├── .gitmodules ├── LICENSE ├── README.md ├── Run_PREFER.ipynb ├── __init__.py ├── analysis_notebooks ├── Best_PREFER_model_VS_RF.ipynb ├── Plot_performance_distributions_for_representation.ipynb ├── README.txt └── TestSet_Bootstrapping.ipynb ├── api_version.txt ├── cddd-environment-light.yml ├── cddd-environment.yml ├── compute_model_based_representations.py ├── config_files ├── config_PREFER_logD.yaml ├── config_PREFER_smalldata.yaml ├── config_PREFER_solub.yaml └── config_model_based_representations.yaml ├── moler-environment-light.yml ├── moler-environment.yml ├── prefer-environment.yml ├── prefer ├── __init__.py ├── azure_ml │ ├── README.md │ ├── aml_config.py │ ├── aml_configuration │ │ └── aml_config.json │ ├── config_logD_azure.yaml │ ├── exceptions.py │ ├── get_model_utils.py │ ├── included_prefixes.json │ ├── model_registration_prefer.py │ ├── model_registration_utils.py │ ├── reproducibility.py │ ├── schedule_global_model_pipeline.py │ ├── telemetry_utils.py │ └── utils.py ├── docs │ ├── PREFER_scheme.png │ └── SaltsMod.txt ├── model_based_representations │ ├── __init__.py │ ├── cddd_wrapper.py │ ├── interface.py │ ├── model_based_representations_factory.py │ ├── models │ │ └── __init__.py │ └── moler_wrapper.py ├── molecule_representations │ ├── __init__.py │ ├── descriptors2D_representations_builder.py │ ├── fingerprints_representations_builder.py │ └── model_representations_builder.py ├── schema │ ├── __init__.py │ └── config.py ├── scripts │ ├── __init__.py │ ├── aml_context.py │ ├── combine_results.py │ ├── get_representations.py │ ├── model_wrapper.py │ ├── run_PREFER.py │ └── utils.py ├── src │ ├── __init__.py │ ├── benchmarking.py │ ├── molecule_representations.py │ ├── molecule_representations_builder.py │ ├── prefer_model_wrapper.py │ └── vector_molecule_representations.py ├── tests │ ├── __init__.py │ ├── data_for_test │ │ └── logDPublic.csv │ ├── file_for_test │ │ ├── config_PREFER_test_custom_autosklearn.yaml │ │ └── logD_desirability_scores.yaml │ ├── test_autosklearn_customization.py │ ├── test_check_input_dataframe.py │ ├── test_data_preparation.py │ ├── test_filtering.py │ ├── test_helpers.py │ ├── test_prefer_model_wrapper.py │ └── test_scripts.py └── utils │ ├── __init__.py │ ├── automation.py │ ├── check_input_dataframe.py │ ├── data_preparation.py │ ├── data_utils.py │ ├── features_scaling.py │ ├── filtering.py │ ├── mapping.py │ ├── models_evaluation.py │ ├── models_utils.py │ ├── post_processing_and_optimization_helpers.py │ ├── random_utils.py │ ├── run_automl.py │ ├── save_load.py │ └── splitting_strategies.py ├── pyproject.toml ├── run_prefer_automation.py ├── setup.py └── small_data_experiments ├── README_smalldata.txt ├── analysis_smalldata_example.ipynb ├── extract_zipped_files.ipynb ├── run_PREFER_smalldata_example.ipynb └── run_prefer_automation_smalldata.py /.gitmodules: -------------------------------------------------------------------------------- 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