Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W A add_date_colorbar() (in module pimmslearn.analyzers.analyzers) add_default_paths() (in module pimmslearn.nb) add_indices() (in module pimmslearn.io) add_metrics() (pimmslearn.models.Metrics method) AETransformer (class in pimmslearn.sklearn.ae_transformer) after_loss() (pimmslearn.models.ae.ModelAdapter method) (pimmslearn.models.ae.ModelAdapterVAE method) after_pred() (pimmslearn.models.ae.DatasetWithTargetAdapter method) (pimmslearn.models.ae.ModelAdapter method) (pimmslearn.models.ae.ModelAdapterVAE method) Analysis (class in pimmslearn.analyzers) AnalyzePeptides (class in pimmslearn.analyzers.analyzers) append_to_filepath() (in module pimmslearn.utils) apply_default_layout() (in module pimmslearn.plotting.plotly) args_from_dict() (in module pimmslearn.nb) as_hex() (pimmslearn.plotting.defaults.ModelColorVisualizer method) assign_colors() (in module pimmslearn.plotting.defaults) Autoencoder (class in pimmslearn.models.ae) AutoEncoderAnalysis (class in pimmslearn.models.ae) B bcolors (class in pimmslearn.io.format) before_batch() (pimmslearn.models.ae.DatasetWithTargetAdapter method) (pimmslearn.models.ae.ModelAdapter method) (pimmslearn.models.ae.ModelAdapterVAE method) BOLD (pimmslearn.io.format.bcolors attribute) build_df_from_pred_batches() (in module pimmslearn.model) C calc_errors_per_bin() (in module pimmslearn.pandas.calc_errors) calc_errors_per_feat() (in module pimmslearn.pandas) (in module pimmslearn.pandas.calc_errors) calc_net_weight_count() (in module pimmslearn.models) calculate_PCs() (pimmslearn.analyzers.analyzers.AnalyzePeptides method) calculte_metrics() (in module pimmslearn.models) cast_object_to_category() (in module pimmslearn.analyzers.analyzers) check_split_integrity() (in module pimmslearn.sampling) class_full_module() (in module pimmslearn.io.format) classname() (in module pimmslearn.io.format) CollabAnalysis (class in pimmslearn.models.collab) CollaborativeFilteringTransformer (class in pimmslearn.sklearn.cf_transformer) collect() (in module pimmslearn.models.collect_dumps) collect_configs() (in module pimmslearn.models.collect_dumps) collect_metrics() (in module pimmslearn.models) (in module pimmslearn.models.collect_dumps) combine_data() (in module pimmslearn.models.collab) compare_indices() (in module pimmslearn.models) compute_kld() (in module pimmslearn.models.vae) compute_moments_shift() (in module pimmslearn.imputation) compute_stats_missing() (in module pimmslearn.data_handling) Config (class in pimmslearn.nb) corr_lower_triangle() (in module pimmslearn.analyzers.analyzers) coverage() (in module pimmslearn.data_handling) create_random_df() (in module pimmslearn.utils) create_random_missing_data() (in module pimmslearn.utils) create_random_missing_data_long() (in module pimmslearn.utils) Cutoffs (class in pimmslearn.analyzers.diff_analysis) D DatasetWithMaskAndNoTarget (class in pimmslearn.io.datasets) DatasetWithTarget (class in pimmslearn.io.datasets) DatasetWithTargetAdapter (class in pimmslearn.models.ae) DatasetWithTargetSpecifyTarget (class in pimmslearn.io.datasets) DataSplits (class in pimmslearn.io.datasplits) decode() (pimmslearn.models.vae.VAE method) decompose_NAs() (in module pimmslearn.pandas.missing_data) describe_peptides() (pimmslearn.analyzers.analyzers.AnalyzePeptides method) df (pimmslearn.analyzers.analyzers.AnalyzePeptides attribute) df_long (pimmslearn.analyzers.analyzers.AnalyzePeptides property) df_wide (pimmslearn.analyzers.analyzers.AnalyzePeptides property) dls (pimmslearn.models.analysis.ModelAnalysis attribute) dump() (pimmslearn.io.datasplits.DataSplits method) (pimmslearn.nb.Config method) dump_json() (in module pimmslearn.io) dump_to_csv() (in module pimmslearn.io) E encode() (pimmslearn.models.vae.VAE method) ENDC (pimmslearn.io.format.bcolors attribute) extend_name() (in module pimmslearn.io) F FAIL (pimmslearn.io.format.bcolors attribute) feat_completness_over_samples (pimmslearn.analyzers.diff_analysis.Cutoffs attribute) feature_frequency() (in module pimmslearn.sampling) filename_tmp (pimmslearn.models.RecorderDump attribute) files (pimmslearn.io.PathsList attribute) fit() (pimmslearn.sklearn.ae_transformer.AETransformer method) (pimmslearn.sklearn.cf_transformer.CollaborativeFilteringTransformer method) flatten_dict_of_dicts() (in module pimmslearn.pandas) fname_stub (pimmslearn.analyzers.analyzers.AnalyzePeptides property) folder (pimmslearn.io.PathsList attribute) forward() (pimmslearn.models.ae.Autoencoder method) (pimmslearn.models.vae.VAE method) frequency_by_index() (in module pimmslearn.sampling) from_csv() (in module pimmslearn.io.load) (pimmslearn.analyzers.analyzers.AnalyzePeptides class method) from_dict() (pimmslearn.nb.Config class method) from_folder() (pimmslearn.io.datasplits.DataSplits class method) from_pickle() (in module pimmslearn.io) (in module pimmslearn.io.load) (pimmslearn.analyzers.analyzers.AnalyzePeptides class method) G gaussian_log_prob() (in module pimmslearn.models.vae) get_absolute_error() (in module pimmslearn.pandas) (in module pimmslearn.pandas.calc_errors) get_columns_accessor() (in module pimmslearn.pandas) get_columns_accessor_from_iterable() (in module pimmslearn.pandas) get_columns_namedtuple() (in module pimmslearn.pandas) get_consecutive_data_indices() (in module pimmslearn.analyzers.analyzers) get_consecutive_dates() (pimmslearn.analyzers.analyzers.AnalyzePeptides method) get_counts_per_bin() (in module pimmslearn.pandas) get_data_for_errors_by_median() (in module pimmslearn.plotting.errors) get_dectection_limit() (pimmslearn.analyzers.analyzers.AnalyzePeptides method) get_df_from_nested_dict() (in module pimmslearn.models) get_disease_association() (in module pimmslearn.databases.diseases) get_dls() (in module pimmslearn.io.dataloaders) get_fname_from_keys() (in module pimmslearn.io) get_last_index_matching_proportion() (in module pimmslearn.pandas) get_latent_space() (in module pimmslearn.model) get_lower_whiskers() (in module pimmslearn.pandas) get_min_max_iterable() (in module pimmslearn.plotting.data) get_missing_values() (in module pimmslearn.models.ae) (in module pimmslearn.models.collab) get_mu_and_logvar() (pimmslearn.models.vae.VAE method) get_params() (in module pimmslearn.nb) get_PCA() (in module pimmslearn.sklearn) (pimmslearn.analyzers.analyzers.AnalyzePeptides method) get_preds_from_df() (in module pimmslearn.models.ae) (pimmslearn.models.ae.AutoEncoderAnalysis method) get_prop_not_na() (pimmslearn.analyzers.analyzers.AnalyzePeptides method) get_record() (in module pimmslearn.pandas.missing_data) get_sorted_not_missing() (in module pimmslearn.data_handling) get_test_dl() (in module pimmslearn.io.dataloaders) (pimmslearn.models.ae.AutoEncoderAnalysis method) get_thresholds() (in module pimmslearn.sampling) get_unique_non_unique_columns() (in module pimmslearn.pandas) H HEADER (pimmslearn.io.format.bcolors attribute) highlight_min() (in module pimmslearn.pandas) I impute_shifted_normal() (in module pimmslearn.imputation) index_to_dict() (in module pimmslearn.pandas) interpolate() (in module pimmslearn.pandas) (pimmslearn.io.datasplits.DataSplits method) inverse_transform() (in module pimmslearn.transform) (pimmslearn.transform.MinMaxScaler method) (pimmslearn.transform.VaepPipeline method) is_wide_format (pimmslearn.io.datasplits.DataSplits attribute) items() (pimmslearn.nb.Config method) K key_map() (in module pimmslearn.pandas) keys() (pimmslearn.nb.Config method) L LatentAnalysis (class in pimmslearn.analyzers.analyzers) learn (pimmslearn.models.analysis.ModelAnalysis attribute) length() (in module pimmslearn.pandas) list_files() (in module pimmslearn.pandas.missing_data) load() (pimmslearn.io.datasplits.DataSplits method) (pimmslearn.models.RecorderDump class method) load_config_file() (in module pimmslearn.models.collect_dumps) load_freq() (in module pimmslearn.io.datasplits) load_items() (in module pimmslearn.io.datasplits) load_json() (in module pimmslearn.io) load_metric_file() (in module pimmslearn.models.collect_dumps) load_predictions() (in module pimmslearn.analyzers.compare_predictions) load_single_csv_pred_file() (in module pimmslearn.analyzers.compare_predictions) load_split_prediction_by_modelkey() (in module pimmslearn.analyzers.compare_predictions) log_transform() (pimmslearn.analyzers.analyzers.AnalyzePeptides method) long_format() (in module pimmslearn.io.datasplits) loss_fct() (in module pimmslearn.models.vae) M main() (in module pimmslearn.cmd_interface.setup_diff_analysis_website) (in module pimmslearn.cmd_interface.setup_imp_cp_website) make_large_descriptors() (in module pimmslearn.plotting) make_pandas_compatible() (in module pimmslearn.transform) Metrics (class in pimmslearn.models) min_feat_in_sample (pimmslearn.analyzers.diff_analysis.Cutoffs attribute) min_max() (in module pimmslearn.plotting.data) MinMaxScaler (class in pimmslearn.transform) model (pimmslearn.models.analysis.ModelAnalysis attribute) ModelAdapter (class in pimmslearn.models.ae) ModelAdapterVAE (class in pimmslearn.models.ae) ModelAnalysis (class in pimmslearn.models.analysis) ModelColorVisualizer (class in pimmslearn.plotting.defaults) module pimmslearn pimmslearn.analyzers pimmslearn.analyzers.analyzers pimmslearn.analyzers.compare_predictions pimmslearn.analyzers.diff_analysis pimmslearn.cmd_interface pimmslearn.cmd_interface.setup_diff_analysis_website pimmslearn.cmd_interface.setup_imp_cp_website pimmslearn.data_handling pimmslearn.databases pimmslearn.databases.diseases pimmslearn.filter pimmslearn.imputation pimmslearn.io pimmslearn.io.dataloaders pimmslearn.io.datasets pimmslearn.io.datasplits pimmslearn.io.format pimmslearn.io.load pimmslearn.io.types pimmslearn.logging pimmslearn.model pimmslearn.models pimmslearn.models.ae pimmslearn.models.analysis pimmslearn.models.collab pimmslearn.models.collect_dumps pimmslearn.models.vae pimmslearn.nb pimmslearn.normalization pimmslearn.pandas pimmslearn.pandas.calc_errors pimmslearn.pandas.missing_data pimmslearn.plotting pimmslearn.plotting.data pimmslearn.plotting.defaults pimmslearn.plotting.errors pimmslearn.plotting.plotly pimmslearn.sampling pimmslearn.sklearn pimmslearn.sklearn.ae_transformer pimmslearn.sklearn.cf_transformer pimmslearn.stats pimmslearn.transform pimmslearn.utils N nan (pimmslearn.io.datasets.PeptideDatasetInMemory attribute) normalize_by_median() (in module pimmslearn.normalization) normalize_sceptre() (in module pimmslearn.normalization) O OKBLUE (pimmslearn.io.format.bcolors attribute) OKCYAN (pimmslearn.io.format.bcolors attribute) OKGREEN (pimmslearn.io.format.bcolors attribute) overwrite_entry() (pimmslearn.nb.Config method) P params (pimmslearn.models.analysis.ModelAnalysis attribute) parse_dict() (in module pimmslearn.io) parse_query_expression() (in module pimmslearn.pandas) PathsList (class in pimmslearn.io) PeptideDatasetInMemory (class in pimmslearn.io.datasets) percent_missing() (in module pimmslearn.pandas.missing_data) percent_non_missing() (in module pimmslearn.pandas.missing_data) pimmslearn module pimmslearn.analyzers module pimmslearn.analyzers.analyzers module pimmslearn.analyzers.compare_predictions module pimmslearn.analyzers.diff_analysis module pimmslearn.cmd_interface module pimmslearn.cmd_interface.setup_diff_analysis_website module pimmslearn.cmd_interface.setup_imp_cp_website module pimmslearn.data_handling module pimmslearn.databases module pimmslearn.databases.diseases module pimmslearn.filter module pimmslearn.imputation module pimmslearn.io module pimmslearn.io.dataloaders module pimmslearn.io.datasets module pimmslearn.io.datasplits module pimmslearn.io.format module pimmslearn.io.load module pimmslearn.io.types module pimmslearn.logging module pimmslearn.model module pimmslearn.models module pimmslearn.models.ae module pimmslearn.models.analysis module pimmslearn.models.collab module pimmslearn.models.collect_dumps module pimmslearn.models.vae module pimmslearn.nb module pimmslearn.normalization module pimmslearn.pandas module pimmslearn.pandas.calc_errors module pimmslearn.pandas.missing_data module pimmslearn.plotting module pimmslearn.plotting.data module pimmslearn.plotting.defaults module pimmslearn.plotting.errors module pimmslearn.plotting.plotly module pimmslearn.sampling module pimmslearn.sklearn module pimmslearn.sklearn.ae_transformer module pimmslearn.sklearn.cf_transformer module pimmslearn.stats module pimmslearn.transform module pimmslearn.utils module plot_by_category() (pimmslearn.analyzers.analyzers.LatentAnalysis method) plot_by_date() (pimmslearn.analyzers.analyzers.LatentAnalysis method) plot_corr_histogram() (in module pimmslearn.analyzers.analyzers) plot_cutoffs() (in module pimmslearn.plotting) plot_date_map() (in module pimmslearn.analyzers.analyzers) plot_errors_binned() (in module pimmslearn.plotting.errors) plot_errors_by_median() (in module pimmslearn.plotting.errors) plot_feat_counts() (in module pimmslearn.plotting) plot_feat_median_over_prop_missing() (in module pimmslearn.plotting.data) plot_histogram_intensities() (in module pimmslearn.plotting.data) plot_loss() (in module pimmslearn.models) (pimmslearn.models.RecorderDump method) (pimmslearn.sklearn.cf_transformer.CollaborativeFilteringTransformer method) plot_missing_dist_boxplots() (in module pimmslearn.plotting.data) plot_missing_dist_highdim() (in module pimmslearn.plotting.data) plot_missing_pattern_histogram() (in module pimmslearn.plotting.data) plot_missing_pattern_violinplot() (in module pimmslearn.plotting.data) plot_observations() (in module pimmslearn.plotting.data) plot_pca() (pimmslearn.analyzers.analyzers.AnalyzePeptides method) plot_rolling_error() (in module pimmslearn.plotting) (in module pimmslearn.plotting.errors) plot_scatter() (in module pimmslearn.analyzers.analyzers) plot_training_losses() (in module pimmslearn.models) prop_unique_index() (in module pimmslearn.pandas) R RecorderDump (class in pimmslearn.models) remove_keys_from_globals() (in module pimmslearn.nb) reparameterize() (pimmslearn.models.vae.VAE method) replace_with() (in module pimmslearn.pandas) resolve_path() (in module pimmslearn.io) resolve_type() (in module pimmslearn.io.types) S sample_data() (in module pimmslearn.sampling) sample_mnar_mcar() (in module pimmslearn.sampling) save() (pimmslearn.models.RecorderDump method) savefig() (in module pimmslearn) (in module pimmslearn.plotting) scatter_plot_w_dates() (in module pimmslearn.analyzers.analyzers) seaborn_scatter() (in module pimmslearn.analyzers.analyzers) search_files() (in module pimmslearn.io) search_subfolders() (in module pimmslearn.io) select_content() (in module pimmslearn.models.collect_dumps) select_dates() (in module pimmslearn.plotting) select_feat() (in module pimmslearn.analyzers.diff_analysis) select_features() (in module pimmslearn.filter) select_max_by() (in module pimmslearn.pandas) select_raw_data() (in module pimmslearn.analyzers.diff_analysis) select_xticks() (in module pimmslearn.plotting) set_fit_request() (pimmslearn.sklearn.ae_transformer.AETransformer method) (pimmslearn.sklearn.cf_transformer.CollaborativeFilteringTransformer method) setup_logger() (in module pimmslearn.logging) setup_logger_w_file() (in module pimmslearn.logging) setup_nb_logger() (in module pimmslearn.logging) split_nb_name() (in module pimmslearn.cmd_interface.setup_diff_analysis_website) (in module pimmslearn.cmd_interface.setup_imp_cp_website) split_prediction_by_mask() (in module pimmslearn.models) stats (pimmslearn.analyzers.analyzers.AnalyzePeptides attribute) stats_by_level() (in module pimmslearn.imputation) T test_y (pimmslearn.io.datasplits.DataSplits attribute) to_long_format() (in module pimmslearn.io.datasplits) (pimmslearn.analyzers.analyzers.AnalyzePeptides method) (pimmslearn.io.datasplits.DataSplits method) to_pickle() (in module pimmslearn.io) to_tensor() (in module pimmslearn.io.datasets) to_wide_format() (pimmslearn.analyzers.analyzers.AnalyzePeptides method) (pimmslearn.io.datasplits.DataSplits method) train_X (pimmslearn.io.datasplits.DataSplits attribute) transform (pimmslearn.models.analysis.ModelAnalysis attribute) transform() (in module pimmslearn.transform) (pimmslearn.sklearn.ae_transformer.AETransformer method) (pimmslearn.sklearn.cf_transformer.CollaborativeFilteringTransformer method) (pimmslearn.transform.MinMaxScaler method) (pimmslearn.transform.VaepPipeline method) U UNDERLINE (pimmslearn.io.format.bcolors attribute) unique_cols() (in module pimmslearn.pandas) update_from_dict() (pimmslearn.nb.Config method) V VAE (class in pimmslearn.models.vae) VaepPipeline (class in pimmslearn.transform) val_y (pimmslearn.io.datasplits.DataSplits attribute) values() (pimmslearn.nb.Config method) verify_df() (in module pimmslearn.io.load) W WARNING (pimmslearn.io.format.bcolors attribute) wide_format() (in module pimmslearn.io.datasplits)
