API Reference

Below are the API pages showing already-implemented candle functionality. Let us know if you have any feedback!

• DATA_PREPROCESSING_UTILS
  • candle.data_preprocessing_utils.quantile_normalization
  • candle.data_preprocessing_utils.generate_cross_validation_partition
• PYTORCH_UTILS
  • candle.pytorch_utils.set_pytorch_threads
  • candle.pytorch_utils.set_pytorch_seed
  • candle.pytorch_utils.get_pytorch_function
  • candle.pytorch_utils.build_pytorch_activation
  • candle.pytorch_utils.build_pytorch_optimizer
  • candle.pytorch_utils.pytorch_initialize
  • candle.pytorch_utils.pytorch_xent
  • candle.pytorch_utils.pytorch_mse
• BENCHMARK_DEF
  • candle.benchmark_def.Benchmark
  • candle.benchmark_def.create_params
• UQ_UTILS
  • candle.uq_utils.UQDistDict
  • candle.uq_utils.generate_index_distribution
  • candle.uq_utils.generate_index_distribution_from_fraction
  • candle.uq_utils.generate_index_distribution_from_blocks
  • candle.uq_utils.generate_index_distribution_from_block_list
  • candle.uq_utils.compute_limits
  • candle.uq_utils.fill_array
  • candle.uq_utils.compute_statistics_homoscedastic_summary
  • candle.uq_utils.compute_statistics_homoscedastic
  • candle.uq_utils.compute_statistics_heteroscedastic
  • candle.uq_utils.compute_statistics_quantile
  • candle.uq_utils.split_data_for_empirical_calibration
  • candle.uq_utils.compute_empirical_calibration_interpolation
• GENERIC_UTILS
  • candle.generic_utils.Progbar
  • candle.generic_utils.get_from_module
  • candle.generic_utils.make_tuple
  • candle.generic_utils.func_dump
  • candle.generic_utils.func_load
  • candle.generic_utils.func_reconstruct_closure
  • candle.generic_utils.display_table
• FEATURE_SELECTION_UTILS
  • candle.feature_selection_utils.select_features_by_missing_values
  • candle.feature_selection_utils.select_features_by_variation
  • candle.feature_selection_utils.select_decorrelated_features
• UQ_KERAS_UTILS
  • candle.uq_keras_utils.AbstentionAdapt_Callback
  • candle.uq_keras_utils.Contamination_Callback
  • candle.uq_keras_utils.abstention_loss
  • candle.uq_keras_utils.sparse_abstention_loss
  • candle.uq_keras_utils.abstention_acc_metric
  • candle.uq_keras_utils.sparse_abstention_acc_metric
  • candle.uq_keras_utils.abstention_metric
  • candle.uq_keras_utils.acc_class_i_metric
  • candle.uq_keras_utils.abstention_acc_class_i_metric
  • candle.uq_keras_utils.abstention_class_i_metric
  • candle.uq_keras_utils.modify_labels
  • candle.uq_keras_utils.add_model_output
  • candle.uq_keras_utils.r2_heteroscedastic_metric
  • candle.uq_keras_utils.mae_heteroscedastic_metric
  • candle.uq_keras_utils.mse_heteroscedastic_metric
  • candle.uq_keras_utils.meanS_heteroscedastic_metric
  • candle.uq_keras_utils.heteroscedastic_loss
  • candle.uq_keras_utils.quantile_loss
  • candle.uq_keras_utils.triple_quantile_loss
  • candle.uq_keras_utils.quantile_metric
  • candle.uq_keras_utils.add_index_to_output
  • candle.uq_keras_utils.contamination_loss
  • candle.uq_keras_utils.mse_contamination_metric
  • candle.uq_keras_utils.mae_contamination_metric
  • candle.uq_keras_utils.r2_contamination_metric
• CKPT_PYTORCH_UTILS
  • candle.ckpt_pytorch_utils.CandleCkptPyTorch
• VIZ_UTILS
  • candle.viz_utils.plot_history
  • candle.viz_utils.plot_scatter
  • candle.viz_utils.plot_error
  • candle.viz_utils.plot_array
  • candle.viz_utils.plot_density_observed_vs_predicted
  • candle.viz_utils.plot_2d_density_sigma_vs_error
  • candle.viz_utils.plot_histogram_error_per_sigma
  • candle.viz_utils.plot_decile_predictions
  • candle.viz_utils.plot_calibration_interpolation
  • candle.viz_utils.plot_calibrated_std
  • candle.viz_utils.plot_contamination
  • candle.viz_utils.plot_metrics
• CKPT_UTILS
  • candle.ckpt_utils.ModelType
  • candle.ckpt_utils.CandleCkptModel
  • candle.ckpt_utils.ParamType
  • candle.ckpt_utils.CandleCkpt
  • candle.ckpt_utils.ParamRequired
  • candle.ckpt_utils.ckpt_parser
  • candle.ckpt_utils.ckpt_defs
• CKPT_KERAS_UTILS
  • candle.ckpt_keras_utils.CandleCkptKeras
• CLR_KERAS_UTILS
  • candle.clr_keras_utils.CyclicLR
  • candle.clr_keras_utils.clr_check_args
  • candle.clr_keras_utils.clr_set_args
  • candle.clr_keras_utils.clr_callback
• DATA_UTILS
  • candle.data_utils.to_categorical
  • candle.data_utils.convert_to_class
  • candle.data_utils.scale_array
  • candle.data_utils.impute_and_scale_array
  • candle.data_utils.drop_impute_and_scale_dataframe
  • candle.data_utils.discretize_dataframe
  • candle.data_utils.discretize_array
  • candle.data_utils.lookup
  • candle.data_utils.load_X_data
  • candle.data_utils.load_X_data2
  • candle.data_utils.load_Xy_one_hot_data
  • candle.data_utils.load_Xy_one_hot_data2
  • candle.data_utils.load_Xy_data2
  • candle.data_utils.load_Xy_data_noheader
  • candle.data_utils.load_csv_data
• HELPER_UTILS
  • candle.helper_utils.fetch_file
  • candle.helper_utils.verify_path
  • candle.helper_utils.set_up_logger
  • candle.helper_utils.eval_string_as_list
  • candle.helper_utils.eval_string_as_list_of_lists
  • candle.helper_utils.str2bool
  • candle.helper_utils.keras_default_config
  • candle.helper_utils.set_seed
• FILE_UTILS
  • candle.file_utils.get_file
  • candle.file_utils.validate_file
  • candle.file_utils.directory_tree_from_parameters
• MODAC_UTILS
  • candle.modac_utils.get_file_from_modac
  • candle.modac_utils.register_file_to_modac
  • candle.modac_utils.authenticate_modac
  • candle.modac_utils.query_yes_no
  • candle.modac_utils.get_dataObject_modac_filesize
  • candle.modac_utils.get_dataObject_modac_md5sum
  • candle.modac_utils.get_dataObject_modac_meta
• NOISE_UTILS
  • candle.noise_utils.add_noise_new
  • candle.noise_utils.add_noise
  • candle.noise_utils.label_flip
  • candle.noise_utils.label_flip_correlated
  • candle.noise_utils.add_gaussian_noise
  • candle.noise_utils.add_column_noise
  • candle.noise_utils.add_cluster_noise
• PARSING_UTILS
  • candle.parsing_utils.ArgumentStruct
  • candle.parsing_utils.ListOfListsAction
  • candle.parsing_utils.ParseDict
  • candle.parsing_utils.ConfigDict
  • candle.parsing_utils.extract_keywords
  • candle.parsing_utils.check_flag_conflicts
  • candle.parsing_utils.check_file_parameters_exists
  • candle.parsing_utils.finalize_parameters
  • candle.parsing_utils.args_overwrite_config
  • candle.parsing_utils.get_choice
  • candle.parsing_utils.parse_from_dictlist
  • candle.parsing_utils.parse_common
• KERAS_UTILS
  • candle.keras_utils.PermanentDropout
  • candle.keras_utils.LoggingCallback
  • candle.keras_utils.TerminateOnTimeOut
  • candle.keras_utils.CandleRemoteMonitor
  • candle.keras_utils.set_parallelism_threads
  • candle.keras_utils.set_seed
  • candle.keras_utils.get_function
  • candle.keras_utils.build_optimizer
  • candle.keras_utils.build_initializer
  • candle.keras_utils.xent
  • candle.keras_utils.r2
  • candle.keras_utils.mae
  • candle.keras_utils.mse
  • candle.keras_utils.covariance
  • candle.keras_utils.corr
  • candle.keras_utils.evaluate_autoencoder
  • candle.keras_utils.register_permanent_dropout
  • candle.keras_utils.compute_trainable_params
• P1_UTILS
  • candle.P1_utils.calculate_concordance_correlation_coefficient
  • candle.P1_utils.generalization_feature_selection
  • candle.P1_utils.coxen_single_drug_gene_selection
  • candle.P1_utils.coxen_multi_drug_gene_selection
  • candle.P1_utils.generate_gene_set_data
  • candle.P1_utils.design_mat
  • candle.P1_utils.it_sol
  • candle.P1_utils.aprior
  • candle.P1_utils.bprior
  • candle.P1_utils.postmean
  • candle.P1_utils.postvar
  • candle.P1_utils.combat_batch_effect_removal