Index

A

ACCURACY (optunaz.config.optconfig.ClassificationScore attribute) activation (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) AdaBoostClassifier (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] AdaBoostClassifier.AdaBoostClassifierParameters (class in optunaz.config.buildconfig) AdaBoostClassifier.Parameters (class in optunaz.config.optconfig), [1] AdaBoostClassifier.Parameters.AdaBoostClassifierParametersLearningRate (class in optunaz.config.optconfig), [1] AdaBoostClassifier.Parameters.AdaBoostClassifierParametersNEstimators (class in optunaz.config.optconfig), [1] add_boolean_guards_for_schema_properties() (in module optunaz.utils.schema) add_ellipsis() (in module optunaz.utils.mlflow) addsibling() (in module optunaz.utils.schema) addSlurmRetry() (optunaz.automl.ModelDispatcher method) addtitles() (in module optunaz.utils.schema) aggregation (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) aggregation_norm (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) algorith_hash (optunaz.utils.tracking.TrackingData attribute) Algorithm (class in optunaz.config) (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig) algorithm (optunaz.config.buildconfig.BuildConfig attribute) ALGORITHM_HASH (optunaz.utils.enums.TrialParams attribute) ALGORITHM_NAME (optunaz.utils.enums.TrialParams attribute) algorithms (optunaz.config.optconfig.OptimizationConfig attribute) ALGORITHMS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_ADABOOSTCLASSIFIER (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_ADABOOSTCLASSIFIER_LEARNING_RATE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_ADABOOSTCLASSIFIER_N_ESTIMATORS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CALIBRATEDCLASSIFIERCV (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CALIBRATEDCLASSIFIERCV_ENSEMBLE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CALIBRATEDCLASSIFIERCV_ESTIMATOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CALIBRATEDCLASSIFIERCV_METHOD (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CALIBRATEDCLASSIFIERCV_N_FOLDS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CALIBRATEDCLASSIFIERCV_PARAMS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_ACTIVATION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_AGGREGATION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_AGGREGATION_NORM (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_BATCH_SIZE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_CLASSIFIER (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_DEPTH (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_DROPOUT (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_ENSEMBLE_SIZE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_EPOCHS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_FEATURES_GENERATOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_FFN_HIDDEN_SIZE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_FFN_NUM_LAYERS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_FINAL_LR_RATIO_EXP (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_FRZN (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_HIDDEN_SIZE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_HYPEROPT_CLASSIFIER (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_HYPEROPT_REGRESSOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_INIT_LR_RATIO_EXP (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_MAX_LR_EXP (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_NUM_ITERS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_PRETRAINED_MODEL (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_REGRESSOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_SEARCH_PARAMETER_LEVEL (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_STARTUP_RANDOM_ITERS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CHEMPROP_WARMUP_EPOCHS_RATIO (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CUSTOM_FILE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CUSTOM_REFIT_MODEL (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CUSTOMCLASSIFIERMODEL (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_CUSTOMREGRESSIONMODEL (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_ESTIMATOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_HIGH (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute)

ALGORITHMS_INTERFACE_SKLEARN (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_INTERFACE_XGBOOST (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_KNEIGHBORS_METRIC (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_KNEIGHBORS_N_NEIGHBORS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_KNEIGHBORS_WEIGHTS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_KNEIGHBORSCLASSIFIER (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_KNEIGHBORSREGRESSOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_LASSO (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_LASSO_ALPHA (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_LOGISTICREGRESSION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_LOGISTICREGRESSION_C (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_LOGISTICREGRESSION_SOLVER (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_LOW (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_MAPIE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_MAPIE_ALPHA (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_MAPIE_ESTIMATOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PLSREGRESSION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PLSREGRESSION_N_COMPONENTS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PRF (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PRF_MAX_DEPTH (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PRF_MAX_FEATURES (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PRF_MINPYSUMLEAF (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PRF_N_ESTIMATORS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PRF_USE_PY_GINI (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_PRF_USE_PY_LEAFS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_Q (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_RF_MAX_DEPTH (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_RF_MAX_FEATURES (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_RF_N_ESTIMATORS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_RFCLASSIFIER (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_RFREGRESSOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_RIDGE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_RIDGE_ALPHA (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_SVC (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_SVC_C (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_SVC_GAMMA (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_SVR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_SVR_C (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_SVR_GAMMA (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_XGBREGRESSOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_XGBREGRESSOR_LEARNING_RATE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_XGBREGRESSOR_MAX_DEPTH (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ALGORITHMS_XGBREGRESSOR_N_ESTIMATORS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) all_cv_test_scores (optunaz.utils.tracking.TrackingData attribute) alpha (optunaz.config.buildconfig.Lasso.LassoParameters attribute) (optunaz.config.buildconfig.Ridge.RidgeParameters attribute) (optunaz.config.optconfig.Lasso.Parameters attribute) (optunaz.config.optconfig.Ridge.Parameters attribute) AmorProt (class in optunaz.utils.preprocessing.transform), [1] AmorProt.Parameters (class in optunaz.utils.preprocessing.transform), [1] AmorProtDescriptors (class in optunaz.descriptors), [1] AmorProtDescriptors.AmorProt (class in optunaz.descriptors) AmorProtDescriptors.Parameters (class in optunaz.descriptors), [1] ArgsError attach_root_path() (in module optunaz.utils.files_paths) ATTRIBUTE_TRIAL_TRAIN_SCORE (optunaz.utils.enums.objective_enum.ObjectiveEnum attribute) AUC_PR_CAL (optunaz.config.optconfig.ClassificationScore attribute) auc_pr_cal() (in module optunaz.metircs) AUTO (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) (optunaz.config.optconfig.PRFClassifierMaxFeatures attribute) (optunaz.config.optconfig.RandomForestMaxFeatures attribute) aux_column (optunaz.datareader.Dataset attribute) aux_transform (optunaz.datareader.Dataset attribute) (optunaz.model_writer.QSARtunaModel attribute) aux_weight_pc (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters attribute) AuxCovariateMissing AuxTransformer (class in optunaz.utils.preprocessing.transform) Avalon (class in optunaz.descriptors), [1] Avalon.Parameters (class in optunaz.descriptors) AVERAGE_PRECISION (optunaz.config.optconfig.ClassificationScore attribute)

B

BALANCED_ACCURACY (optunaz.config.optconfig.ClassificationScore attribute) base (optunaz.utils.preprocessing.transform.ModelDataTransform.Parameters attribute) base_chemprop_params() (in module optunaz.three_step_opt_build_merge) base_dict (optunaz.utils.preprocessing.transform.ModelDataTransform attribute) base_negation (optunaz.utils.preprocessing.transform.ModelDataTransform attribute) basename_from_config() (in module optunaz.optbuild) batch_size (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) BEDROC (optunaz.config.optconfig.ClassificationScore attribute) bedroc_score() (in module optunaz.metircs) best_trial (optunaz.config.buildconfig.BuildConfig.Metadata attribute) best_value (optunaz.config.buildconfig.BuildConfig.Metadata attribute) bin_edges (optunaz.utils.tracking.Calpoint attribute) bins (optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit attribute) (optunaz.utils.preprocessing.splitter.ScaffoldSplit attribute) (optunaz.utils.preprocessing.splitter.Stratified attribute)

bootstrap (optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters attribute) build() (in module optunaz.builder) build_best() (in module optunaz.three_step_opt_build_merge) build_merged() (in module optunaz.three_step_opt_build_merge) build_with_al() (in module optunaz.optbuild) BuildConfig (class in optunaz.config.buildconfig) buildconfig (optunaz.utils.tracking.TrackingData attribute) BuildConfig.Metadata (class in optunaz.config.buildconfig) BuildConfig.Settings (class in optunaz.config.buildconfig) buildconfig_best() (in module optunaz.three_step_opt_build_merge) buildconfig_from_trial() (in module optunaz.config.build_from_opt) BUILDING (optunaz.config.Task attribute) BuildingConfigurationEnum (class in optunaz.utils.enums.building_configuration_enum) BuildTrackingData (class in optunaz.utils.tracking) butina_cluster (optunaz.utils.preprocessing.splitter.ScaffoldSplit attribute) butina_cluster() (in module optunaz.utils.preprocessing.splitter)

C

C (optunaz.config.buildconfig.LogisticRegression.LogisticRegressionParameters attribute) (optunaz.config.buildconfig.SVC.SVCParameters attribute) (optunaz.config.buildconfig.SVR.SVRParameters attribute) (optunaz.config.optconfig.LogisticRegression.Parameters attribute) (optunaz.config.optconfig.SVC.Parameters attribute) (optunaz.config.optconfig.SVR.Parameters attribute) cache (optunaz.objective.Objective attribute) cal_points (optunaz.utils.tracking.BuildTrackingData attribute) calcSlurmMem() (optunaz.automl.ModelDispatcher static method) calculate_from_mol() (optunaz.descriptors.Avalon method) (optunaz.descriptors.ECFP method), [1] (optunaz.descriptors.ECFP_counts method), [1] (optunaz.descriptors.MACCS_keys method), [1] (optunaz.descriptors.PathFP method), [1] (optunaz.descriptors.RdkitDescriptor method) (optunaz.descriptors.UnscaledMAPC method), [1] (optunaz.descriptors.UnscaledPhyschemDescriptors method), [1] calculate_from_smi() (optunaz.descriptors.AmorProtDescriptors method), [1] (optunaz.descriptors.CanonicalSmiles method) (optunaz.descriptors.CompositeDescriptor method), [1] (optunaz.descriptors.GenericScaffold method) (optunaz.descriptors.MolDescriptor method) (optunaz.descriptors.PrecomputedDescriptorFromFile method), [1] (optunaz.descriptors.RdkitDescriptor method) (optunaz.descriptors.Scaffold method) (optunaz.descriptors.ScaledDescriptor method), [1] (optunaz.descriptors.SmilesAndSideInfoFromFile method), [1] (optunaz.descriptors.SmilesFromFile method), [1] (optunaz.descriptors.UnscaledJazzyDescriptors method), [1] (optunaz.descriptors.UnscaledZScalesDescriptors method), [1], [2] (optunaz.descriptors.ValidDescriptor method) CALIBRATED_SET (optunaz.utils.enums.interface_enum.InterfaceEnum attribute) CalibratedClassifierCVEnsemble (class in optunaz.config.optconfig) CalibratedClassifierCVMethod (class in optunaz.config.optconfig) CalibratedClassifierCVWithVA (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] CalibratedClassifierCVWithVA.CalibratedClassifierCVParameters (class in optunaz.config.buildconfig) CalibratedClassifierCVWithVA.Parameters (class in optunaz.config.optconfig), [1] calibration_analysis() (in module optunaz.evaluate) Calpoint (class in optunaz.utils.tracking) CanonicalSmiles (class in optunaz.descriptors) CanonicalSmiles.Parameters (class in optunaz.descriptors) check_invalid_descriptor_param() (in module optunaz.config.build_from_opt) check_precomp_args() (in module optunaz.predict) check_sets() (optunaz.datareader.Dataset method) checkIfRetrainingProcessed() (optunaz.automl.ModelDispatcher method) checkisLocked() (optunaz.automl.ModelDispatcher method) checkRunningSlurmJobs() (optunaz.automl.ModelDispatcher method) checkSaveTemporalModel() (optunaz.automl.ModelDispatcher method) checkSkipped() (optunaz.automl.ModelDispatcher method) checkSlurmStatusAndNextProcedure() (optunaz.automl.ModelDispatcher method) CHEMPROP_SET (optunaz.utils.enums.interface_enum.InterfaceEnum attribute) ChemPropActivation (class in optunaz.config.optconfig) ChemPropAggregation (class in optunaz.config.optconfig) ChemPropClassifier (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] ChemPropClassifier.ChemPropClassifierParameters (class in optunaz.config.buildconfig) ChemPropClassifier.Parameters (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersAggregation_Norm (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersBatch_Size (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersDepth (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersDropout (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersFFN_Hidden_Size (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersFFN_Num_Layers (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersHidden_Size (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersInit_Lr_Ratio_Exp (class in optunaz.config.optconfig), [1]

ChemPropClassifier.Parameters.ChemPropParametersMax_Lr_Exp (class in optunaz.config.optconfig), [1] ChemPropClassifier.Parameters.ChemPropParametersWarmup_Epochs_Ratio (class in optunaz.config.optconfig), [1] ChemPropFeatures_Generator (class in optunaz.config.optconfig) ChemPropFrzn (class in optunaz.config.optconfig) ChemPropHyperoptClassifier (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters (class in optunaz.config.buildconfig) ChemPropHyperoptClassifier.Parameters (class in optunaz.config.optconfig), [1] ChemPropHyperoptRegressor (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters (class in optunaz.config.buildconfig) ChemPropHyperoptRegressor.Parameters (class in optunaz.config.optconfig), [1] ChemPropRegressor (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] ChemPropRegressor.ChemPropRegressorParameters (class in optunaz.config.buildconfig) ChemPropRegressor.Parameters (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersAggregation_Norm (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersBatch_Size (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersDepth (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersDropout (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersFFN_Hidden_Size (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersFFN_Num_Layers (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersHidden_Size (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersInit_Lr_Ratio_Exp (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersMax_Lr_Exp (class in optunaz.config.optconfig), [1] ChemPropRegressor.Parameters.ChemPropParametersWarmup_Epochs_Ratio (class in optunaz.config.optconfig), [1] ChemPropRegressorPretrained (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] ChemPropRegressorPretrained.ChemPropRegressorPretrainedParameters (class in optunaz.config.buildconfig) ChemPropRegressorPretrained.Parameters (class in optunaz.config.optconfig), [1] ChemPropRegressorPretrained.Parameters.ChemPropParametersEpochs (class in optunaz.config.optconfig), [1] ChemPropSearch_Parameter_Level (class in optunaz.config.optconfig) CLASSIFICATION (optunaz.config.ModelMode attribute) ClassificationScore (class in optunaz.config.optconfig) column_name (optunaz.utils.preprocessing.splitter.Predefined attribute) CompositeDescriptor (class in optunaz.descriptors), [1] CompositeDescriptor.Parameters (class in optunaz.descriptors), [1] CONCORDANCE_INDEX (optunaz.config.optconfig.ClassificationScore attribute) concordance_index() (in module optunaz.metircs) ConfigurationEnum (class in optunaz.utils.enums.configuration_enum) conversion (optunaz.utils.preprocessing.transform.ModelDataTransform.Parameters attribute) convert() (in module optunaz.convert) copy_path_for_scaled_descriptor() (in module optunaz.config.optconfig) copytitle() (in module optunaz.utils.schema) create_dependency() (in module optunaz.utils.schema) CROSS_VALIDATE_FIT_TIME (optunaz.utils.enums.return_values_enum.SklearnReturnValueEnum attribute) (optunaz.utils.enums.return_values_enum.XGBoostReturnValueEnum attribute) CROSS_VALIDATE_SCORE_TIME (optunaz.utils.enums.return_values_enum.SklearnReturnValueEnum attribute) (optunaz.utils.enums.return_values_enum.XGBoostReturnValueEnum attribute) CROSS_VALIDATE_TEST_SCORE (optunaz.utils.enums.return_values_enum.SklearnReturnValueEnum attribute) (optunaz.utils.enums.return_values_enum.XGBoostReturnValueEnum attribute) CROSS_VALIDATE_TRAIN_SCORE (optunaz.utils.enums.return_values_enum.SklearnReturnValueEnum attribute) (optunaz.utils.enums.return_values_enum.XGBoostReturnValueEnum attribute) cross_validation (optunaz.config.buildconfig.BuildConfig.Metadata attribute) (optunaz.config.optconfig.OptimizationConfig.Settings attribute) CustomClassificationModel (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] CustomClassificationModel.CustomClassificationEstimator (class in optunaz.config.buildconfig) CustomClassificationModel.CustomClassificationModelParameters (class in optunaz.config.buildconfig) CustomClassificationModel.Parameters (class in optunaz.config.optconfig), [1] CustomRegressionModel (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] CustomRegressionModel.CustomRegressionEstimator (class in optunaz.config.buildconfig) CustomRegressionModel.CustomRegressionModelParameters (class in optunaz.config.buildconfig) CustomRegressionModel.Parameters (class in optunaz.config.optconfig), [1] cv_split_strategy (optunaz.config.optconfig.OptimizationConfig.Settings attribute)

D

data (optunaz.config.buildconfig.BuildConfig attribute) (optunaz.config.optconfig.OptimizationConfig attribute) DATA (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DATA_DATASET (optunaz.utils.enums.prediction_configuration_enum.PredictionConfigurationEnum attribute) DATA_INPUTCOLUMN (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DATA_RESPONSECOLUMN (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DATA_TEST (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DATA_TRAINING (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) Datapoint (class in optunaz.utils.tracking) Dataset (class in optunaz.datareader) DataTransform (class in optunaz.utils.preprocessing.transform) DataTransformError dedup() (optunaz.utils.preprocessing.deduplicator.Deduplicator method) (optunaz.utils.preprocessing.deduplicator.KeepAllNoDeduplication method) (optunaz.utils.preprocessing.deduplicator.KeepAvg method), [1] (optunaz.utils.preprocessing.deduplicator.KeepFirst method) (optunaz.utils.preprocessing.deduplicator.KeepLast method) (optunaz.utils.preprocessing.deduplicator.KeepMax method) (optunaz.utils.preprocessing.deduplicator.KeepMedian method), [1] (optunaz.utils.preprocessing.deduplicator.KeepMin method) (optunaz.utils.preprocessing.deduplicator.KeepRandom method) deduplicate() (in module optunaz.datareader) deduplication_strategy (optunaz.datareader.Dataset attribute) Deduplicator (class in optunaz.utils.preprocessing.deduplicator) delimiter (optunaz.utils.preprocessing.transform.VectorFromColumn.Parameters attribute) delsibling() (in module optunaz.utils.schema) depth (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) description (optunaz.config.optconfig.OptimizationConfig attribute) descriptor (optunaz.config.buildconfig.BuildConfig attribute) (optunaz.descriptors.JazzyDescriptors.Parameters attribute), [1] (optunaz.descriptors.MAPC.Parameters attribute), [1] (optunaz.descriptors.PhyschemDescriptors.Parameters attribute), [1] (optunaz.descriptors.ScaledDescriptor.ScaledDescriptorParameters attribute) (optunaz.descriptors.ZScalesDescriptors.Parameters attribute), [1], [2] (optunaz.model_writer.QSARtunaModel attribute) DESCRIPTOR (optunaz.utils.enums.TrialParams attribute) descriptor_from_config() (in module optunaz.descriptors) descriptors (optunaz.config.optconfig.OptimizationConfig attribute) (optunaz.descriptors.CompositeDescriptor.Parameters attribute) DESCRIPTORS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_AMORPROT (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_AVALON (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_AVALON_NBITS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute)

DESCRIPTORS_COMPOSITE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_ECFP (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_ECFP_NBITS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_ECFP_RADIUS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_ECFPCOUNTS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_ECFPCOUNTS_RADIUS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_ECFPCOUNTS_USEFEATURES (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_JAZZY (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_JAZZY_JAZZYNAMES (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_MACCSKEYS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_MAPC (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_MAPC_MAXRADIUS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_MAPC_NPERMUTATIONS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PATHFP (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PATHFP_FPSIZE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PATHFP_MAXPATH (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PHYSCHEM (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PHYSCHEM_RDKITNAMES (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PRECOMPUTED (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PRECOMPUTED_FILE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PRECOMPUTED_INPUT_COLUMNN (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_PRECOMPUTED_RESPONSE_COLUMN (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_SCALED (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_SCALED_DESCRIPTOR (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_SCALED_DESCRIPTOR_PARAMETERS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_SMILES (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_SMILES_AND_SI (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_SMILES_AND_SI_AUX_WEIGHT_PC (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_SMILES_AND_SI_FILE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_SMILES_AND_SI_INPUT_COLUMN (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_UNSC_JAZZY (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_UNSC_MAPC (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_UNSC_PHYSCHEM (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_UNSC_ZSCALES (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) DESCRIPTORS_ZSCALES (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) detect_mode_from_algs() (in module optunaz.config.optconfig) direction (optunaz.config.buildconfig.BuildConfig.Settings attribute) (optunaz.config.optconfig.OptimizationConfig.Settings attribute) dispatcher_process() (in module optunaz.automl) DISTANCE (optunaz.config.optconfig.KNeighborsWeights attribute) doctitle() (in module optunaz.schemagen) doTemporalPredictions() (optunaz.automl.ModelDispatcher method) dropout (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute)

E

ECFP (class in optunaz.descriptors), [1] ECFP.Parameters (class in optunaz.descriptors), [1] ECFP_counts (class in optunaz.descriptors), [1] ECFP_counts.Parameters (class in optunaz.descriptors), [1] ELU (optunaz.config.optconfig.ChemPropActivation attribute) encode_name() (in module optunaz.config.build_from_opt) ensemble (optunaz.config.buildconfig.CalibratedClassifierCVWithVA.CalibratedClassifierCVParameters attribute) (optunaz.config.optconfig.CalibratedClassifierCVWithVA.Parameters attribute) ensemble_size (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropHyperoptClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropHyperoptRegressor.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) epochs (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.buildconfig.ChemPropRegressorPretrained.ChemPropRegressorPretrainedParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropHyperoptClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropHyperoptRegressor.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters attribute) estimator (optunaz.config.buildconfig.CalibratedClassifierCVWithVA.CalibratedClassifierCVParameters attribute) (optunaz.config.buildconfig.Mapie.MapieParameters attribute) (optunaz.config.optconfig.CalibratedClassifierCVWithVA.Parameters attribute) (optunaz.config.optconfig.Mapie.Parameters attribute)

estimator() (optunaz.config.buildconfig.AdaBoostClassifier method) (optunaz.config.buildconfig.Algorithm method) (optunaz.config.buildconfig.CalibratedClassifierCVWithVA method) (optunaz.config.buildconfig.ChemPropClassifier method) (optunaz.config.buildconfig.ChemPropHyperoptClassifier method) (optunaz.config.buildconfig.ChemPropHyperoptRegressor method) (optunaz.config.buildconfig.ChemPropRegressor method) (optunaz.config.buildconfig.ChemPropRegressorPretrained method) (optunaz.config.buildconfig.CustomClassificationModel method) (optunaz.config.buildconfig.CustomRegressionModel method) (optunaz.config.buildconfig.KNeighborsClassifier method) (optunaz.config.buildconfig.KNeighborsRegressor method) (optunaz.config.buildconfig.Lasso method) (optunaz.config.buildconfig.LogisticRegression method) (optunaz.config.buildconfig.Mapie method) (optunaz.config.buildconfig.PLSRegression method) (optunaz.config.buildconfig.PRFClassifier method) (optunaz.config.buildconfig.RandomForestClassifier method) (optunaz.config.buildconfig.RandomForestRegressor method) (optunaz.config.buildconfig.Ridge method) (optunaz.config.buildconfig.SVC method) (optunaz.config.buildconfig.SVR method) (optunaz.config.buildconfig.XGBRegressor method) EUCLIDEAN (optunaz.config.optconfig.KNeighborsMetric attribute) expected (optunaz.utils.tracking.Datapoint attribute) explain() (optunaz.model_writer.Predictor method) explain_ECFP() (in module optunaz.explainability) EXPLAINED_VARIANCE (optunaz.config.optconfig.RegressionScore attribute) ExplainPreds() (in module optunaz.explainability) EXTRA_COLUMN_BESTHIT (optunaz.utils.enums.objective_enum.ObjectiveEnum attribute)

F

F1 (optunaz.config.optconfig.ClassificationScore attribute) F1_MACRO (optunaz.config.optconfig.ClassificationScore attribute) F1_MICRO (optunaz.config.optconfig.ClassificationScore attribute) F1_WEIGHTED (optunaz.config.optconfig.ClassificationScore attribute) FALSE (optunaz.config.optconfig.CalibratedClassifierCVEnsemble attribute) (optunaz.utils.preprocessing.transform.LogNegative attribute) fd_bin() (in module optunaz.utils.preprocessing.splitter) features_generator (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropHyperoptClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropHyperoptRegressor.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) ffn_hidden_size (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) ffn_num_layers (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute)

file (optunaz.descriptors.PrecomputedDescriptorFromFile.Parameters attribute) (optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters attribute) file_format (optunaz.config.Visualization attribute) file_path (optunaz.descriptors.UnfittedSklearnScaler.MolData attribute) final_lr_ratio_exp (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) fingerprint() (optunaz.descriptors.AmorProtDescriptors.AmorProt method) first_run (optunaz.automl.ModelAutoML property) fit() (optunaz.config.buildconfig.CustomClassificationModel.CustomClassificationEstimator method) (optunaz.config.buildconfig.CustomRegressionModel.CustomRegressionEstimator method) FittedSklearnScaler (class in optunaz.descriptors) fp_info() (optunaz.descriptors.CompositeDescriptor method) fpSize (optunaz.descriptors.PathFP.Parameters attribute) frac_pred (optunaz.utils.tracking.Calpoint attribute) frac_true (optunaz.utils.tracking.Calpoint attribute) fraction (optunaz.utils.preprocessing.splitter.Random attribute) (optunaz.utils.preprocessing.splitter.Stratified attribute) (optunaz.utils.preprocessing.splitter.Temporal attribute) frzn (optunaz.config.buildconfig.ChemPropRegressorPretrained.ChemPropRegressorPretrainedParameters attribute) (optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters attribute)

G

gamma (optunaz.config.buildconfig.SVC.SVCParameters attribute) (optunaz.config.buildconfig.SVR.SVRParameters attribute) (optunaz.config.optconfig.SVC.Parameters attribute) (optunaz.config.optconfig.SVR.Parameters attribute) GENERAL_ALGORITHM_NAME (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) GENERAL_CLASSIFIER (optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum attribute) GENERAL_DISABLED (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) GENERAL_HYPERPARAMETERS (optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum attribute) GENERAL_NAME (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) GENERAL_PARAMETERS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) GENERAL_REGRESSOR (optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum attribute) GenericScaffold (class in optunaz.descriptors) GenericScaffold.Parameters (class in optunaz.descriptors) get_authorization_header() (in module optunaz.utils.tracking) get_ecfp_fpinfo() (in module optunaz.explainability) get_ecfpcount_fpinfo() (in module optunaz.explainability) get_fitted_scaler() (optunaz.descriptors.FittedSklearnScaler method) get_fitted_scaler_for_fp() (optunaz.descriptors.UnfittedSklearnScaler method) get_fp_info() (in module optunaz.explainability) get_merged_sets() (optunaz.datareader.Dataset method) get_merged_train_score() (in module optunaz.evaluate) get_metadata() (in module optunaz.model_writer)

get_n_splits() (optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit method) (optunaz.utils.preprocessing.splitter.ScaffoldSplit method) (optunaz.utils.preprocessing.splitter.SklearnSplitter method) get_scores() (in module optunaz.evaluate) get_sets() (optunaz.datareader.Dataset method) get_sklearn_splitter() (optunaz.utils.preprocessing.splitter.KFold method) (optunaz.utils.preprocessing.splitter.NoSplitting method) (optunaz.utils.preprocessing.splitter.Predefined method) (optunaz.utils.preprocessing.splitter.Random method) (optunaz.utils.preprocessing.splitter.ScaffoldSplit method) (optunaz.utils.preprocessing.splitter.Splitter method) (optunaz.utils.preprocessing.splitter.Stratified method) (optunaz.utils.preprocessing.splitter.Temporal method) get_train_test_scores() (in module optunaz.evaluate) get_transform() (in module optunaz.model_writer) getAllRetrainingData() (optunaz.automl.ModelAutoML method) getref() (in module optunaz.utils.schema) getRetrainingData() (optunaz.automl.ModelAutoML method) getSlurmRetry() (optunaz.automl.ModelDispatcher method) GroupingSplitter (class in optunaz.utils.preprocessing.splitter) groups() (optunaz.utils.preprocessing.splitter.GroupingSplitter method) (optunaz.utils.preprocessing.splitter.Predefined method) (optunaz.utils.preprocessing.splitter.ScaffoldSplit method), [1]

H

hidden_size (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) high (optunaz.config.optconfig.AdaBoostClassifier.Parameters.AdaBoostClassifierParametersLearningRate attribute) (optunaz.config.optconfig.AdaBoostClassifier.Parameters.AdaBoostClassifierParametersNEstimators attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersAggregation_Norm attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersBatch_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDepth attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDropout attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Hidden_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Num_Layers attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersHidden_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersInit_Lr_Ratio_Exp attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersMax_Lr_Exp attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersWarmup_Epochs_Ratio attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersAggregation_Norm attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersBatch_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDepth attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDropout attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Hidden_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Num_Layers attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersHidden_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersInit_Lr_Ratio_Exp attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersMax_Lr_Exp attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersWarmup_Epochs_Ratio attribute) (optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters.ChemPropParametersEpochs attribute) (optunaz.config.optconfig.KNeighborsClassifier.Parameters.KNeighborsClassifierParametersN_Neighbors attribute) (optunaz.config.optconfig.KNeighborsRegressor.Parameters.KNeighborsRegressorParametersN_Neighbors attribute) (optunaz.config.optconfig.Lasso.Parameters.LassoParametersAlpha attribute) (optunaz.config.optconfig.LogisticRegression.Parameters.LogisticRegressionParametersParameterC attribute) (optunaz.config.optconfig.PLSRegression.Parameters.NComponents attribute) (optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersMaxDepth attribute) (optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersMinPySumLeaf attribute) (optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersNEstimators attribute) (optunaz.config.optconfig.RandomForestClassifier.Parameters.RandomForestClassifierParametersMaxDepth attribute) (optunaz.config.optconfig.RandomForestClassifier.Parameters.RandomForestClassifierParametersNEstimators attribute) (optunaz.config.optconfig.RandomForestRegressor.Parameters.RandomForestRegressorParametersMaxDepth attribute) (optunaz.config.optconfig.RandomForestRegressor.Parameters.RandomForestRegressorParametersNEstimators attribute) (optunaz.config.optconfig.Ridge.Parameters.Alpha attribute) (optunaz.config.optconfig.SVC.Parameters.Gamma attribute) (optunaz.config.optconfig.SVC.Parameters.SVCParametersParameterC attribute) (optunaz.config.optconfig.SVR.Parameters.SVRParametersGamma attribute) (optunaz.config.optconfig.SVR.Parameters.SVRParametersParameterC attribute) (optunaz.config.optconfig.XGBRegressor.Parameters.LearningRate attribute) (optunaz.config.optconfig.XGBRegressor.Parameters.MaxDepth attribute) (optunaz.config.optconfig.XGBRegressor.Parameters.NEstimators attribute) (optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters.Aux_Weight_Pc attribute)

HistogramStratifiedShuffleSplit (class in optunaz.utils.preprocessing.splitter)

I

increaseJobCpu() (optunaz.automl.ModelDispatcher method) increaseJobMem() (optunaz.automl.ModelDispatcher method) increaseJobTime() (optunaz.automl.ModelDispatcher method) inference_parameters() (optunaz.descriptors.PrecomputedDescriptorFromFile method), [1] init_lr_ratio_exp (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) initProcessedTimepoints() (optunaz.automl.ModelAutoML method) input_column (optunaz.datareader.Dataset attribute) (optunaz.descriptors.PrecomputedDescriptorFromFile.Parameters attribute) (optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters attribute)

InterfaceEnum (class in optunaz.utils.enums.interface_enum) intermediate_test_dataset_file (optunaz.datareader.Dataset attribute) intermediate_training_dataset_file (optunaz.datareader.Dataset attribute) InternalTrackingCallback (class in optunaz.utils.tracking) isanyof() (in module optunaz.config.optconfig) ISOTONIC (optunaz.config.optconfig.CalibratedClassifierCVMethod attribute) isTrained() (optunaz.automl.ModelDispatcher method) isvalid() (in module optunaz.datareader)

J

JACCARD (optunaz.config.optconfig.ClassificationScore attribute) JACCARD_MACRO (optunaz.config.optconfig.ClassificationScore attribute) JACCARD_MICRO (optunaz.config.optconfig.ClassificationScore attribute) JACCARD_WEIGHTED (optunaz.config.optconfig.ClassificationScore attribute) jazzy_filters (optunaz.descriptors.JazzyDescriptors.Parameters attribute) (optunaz.descriptors.UnscaledJazzyDescriptors.Parameters attribute)

jazzy_names (optunaz.descriptors.JazzyDescriptors.Parameters attribute) (optunaz.descriptors.UnscaledJazzyDescriptors.Parameters attribute) JazzyDescriptors (class in optunaz.descriptors), [1] JazzyDescriptors.Parameters (class in optunaz.descriptors), [1] JPEG (optunaz.config.Visualization.ImageFileFormat attribute) JPG (optunaz.config.Visualization.ImageFileFormat attribute)

K

KeepAllNoDeduplication (class in optunaz.utils.preprocessing.deduplicator), [1] KeepAvg (class in optunaz.utils.preprocessing.deduplicator), [1] KeepFirst (class in optunaz.utils.preprocessing.deduplicator), [1] KeepLast (class in optunaz.utils.preprocessing.deduplicator), [1] KeepMax (class in optunaz.utils.preprocessing.deduplicator), [1] KeepMedian (class in optunaz.utils.preprocessing.deduplicator), [1] KeepMin (class in optunaz.utils.preprocessing.deduplicator), [1] KeepRandom (class in optunaz.utils.preprocessing.deduplicator), [1] KFold (class in optunaz.utils.preprocessing.splitter) KNeighborsClassifier (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1]

KNeighborsClassifier.KNeighborsClassifierParameters (class in optunaz.config.buildconfig) KNeighborsClassifier.Parameters (class in optunaz.config.optconfig), [1] KNeighborsClassifier.Parameters.KNeighborsClassifierParametersN_Neighbors (class in optunaz.config.optconfig), [1] KNeighborsMetric (class in optunaz.config.optconfig) KNeighborsRegressor (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] KNeighborsRegressor.KNeighborsRegressorParameters (class in optunaz.config.buildconfig) KNeighborsRegressor.Parameters (class in optunaz.config.optconfig), [1] KNeighborsRegressor.Parameters.KNeighborsRegressorParametersN_Neighbors (class in optunaz.config.optconfig), [1] KNeighborsWeights (class in optunaz.config.optconfig)

L

L1 (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) L2 (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) L3 (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) L4 (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) L5 (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) L6 (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) L7 (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) L8 (optunaz.config.optconfig.ChemPropSearch_Parameter_Level attribute) Lasso (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] Lasso.LassoParameters (class in optunaz.config.buildconfig) Lasso.Parameters (class in optunaz.config.optconfig), [1] Lasso.Parameters.LassoParametersAlpha (class in optunaz.config.optconfig), [1] last_timepoint (optunaz.automl.ModelAutoML property) LEAKYRELU (optunaz.config.optconfig.ChemPropActivation attribute) learning_rate (optunaz.config.buildconfig.AdaBoostClassifier.AdaBoostClassifierParameters attribute) (optunaz.config.buildconfig.XGBRegressor.XGBRegressorParameters attribute) (optunaz.config.optconfig.AdaBoostClassifier.Parameters attribute) (optunaz.config.optconfig.XGBRegressor.Parameters attribute) leave_out (optunaz.utils.preprocessing.splitter.Random attribute) (optunaz.utils.preprocessing.splitter.Stratified attribute) load_df_from_file() (in module optunaz.utils) loadJSON() (in module optunaz.utils.load_json) LOG (optunaz.utils.preprocessing.transform.LogBase attribute) LOG10 (optunaz.utils.preprocessing.transform.LogBase attribute) LOG2 (optunaz.config.optconfig.PRFClassifierMaxFeatures attribute) (optunaz.config.optconfig.RandomForestMaxFeatures attribute) (optunaz.utils.preprocessing.transform.LogBase attribute) log_scores() (in module optunaz.three_step_opt_build_merge) log_transform (optunaz.datareader.Dataset attribute) log_transform_base (optunaz.datareader.Dataset attribute) log_transform_negative (optunaz.datareader.Dataset attribute) log_transform_unit_conversion (optunaz.datareader.Dataset attribute) LogBase (class in optunaz.utils.preprocessing.transform) LogisticRegression (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] LogisticRegression.LogisticRegressionParameters (class in optunaz.config.buildconfig) LogisticRegression.Parameters (class in optunaz.config.optconfig), [1] LogisticRegression.Parameters.LogisticRegressionParametersParameterC (class in optunaz.config.optconfig), [1] LogNegative (class in optunaz.utils.preprocessing.transform) low (optunaz.config.optconfig.AdaBoostClassifier.Parameters.AdaBoostClassifierParametersLearningRate attribute) (optunaz.config.optconfig.AdaBoostClassifier.Parameters.AdaBoostClassifierParametersNEstimators attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersAggregation_Norm attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersBatch_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDepth attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDropout attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Hidden_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Num_Layers attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersHidden_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersInit_Lr_Ratio_Exp attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersMax_Lr_Exp attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersWarmup_Epochs_Ratio attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersAggregation_Norm attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersBatch_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDepth attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDropout attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Hidden_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Num_Layers attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersHidden_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersInit_Lr_Ratio_Exp attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersMax_Lr_Exp attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersWarmup_Epochs_Ratio attribute) (optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters.ChemPropParametersEpochs attribute) (optunaz.config.optconfig.KNeighborsClassifier.Parameters.KNeighborsClassifierParametersN_Neighbors attribute) (optunaz.config.optconfig.KNeighborsRegressor.Parameters.KNeighborsRegressorParametersN_Neighbors attribute) (optunaz.config.optconfig.Lasso.Parameters.LassoParametersAlpha attribute) (optunaz.config.optconfig.LogisticRegression.Parameters.LogisticRegressionParametersParameterC attribute) (optunaz.config.optconfig.PLSRegression.Parameters.NComponents attribute) (optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersMaxDepth attribute) (optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersMinPySumLeaf attribute) (optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersNEstimators attribute) (optunaz.config.optconfig.RandomForestClassifier.Parameters.RandomForestClassifierParametersMaxDepth attribute) (optunaz.config.optconfig.RandomForestClassifier.Parameters.RandomForestClassifierParametersNEstimators attribute) (optunaz.config.optconfig.RandomForestRegressor.Parameters.RandomForestRegressorParametersMaxDepth attribute) (optunaz.config.optconfig.RandomForestRegressor.Parameters.RandomForestRegressorParametersNEstimators attribute) (optunaz.config.optconfig.Ridge.Parameters.Alpha attribute) (optunaz.config.optconfig.SVC.Parameters.Gamma attribute) (optunaz.config.optconfig.SVC.Parameters.SVCParametersParameterC attribute) (optunaz.config.optconfig.SVR.Parameters.SVRParametersGamma attribute) (optunaz.config.optconfig.SVR.Parameters.SVRParametersParameterC attribute) (optunaz.config.optconfig.XGBRegressor.Parameters.LearningRate attribute) (optunaz.config.optconfig.XGBRegressor.Parameters.MaxDepth attribute) (optunaz.config.optconfig.XGBRegressor.Parameters.NEstimators attribute) (optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters.Aux_Weight_Pc attribute)

M

MACCS_keys (class in optunaz.descriptors), [1] MACCS_keys.Parameters (class in optunaz.descriptors), [1] main() (in module optunaz.automl) (in module optunaz.convert) (in module optunaz.optbuild) (in module optunaz.predict) (in module optunaz.schemagen) make_scaffold_generic (optunaz.utils.preprocessing.splitter.ScaffoldSplit attribute) MANHATTAN (optunaz.config.optconfig.KNeighborsMetric attribute) MAPC (class in optunaz.descriptors), [1] MAPC.Parameters (class in optunaz.descriptors), [1] Mapie (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] Mapie.MapieParameters (class in optunaz.config.buildconfig) Mapie.Parameters (class in optunaz.config.optconfig), [1] mapie_alpha (optunaz.config.buildconfig.Mapie.MapieParameters attribute) (optunaz.config.optconfig.Mapie.Parameters attribute) max_depth (optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters attribute) (optunaz.config.buildconfig.RandomForestClassifier.RandomForestParameters attribute) (optunaz.config.buildconfig.RandomForestRegressor.RandomForestParameters attribute) (optunaz.config.buildconfig.XGBRegressor.XGBRegressorParameters attribute) (optunaz.config.optconfig.PRFClassifier.Parameters attribute) (optunaz.config.optconfig.RandomForestClassifier.Parameters attribute) (optunaz.config.optconfig.RandomForestRegressor.Parameters attribute) (optunaz.config.optconfig.XGBRegressor.Parameters attribute) MAX_ERROR (optunaz.config.optconfig.RegressionScore attribute) max_features (optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters attribute) (optunaz.config.buildconfig.RandomForestClassifier.RandomForestParameters attribute) (optunaz.config.buildconfig.RandomForestRegressor.RandomForestParameters attribute) (optunaz.config.optconfig.PRFClassifier.Parameters attribute) (optunaz.config.optconfig.RandomForestClassifier.Parameters attribute) (optunaz.config.optconfig.RandomForestRegressor.Parameters attribute) max_lr_exp (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) MAXIMIZATION (optunaz.config.OptimizationDirection attribute) maxPath (optunaz.descriptors.PathFP.Parameters attribute) maxRadius (optunaz.descriptors.MAPC.Parameters attribute) (optunaz.descriptors.UnscaledMAPC.Parameters attribute) md5_hash() (in module optunaz.utils) MEAN (optunaz.config.optconfig.ChemPropAggregation attribute) merge() (in module optunaz.datareader) meta() (in module optunaz.automl) metadata (optunaz.config.buildconfig.BuildConfig attribute) (optunaz.model_writer.QSARtunaModel attribute) METADATA (optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum attribute) METADATA_BESTTRIAL (optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum attribute) METADATA_BESTVALUE (optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum attribute) method (optunaz.config.buildconfig.CalibratedClassifierCVWithVA.CalibratedClassifierCVParameters attribute) (optunaz.config.optconfig.CalibratedClassifierCVWithVA.Parameters attribute) metric (optunaz.config.buildconfig.KNeighborsClassifier.KNeighborsClassifierParameters attribute) (optunaz.config.buildconfig.KNeighborsRegressor.KNeighborsRegressorParameters attribute) (optunaz.config.optconfig.KNeighborsClassifier.Parameters attribute) (optunaz.config.optconfig.KNeighborsRegressor.Parameters attribute) min_py_sum_leaf (optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters attribute) (optunaz.config.optconfig.PRFClassifier.Parameters attribute) minimise_std_dev (optunaz.config.optconfig.OptimizationConfig.Settings attribute) MINIMIZATION (optunaz.config.OptimizationDirection attribute) MINKOWSKI (optunaz.config.optconfig.KNeighborsMetric attribute) mkdict() (in module optunaz.utils) MLflowCallback (class in optunaz.utils.mlflow)

MlflowLogParams (class in optunaz.utils.enums) mode (optunaz.config.buildconfig.BuildConfig.Settings attribute) (optunaz.config.optconfig.OptimizationConfig attribute) (optunaz.config.optconfig.OptimizationConfig.Settings attribute) (optunaz.model_writer.QSARtunaModel attribute) ModelAutoML (class in optunaz.automl) ModelDataTransform (class in optunaz.utils.preprocessing.transform), [1] ModelDataTransform.Parameters (class in optunaz.utils.preprocessing.transform), [1] ModelDispatcher (class in optunaz.automl) ModelMode (class in optunaz.config) ModelRunnerDataframeEnum (class in optunaz.utils.enums.model_runner_enum) module optunaz optunaz.automl optunaz.builder optunaz.config optunaz.config.build_from_opt optunaz.config.buildconfig optunaz.config.optconfig optunaz.convert optunaz.datareader optunaz.descriptors optunaz.evaluate optunaz.explainability optunaz.metircs optunaz.model_writer optunaz.objective optunaz.optbuild optunaz.predict optunaz.schemagen optunaz.three_step_opt_build_merge optunaz.utils optunaz.utils.enums optunaz.utils.enums.building_configuration_enum optunaz.utils.enums.configuration_enum optunaz.utils.enums.interface_enum optunaz.utils.enums.model_runner_enum optunaz.utils.enums.objective_enum optunaz.utils.enums.optimization_configuration_enum optunaz.utils.enums.prediction_configuration_enum optunaz.utils.enums.return_values_enum optunaz.utils.enums.visualization_enum optunaz.utils.files_paths optunaz.utils.load_json optunaz.utils.mlflow optunaz.utils.preprocessing optunaz.utils.preprocessing.deduplicator optunaz.utils.preprocessing.splitter optunaz.utils.preprocessing.transform optunaz.utils.retraining optunaz.utils.schema optunaz.utils.tracking optunaz.visualizer mol_data (optunaz.descriptors.UnfittedSklearnScaler attribute) mol_from_smi() (in module optunaz.descriptors) MolDescriptor (class in optunaz.descriptors) MORGAN (optunaz.config.optconfig.ChemPropFeatures_Generator attribute) MORGAN_COUNT (optunaz.config.optconfig.ChemPropFeatures_Generator attribute) move_up_directory() (in module optunaz.utils.files_paths) MPNN (optunaz.config.optconfig.ChemPropFrzn attribute) MPNN_FIRST_FFN (optunaz.config.optconfig.ChemPropFrzn attribute) MPNN_LAST_FFN (optunaz.config.optconfig.ChemPropFrzn attribute)

N

n_chemprop_trials (optunaz.config.optconfig.OptimizationConfig.Settings attribute) n_components (optunaz.config.buildconfig.PLSRegression.PLSParameters attribute) (optunaz.config.optconfig.PLSRegression.Parameters attribute) n_estimators (optunaz.config.buildconfig.AdaBoostClassifier.AdaBoostClassifierParameters attribute) (optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters attribute) (optunaz.config.buildconfig.RandomForestClassifier.RandomForestParameters attribute) (optunaz.config.buildconfig.RandomForestRegressor.RandomForestParameters attribute) (optunaz.config.buildconfig.XGBRegressor.XGBRegressorParameters attribute) (optunaz.config.optconfig.AdaBoostClassifier.Parameters attribute) (optunaz.config.optconfig.PRFClassifier.Parameters attribute) (optunaz.config.optconfig.RandomForestClassifier.Parameters attribute) (optunaz.config.optconfig.RandomForestRegressor.Parameters attribute) (optunaz.config.optconfig.XGBRegressor.Parameters attribute) n_folds (optunaz.config.buildconfig.CalibratedClassifierCVWithVA.CalibratedClassifierCVParameters attribute) (optunaz.config.optconfig.CalibratedClassifierCVWithVA.Parameters attribute) n_jobs (optunaz.config.optconfig.OptimizationConfig.Settings attribute) n_neighbors (optunaz.config.buildconfig.KNeighborsClassifier.KNeighborsClassifierParameters attribute) (optunaz.config.buildconfig.KNeighborsRegressor.KNeighborsRegressorParameters attribute) (optunaz.config.optconfig.KNeighborsClassifier.Parameters attribute) (optunaz.config.optconfig.KNeighborsRegressor.Parameters attribute) n_splits (optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit attribute) n_startup_trials (optunaz.config.optconfig.OptimizationConfig.Settings attribute) n_trials (optunaz.config.buildconfig.BuildConfig.Metadata attribute) (optunaz.config.buildconfig.BuildConfig.Settings attribute) (optunaz.config.optconfig.OptimizationConfig.Settings attribute) name (optunaz.config.buildconfig.AdaBoostClassifier attribute) (optunaz.config.buildconfig.BuildConfig.Metadata attribute) (optunaz.config.buildconfig.CalibratedClassifierCVWithVA attribute) (optunaz.config.buildconfig.ChemPropClassifier attribute) (optunaz.config.buildconfig.ChemPropHyperoptClassifier attribute) (optunaz.config.buildconfig.ChemPropHyperoptRegressor attribute) (optunaz.config.buildconfig.ChemPropRegressor attribute) (optunaz.config.buildconfig.ChemPropRegressorPretrained attribute) (optunaz.config.buildconfig.CustomClassificationModel attribute) (optunaz.config.buildconfig.CustomRegressionModel attribute) (optunaz.config.buildconfig.KNeighborsClassifier attribute) (optunaz.config.buildconfig.KNeighborsRegressor attribute) (optunaz.config.buildconfig.Lasso attribute) (optunaz.config.buildconfig.LogisticRegression attribute) (optunaz.config.buildconfig.Mapie attribute) (optunaz.config.buildconfig.PLSRegression attribute) (optunaz.config.buildconfig.PRFClassifier attribute) (optunaz.config.buildconfig.RandomForestClassifier attribute) (optunaz.config.buildconfig.RandomForestRegressor attribute) (optunaz.config.buildconfig.Ridge attribute) (optunaz.config.buildconfig.SVC attribute) (optunaz.config.buildconfig.SVR attribute) (optunaz.config.buildconfig.XGBRegressor attribute) (optunaz.config.optconfig.AdaBoostClassifier attribute) (optunaz.config.optconfig.CalibratedClassifierCVWithVA attribute) (optunaz.config.optconfig.ChemPropClassifier attribute) (optunaz.config.optconfig.ChemPropHyperoptClassifier attribute) (optunaz.config.optconfig.ChemPropHyperoptRegressor attribute) (optunaz.config.optconfig.ChemPropRegressor attribute) (optunaz.config.optconfig.ChemPropRegressorPretrained attribute) (optunaz.config.optconfig.CustomClassificationModel attribute) (optunaz.config.optconfig.CustomRegressionModel attribute) (optunaz.config.optconfig.KNeighborsClassifier attribute) (optunaz.config.optconfig.KNeighborsRegressor attribute) (optunaz.config.optconfig.Lasso attribute) (optunaz.config.optconfig.LogisticRegression attribute) (optunaz.config.optconfig.Mapie attribute) (optunaz.config.optconfig.OptimizationConfig attribute) (optunaz.config.optconfig.PLSRegression attribute) (optunaz.config.optconfig.PRFClassifier attribute) (optunaz.config.optconfig.RandomForestClassifier attribute) (optunaz.config.optconfig.RandomForestRegressor attribute) (optunaz.config.optconfig.Ridge attribute) (optunaz.config.optconfig.SVC attribute) (optunaz.config.optconfig.SVR attribute) (optunaz.config.optconfig.XGBRegressor attribute) (optunaz.descriptors.AmorProtDescriptors attribute) (optunaz.descriptors.Avalon attribute) (optunaz.descriptors.CanonicalSmiles attribute) (optunaz.descriptors.CompositeDescriptor attribute) (optunaz.descriptors.ECFP attribute) (optunaz.descriptors.ECFP_counts attribute) (optunaz.descriptors.FittedSklearnScaler attribute) (optunaz.descriptors.GenericScaffold attribute) (optunaz.descriptors.JazzyDescriptors attribute) (optunaz.descriptors.MACCS_keys attribute) (optunaz.descriptors.MAPC attribute) (optunaz.descriptors.PathFP attribute) (optunaz.descriptors.PhyschemDescriptors attribute) (optunaz.descriptors.PrecomputedDescriptorFromFile attribute) (optunaz.descriptors.Scaffold attribute) (optunaz.descriptors.ScaledDescriptor attribute) (optunaz.descriptors.SmilesAndSideInfoFromFile attribute) (optunaz.descriptors.SmilesFromFile attribute) (optunaz.descriptors.UnfittedSklearnScaler attribute) (optunaz.descriptors.UnscaledJazzyDescriptors attribute) (optunaz.descriptors.UnscaledMAPC attribute) (optunaz.descriptors.UnscaledPhyschemDescriptors attribute) (optunaz.descriptors.UnscaledZScalesDescriptors attribute) (optunaz.descriptors.ValidDescriptor attribute) (optunaz.descriptors.ZScalesDescriptors attribute) (optunaz.utils.preprocessing.deduplicator.KeepAllNoDeduplication attribute) (optunaz.utils.preprocessing.deduplicator.KeepAvg attribute) (optunaz.utils.preprocessing.deduplicator.KeepFirst attribute) (optunaz.utils.preprocessing.deduplicator.KeepLast attribute) (optunaz.utils.preprocessing.deduplicator.KeepMax attribute) (optunaz.utils.preprocessing.deduplicator.KeepMedian attribute) (optunaz.utils.preprocessing.deduplicator.KeepMin attribute) (optunaz.utils.preprocessing.deduplicator.KeepRandom attribute) (optunaz.utils.preprocessing.splitter.KFold attribute) (optunaz.utils.preprocessing.splitter.NoSplitting attribute) (optunaz.utils.preprocessing.splitter.Predefined attribute) (optunaz.utils.preprocessing.splitter.Random attribute) (optunaz.utils.preprocessing.splitter.ScaffoldSplit attribute) (optunaz.utils.preprocessing.splitter.Stratified attribute) (optunaz.utils.preprocessing.splitter.Temporal attribute) (optunaz.utils.preprocessing.transform.AmorProt attribute) (optunaz.utils.preprocessing.transform.ModelDataTransform attribute) (optunaz.utils.preprocessing.transform.PTRTransform attribute) (optunaz.utils.preprocessing.transform.VectorFromColumn attribute) (optunaz.utils.preprocessing.transform.ZScales attribute)

NameParameterDataclass (class in optunaz.config) nBits (optunaz.descriptors.Avalon.Parameters attribute) (optunaz.descriptors.ECFP.Parameters attribute) (optunaz.descriptors.ECFP_counts.Parameters attribute) NEG_BRIER_SCORE (optunaz.config.optconfig.ClassificationScore attribute) NEG_MEAN_ABSOLUTE_ERROR (optunaz.config.optconfig.RegressionScore attribute) NEG_MEAN_SQUARED_ERROR (optunaz.config.optconfig.RegressionScore attribute) NEG_MEDIAN_ABSOLUTE_ERROR (optunaz.config.optconfig.RegressionScore attribute) negation (optunaz.utils.preprocessing.transform.ModelDataTransform.Parameters attribute) new() (optunaz.config.NameParameterDataclass class method) new_syn_data_frac (optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters attribute) NoDifferingRetrainingData NONE (optunaz.config.optconfig.ChemPropFeatures_Generator attribute) (optunaz.config.optconfig.ChemPropFrzn attribute) NoNewRetrainingData NoPreviousModel NoRetrainingDataConvention NORM (optunaz.config.optconfig.ChemPropAggregation attribute) NoSplitting (class in optunaz.utils.preprocessing.splitter) NoValidDescriptors NoValidSmiles nPermutations (optunaz.descriptors.MAPC.Parameters attribute) (optunaz.descriptors.UnscaledMAPC.Parameters attribute) null_scores() (in module optunaz.objective) num_iters (optunaz.config.buildconfig.ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters attribute) (optunaz.config.optconfig.ChemPropHyperoptClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropHyperoptRegressor.Parameters attribute) numpy_from_rdkit() (in module optunaz.descriptors)

O

Objective (class in optunaz.objective) ObjectiveEnum (class in optunaz.utils.enums.objective_enum) optconfig (optunaz.objective.Objective attribute) OPTCONFIG (optunaz.utils.enums.StudyUserAttrs attribute) optconfig (optunaz.utils.mlflow.MLflowCallback attribute) (optunaz.utils.tracking.InternalTrackingCallback attribute) OPTIMIZATION (optunaz.config.Task attribute) OptimizationConfig (class in optunaz.config.optconfig) OptimizationConfig.Settings (class in optunaz.config.optconfig) OptimizationConfigurationEnum (class in optunaz.utils.enums.optimization_configuration_enum) OptimizationDirection (class in optunaz.config) optimize() (in module optunaz.three_step_opt_build_merge) optuna_storage (optunaz.config.optconfig.OptimizationConfig.Settings attribute) OPTUNA_SYSTEM_ATTRS_INTERMEDIATE_VALUES (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) OPTUNA_SYSTEM_ATTRS_NUMBER (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) OPTUNA_SYSTEM_ATTRS_TRIAL_ID (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) optunaz module optunaz.automl module optunaz.builder module optunaz.config module optunaz.config.build_from_opt module optunaz.config.buildconfig module optunaz.config.optconfig module optunaz.convert module optunaz.datareader module optunaz.descriptors module optunaz.evaluate module optunaz.explainability module optunaz.metircs module optunaz.model_writer module optunaz.objective module optunaz.optbuild module optunaz.predict module

optunaz.schemagen module optunaz.three_step_opt_build_merge module optunaz.utils module optunaz.utils.enums module optunaz.utils.enums.building_configuration_enum module optunaz.utils.enums.configuration_enum module optunaz.utils.enums.interface_enum module optunaz.utils.enums.model_runner_enum module optunaz.utils.enums.objective_enum module optunaz.utils.enums.optimization_configuration_enum module optunaz.utils.enums.prediction_configuration_enum module optunaz.utils.enums.return_values_enum module optunaz.utils.enums.visualization_enum module optunaz.utils.files_paths module optunaz.utils.load_json module optunaz.utils.mlflow module optunaz.utils.preprocessing module optunaz.utils.preprocessing.deduplicator module optunaz.utils.preprocessing.splitter module optunaz.utils.preprocessing.transform module optunaz.utils.retraining module optunaz.utils.schema module optunaz.utils.tracking module optunaz.visualizer module output_folder (optunaz.config.Visualization attribute)

P

parallel_compute_descriptor() (optunaz.descriptors.MolDescriptor method) parameters (optunaz.config.buildconfig.AdaBoostClassifier attribute) (optunaz.config.buildconfig.CalibratedClassifierCVWithVA attribute) (optunaz.config.buildconfig.ChemPropClassifier attribute) (optunaz.config.buildconfig.ChemPropHyperoptClassifier attribute) (optunaz.config.buildconfig.ChemPropHyperoptRegressor attribute) (optunaz.config.buildconfig.ChemPropRegressor attribute) (optunaz.config.buildconfig.ChemPropRegressorPretrained attribute) (optunaz.config.buildconfig.CustomClassificationModel attribute) (optunaz.config.buildconfig.CustomRegressionModel attribute) (optunaz.config.buildconfig.KNeighborsClassifier attribute) (optunaz.config.buildconfig.KNeighborsRegressor attribute) (optunaz.config.buildconfig.Lasso attribute) (optunaz.config.buildconfig.LogisticRegression attribute) (optunaz.config.buildconfig.Mapie attribute) (optunaz.config.buildconfig.PLSRegression attribute) (optunaz.config.buildconfig.PRFClassifier attribute) (optunaz.config.buildconfig.RandomForestClassifier attribute) (optunaz.config.buildconfig.RandomForestRegressor attribute) (optunaz.config.buildconfig.Ridge attribute) (optunaz.config.buildconfig.SVC attribute) (optunaz.config.buildconfig.SVR attribute) (optunaz.config.buildconfig.XGBRegressor attribute) (optunaz.config.optconfig.AdaBoostClassifier attribute) (optunaz.config.optconfig.CalibratedClassifierCVWithVA attribute) (optunaz.config.optconfig.ChemPropClassifier attribute) (optunaz.config.optconfig.ChemPropHyperoptClassifier attribute) (optunaz.config.optconfig.ChemPropHyperoptRegressor attribute) (optunaz.config.optconfig.ChemPropRegressor attribute) (optunaz.config.optconfig.ChemPropRegressorPretrained attribute) (optunaz.config.optconfig.CustomClassificationModel attribute) (optunaz.config.optconfig.CustomRegressionModel attribute) (optunaz.config.optconfig.KNeighborsClassifier attribute) (optunaz.config.optconfig.KNeighborsRegressor attribute) (optunaz.config.optconfig.Lasso attribute) (optunaz.config.optconfig.LogisticRegression attribute) (optunaz.config.optconfig.Mapie attribute) (optunaz.config.optconfig.PLSRegression attribute) (optunaz.config.optconfig.PRFClassifier attribute) (optunaz.config.optconfig.RandomForestClassifier attribute) (optunaz.config.optconfig.RandomForestRegressor attribute) (optunaz.config.optconfig.Ridge attribute) (optunaz.config.optconfig.SVC attribute) (optunaz.config.optconfig.SVR attribute) (optunaz.config.optconfig.XGBRegressor attribute) (optunaz.descriptors.AmorProtDescriptors attribute) (optunaz.descriptors.Avalon attribute) (optunaz.descriptors.CanonicalSmiles attribute) (optunaz.descriptors.CompositeDescriptor attribute) (optunaz.descriptors.ECFP attribute) (optunaz.descriptors.ECFP_counts attribute) (optunaz.descriptors.GenericScaffold attribute) (optunaz.descriptors.JazzyDescriptors attribute) (optunaz.descriptors.MACCS_keys attribute) (optunaz.descriptors.MAPC attribute) (optunaz.descriptors.PathFP attribute) (optunaz.descriptors.PhyschemDescriptors attribute) (optunaz.descriptors.PrecomputedDescriptorFromFile attribute) (optunaz.descriptors.Scaffold attribute) (optunaz.descriptors.ScaledDescriptor attribute) (optunaz.descriptors.SmilesAndSideInfoFromFile attribute) (optunaz.descriptors.SmilesFromFile attribute) (optunaz.descriptors.UnscaledJazzyDescriptors attribute) (optunaz.descriptors.UnscaledMAPC attribute) (optunaz.descriptors.UnscaledPhyschemDescriptors attribute) (optunaz.descriptors.UnscaledZScalesDescriptors attribute) (optunaz.descriptors.ValidDescriptor attribute) (optunaz.descriptors.ZScalesDescriptors attribute) (optunaz.utils.preprocessing.transform.AmorProt attribute) (optunaz.utils.preprocessing.transform.ModelDataTransform attribute) (optunaz.utils.preprocessing.transform.PTRTransform attribute) (optunaz.utils.preprocessing.transform.VectorFromColumn attribute) (optunaz.utils.preprocessing.transform.ZScales attribute)

patch_schema_generic() (in module optunaz.schemagen) patch_schema_optunaz() (in module optunaz.schemagen) PathFP (class in optunaz.descriptors), [1] PathFP.Parameters (class in optunaz.descriptors), [1] PDF (optunaz.config.Visualization.ImageFileFormat attribute) perform_ptr() (in module optunaz.model_writer) PhyschemDescriptors (class in optunaz.descriptors), [1] PhyschemDescriptors.Parameters (class in optunaz.descriptors), [1] plot_by_configuration() (optunaz.visualizer.Visualizer method) plot_contour (optunaz.config.Visualization.Plots attribute) plot_contour() (optunaz.visualizer.Visualizer method) plot_history (optunaz.config.Visualization.Plots attribute) plot_history() (optunaz.visualizer.Visualizer static method) plot_parallel_coordinate (optunaz.config.Visualization.Plots attribute) plot_parallel_coordinate() (optunaz.visualizer.Visualizer method) plot_slice (optunaz.config.Visualization.Plots attribute) plot_slice() (optunaz.visualizer.Visualizer method) plots (optunaz.config.Visualization attribute) PLSRegression (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] PLSRegression.Parameters (class in optunaz.config.optconfig), [1] PLSRegression.Parameters.NComponents (class in optunaz.config.optconfig), [1] PLSRegression.PLSParameters (class in optunaz.config.buildconfig) PNG (optunaz.config.Visualization.ImageFileFormat attribute) PRECISION (optunaz.config.optconfig.ClassificationScore attribute) PRECISION_MACRO (optunaz.config.optconfig.ClassificationScore attribute) PRECISION_MICRO (optunaz.config.optconfig.ClassificationScore attribute) PRECISION_WEIGHTED (optunaz.config.optconfig.ClassificationScore attribute) PrecomputedDescriptorFromFile (class in optunaz.descriptors), [1] PrecomputedDescriptorFromFile.Parameters (class in optunaz.descriptors), [1] PrecomputedError Predefined (class in optunaz.utils.preprocessing.splitter), [1] predict() (optunaz.config.buildconfig.CustomClassificationModel.CustomClassificationEstimator method) (optunaz.config.buildconfig.CustomRegressionModel.CustomRegressionEstimator method) (optunaz.model_writer.Predictor method) predict_from_smiles() (optunaz.model_writer.QSARtunaModel method) predict_proba() (optunaz.config.buildconfig.CustomClassificationModel.CustomClassificationEstimator method) (optunaz.model_writer.Predictor method) predict_uncert() (optunaz.model_writer.Predictor method) predicted (optunaz.utils.tracking.Datapoint attribute) PREDICTION (optunaz.config.Task attribute) PredictionConfigurationEnum (class in optunaz.utils.enums.prediction_configuration_enum) Predictor (class in optunaz.model_writer) predictor (optunaz.model_writer.QSARtunaModel attribute) preexisting_model (optunaz.config.buildconfig.CustomClassificationModel.CustomClassificationModelParameters attribute) (optunaz.config.buildconfig.CustomRegressionModel.CustomRegressionModelParameters attribute) (optunaz.config.optconfig.CustomClassificationModel.Parameters attribute) (optunaz.config.optconfig.CustomRegressionModel.Parameters attribute) PRELU (optunaz.config.optconfig.ChemPropActivation attribute) prep_build() (in module optunaz.convert) prepare_dispatcher() (in module optunaz.automl) prepare_tags() (optunaz.utils.mlflow.MLflowCallback method) pretrained_model (optunaz.automl.ModelDispatcher property) (optunaz.config.buildconfig.ChemPropRegressorPretrained.ChemPropRegressorPretrainedParameters attribute) (optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters attribute) PRF_SET (optunaz.utils.enums.interface_enum.InterfaceEnum attribute) PRFClassifier (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] PRFClassifier.Parameters (class in optunaz.config.optconfig), [1] PRFClassifier.Parameters.PRFClassifierParametersMaxDepth (class in optunaz.config.optconfig), [1] PRFClassifier.Parameters.PRFClassifierParametersMinPySumLeaf (class in optunaz.config.optconfig), [1] PRFClassifier.Parameters.PRFClassifierParametersNEstimators (class in optunaz.config.optconfig), [1] PRFClassifier.PRFClassifierParameters (class in optunaz.config.buildconfig) PRFClassifierMaxFeatures (class in optunaz.config.optconfig) probabilistic_threshold_representation (optunaz.datareader.Dataset attribute) probabilistic_threshold_representation_std (optunaz.datareader.Dataset attribute) probabilistic_threshold_representation_threshold (optunaz.datareader.Dataset attribute) process_retraining_task() (in module optunaz.automl) processed_timepoints (optunaz.automl.ModelAutoML property) processQuorum() (optunaz.automl.ModelDispatcher method) processRetraining() (optunaz.automl.ModelDispatcher method) processTrain() (optunaz.automl.ModelDispatcher method) PTRTransform (class in optunaz.utils.preprocessing.transform), [1] PTRTransform.Parameters (class in optunaz.utils.preprocessing.transform), [1]

Q

q (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersAggregation_Norm attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersBatch_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDepth attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDropout attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Hidden_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Num_Layers attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersHidden_Size attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersWarmup_Epochs_Ratio attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersAggregation_Norm attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersBatch_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDepth attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDropout attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Hidden_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Num_Layers attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersHidden_Size attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersWarmup_Epochs_Ratio attribute) (optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters.ChemPropParametersEpochs attribute) (optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters.Aux_Weight_Pc attribute)

QSARtunaModel (class in optunaz.model_writer)

R

R2 (optunaz.config.optconfig.RegressionScore attribute) radius (optunaz.descriptors.ECFP.Parameters attribute) (optunaz.descriptors.ECFP_counts.Parameters attribute) Random (class in optunaz.utils.preprocessing.splitter), [1] random_seed (optunaz.config.optconfig.OptimizationConfig.Settings attribute) random_state (optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit attribute) (optunaz.utils.preprocessing.splitter.KFold attribute) (optunaz.utils.preprocessing.splitter.ScaffoldSplit attribute) RandomForestClassifier (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] RandomForestClassifier.Parameters (class in optunaz.config.optconfig), [1] RandomForestClassifier.Parameters.RandomForestClassifierParametersMaxDepth (class in optunaz.config.optconfig), [1] RandomForestClassifier.Parameters.RandomForestClassifierParametersNEstimators (class in optunaz.config.optconfig), [1] RandomForestClassifier.RandomForestParameters (class in optunaz.config.buildconfig) RandomForestMaxFeatures (class in optunaz.config.optconfig) RandomForestRegressor (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] RandomForestRegressor.Parameters (class in optunaz.config.optconfig), [1] RandomForestRegressor.Parameters.RandomForestRegressorParametersMaxDepth (class in optunaz.config.optconfig), [1] RandomForestRegressor.Parameters.RandomForestRegressorParametersNEstimators (class in optunaz.config.optconfig), [1] RandomForestRegressor.RandomForestParameters (class in optunaz.config.buildconfig) RDKIT_2D (optunaz.config.optconfig.ChemPropFeatures_Generator attribute) RDKIT_2D_NORMALIZED (optunaz.config.optconfig.ChemPropFeatures_Generator attribute) rdkit_names (optunaz.descriptors.PhyschemDescriptors.Parameters attribute) (optunaz.descriptors.UnscaledPhyschemDescriptors.Parameters attribute) RdkitDescriptor (class in optunaz.descriptors) read_data() (in module optunaz.datareader) RECALL (optunaz.config.optconfig.ClassificationScore attribute) RECALL_MACRO (optunaz.config.optconfig.ClassificationScore attribute) RECALL_MICRO (optunaz.config.optconfig.ClassificationScore attribute) RECALL_WEIGHTED (optunaz.config.optconfig.ClassificationScore attribute) refit_model (optunaz.config.buildconfig.CustomClassificationModel.CustomClassificationModelParameters attribute) (optunaz.config.buildconfig.CustomRegressionModel.CustomRegressionModelParameters attribute) (optunaz.config.optconfig.CustomClassificationModel.Parameters attribute) (optunaz.config.optconfig.CustomRegressionModel.Parameters attribute)

REGRESSION (optunaz.config.ModelMode attribute) RegressionScore (class in optunaz.config.optconfig) RELU (optunaz.config.optconfig.ChemPropActivation attribute) remove_algo_hash() (in module optunaz.config.build_from_opt) remove_failed_idx() (in module optunaz.utils) remove_schema_properties() (in module optunaz.utils.schema) removeprefix() (in module optunaz.utils.tracking) replaceenum() (in module optunaz.utils.schema) replacekey() (in module optunaz.utils.schema) replacevalue() (in module optunaz.utils.schema) response_column (optunaz.datareader.Dataset attribute) (optunaz.descriptors.PrecomputedDescriptorFromFile.Parameters attribute) response_column_name (optunaz.utils.tracking.BuildTrackingData attribute) response_type (optunaz.datareader.Dataset attribute) resubmitAnyFailedJobs() (optunaz.automl.ModelDispatcher method) RetrainingHeadersIssue RetrainingIsAlreadyProcessed RetrainingIsLocked returnRdkit (optunaz.descriptors.ECFP.Parameters attribute) reverse_dict (optunaz.utils.preprocessing.transform.ModelDataTransform attribute) reverse_transform() (optunaz.utils.preprocessing.transform.ModelDataTransform method) (optunaz.utils.preprocessing.transform.PTRTransform method) reverse_transform_df() (optunaz.utils.preprocessing.transform.ModelDataTransform method) reverse_transform_one() (optunaz.utils.preprocessing.transform.ModelDataTransform method) Ridge (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] Ridge.Parameters (class in optunaz.config.optconfig), [1] Ridge.Parameters.Alpha (class in optunaz.config.optconfig), [1] Ridge.RidgeParameters (class in optunaz.config.buildconfig) ROC_AUC (optunaz.config.optconfig.ClassificationScore attribute) round_scores() (in module optunaz.utils.tracking) run_study() (in module optunaz.three_step_opt_build_merge) runShap() (in module optunaz.explainability)

S

SamePreviousModel save_intermediate_files (optunaz.datareader.Dataset attribute) save_model() (in module optunaz.model_writer) saved_params (optunaz.descriptors.FittedSklearnScaler attribute) Scaffold (class in optunaz.descriptors) Scaffold.Parameters (class in optunaz.descriptors) ScaffoldSplit (class in optunaz.utils.preprocessing.splitter), [1] ScaledDescriptor (class in optunaz.descriptors), [1] ScaledDescriptor.ScaledDescriptorParameters (class in optunaz.descriptors), [1] scaler (optunaz.descriptors.JazzyDescriptors.Parameters attribute) (optunaz.descriptors.MAPC.Parameters attribute) (optunaz.descriptors.PhyschemDescriptors.Parameters attribute) (optunaz.descriptors.ScaledDescriptor.ScaledDescriptorParameters attribute) (optunaz.descriptors.ZScalesDescriptors.Parameters attribute) ScalingFittingError scoring (optunaz.config.buildconfig.BuildConfig.Settings attribute) (optunaz.config.optconfig.OptimizationConfig.Settings attribute) (optunaz.utils.tracking.TrackingData attribute) search_parameter_level (optunaz.config.buildconfig.ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters attribute) (optunaz.config.optconfig.ChemPropHyperoptClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropHyperoptRegressor.Parameters attribute) seed (optunaz.utils.preprocessing.deduplicator.KeepRandom attribute) (optunaz.utils.preprocessing.splitter.Random attribute) (optunaz.utils.preprocessing.splitter.Stratified attribute) SELU (optunaz.config.optconfig.ChemPropActivation attribute) SET (optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum attribute) set_algo_hashes() (optunaz.config.optconfig.OptimizationConfig method) set_build_cache() (in module optunaz.config.build_from_opt) set_cache() (optunaz.config.optconfig.OptimizationConfig method) set_default_output_names() (in module optunaz.optbuild) set_inference_params() (in module optunaz.predict) set_score_request() (optunaz.config.buildconfig.CustomClassificationModel.CustomClassificationEstimator method) (optunaz.config.buildconfig.CustomRegressionModel.CustomRegressionEstimator method) set_unfitted_scaler_data() (optunaz.descriptors.ScaledDescriptor method) setDispatcherVariables() (optunaz.automl.ModelDispatcher method) setJobLocked() (optunaz.automl.ModelDispatcher method) setProcessedTimepoints() (optunaz.automl.ModelAutoML method) setRetrainingData() (optunaz.automl.ModelAutoML method) setSkippedTimepoint() (optunaz.automl.ModelDispatcher method) settings (optunaz.config.buildconfig.BuildConfig attribute) (optunaz.config.optconfig.OptimizationConfig attribute) SETTINGS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) SETTINGS_CROSS_VALIDATION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) SETTINGS_DIRECTION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) SETTINGS_MODE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) SETTINGS_MODE_CLASSIFICATION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) SETTINGS_MODE_REGRESSION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) SETTINGS_N_JOBS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) SETTINGS_N_TRIALS (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) SETTINGS_SHUFFLE (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) ShapExplainer() (in module optunaz.explainability) shorten_names() (in module optunaz.utils.mlflow) shuffle (optunaz.config.buildconfig.BuildConfig.Metadata attribute) (optunaz.config.optconfig.OptimizationConfig.Settings attribute) (optunaz.utils.preprocessing.splitter.KFold attribute)

SIGMOID (optunaz.config.optconfig.CalibratedClassifierCVMethod attribute) SKLEARN_SET (optunaz.utils.enums.interface_enum.InterfaceEnum attribute) SklearnReturnValueEnum (class in optunaz.utils.enums.return_values_enum) SklearnSplitter (class in optunaz.utils.preprocessing.splitter) SlurmJobSkip SlurmMemoryExceeded SlurmNoLog SlurmParseError SlurmTimeLimitExceeded SMILES (optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum attribute) smiles (optunaz.utils.tracking.Datapoint attribute) smiles_column (optunaz.descriptors.UnfittedSklearnScaler.MolData attribute) SmilesAndSideInfoFromFile (class in optunaz.descriptors), [1] SmilesAndSideInfoFromFile.Parameters (class in optunaz.descriptors), [1] SmilesAndSideInfoFromFile.Parameters.Aux_Weight_Pc (class in optunaz.descriptors), [1] SmilesFromFile (class in optunaz.descriptors), [1] SmilesFromFile.Parameters (class in optunaz.descriptors), [1] solver (optunaz.config.buildconfig.LogisticRegression.LogisticRegressionParameters attribute) (optunaz.config.optconfig.LogisticRegression.Parameters attribute) split() (in module optunaz.datareader) (optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit method) (optunaz.utils.preprocessing.splitter.KFold method) (optunaz.utils.preprocessing.splitter.NoSplitting method) (optunaz.utils.preprocessing.splitter.Predefined method), [1] (optunaz.utils.preprocessing.splitter.ScaffoldSplit method), [1] (optunaz.utils.preprocessing.splitter.SklearnSplitter method) (optunaz.utils.preprocessing.splitter.Splitter method) (optunaz.utils.preprocessing.splitter.Temporal method), [1] split_chemprop (optunaz.config.optconfig.OptimizationConfig.Settings attribute) split_optimize() (in module optunaz.three_step_opt_build_merge) split_strategy (optunaz.datareader.Dataset attribute) Splitter (class in optunaz.utils.preprocessing.splitter) SQRT (optunaz.config.optconfig.PRFClassifierMaxFeatures attribute) (optunaz.config.optconfig.RandomForestMaxFeatures attribute) std (optunaz.utils.preprocessing.transform.PTRTransform.Parameters attribute) Stratified (class in optunaz.utils.preprocessing.splitter), [1] stratify() (in module optunaz.utils.preprocessing.splitter) StudyUserAttrs (class in optunaz.utils.enums) submitJob() (optunaz.automl.ModelDispatcher method) suggest_alg_params() (in module optunaz.config.build_from_opt) suggest_aux_params() (in module optunaz.config.build_from_opt) SUM (optunaz.config.optconfig.ChemPropAggregation attribute) SVC (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] SVC.Parameters (class in optunaz.config.optconfig), [1] SVC.Parameters.Gamma (class in optunaz.config.optconfig), [1] SVC.Parameters.SVCParametersParameterC (class in optunaz.config.optconfig), [1] SVC.SVCParameters (class in optunaz.config.buildconfig) SVG (optunaz.config.Visualization.ImageFileFormat attribute) SVR (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1] SVR.Parameters (class in optunaz.config.optconfig), [1] SVR.Parameters.SVRParametersGamma (class in optunaz.config.optconfig), [1] SVR.Parameters.SVRParametersParameterC (class in optunaz.config.optconfig), [1] SVR.SVRParameters (class in optunaz.config.buildconfig)

T

T() (optunaz.descriptors.AmorProtDescriptors.AmorProt method) TANH (optunaz.config.optconfig.ChemPropActivation attribute) Task (class in optunaz.config) task (optunaz.config.buildconfig.BuildConfig attribute) (optunaz.config.optconfig.OptimizationConfig attribute) TASK (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) TASK_BUILDING (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) TASK_OPTIMIZATION (optunaz.utils.enums.configuration_enum.ConfigurationEnum attribute) Temporal (class in optunaz.utils.preprocessing.splitter), [1] TemporalPredsPredicted TEST (optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum attribute) test_dataset_file (optunaz.datareader.Dataset attribute) test_fraction (optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit attribute) test_points (optunaz.utils.tracking.BuildTrackingData attribute) TEST_SCORES (optunaz.utils.enums.TrialUserAttrs attribute) test_scores (optunaz.utils.tracking.BuildTrackingData attribute) threshold (optunaz.utils.preprocessing.transform.PTRTransform.Parameters attribute) TimepointSkipped tmp_buildconfig() (optunaz.utils.mlflow.MLflowCallback method) track_build() (in module optunaz.utils.tracking) track_to_mlflow (optunaz.config.optconfig.OptimizationConfig.Settings attribute) tracking_rest_endpoint (optunaz.config.buildconfig.BuildConfig.Settings attribute) (optunaz.config.optconfig.OptimizationConfig.Settings attribute) tracking_uri (optunaz.utils.mlflow.MLflowCallback attribute) TrackingData (class in optunaz.utils.tracking) TRAIN (optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum attribute) train_aux (optunaz.objective.Objective attribute)

TRAIN_SCORES (optunaz.utils.enums.TrialUserAttrs attribute) train_size (optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit attribute) train_smiles (optunaz.objective.Objective attribute) train_y (optunaz.objective.Objective attribute) training_dataset_file (optunaz.datareader.Dataset attribute) transform (optunaz.model_writer.QSARtunaModel attribute) transform() (in module optunaz.datareader) (optunaz.utils.preprocessing.transform.AmorProt method) (optunaz.utils.preprocessing.transform.AuxTransformer method) (optunaz.utils.preprocessing.transform.DataTransform method) (optunaz.utils.preprocessing.transform.ModelDataTransform method) (optunaz.utils.preprocessing.transform.PTRTransform method) (optunaz.utils.preprocessing.transform.VectorFromColumn method) (optunaz.utils.preprocessing.transform.ZScales method) transform_df() (optunaz.utils.preprocessing.transform.ModelDataTransform method) transform_one() (optunaz.utils.preprocessing.transform.ModelDataTransform method) TRIAL_NUMBER (optunaz.utils.enums.MlflowLogParams attribute) trial_number (optunaz.utils.tracking.TrackingData attribute) trial_number_offset (optunaz.utils.mlflow.MLflowCallback attribute) (optunaz.utils.tracking.InternalTrackingCallback attribute) trial_state (optunaz.utils.tracking.TrackingData attribute) trial_value (optunaz.utils.tracking.TrackingData attribute) TrialParams (class in optunaz.utils.enums) TrialUserAttrs (class in optunaz.utils.enums) TRUE (optunaz.config.optconfig.CalibratedClassifierCVEnsemble attribute) (optunaz.utils.preprocessing.transform.LogNegative attribute) type_base_schema() (in module optunaz.schemagen)

U

UncertaintyError UnfittedSklearnScaler (class in optunaz.descriptors) UnfittedSklearnScaler.MolData (class in optunaz.descriptors) UNIFORM (optunaz.config.optconfig.KNeighborsWeights attribute) UnscaledJazzyDescriptors (class in optunaz.descriptors), [1] UnscaledJazzyDescriptors.Parameters (class in optunaz.descriptors), [1] UnscaledMAPC (class in optunaz.descriptors), [1] UnscaledMAPC.Parameters (class in optunaz.descriptors), [1] UnscaledPhyschemDescriptors (class in optunaz.descriptors), [1]

UnscaledPhyschemDescriptors.Parameters (class in optunaz.descriptors), [1] UnscaledZScalesDescriptors (class in optunaz.descriptors), [1], [2] UnscaledZScalesDescriptors.Parameters (class in optunaz.descriptors), [1], [2] use_cache (optunaz.config.optconfig.OptimizationConfig.Settings attribute) use_py_gini (optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters attribute) (optunaz.config.optconfig.PRFClassifier.Parameters attribute) use_py_leafs (optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters attribute) (optunaz.config.optconfig.PRFClassifier.Parameters attribute) use_xvfb (optunaz.config.Visualization attribute) useFeatures (optunaz.descriptors.ECFP_counts.Parameters attribute)

V

validate_args() (in module optunaz.automl) (in module optunaz.predict) validate_aux() (in module optunaz.predict) validate_cls_input() (in module optunaz.metircs) validate_set_precomputed() (in module optunaz.predict) validate_uncertainty() (in module optunaz.predict) ValidDescriptor (class in optunaz.descriptors) ValidDescriptor.Parameters (class in optunaz.descriptors) VectorFromColumn (class in optunaz.utils.preprocessing.transform), [1] VectorFromColumn.Parameters (class in optunaz.utils.preprocessing.transform), [1] VENNABERS (optunaz.config.optconfig.CalibratedClassifierCVMethod attribute) Visualization (class in optunaz.config) visualization (optunaz.config.buildconfig.BuildConfig.Metadata attribute) (optunaz.config.optconfig.OptimizationConfig attribute)

VISUALIZATION (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) Visualization.ImageFileFormat (class in optunaz.config) Visualization.Plots (class in optunaz.config) VISUALIZATION_CLASSIFIER (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_FILE_FORMAT (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_OUTPUT_FOLDER (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_PLOTS (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_PLOTS_CONTOUR (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_PLOTS_HISTORY (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_PLOTS_PARALLEL_COORDINATE (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_PLOTS_SLICE (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_REGRESSOR (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VISUALIZATION_USE_XVFB (optunaz.utils.enums.visualization_enum.VisualizationEnum attribute) VisualizationEnum (class in optunaz.utils.enums.visualization_enum) Visualizer (class in optunaz.visualizer)

W

warmup_epochs_ratio (optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters attribute) (optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters attribute) (optunaz.config.optconfig.ChemPropClassifier.Parameters attribute) (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute) weights (optunaz.config.buildconfig.KNeighborsClassifier.KNeighborsClassifierParameters attribute) (optunaz.config.buildconfig.KNeighborsRegressor.KNeighborsRegressorParameters attribute) (optunaz.config.optconfig.KNeighborsClassifier.Parameters attribute) (optunaz.config.optconfig.KNeighborsRegressor.Parameters attribute)

wrap_model() (in module optunaz.model_writer) writeDataset() (optunaz.automl.ModelDispatcher method) writeJson() (optunaz.automl.ModelDispatcher method) writeSlurm() (optunaz.automl.ModelDispatcher method)

X

XGBOOST_SET (optunaz.utils.enums.interface_enum.InterfaceEnum attribute) XGBoostReturnValueEnum (class in optunaz.utils.enums.return_values_enum) XGBRegressor (class in optunaz.config.buildconfig) (class in optunaz.config.optconfig), [1]

XGBRegressor.Parameters (class in optunaz.config.optconfig), [1] XGBRegressor.Parameters.LearningRate (class in optunaz.config.optconfig), [1] XGBRegressor.Parameters.MaxDepth (class in optunaz.config.optconfig), [1] XGBRegressor.Parameters.NEstimators (class in optunaz.config.optconfig), [1] XGBRegressor.XGBRegressorParameters (class in optunaz.config.buildconfig)

Y

Y_PRED (optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum attribute)

Y_TRUE (optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum attribute)

Z

ZScales (class in optunaz.utils.preprocessing.transform), [1] ZScales.Parameters (class in optunaz.utils.preprocessing.transform), [1]

ZScalesDescriptors (class in optunaz.descriptors), [1], [2] ZScalesDescriptors.Parameters (class in optunaz.descriptors), [1], [2]