OpenADMET Models documentation

openadmet-models

Index

Symbols

--accelerator command line option --aq-fxn command line option --best-y command line option --beta command line option --debug command line option, [1] --input-col command line option --input-path command line option --label-types command line option --labels command line option --model-dir command line option

--model-dirs command line option --model-stats-fns command line option --mt-id command line option --output-csv command line option --output-dir command line option, [1] --recipe-path command line option --report command line option --tag command line option --task-names command line option --xi command line option

A

accelerator (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNModelBase attribute) (openadmet.models.trainer.lightning.LightningTrainer attribute) accumulate_grad_batches (openadmet.models.trainer.lightning.LightningTrainer attribute) active_metrics (openadmet.models.eval.cross_validation.CrossValidationBase property) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation property) (openadmet.models.eval.regression.RegressionMetrics property)

aggregation (openadmet.models.architecture.chemprop.ChemPropModel attribute) axes_labels (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.regression.RegressionPlots attribute)

B

batch_norm (openadmet.models.architecture.chemprop.ChemPropModel attribute) boosting_type (openadmet.models.architecture.lgbm.LGBMModelBase attribute) bootstrap (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) bootstrap_confidence_level (openadmet.models.eval.classification.ClassificationMetrics attribute) (openadmet.models.eval.regression.RegressionMetrics attribute) break_ties (openadmet.models.architecture.svm.SVMClassifierModel attribute) build() (openadmet.models.active_learning.ensemble_base.EnsembleBase method) (openadmet.models.architecture.catboost.CatBoostModelBase method) (openadmet.models.architecture.chemprop.ChemPropModel method) (openadmet.models.architecture.dummy.DummyModelBase method) (openadmet.models.architecture.lgbm.LGBMModelBase method) (openadmet.models.architecture.model_base.ModelBase method) (openadmet.models.architecture.rf.RFModelBase method) (openadmet.models.architecture.svm.SVMModelBase method) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase method) (openadmet.models.architecture.tabpfn.TabPFNModelBase method) (openadmet.models.architecture.xgboost.XGBoostModelBase method) (openadmet.models.trainer.lightning.LightningTrainer method) (openadmet.models.trainer.sklearn.SKlearnBasicTrainer method) (openadmet.models.trainer.sklearn.SKLearnSearchTrainer method) (openadmet.models.trainer.trainer_base.TrainerBase method)

C

C (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) cache_size (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) calibrate_uncertainty() (openadmet.models.active_learning.committee.CommitteeRegressor method) calibrated (openadmet.models.active_learning.committee.CommitteeRegressor property) calibration_plot() (openadmet.models.eval.uncertainty.UncertaintyPlots static method) CatBoostClassifierModel (class in openadmet.models.architecture.catboost) CatBoostModelBase (class in openadmet.models.architecture.catboost) CatBoostRegressorModel (class in openadmet.models.architecture.catboost) ccp_alpha (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) ChemPropModel (class in openadmet.models.architecture.chemprop) ciplot() (openadmet.models.eval.regression.RegressionPlots static method) class_weight (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.svm.SVMClassifierModel attribute) ClassificationMetrics (class in openadmet.models.eval.classification) ClassificationPlots (class in openadmet.models.eval.classification) coef0 (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) colsample_bytree (openadmet.models.architecture.lgbm.LGBMModelBase attribute) command line option --accelerator --aq-fxn --best-y --beta --debug, [1] --input-col --input-path --label-types --labels --model-dir --model-dirs --model-stats-fns --mt-id --output-csv --output-dir, [1] --recipe-path --report --tag --task-names --xi

CommitteeRegressor (class in openadmet.models.active_learning.committee) compare() (openadmet.models.comparison.compare_base.ComparisonBase method) ComparisonBase (class in openadmet.models.comparison.compare_base) concatenate() (openadmet.models.features.combine.FeatureConcatenator static method) confidence_level (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) configure_optimizers() (in module openadmet.models.architecture.chemprop) (openadmet.models.architecture.model_base.LightningModuleBase method) constant (openadmet.models.architecture.dummy.DummyClassifierModel attribute) (openadmet.models.architecture.dummy.DummyRegressorModel attribute) criterion (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) CrossValidationBase (class in openadmet.models.eval.cross_validation)

D

decision_function_shape (openadmet.models.architecture.svm.SVMClassifierModel attribute) DeepLearningFeaturizer (class in openadmet.models.features.feature_base) degree (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) depth (openadmet.models.architecture.chemprop.ChemPropModel attribute) descr_type (openadmet.models.features.molfeat_properties.DescriptorFeaturizer attribute) DescriptorFeaturizer (class in openadmet.models.features.molfeat_properties) deserialize() (openadmet.models.architecture.model_base.ModelBase method) deterministic (openadmet.models.trainer.lightning.LightningTrainer attribute) devices (openadmet.models.trainer.lightning.LightningTrainer attribute)

do_stats (openadmet.models.eval.regression.RegressionPlots attribute) dpi (openadmet.models.eval.classification.ClassificationPlots attribute) (openadmet.models.eval.regression.RegressionPlots attribute) (openadmet.models.eval.uncertainty.UncertaintyPlots attribute) dropout (openadmet.models.architecture.chemprop.ChemPropModel attribute) dtype (openadmet.models.features.molfeat_fingerprint.FingerprintFeaturizer attribute) (openadmet.models.features.molfeat_properties.DescriptorFeaturizer attribute) DummyClassifierModel (class in openadmet.models.architecture.dummy) DummyModelBase (class in openadmet.models.architecture.dummy) DummyRegressorModel (class in openadmet.models.architecture.dummy)

E

early_stopping (openadmet.models.trainer.lightning.LightningTrainer attribute) early_stopping_min_delta (openadmet.models.trainer.lightning.LightningTrainer attribute) early_stopping_mode (openadmet.models.trainer.lightning.LightningTrainer attribute) early_stopping_patience (openadmet.models.trainer.lightning.LightningTrainer attribute) EnsembleBase (class in openadmet.models.active_learning.ensemble_base) epsilon (openadmet.models.architecture.svm.SVMRegressorModel attribute) estimator (openadmet.models.architecture.model_base.ModelBase property) EvalBase (class in openadmet.models.eval.eval_base) EvalBase.Config (class in openadmet.models.eval.eval_base) evaluate() (openadmet.models.eval.binary.PosthocBinaryMetrics method) (openadmet.models.eval.classification.ClassificationMetrics method) (openadmet.models.eval.classification.ClassificationPlots method) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation method) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation method) (openadmet.models.eval.eval_base.EvalBase method) (openadmet.models.eval.regression.RegressionMetrics method) (openadmet.models.eval.regression.RegressionPlots method) (openadmet.models.eval.uncertainty.UncertaintyMetrics method) (openadmet.models.eval.uncertainty.UncertaintyPlots method)

expected_improvement() (in module openadmet.models.active_learning.acquisition) exploitation() (in module openadmet.models.active_learning.acquisition) extra (openadmet.models.eval.eval_base.EvalBase.Config attribute)

F

fast_dev_run (openadmet.models.trainer.lightning.LightningTrainer attribute) FeatureConcatenator (class in openadmet.models.features.combine) featurize() (openadmet.models.features.combine.FeatureConcatenator method) (openadmet.models.features.feature_base.DeepLearningFeaturizer method) (openadmet.models.features.feature_base.FeaturizerBase method) (openadmet.models.features.molfeat_fingerprint.FingerprintFeaturizer method) (openadmet.models.features.molfeat_properties.DescriptorFeaturizer method) FeaturizerBase (class in openadmet.models.features.feature_base) featurizers (openadmet.models.features.combine.FeatureConcatenator attribute) ffn_hidden_dim (openadmet.models.architecture.chemprop.ChemPropModel attribute) ffn_lr (openadmet.models.architecture.chemprop.ChemPropModel attribute)

ffn_num_layers (openadmet.models.architecture.chemprop.ChemPropModel attribute) ffn_weight_decay (openadmet.models.architecture.chemprop.ChemPropModel attribute) final_lr (openadmet.models.architecture.chemprop.ChemPropModel attribute) FingerprintFeaturizer (class in openadmet.models.features.molfeat_fingerprint) fit_reg (openadmet.models.eval.regression.RegressionPlots attribute) fp_type (openadmet.models.features.molfeat_fingerprint.FingerprintFeaturizer attribute) freeze_weights() (openadmet.models.architecture.chemprop.ChemPropModel method) (openadmet.models.architecture.model_base.LightningModelBase method) from_chemeleon (openadmet.models.architecture.chemprop.ChemPropModel attribute) from_foundation (openadmet.models.architecture.chemprop.ChemPropModel attribute) from_params() (openadmet.models.active_learning.ensemble_base.EnsembleBase method)

G

gamma (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) get_comparison_class() (in module openadmet.models.comparison.compare_base) get_ensemble_class() (in module openadmet.models.active_learning.ensemble_base) get_eval_class() (in module openadmet.models.eval.eval_base) get_featurizer_class() (in module openadmet.models.features.feature_base) get_mod_class() (in module openadmet.models.architecture.model_base) get_precision_recall() (openadmet.models.eval.binary.PosthocBinaryMetrics method)

get_stat_caption() (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation method) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation method) (openadmet.models.eval.regression.RegressionMetrics method) get_stat_dict() (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation method) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation method) (openadmet.models.eval.regression.RegressionMetrics method) get_t_true_and_t_pred() (in module openadmet.models.eval.eval_base) get_trainer_class() (in module openadmet.models.trainer.trainer_base) gradient_clip_val (openadmet.models.trainer.lightning.LightningTrainer attribute)

I

ignore_pretraining_limits (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNModelBase attribute) importance_type (openadmet.models.architecture.lgbm.LGBMModelBase attribute)

init_lr (openadmet.models.architecture.chemprop.ChemPropModel attribute) is_cross_val (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.eval_base.EvalBase attribute)

K

kernel (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute)

L

learning_rate (openadmet.models.architecture.lgbm.LGBMModelBase attribute) LGBMClassifierModel (class in openadmet.models.architecture.lgbm) LGBMModelBase (class in openadmet.models.architecture.lgbm) LGBMRegressorModel (class in openadmet.models.architecture.lgbm) LightningModelBase (class in openadmet.models.architecture.model_base) LightningModuleBase (class in openadmet.models.architecture.model_base)

LightningTrainer (class in openadmet.models.trainer.lightning) limit_train_batches (openadmet.models.trainer.lightning.LightningTrainer attribute) limit_val_batches (openadmet.models.trainer.lightning.LightningTrainer attribute) load() (openadmet.models.architecture.model_base.LightningModelBase method) (openadmet.models.architecture.model_base.ModelBase method) (openadmet.models.architecture.model_base.PickleableModelBase method)

M

make_new() (openadmet.models.architecture.chemprop.ChemPropModel method) (openadmet.models.architecture.model_base.LightningModelBase method) (openadmet.models.architecture.model_base.PickleableModelBase method) (openadmet.models.trainer.lightning.LightningTrainer method) mask_nans() (in module openadmet.models.eval.eval_base) mask_nans_std() (in module openadmet.models.eval.eval_base) max_depth (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) max_epochs (openadmet.models.trainer.lightning.LightningTrainer attribute) max_features (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) max_iter (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) max_leaf_nodes (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) max_lr (openadmet.models.architecture.chemprop.ChemPropModel attribute) max_samples (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) max_time (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) max_uncertainty_reduction() (in module openadmet.models.active_learning.acquisition) max_val (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.regression.RegressionPlots attribute) MaxDissimilaritySplitter (class in openadmet.models.split.scaffold) message_hidden_dim (openadmet.models.architecture.chemprop.ChemPropModel attribute) messages (openadmet.models.architecture.chemprop.ChemPropModel attribute) metric_list (openadmet.models.architecture.chemprop.ChemPropModel attribute) metric_names (openadmet.models.eval.classification.ClassificationMetrics property) (openadmet.models.eval.cross_validation.CrossValidationBase property) (openadmet.models.eval.regression.RegressionMetrics property) (openadmet.models.eval.uncertainty.UncertaintyMetrics property) min_child_samples (openadmet.models.architecture.lgbm.LGBMModelBase attribute) min_child_weight (openadmet.models.architecture.lgbm.LGBMModelBase attribute) min_impurity_decrease (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) min_samples_leaf (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) min_samples_split (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) min_split_gain (openadmet.models.architecture.lgbm.LGBMModelBase attribute) min_val (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.regression.RegressionPlots attribute) min_weight_fraction_leaf (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) mod_class (openadmet.models.architecture.catboost.CatBoostClassifierModel attribute) (openadmet.models.architecture.catboost.CatBoostModelBase attribute) (openadmet.models.architecture.catboost.CatBoostRegressorModel attribute) (openadmet.models.architecture.dummy.DummyClassifierModel attribute) (openadmet.models.architecture.dummy.DummyModelBase attribute) (openadmet.models.architecture.dummy.DummyRegressorModel attribute) (openadmet.models.architecture.lgbm.LGBMClassifierModel attribute) (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.lgbm.LGBMRegressorModel attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFModelBase attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMModelBase attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNModelBase attribute) (openadmet.models.architecture.xgboost.XGBClassifierModel attribute) (openadmet.models.architecture.xgboost.XGBoostModelBase attribute) (openadmet.models.architecture.xgboost.XGBRegressorModel attribute) model (openadmet.models.trainer.trainer_base.TrainerBase property) model_config (openadmet.models.active_learning.committee.CommitteeRegressor attribute) (openadmet.models.active_learning.ensemble_base.EnsembleBase attribute) (openadmet.models.architecture.catboost.CatBoostClassifierModel attribute) (openadmet.models.architecture.catboost.CatBoostModelBase attribute) (openadmet.models.architecture.catboost.CatBoostRegressorModel attribute) (openadmet.models.architecture.chemprop.ChemPropModel attribute) (openadmet.models.architecture.dummy.DummyClassifierModel attribute) (openadmet.models.architecture.dummy.DummyModelBase attribute) (openadmet.models.architecture.dummy.DummyRegressorModel attribute) (openadmet.models.architecture.lgbm.LGBMClassifierModel attribute) (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.lgbm.LGBMRegressorModel attribute) (openadmet.models.architecture.model_base.LightningModelBase attribute) (openadmet.models.architecture.model_base.ModelBase attribute) (openadmet.models.architecture.model_base.PickleableModelBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFModelBase attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMModelBase attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) (openadmet.models.architecture.tabpfn.TabPFNClassifierModel attribute) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNPostHocClassifierModel attribute) (openadmet.models.architecture.tabpfn.TabPFNPostHocRegressorModel attribute) (openadmet.models.architecture.tabpfn.TabPFNRegressorModel attribute) (openadmet.models.architecture.xgboost.XGBClassifierModel attribute) (openadmet.models.architecture.xgboost.XGBoostModelBase attribute) (openadmet.models.architecture.xgboost.XGBRegressorModel attribute) (openadmet.models.comparison.compare_base.ComparisonBase attribute) (openadmet.models.eval.binary.PosthocBinaryMetrics attribute) (openadmet.models.eval.classification.ClassificationMetrics attribute) (openadmet.models.eval.classification.ClassificationPlots attribute) (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.eval_base.EvalBase attribute) (openadmet.models.eval.regression.RegressionMetrics attribute) (openadmet.models.eval.regression.RegressionPlots attribute) (openadmet.models.eval.uncertainty.UncertaintyMetrics attribute) (openadmet.models.eval.uncertainty.UncertaintyPlots attribute) (openadmet.models.features.combine.FeatureConcatenator attribute) (openadmet.models.features.feature_base.DeepLearningFeaturizer attribute) (openadmet.models.features.feature_base.FeaturizerBase attribute) (openadmet.models.features.feature_base.MolfeatFeaturizer attribute) (openadmet.models.features.molfeat_fingerprint.FingerprintFeaturizer attribute) (openadmet.models.features.molfeat_properties.DescriptorFeaturizer attribute) (openadmet.models.split.scaffold.MaxDissimilaritySplitter attribute) (openadmet.models.split.scaffold.PerimeterSplitter attribute) (openadmet.models.split.scaffold.ScaffoldSplitter attribute) (openadmet.models.split.sklearn.ShuffleSplitter attribute) (openadmet.models.trainer.lightning.LightningTrainer attribute) (openadmet.models.trainer.sklearn.SKlearnBasicTrainer attribute) (openadmet.models.trainer.sklearn.SKLearnGridSearchTrainer attribute) (openadmet.models.trainer.sklearn.SKLearnSearchTrainer attribute) (openadmet.models.trainer.sklearn.SKLearnTrainer attribute) (openadmet.models.trainer.trainer_base.TrainerBase attribute)

model_post_init() (openadmet.models.active_learning.committee.CommitteeRegressor method) (openadmet.models.active_learning.ensemble_base.EnsembleBase method) (openadmet.models.architecture.catboost.CatBoostClassifierModel method) (openadmet.models.architecture.catboost.CatBoostModelBase method) (openadmet.models.architecture.catboost.CatBoostRegressorModel method) (openadmet.models.architecture.chemprop.ChemPropModel method) (openadmet.models.architecture.dummy.DummyClassifierModel method) (openadmet.models.architecture.dummy.DummyModelBase method) (openadmet.models.architecture.dummy.DummyRegressorModel method) (openadmet.models.architecture.lgbm.LGBMClassifierModel method) (openadmet.models.architecture.lgbm.LGBMModelBase method) (openadmet.models.architecture.lgbm.LGBMRegressorModel method) (openadmet.models.architecture.model_base.LightningModelBase method) (openadmet.models.architecture.model_base.ModelBase method) (openadmet.models.architecture.model_base.PickleableModelBase method) (openadmet.models.architecture.rf.RFClassifierModel method) (openadmet.models.architecture.rf.RFModelBase method) (openadmet.models.architecture.rf.RFRegressorModel method) (openadmet.models.architecture.svm.SVMClassifierModel method) (openadmet.models.architecture.svm.SVMModelBase method) (openadmet.models.architecture.svm.SVMRegressorModel method) (openadmet.models.architecture.tabpfn.TabPFNClassifierModel method) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase method) (openadmet.models.architecture.tabpfn.TabPFNModelBase method) (openadmet.models.architecture.tabpfn.TabPFNPostHocClassifierModel method) (openadmet.models.architecture.tabpfn.TabPFNPostHocRegressorModel method) (openadmet.models.architecture.tabpfn.TabPFNRegressorModel method) (openadmet.models.architecture.xgboost.XGBClassifierModel method) (openadmet.models.architecture.xgboost.XGBoostModelBase method) (openadmet.models.architecture.xgboost.XGBRegressorModel method) (openadmet.models.eval.classification.ClassificationMetrics method) (openadmet.models.eval.cross_validation.CrossValidationBase method) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation method) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation method) (openadmet.models.eval.regression.RegressionMetrics method) (openadmet.models.eval.uncertainty.UncertaintyMetrics method) (openadmet.models.eval.uncertainty.UncertaintyPlots method) (openadmet.models.features.feature_base.MolfeatFeaturizer method) (openadmet.models.features.molfeat_fingerprint.FingerprintFeaturizer method) (openadmet.models.features.molfeat_properties.DescriptorFeaturizer method) (openadmet.models.trainer.lightning.LightningTrainer method) (openadmet.models.trainer.sklearn.SKlearnBasicTrainer method) (openadmet.models.trainer.sklearn.SKLearnGridSearchTrainer method) (openadmet.models.trainer.sklearn.SKLearnSearchTrainer method) (openadmet.models.trainer.sklearn.SKLearnTrainer method) (openadmet.models.trainer.trainer_base.TrainerBase method) ModelBase (class in openadmet.models.architecture.model_base) models (openadmet.models.active_learning.ensemble_base.EnsembleBase attribute) module openadmet.models.active_learning.acquisition openadmet.models.active_learning.committee openadmet.models.active_learning.ensemble_base openadmet.models.architecture.catboost openadmet.models.architecture.chemprop openadmet.models.architecture.dummy openadmet.models.architecture.lgbm openadmet.models.architecture.model_base openadmet.models.architecture.rf openadmet.models.architecture.svm openadmet.models.architecture.tabpfn openadmet.models.architecture.xgboost openadmet.models.comparison.compare_base openadmet.models.eval.binary openadmet.models.eval.classification openadmet.models.eval.cross_validation openadmet.models.eval.eval_base openadmet.models.eval.regression openadmet.models.eval.uncertainty openadmet.models.eval.utils openadmet.models.features.combine openadmet.models.features.feature_base openadmet.models.features.molfeat_fingerprint openadmet.models.features.molfeat_properties openadmet.models.split.scaffold openadmet.models.split.sklearn openadmet.models.trainer.lightning openadmet.models.trainer.sklearn openadmet.models.trainer.trainer_base MolfeatFeaturizer (class in openadmet.models.features.feature_base) monitor_metric (openadmet.models.architecture.chemprop.ChemPropModel attribute) (openadmet.models.architecture.model_base.LightningModuleBase attribute) monotonic_cst (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) mpnn_lr (openadmet.models.architecture.chemprop.ChemPropModel attribute) mpnn_weight_decay (openadmet.models.architecture.chemprop.ChemPropModel attribute)

N

n_estimators (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) n_jobs (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) (openadmet.models.features.molfeat_fingerprint.FingerprintFeaturizer attribute) (openadmet.models.features.molfeat_properties.DescriptorFeaturizer attribute)

n_models (openadmet.models.active_learning.ensemble_base.EnsembleBase property) n_repeats (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation attribute) n_resamples (openadmet.models.eval.eval_base.EvalBase attribute) n_splits (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation attribute) n_tasks (openadmet.models.architecture.chemprop.ChemPropModel attribute) normalized_targets (openadmet.models.architecture.chemprop.ChemPropModel attribute) num_leaves (openadmet.models.architecture.lgbm.LGBMModelBase attribute)

O

objective (openadmet.models.architecture.lgbm.LGBMModelBase attribute) oob_score (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) openadmet.models.active_learning.acquisition module openadmet.models.active_learning.committee module openadmet.models.active_learning.ensemble_base module openadmet.models.architecture.catboost module openadmet.models.architecture.chemprop module openadmet.models.architecture.dummy module openadmet.models.architecture.lgbm module openadmet.models.architecture.model_base module openadmet.models.architecture.rf module openadmet.models.architecture.svm module openadmet.models.architecture.tabpfn module openadmet.models.architecture.xgboost module openadmet.models.comparison.compare_base module openadmet.models.eval.binary module openadmet.models.eval.classification module

openadmet.models.eval.cross_validation module openadmet.models.eval.eval_base module openadmet.models.eval.regression module openadmet.models.eval.uncertainty module openadmet.models.eval.utils module openadmet.models.features.combine module openadmet.models.features.feature_base module openadmet.models.features.molfeat_fingerprint module openadmet.models.features.molfeat_properties module openadmet.models.split.scaffold module openadmet.models.split.sklearn module openadmet.models.trainer.lightning module openadmet.models.trainer.sklearn module openadmet.models.trainer.trainer_base module optimizer (openadmet.models.architecture.model_base.LightningModuleBase attribute) optimizer_lr (openadmet.models.architecture.model_base.LightningModuleBase attribute) optimizer_weight_decay (openadmet.models.architecture.model_base.LightningModuleBase attribute) output_dir (openadmet.models.trainer.lightning.LightningTrainer attribute)

P

param_grid (openadmet.models.trainer.sklearn.SKLearnGridSearchTrainer attribute) pct_within_1_log_unit() (in module openadmet.models.eval.regression) PerimeterSplitter (class in openadmet.models.split.scaffold) phe_init_args (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) pickleable (openadmet.models.architecture.model_base.PickleableModelBase attribute) PickleableModelBase (class in openadmet.models.architecture.model_base) plot_confusion_matrix() (openadmet.models.eval.binary.PosthocBinaryMetrics method) plot_errbars (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.regression.RegressionPlots attribute) plot_posthoc_classification() (openadmet.models.eval.binary.PosthocBinaryMetrics method) plot_uncertainty_calibration() (openadmet.models.active_learning.committee.CommitteeRegressor method) plots (openadmet.models.eval.classification.ClassificationPlots attribute) (openadmet.models.eval.regression.RegressionPlots attribute) PosthocBinaryMetrics (class in openadmet.models.eval.binary) pr_auc_score() (in module openadmet.models.eval.classification) pr_curve() (openadmet.models.eval.classification.ClassificationPlots method) precision (openadmet.models.trainer.lightning.LightningTrainer attribute) predict() (openadmet.models.active_learning.committee.CommitteeRegressor method) (openadmet.models.architecture.catboost.CatBoostModelBase method) (openadmet.models.architecture.chemprop.ChemPropModel method) (openadmet.models.architecture.dummy.DummyModelBase method) (openadmet.models.architecture.lgbm.LGBMModelBase method) (openadmet.models.architecture.model_base.ModelBase method) (openadmet.models.architecture.rf.RFModelBase method) (openadmet.models.architecture.svm.SVMModelBase method) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase method) (openadmet.models.architecture.tabpfn.TabPFNModelBase method) (openadmet.models.architecture.xgboost.XGBoostModelBase method)

predict_proba() (openadmet.models.architecture.catboost.CatBoostClassifierModel method) (openadmet.models.architecture.lgbm.LGBMClassifierModel method) (openadmet.models.architecture.rf.RFClassifierModel method) (openadmet.models.architecture.svm.SVMClassifierModel method) (openadmet.models.architecture.tabpfn.TabPFNPostHocClassifierModel method) (openadmet.models.architecture.xgboost.XGBClassifierModel method) probability (openadmet.models.architecture.svm.SVMClassifierModel attribute) probability_improvement() (in module openadmet.models.active_learning.acquisition) pXC50 (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.regression.RegressionMetrics attribute) (openadmet.models.eval.regression.RegressionPlots attribute) PytorchLightningRepeatedKFoldCrossValidation (class in openadmet.models.eval.cross_validation)

Q

quantile (openadmet.models.architecture.dummy.DummyRegressorModel attribute)

query() (openadmet.models.active_learning.committee.CommitteeRegressor method)

R

random_state (openadmet.models.architecture.dummy.DummyClassifierModel attribute) (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNModelBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation attribute) reduce_lr_factor (openadmet.models.architecture.chemprop.ChemPropModel attribute) reduce_lr_patience (openadmet.models.architecture.chemprop.ChemPropModel attribute) reg_alpha (openadmet.models.architecture.lgbm.LGBMModelBase attribute) reg_lambda (openadmet.models.architecture.lgbm.LGBMModelBase attribute) regplot() (openadmet.models.eval.regression.RegressionPlots static method) RegressionMetrics (class in openadmet.models.eval.regression) RegressionPlots (class in openadmet.models.eval.regression)

relative_absolute_error() (in module openadmet.models.eval.regression) repeated_group_k_fold() (in module openadmet.models.eval.cross_validation) report() (openadmet.models.eval.binary.PosthocBinaryMetrics method) (openadmet.models.eval.classification.ClassificationMetrics method) (openadmet.models.eval.classification.ClassificationPlots method) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation method) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation method) (openadmet.models.eval.eval_base.EvalBase method) (openadmet.models.eval.regression.RegressionMetrics method) (openadmet.models.eval.regression.RegressionPlots method) (openadmet.models.eval.uncertainty.UncertaintyMetrics method) (openadmet.models.eval.uncertainty.UncertaintyPlots method) resolve_hyperparameters() (openadmet.models.architecture.chemprop.ChemPropModel method) RFClassifierModel (class in openadmet.models.architecture.rf) RFModelBase (class in openadmet.models.architecture.rf) RFRegressorModel (class in openadmet.models.architecture.rf) roc_curve() (openadmet.models.eval.classification.ClassificationPlots method)

S

safe_index() (in module openadmet.models.split.scaffold) save() (openadmet.models.active_learning.committee.CommitteeRegressor method) (openadmet.models.architecture.model_base.LightningModelBase method) (openadmet.models.architecture.model_base.ModelBase method) (openadmet.models.architecture.model_base.PickleableModelBase method) ScaffoldSplitter (class in openadmet.models.split.scaffold) scheduler (openadmet.models.architecture.chemprop.ChemPropModel attribute) (openadmet.models.architecture.model_base.LightningModuleBase attribute) scheduler_factor (openadmet.models.architecture.model_base.LightningModuleBase attribute) scheduler_patience (openadmet.models.architecture.model_base.LightningModuleBase attribute) search (openadmet.models.trainer.sklearn.SKLearnSearchTrainer property) serialize() (openadmet.models.active_learning.committee.CommitteeRegressor method) (openadmet.models.architecture.chemprop.ChemPropModel method) (openadmet.models.architecture.model_base.LightningModelBase method) (openadmet.models.architecture.model_base.ModelBase method) (openadmet.models.architecture.model_base.PickleableModelBase method) set_n_tasks() (openadmet.models.architecture.chemprop.ChemPropModel method) shrinking (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute)

ShuffleSplitter (class in openadmet.models.split.sklearn) SKlearnBasicTrainer (class in openadmet.models.trainer.sklearn) SKLearnGridSearchTrainer (class in openadmet.models.trainer.sklearn) SKLearnRepeatedKFoldCrossValidation (class in openadmet.models.eval.cross_validation) SKLearnSearchTrainer (class in openadmet.models.trainer.sklearn) SKLearnTrainer (class in openadmet.models.trainer.sklearn) split() (openadmet.models.split.scaffold.MaxDissimilaritySplitter method) (openadmet.models.split.scaffold.PerimeterSplitter method) (openadmet.models.split.scaffold.ScaffoldSplitter method) (openadmet.models.split.sklearn.ShuffleSplitter method) stat_and_bootstrap() (openadmet.models.eval.eval_base.EvalBase method) stats_to_json() (openadmet.models.eval.binary.PosthocBinaryMetrics method) strategy (openadmet.models.architecture.dummy.DummyClassifierModel attribute) (openadmet.models.architecture.dummy.DummyRegressorModel attribute) subsample (openadmet.models.architecture.lgbm.LGBMModelBase attribute) subsample_for_bin (openadmet.models.architecture.lgbm.LGBMModelBase attribute) subsample_freq (openadmet.models.architecture.lgbm.LGBMModelBase attribute) SVMClassifierModel (class in openadmet.models.architecture.svm) SVMModelBase (class in openadmet.models.architecture.svm) SVMRegressorModel (class in openadmet.models.architecture.svm)

T

TabPFNClassifierModel (class in openadmet.models.architecture.tabpfn) TabPFNExtensionModelBase (class in openadmet.models.architecture.tabpfn) TabPFNModelBase (class in openadmet.models.architecture.tabpfn) TabPFNPostHocClassifierModel (class in openadmet.models.architecture.tabpfn) TabPFNPostHocRegressorModel (class in openadmet.models.architecture.tabpfn) TabPFNRegressorModel (class in openadmet.models.architecture.tabpfn) task_names (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation property) (openadmet.models.eval.regression.RegressionMetrics property) (openadmet.models.eval.uncertainty.UncertaintyMetrics property) title (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.regression.RegressionPlots attribute) tol (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) train() (openadmet.models.architecture.catboost.CatBoostModelBase method) (openadmet.models.architecture.chemprop.ChemPropModel method) (openadmet.models.architecture.dummy.DummyModelBase method) (openadmet.models.architecture.lgbm.LGBMModelBase method) (openadmet.models.architecture.model_base.ModelBase method) (openadmet.models.architecture.rf.RFModelBase method) (openadmet.models.architecture.svm.SVMModelBase method) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase method) (openadmet.models.architecture.tabpfn.TabPFNModelBase method) (openadmet.models.architecture.xgboost.XGBoostModelBase method) (openadmet.models.trainer.lightning.LightningTrainer method) (openadmet.models.trainer.sklearn.SKlearnBasicTrainer method) (openadmet.models.trainer.sklearn.SKLearnGridSearchTrainer method) (openadmet.models.trainer.trainer_base.TrainerBase method) TrainerBase (class in openadmet.models.trainer.trainer_base) transformer (openadmet.models.features.feature_base.MolfeatFeaturizer property)

type (openadmet.models.active_learning.committee.CommitteeRegressor attribute) (openadmet.models.active_learning.ensemble_base.EnsembleBase attribute) (openadmet.models.architecture.catboost.CatBoostClassifierModel attribute) (openadmet.models.architecture.catboost.CatBoostModelBase attribute) (openadmet.models.architecture.catboost.CatBoostRegressorModel attribute) (openadmet.models.architecture.chemprop.ChemPropModel attribute) (openadmet.models.architecture.dummy.DummyClassifierModel attribute) (openadmet.models.architecture.dummy.DummyModelBase attribute) (openadmet.models.architecture.dummy.DummyRegressorModel attribute) (openadmet.models.architecture.lgbm.LGBMClassifierModel attribute) (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.lgbm.LGBMRegressorModel attribute) (openadmet.models.architecture.model_base.LightningModelBase attribute) (openadmet.models.architecture.model_base.LightningModuleBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFModelBase attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMModelBase attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) (openadmet.models.architecture.tabpfn.TabPFNClassifierModel attribute) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNPostHocClassifierModel attribute) (openadmet.models.architecture.tabpfn.TabPFNPostHocRegressorModel attribute) (openadmet.models.architecture.tabpfn.TabPFNRegressorModel attribute) (openadmet.models.architecture.xgboost.XGBClassifierModel attribute) (openadmet.models.architecture.xgboost.XGBoostModelBase attribute) (openadmet.models.architecture.xgboost.XGBRegressorModel attribute) (openadmet.models.features.molfeat_fingerprint.FingerprintFeaturizer attribute) (openadmet.models.features.molfeat_properties.DescriptorFeaturizer attribute)

U

UncertaintyMetrics (class in openadmet.models.eval.uncertainty) UncertaintyPlots (class in openadmet.models.eval.uncertainty) upper_confidence_bound() (in module openadmet.models.active_learning.acquisition) use_wandb (openadmet.models.eval.classification.ClassificationMetrics attribute) (openadmet.models.eval.classification.ClassificationPlots attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.regression.RegressionMetrics attribute) (openadmet.models.eval.regression.RegressionPlots attribute) (openadmet.models.eval.uncertainty.UncertaintyMetrics attribute) (openadmet.models.eval.uncertainty.UncertaintyPlots attribute) (openadmet.models.trainer.lightning.LightningTrainer attribute)

V

validate_scheduler_params() (openadmet.models.architecture.chemprop.ChemPropModel method) verbose (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute)

W

wandb_logger (openadmet.models.trainer.lightning.LightningTrainer attribute) wandb_project (openadmet.models.trainer.lightning.LightningTrainer attribute) warm_start (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) warmup_epochs (openadmet.models.architecture.chemprop.ChemPropModel attribute) weight_decay (openadmet.models.architecture.chemprop.ChemPropModel attribute) wrap_ktau() (in module openadmet.models.eval.cross_validation) wrap_spearmanr() (in module openadmet.models.eval.cross_validation)

write_report() (openadmet.models.eval.classification.ClassificationMetrics method) (openadmet.models.eval.classification.ClassificationPlots method) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation method) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation method) (openadmet.models.eval.regression.RegressionMetrics method) (openadmet.models.eval.regression.RegressionPlots method) (openadmet.models.eval.uncertainty.UncertaintyMetrics method) (openadmet.models.eval.uncertainty.UncertaintyPlots method)

X

XGBClassifierModel (class in openadmet.models.architecture.xgboost)

XGBoostModelBase (class in openadmet.models.architecture.xgboost) XGBRegressorModel (class in openadmet.models.architecture.xgboost)