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Installation
Getting Started
Usage Examples
CANDLE Compliance Example
CANDLE Checkpoint Examples
API Reference
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
Tutorials
Writing candle compliant code
MNIST example
.. Cite CANDLE LIB
For developers
Contributor's Guide
GitHub Issues
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CANDLE Supervisor
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.rst
.pdf
candle.P1_utils.design_mat
Contents
design_mat()
candle.P1_utils.design_mat
#
candle.P1_utils.
design_mat
(
mod
,
numerical_covariates
,
batch_levels
)
#
Contents
design_mat()
