optunaz.utils.enums package

Submodules

optunaz.utils.enums.building_configuration_enum module

class optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum

Bases: ConfigurationEnum

This “Enum” serves to store all the strings used in parsing the building configurations. Note, that validity checks are not performed, but referred to JSON Schema validations.

GENERAL_HYPERPARAMETERS = 'hyper_parameters'

GENERAL_REGRESSOR = 'regressor'

GENERAL_CLASSIFIER = 'classifier'

METADATA = 'metadata'

METADATA_BESTTRIAL = 'best_trial'

METADATA_BESTVALUE = 'best_value'

optunaz.utils.enums.configuration_enum module

class optunaz.utils.enums.configuration_enum.ConfigurationEnum

Bases: object

This “Enum” serves to store all the strings used in parsing all configurations. Note, that validity checks are not performed, but referred to JSON Schema validations.

GENERAL_DISABLED = 'disabled'

GENERAL_PARAMETERS = 'parameters'

TASK = 'task'

TASK_OPTIMIZATION = 'optimization'

TASK_BUILDING = 'building'

DATA = 'data'

DATA_INPUTCOLUMN = 'input_column'

DATA_RESPONSECOLUMN = 'response_column'

DATA_TRAINING = 'training'

DATA_TEST = 'test'

DESCRIPTORS = 'descriptors'

DESCRIPTORS_AVALON = 'Avalon'

DESCRIPTORS_AVALON_NBITS = 'nBits'

DESCRIPTORS_ECFP = 'ECFP'

DESCRIPTORS_ECFP_RADIUS = 'radius'

DESCRIPTORS_ECFP_NBITS = 'nBits'

DESCRIPTORS_ECFPCOUNTS = 'ECFP_counts'

DESCRIPTORS_ECFPCOUNTS_RADIUS = 'radius'

DESCRIPTORS_ECFPCOUNTS_USEFEATURES = 'useFeatures'

DESCRIPTORS_PATHFP = 'PathFP'

DESCRIPTORS_PATHFP_MAXPATH = 'maxPath'

DESCRIPTORS_PATHFP_FPSIZE = 'fpSize'

DESCRIPTORS_MACCSKEYS = 'MACCS_keys'

DESCRIPTORS_UNSC_PHYSCHEM = 'UnscaledPhyschemDescriptors'

DESCRIPTORS_PHYSCHEM = 'PhyschemDescriptors'

DESCRIPTORS_PHYSCHEM_RDKITNAMES = 'rdkit_names'

DESCRIPTORS_AMORPROT = 'AmorProtDescriptors'

DESCRIPTORS_UNSC_MAPC = 'UnscaledMAPC'

DESCRIPTORS_MAPC = 'MAPC'

DESCRIPTORS_MAPC_MAXRADIUS = 'maxRadius'

DESCRIPTORS_MAPC_NPERMUTATIONS = 'nPermutations'

DESCRIPTORS_UNSC_JAZZY = 'UnscaledJazzyDescriptors'

DESCRIPTORS_JAZZY = 'JazzyDescriptors'

DESCRIPTORS_JAZZY_JAZZYNAMES = 'jazzy_names'

DESCRIPTORS_PRECOMPUTED = 'PrecomputedDescriptorFromFile'

DESCRIPTORS_PRECOMPUTED_FILE = 'file'

DESCRIPTORS_PRECOMPUTED_INPUT_COLUMNN = 'input_column'

DESCRIPTORS_PRECOMPUTED_RESPONSE_COLUMN = 'response_column'

DESCRIPTORS_UNSC_ZSCALES = 'UnscaledZScalesDescriptors'

DESCRIPTORS_ZSCALES = 'ZScalesDescriptors'

DESCRIPTORS_SMILES = 'SmilesFromFile'

DESCRIPTORS_SMILES_AND_SI = 'SmilesAndSideInfoFromFile'

DESCRIPTORS_SMILES_AND_SI_FILE = 'file'

DESCRIPTORS_SMILES_AND_SI_INPUT_COLUMN = 'input_column'

DESCRIPTORS_SMILES_AND_SI_AUX_WEIGHT_PC = 'aux_weight_pc'

DESCRIPTORS_SCALED = 'ScaledDescriptor'

DESCRIPTORS_SCALED_DESCRIPTOR = 'descriptor'

DESCRIPTORS_SCALED_DESCRIPTOR_PARAMETERS = 'parameters'

DESCRIPTORS_COMPOSITE = 'CompositeDescriptor'

SETTINGS = 'settings'

SETTINGS_MODE = 'mode'

SETTINGS_MODE_REGRESSION = 'regression'

SETTINGS_MODE_CLASSIFICATION = 'classification'

SETTINGS_CROSS_VALIDATION = 'cross_validation'

SETTINGS_DIRECTION = 'direction'

SETTINGS_N_TRIALS = 'n_trials'

SETTINGS_N_JOBS = 'n_jobs'

SETTINGS_SHUFFLE = 'shuffle'

ALGORITHMS = 'algorithms'

ALGORITHMS_LOW = 'low'

ALGORITHMS_HIGH = 'high'

ALGORITHMS_Q = 'q'

ALGORITHMS_INTERFACE_SKLEARN = 'sklearn'

ALGORITHMS_INTERFACE_XGBOOST = 'xgboost'

ALGORITHMS_RFREGRESSOR = 'RandomForestRegressor'

ALGORITHMS_RFCLASSIFIER = 'RandomForestClassifier'

ALGORITHMS_RF_MAX_FEATURES = 'max_features'

ALGORITHMS_RF_MAX_DEPTH = 'max_depth'

ALGORITHMS_RF_N_ESTIMATORS = 'n_estimators'

ALGORITHMS_SVR = 'SVR'

ALGORITHMS_SVR_C = 'C'

ALGORITHMS_SVR_GAMMA = 'gamma'

ALGORITHMS_SVC = 'SVC'

ALGORITHMS_SVC_C = 'C'

ALGORITHMS_SVC_GAMMA = 'gamma'

ALGORITHMS_LASSO = 'Lasso'

ALGORITHMS_LASSO_ALPHA = 'alpha'

ALGORITHMS_KNEIGHBORSCLASSIFIER = 'KNeighborsClassifier'

ALGORITHMS_KNEIGHBORSREGRESSOR = 'KNeighborsRegressor'

ALGORITHMS_KNEIGHBORS_N_NEIGHBORS = 'n_neighbors'

ALGORITHMS_KNEIGHBORS_METRIC = 'metric'

ALGORITHMS_KNEIGHBORS_WEIGHTS = 'weights'

ALGORITHMS_RIDGE = 'Ridge'

ALGORITHMS_RIDGE_ALPHA = 'alpha'

ALGORITHMS_PLSREGRESSION = 'PLSRegression'

ALGORITHMS_PLSREGRESSION_N_COMPONENTS = 'n_components'

ALGORITHMS_LOGISTICREGRESSION = 'LogisticRegression'

ALGORITHMS_LOGISTICREGRESSION_SOLVER = 'solver'

ALGORITHMS_LOGISTICREGRESSION_C = 'C'

ALGORITHMS_ADABOOSTCLASSIFIER = 'AdaBoostClassifier'

ALGORITHMS_ADABOOSTCLASSIFIER_N_ESTIMATORS = 'n_estimators'

ALGORITHMS_ADABOOSTCLASSIFIER_LEARNING_RATE = 'learning_rate'

ALGORITHMS_XGBREGRESSOR = 'XGBregressor'

ALGORITHMS_XGBREGRESSOR_MAX_DEPTH = 'max_depth'

ALGORITHMS_XGBREGRESSOR_N_ESTIMATORS = 'n_estimators'

ALGORITHMS_XGBREGRESSOR_LEARNING_RATE = 'learning_rate'

ALGORITHMS_PRF = 'PRFClassifier'

ALGORITHMS_PRF_MAX_FEATURES = 'max_features'

ALGORITHMS_PRF_MAX_DEPTH = 'max_depth'

ALGORITHMS_PRF_N_ESTIMATORS = 'n_estimators'

ALGORITHMS_PRF_MINPYSUMLEAF = 'min_py_sum_leaf'

ALGORITHMS_PRF_USE_PY_GINI = 'use_py_gini'

ALGORITHMS_PRF_USE_PY_LEAFS = 'use_py_leafs'

ALGORITHMS_CHEMPROP = 'BaseChemProp'

ALGORITHMS_CHEMPROP_REGRESSOR = 'ChemPropRegressor'

ALGORITHMS_CHEMPROP_HYPEROPT_REGRESSOR = 'ChemPropHyperoptRegressor'

ALGORITHMS_CHEMPROP_CLASSIFIER = 'ChemPropClassifier'

ALGORITHMS_CHEMPROP_HYPEROPT_CLASSIFIER = 'ChemPropHyperoptClassifier'

ALGORITHMS_CHEMPROP_ACTIVATION = 'activation'

ALGORITHMS_CHEMPROP_AGGREGATION = 'aggregation'

ALGORITHMS_CHEMPROP_AGGREGATION_NORM = 'aggregation_norm'

ALGORITHMS_CHEMPROP_BATCH_SIZE = 'batch_size'

ALGORITHMS_CHEMPROP_DEPTH = 'depth'

ALGORITHMS_CHEMPROP_DROPOUT = 'dropout'

ALGORITHMS_CHEMPROP_EPOCHS = 'epochs'

ALGORITHMS_CHEMPROP_ENSEMBLE_SIZE = 'ensemble_size'

ALGORITHMS_CHEMPROP_FEATURES_GENERATOR = 'features_generator'

ALGORITHMS_CHEMPROP_FFN_HIDDEN_SIZE = 'ffn_hidden_size'

ALGORITHMS_CHEMPROP_FFN_NUM_LAYERS = 'ffn_num_layers'

ALGORITHMS_CHEMPROP_FRZN = 'frzn'

ALGORITHMS_CHEMPROP_FINAL_LR_RATIO_EXP = 'final_lr_ratio_exp'

ALGORITHMS_CHEMPROP_HIDDEN_SIZE = 'hidden_size'

ALGORITHMS_CHEMPROP_NUM_ITERS = 'num_iters'

ALGORITHMS_CHEMPROP_INIT_LR_RATIO_EXP = 'init_lr_ratio_exp'

ALGORITHMS_CHEMPROP_MAX_LR_EXP = 'max_lr_exp'

ALGORITHMS_CHEMPROP_PRETRAINED_MODEL = 'pretrained_model'

ALGORITHMS_CHEMPROP_SEARCH_PARAMETER_LEVEL = 'search_parameter_level'

ALGORITHMS_CHEMPROP_STARTUP_RANDOM_ITERS = 'startup_random_iters'

ALGORITHMS_CHEMPROP_WARMUP_EPOCHS_RATIO = 'warmup_epochs_ratio'

ALGORITHMS_CALIBRATEDCLASSIFIERCV = 'CalibratedClassifierCVWithVA'

ALGORITHMS_CALIBRATEDCLASSIFIERCV_ENSEMBLE = 'ensemble'

ALGORITHMS_CALIBRATEDCLASSIFIERCV_ESTIMATOR = 'estimator'

ALGORITHMS_CALIBRATEDCLASSIFIERCV_METHOD = 'method'

ALGORITHMS_CALIBRATEDCLASSIFIERCV_N_FOLDS = 'n_folds'

ALGORITHMS_CALIBRATEDCLASSIFIERCV_PARAMS = 'calibrated_params'

ALGORITHMS_MAPIE = 'Mapie'

ALGORITHMS_MAPIE_ALPHA = 'mapie_alpha'

optunaz.utils.enums.interface_enum module

class optunaz.utils.enums.interface_enum.InterfaceEnum

Bases: object

This “Enum” serves as storage for the interface specifications.

SKLEARN_SET = {'AdaBoostClassifier', 'Lasso', 'LogisticRegression', 'PLSRegression', 'RandomForestClassifier', 'RandomForestRegressor', 'Ridge', 'SVC', 'SVR'}

XGBOOST_SET = {'XGBregressor'}

CHEMPROP_SET = {'BaseChemProp', 'ChemPropClassifier', 'ChemPropRegressor'}

PRF_SET = {'PRFClassifier'}

CALIBRATED_SET = {'CalibratedClassifierCVWithVA', 'Mapie'}

optunaz.utils.enums.model_runner_enum module

class optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum

Bases: object

This “Enum” serves as storage for the column names used in the dataframe construction in the ModelRunner.

Y_PRED = 'y_pred'

Y_TRUE = 'y_true'

SET = 'set'

TRAIN = 'train'

TEST = 'test'

SMILES = 'smiles'

optunaz.utils.enums.objective_enum module

class optunaz.utils.enums.objective_enum.ObjectiveEnum

Bases: object

This “Enum” serves to store all the strings appearing in the objective function (and its return values).

ATTRIBUTE_TRIAL_TRAIN_SCORE = 'train_score'

EXTRA_COLUMN_BESTHIT = 'bestHit'

optunaz.utils.enums.optimization_configuration_enum module

class optunaz.utils.enums.optimization_configuration_enum.OptimizationConfigurationEnum

Bases: ConfigurationEnum

This “Enum” serves to store all the strings used in parsing the optimization configurations. Note, that validity checks are not performed, but referred to JSON Schema validations.

optunaz.utils.enums.prediction_configuration_enum module

class optunaz.utils.enums.prediction_configuration_enum.PredictionConfigurationEnum

Bases: ConfigurationEnum

This “Enum” serves to store all the strings used in parsing the prediction configurations. Note, that validity checks are not performed, but referred to JSON Schema validations.

DATA_DATASET = 'dataset'

optunaz.utils.enums.return_values_enum module

class optunaz.utils.enums.return_values_enum.SklearnReturnValueEnum

Bases: object

This “Enum” serves as storage for the return value keys using “sklearn”.

CROSS_VALIDATE_FIT_TIME = 'fit_time'

CROSS_VALIDATE_SCORE_TIME = 'score_time'

CROSS_VALIDATE_TEST_SCORE = 'test_score'

CROSS_VALIDATE_TRAIN_SCORE = 'train_score'

class optunaz.utils.enums.return_values_enum.XGBoostReturnValueEnum

Bases: object

This “Enum” serves as storage for the return value keys using “XGBoost”.

CROSS_VALIDATE_FIT_TIME = 'fit_time'

CROSS_VALIDATE_SCORE_TIME = 'score_time'

CROSS_VALIDATE_TEST_SCORE = 'test_score'

CROSS_VALIDATE_TRAIN_SCORE = 'train_score'

optunaz.utils.enums.visualization_enum module

class optunaz.utils.enums.visualization_enum.VisualizationEnum

Bases: object

This “Enum” serves to store all the strings used to specify optional visualizations. Note, that validity checks are not performed, but referred to JSON Schema validations.

VISUALIZATION_REGRESSOR = 'regressor'

VISUALIZATION_CLASSIFIER = 'classifier'

VISUALIZATION = 'visualization'

VISUALIZATION_USE_XVFB = 'use_xvfb'

VISUALIZATION_OUTPUT_FOLDER = 'output_folder'

VISUALIZATION_FILE_FORMAT = 'file_format'

VISUALIZATION_PLOTS = 'plots'

VISUALIZATION_PLOTS_HISTORY = 'plot_history'

VISUALIZATION_PLOTS_CONTOUR = 'plot_contour'

VISUALIZATION_PLOTS_PARALLEL_COORDINATE = 'plot_parallel_coordinate'

VISUALIZATION_PLOTS_SLICE = 'plot_slice'

OPTUNA_SYSTEM_ATTRS_NUMBER = '_number'

OPTUNA_SYSTEM_ATTRS_INTERMEDIATE_VALUES = 'intermediate_values'

OPTUNA_SYSTEM_ATTRS_TRIAL_ID = 'trial_id'

Module contents

class optunaz.utils.enums.StudyUserAttrs(value)

Bases: str, Enum

Dict keys for User Parameters of Optuna Study objects.

OPTCONFIG = 'optconfig'

class optunaz.utils.enums.TrialUserAttrs(value)

Bases: str, Enum

Dict keys for User Parameters of Optuna Trial objects.

TRAIN_SCORES = 'train_scores'

TEST_SCORES = 'test_scores'

class optunaz.utils.enums.TrialParams(value)

Bases: str, Enum

Dict keys for Parameters of Optuna Trial objects.

DESCRIPTOR = 'descriptor'

ALGORITHM_NAME = 'algorithm_name'

ALGORITHM_HASH = 'algorithm_hash'

class optunaz.utils.enums.MlflowLogParams(value)

Bases: str, Enum

Dict keys for Parameters of MLflow Logs.

TRIAL_NUMBER = 'trial_number'