport attribute) boosting_stepno (structboost.BAEConfig attribute) C coefficient_cond_mean (structboost.StabilitySelectionResult attribute) coefficient_mean (structboost.StabilitySelectionResult property) coefficient_sd (structboost.StabilitySelectionResult attribute) column_info (structboost.ObsCovariateEncoding attribute) column_norms_sq() (in module structboost) compute_covariance_cache() (in module structboost) counts (structboost.SimulationResult attribute) D database_references (structboost.DimensionAnnotation attribute) decoder_activation (structboost.BAEConfig attribute) decoder_delta (structboost.TrainingReport attribute) decoder_grad_norm (structboost.TrainingReport attribute) decoder_hidden_dims (structboost.BAEConfig attribute) decoder_lr (structboost.BAEConfig attribute) decoder_weight_decay (structboost.BAEConfig attribute) device (structboost.BAEConfig attribute) diagnostics (structboost.BAEConfig attribute) dim_match_quality (structboost.StabilitySelectionResult attribute) dimension (structboost.DimensionAnnotation attribute) (structboost.DimensionGeneRanking attribute) DimensionAnnotation (class in structboost) DimensionGeneRanking (class in structboost) disentanglement (structboost.BAEConfig attribute) disentanglement_alpha (structboost.BAEConfig attribute) disentanglement_lambda (structboost.BAEConfig attribute) E early_stopping_patience (structboost.BAEConfig attribute) enable_early_stopping (structboost.BAEConfig attribute) encode_obs_covariates() (in module structboost) encoded (structboost.ObsCovariateEncoding attribute) encoded_columns (structboost.ObsCovariateEncoding attribute) encoder_delta (structboost.TrainingReport attribute) encoder_weight_norm (structboost.TrainingReport attribute) expected_false_positives (structboost.StabilitySelectionResult attribute) export_interactive_html() (in module structboost) extract_gene_rankings() (in module structboost) F fit() (structboost.BAE method) fit_transform() (structboost.BAE method) fitted_prior_weights (structboost.BAE property) forward() (structboost.BAE method) frequency (structboost.StabilitySelectionResult attribute) from_dict() (structboost.TrainingReport class method) from_reference() (structboost.BAE class method) G gene_level (structboost.SimulationResult attribute) gene_means (structboost.SimulationResult attribute) gene_names (structboost.GeneRanking attribute) GeneRanking (class in structboost) get_encoder_weights() (structboost.BAE method) get_latent() (structboost.BAE method) get_splitsoftmax_encoder_weights() (structboost.BAE method) H hierarchy (structboost.SimulationResult attribute) I iteration (structboost.TrainingReport attribute) L latent_dim (structboost.BAEConfig attribute) latent_var_per_dim (structboost.TrainingReport attribute) leaf_paths (structboost.SimulationResult attribute) linear_ceiling() (in module structboost) load() (structboost.BAE class method) looks_like_ensembl() (in module structboost) loss_post_boost (structboost.TrainingReport attribute) loss_post_decoder (structboost.TrainingReport attribute) loss_pre_boost (structboost.TrainingReport attribute) M marker_genes (structboost.SimulationResult property) marker_mask (structboost.SimulationResult attribute) max_iterations (structboost.BAEConfig attribute) mean (structboost.ObsCovariateEncoding attribute) min_dim_cosine (structboost.TrainingReport attribute) mode (structboost.StabilitySelectionResult attribute) N n_columns (structboost.ObsCovariateEncoding attribute) n_iterations (structboost.StabilitySelectionResult attribute) (structboost.TrainingReport property) n_prior_dims (structboost.BAE property) n_runs (structboost.StabilitySelectionResult property) n_selected (structboost.TrainingReport attribute) n_selected_genes (structboost.DimensionGeneRanking attribute) n_selected_per_dim (structboost.TrainingReport attribute) n_subsamples (structboost.StabilitySelectionResult attribute) negative_annotation (structboost.DimensionAnnotation attribute) negative_genes (structboost.DimensionGeneRanking attribute) novel_weights (structboost.BAE property) nuisance_ridge (structboost.BAEConfig attribute) O obs_columns (structboost.ObsCovariateEncoding attribute) ObsCovariateEncoding (class in structboost) overall_annotation (structboost.DimensionAnnotation attribute) P params (structboost.SimulationResult attribute) plot_boosting_coefficient_paths() (in module structboost) plot_top_boosting_coefficients() (in module structboost) plot_training_diagnostics() (in module structboost) positive_annotation (structboost.DimensionAnnotation attribute) positive_genes (structboost.DimensionGeneRanking attribute) prior_mode (structboost.BAEConfig attribute) prior_weights (structboost.BAE property) R read_encoder_weights() (in module structboost) reconstruct() (structboost.BAE method) S save() (structboost.BAE method) SCALED_LATENT_KEY (structboost.BAE attribute) seed (structboost.BAEConfig attribute) selection (structboost.AllboostHistory attribute) sign_consistency (structboost.StabilitySelectionResult attribute) sim_scrnaseq_anndata() (in module structboost) sim_scrnaseq_data() (in module structboost) SimulationResult (class in structboost) size_factors (structboost.SimulationResult attribute) split_softmax (structboost.BAEConfig attribute) stability_selection() (in module structboost) (structboost.BAE method) StabilitySelectionResult (class in structboost) stable_encoder() (structboost.StabilitySelectionResult method) stable_support (structboost.StabilitySelectionResult attribute) stage_labels (structboost.SimulationResult attribute) stage_sizes (structboost.SimulationResult attribute) std (structboost.ObsCovariateEncoding attribute) subsample_frac (structboost.StabilitySelectionResult attribute) support_jaccard (structboost.TrainingReport attribute) T target_grad_norm (structboost.TrainingReport attribute) target_optim_lr (structboost.BAEConfig attribute) threshold (structboost.StabilitySelectionResult attribute) to_dict() (structboost.TrainingReport method) train_loss (structboost.TrainingReport attribute) training_history (structboost.BAE property) training_report (structboost.BAE property) TrainingReport (class in structboost) transfer_diagnostics() (structboost.BAE method) transform() (structboost.BAE method) transform_obs_covariates() (in module structboost) transform_splitsoftmax() (structboost.BAE method) W weight_change_rel (structboost.TrainingReport attribute) weights (structboost.GeneRanking attribute) write_annotations_to_h5ad() (in module structboost) write_encoder_weights() (in module structboost)