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.tabicl.TabICLModelBase attribute) (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)

anvil_dir (openadmet.models.anvil.specification.DataSpec attribute) AnvilDeepLearningWorkflow (class in openadmet.models.anvil.workflow) AnvilSection (class in openadmet.models.anvil.specification) AnvilSpecification (class in openadmet.models.anvil.specification) AnvilWorkflow (class in openadmet.models.anvil.workflow) AnvilWorkflowBase (class in openadmet.models.anvil.workflow_base) authors (openadmet.models.anvil.specification.Metadata 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) batch_size (openadmet.models.architecture.tabicl.TabICLModelBase attribute) (openadmet.models.features.chemprop.ChemPropFeaturizer attribute) biotargets (openadmet.models.anvil.specification.Metadata 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) bootstrap_seed (openadmet.models.anvil.specification.EnsembleSpec 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.tabicl.TabICLModelBase 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)

build_number (openadmet.models.anvil.specification.Metadata attribute)

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_method (openadmet.models.anvil.specification.EnsembleSpec attribute) calibration_plot() (openadmet.models.eval.uncertainty.UncertaintyPlots static method) cat_entry (openadmet.models.anvil.specification.DataSpec attribute) catalog (openadmet.models.anvil.specification.DataSpec property) 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) check_finetuning_paths() (openadmet.models.anvil.workflow.AnvilDeepLearningWorkflow method) check_freeze_weights() (openadmet.models.anvil.specification.ModelSpec method) check_if_val_needed() (openadmet.models.anvil.workflow.AnvilDeepLearningWorkflow method) (openadmet.models.anvil.workflow.AnvilWorkflow method) check_model_trainer_compatibility() (openadmet.models.anvil.workflow_base.AnvilWorkflowBase method) check_multitask_compatibility() (openadmet.models.anvil.workflow_base.AnvilWorkflowBase method) check_no_finetuning() (openadmet.models.anvil.workflow.AnvilWorkflow method) check_no_transform() (openadmet.models.anvil.workflow.AnvilDeepLearningWorkflow method) check_paths() (openadmet.models.anvil.specification.EnsembleSpec method) (openadmet.models.anvil.specification.ModelSpec method) check_resource_test_train() (openadmet.models.anvil.specification.DataSpec method) check_trainer_cv_compatibility() (openadmet.models.anvil.workflow_base.AnvilWorkflowBase method) ChemPropFeaturizer (class in openadmet.models.features.chemprop) 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) 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

data (openadmet.models.anvil.specification.AnvilSpecification attribute) data_spec (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) dataset_to_dataloader() (openadmet.models.features.chemprop.ChemPropFeaturizer static method) DataSpec (class in openadmet.models.anvil.specification) debug (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) 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) description (openadmet.models.anvil.specification.Metadata 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) driver (openadmet.models.anvil.specification.Metadata attribute) dropna (openadmet.models.anvil.specification.DataSpec 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) email (openadmet.models.anvil.specification.Metadata attribute) ensemble (openadmet.models.anvil.specification.ProcedureSpec attribute) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) ensemble_kwargs (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) EnsembleBase (class in openadmet.models.active_learning.ensemble_base) EnsembleSpec (class in openadmet.models.anvil.specification) ensure_2d() (in module openadmet.models.eval.utils) epsilon (openadmet.models.architecture.svm.SVMRegressorModel attribute) estimator (openadmet.models.architecture.model_base.ModelBase property) eval (openadmet.models.anvil.specification.ReportSpec attribute) EvalBase (class in openadmet.models.eval.eval_base)

EvalBase.Config (class in openadmet.models.eval.eval_base) evals (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) EvalSpec (class in openadmet.models.anvil.specification) 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) feat (openadmet.models.anvil.specification.ProcedureSpec attribute) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) FeatureConcatenator (class in openadmet.models.features.combine) FeatureSpec (class in openadmet.models.anvil.specification) featurize() (openadmet.models.features.chemprop.ChemPropFeaturizer method) (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.anvil.specification.ModelSpec attribute) freeze_weights() (openadmet.models.architecture.chemprop.ChemPropModel 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) input_col (openadmet.models.anvil.specification.DataSpec 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) 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.ModelBase method) (openadmet.models.architecture.model_base.PickleableModelBase method) load_anvil_model_and_metadata() (in module openadmet.models.inference.inference)

M

make_new() (openadmet.models.architecture.chemprop.ChemPropModel method) (openadmet.models.architecture.model_base.PickleableModelBase method) (openadmet.models.features.chemprop.ChemPropFeaturizer 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) Metadata (class in openadmet.models.anvil.specification) metadata (openadmet.models.anvil.specification.AnvilSpecification attribute) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase 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) model (openadmet.models.anvil.specification.ProcedureSpec attribute) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) (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.anvil.specification.AnvilSection attribute) (openadmet.models.anvil.specification.AnvilSpecification attribute) (openadmet.models.anvil.specification.DataSpec attribute) (openadmet.models.anvil.specification.EnsembleSpec attribute) (openadmet.models.anvil.specification.EvalSpec attribute) (openadmet.models.anvil.specification.FeatureSpec attribute) (openadmet.models.anvil.specification.Metadata attribute) (openadmet.models.anvil.specification.ModelSpec attribute) (openadmet.models.anvil.specification.ProcedureSpec attribute) (openadmet.models.anvil.specification.ReportSpec attribute) (openadmet.models.anvil.specification.SpecBase attribute) (openadmet.models.anvil.specification.SplitSpec attribute) (openadmet.models.anvil.specification.TrainerSpec attribute) (openadmet.models.anvil.specification.TransformSpec attribute) (openadmet.models.anvil.workflow.AnvilDeepLearningWorkflow attribute) (openadmet.models.anvil.workflow.AnvilWorkflow attribute) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase 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.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.tabicl.TabICLClassifierModel attribute) (openadmet.models.architecture.tabicl.TabICLModelBase attribute) (openadmet.models.architecture.tabicl.TabICLRegressorModel 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.chemprop.ChemPropFeaturizer 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_kwargs (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) model_post_init() (openadmet.models.active_learning.committee.CommitteeRegressor method) (openadmet.models.active_learning.ensemble_base.EnsembleBase method) (openadmet.models.anvil.specification.DataSpec method) (openadmet.models.anvil.workflow.AnvilDeepLearningWorkflow method) (openadmet.models.anvil.workflow.AnvilWorkflow 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.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.tabicl.TabICLClassifierModel method) (openadmet.models.architecture.tabicl.TabICLModelBase method) (openadmet.models.architecture.tabicl.TabICLRegressorModel 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) ModelSpec (class in openadmet.models.anvil.specification) module openadmet.models.active_learning.acquisition openadmet.models.active_learning.committee openadmet.models.active_learning.ensemble_base openadmet.models.anvil.specification openadmet.models.anvil.workflow openadmet.models.anvil.workflow_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.tabicl 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.chemprop openadmet.models.features.combine openadmet.models.features.feature_base openadmet.models.features.molfeat_fingerprint openadmet.models.features.molfeat_properties openadmet.models.inference.inference 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) monitor_metric_mode (openadmet.models.architecture.chemprop.ChemPropModel 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) (openadmet.models.architecture.tabicl.TabICLModelBase attribute) n_jobs (openadmet.models.architecture.lgbm.LGBMModelBase attribute) (openadmet.models.architecture.rf.RFClassifierModel attribute) (openadmet.models.architecture.rf.RFRegressorModel attribute) (openadmet.models.features.chemprop.ChemPropFeaturizer 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) (openadmet.models.anvil.specification.EnsembleSpec attribute)

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) name (openadmet.models.anvil.specification.Metadata attribute) no_ensemble_cross_val() (openadmet.models.anvil.workflow_base.AnvilWorkflowBase method) normalize_targets (openadmet.models.features.chemprop.ChemPropFeaturizer 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) offload_mode (openadmet.models.architecture.tabicl.TabICLModelBase 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.anvil.specification module openadmet.models.anvil.workflow module openadmet.models.anvil.workflow_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.tabicl 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.chemprop 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.inference.inference 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 output_dir (openadmet.models.trainer.lightning.LightningTrainer attribute)

P

param_grid (openadmet.models.trainer.sklearn.SKLearnGridSearchTrainer attribute) param_path (openadmet.models.anvil.specification.ModelSpec attribute) param_paths (openadmet.models.anvil.specification.EnsembleSpec attribute) params (openadmet.models.anvil.specification.AnvilSection attribute) (openadmet.models.anvil.specification.FeatureSpec 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() (in module openadmet.models.inference.inference) (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.tabicl.TabICLModelBase 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.tabicl.TabICLClassifierModel 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) procedure (openadmet.models.anvil.specification.AnvilSpecification attribute) ProcedureSpec (class in openadmet.models.anvil.specification) 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_seed (openadmet.models.anvil.specification.ProcedureSpec attribute) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) (openadmet.models.architecture.catboost.CatBoostModelBase attribute) (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.tabicl.TabICLModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNExtensionModelBase attribute) (openadmet.models.architecture.tabpfn.TabPFNModelBase attribute) (openadmet.models.architecture.xgboost.XGBoostModelBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.cross_validation.SKLearnRepeatedKFoldCrossValidation attribute) (openadmet.models.features.feature_base.DeepLearningFeaturizer attribute) read() (openadmet.models.anvil.specification.DataSpec method) 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.anvil.specification.AnvilSpecification attribute) 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) ReportSpec (class in openadmet.models.anvil.specification) resolve_hyperparameters() (openadmet.models.architecture.chemprop.ChemPropModel method) resolved_output_dir (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) resource (openadmet.models.anvil.specification.DataSpec attribute) 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) run() (openadmet.models.anvil.specification.AnvilSpecification method) (openadmet.models.anvil.workflow.AnvilDeepLearningWorkflow method) (openadmet.models.anvil.workflow.AnvilWorkflow method) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase method)

S

safe_index() (in module openadmet.models.split.scaffold) save() (openadmet.models.active_learning.committee.CommitteeRegressor 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) search (openadmet.models.trainer.sklearn.SKLearnSearchTrainer property) section_name (openadmet.models.anvil.specification.AnvilSection attribute) (openadmet.models.anvil.specification.EnsembleSpec attribute) (openadmet.models.anvil.specification.EvalSpec attribute) (openadmet.models.anvil.specification.FeatureSpec attribute) (openadmet.models.anvil.specification.ModelSpec attribute) (openadmet.models.anvil.specification.ProcedureSpec attribute) (openadmet.models.anvil.specification.ReportSpec attribute) (openadmet.models.anvil.specification.SplitSpec attribute) (openadmet.models.anvil.specification.TrainerSpec attribute) (openadmet.models.anvil.specification.TransformSpec attribute) serial_path (openadmet.models.anvil.specification.ModelSpec attribute) serial_paths (openadmet.models.anvil.specification.EnsembleSpec attribute) serialize() (openadmet.models.active_learning.committee.CommitteeRegressor method) (openadmet.models.architecture.chemprop.ChemPropModel 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)

shuffle (openadmet.models.features.chemprop.ChemPropFeaturizer 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) SpecBase (class in openadmet.models.anvil.specification) split (openadmet.models.anvil.specification.ProcedureSpec attribute) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) 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) SplitSpec (class in openadmet.models.anvil.specification) 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

TabICLClassifierModel (class in openadmet.models.architecture.tabicl) TabICLModelBase (class in openadmet.models.architecture.tabicl) TabICLRegressorModel (class in openadmet.models.architecture.tabicl) 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) tag (openadmet.models.anvil.specification.Metadata attribute) tags (openadmet.models.anvil.specification.Metadata attribute) target_cols (openadmet.models.anvil.specification.DataSpec attribute) task_names (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation property) (openadmet.models.eval.regression.RegressionMetrics property) (openadmet.models.eval.uncertainty.UncertaintyMetrics property) template_anvil_dir() (openadmet.models.anvil.specification.DataSpec method) (openadmet.models.anvil.specification.EnsembleSpec method) (openadmet.models.anvil.specification.ModelSpec method) (openadmet.models.anvil.specification.ProcedureSpec method) template_resource() (openadmet.models.anvil.specification.DataSpec method) test_resource (openadmet.models.anvil.specification.DataSpec attribute) title (openadmet.models.eval.cross_validation.CrossValidationBase attribute) (openadmet.models.eval.cross_validation.PytorchLightningRepeatedKFoldCrossValidation attribute) (openadmet.models.eval.regression.RegressionPlots attribute) to_class() (openadmet.models.anvil.specification.AnvilSection method) to_multi_yaml() (openadmet.models.anvil.specification.AnvilSpecification method) to_recipe() (openadmet.models.anvil.specification.AnvilSpecification method) to_workflow() (openadmet.models.anvil.specification.AnvilSpecification method) to_yaml() (openadmet.models.anvil.specification.DataSpec method) (openadmet.models.anvil.specification.SpecBase method) tol (openadmet.models.architecture.svm.SVMClassifierModel attribute) (openadmet.models.architecture.svm.SVMRegressorModel attribute) train (openadmet.models.anvil.specification.ProcedureSpec 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.tabicl.TabICLModelBase 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)

train_resource (openadmet.models.anvil.specification.DataSpec attribute) trainer (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) TrainerBase (class in openadmet.models.trainer.trainer_base) TrainerSpec (class in openadmet.models.anvil.specification) transform (openadmet.models.anvil.specification.ProcedureSpec attribute) (openadmet.models.anvil.workflow_base.AnvilWorkflowBase attribute) transformer (openadmet.models.features.feature_base.MolfeatFeaturizer property) TransformSpec (class in openadmet.models.anvil.specification) type (openadmet.models.active_learning.committee.CommitteeRegressor attribute) (openadmet.models.active_learning.ensemble_base.EnsembleBase attribute) (openadmet.models.anvil.specification.AnvilSection attribute) (openadmet.models.anvil.specification.DataSpec attribute) (openadmet.models.anvil.specification.FeatureSpec 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.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.tabicl.TabICLClassifierModel attribute) (openadmet.models.architecture.tabicl.TabICLModelBase attribute) (openadmet.models.architecture.tabicl.TabICLRegressorModel 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_amp (openadmet.models.architecture.tabicl.TabICLModelBase attribute) use_bagging (openadmet.models.anvil.specification.EnsembleSpec attribute) use_fa3 (openadmet.models.architecture.tabicl.TabICLModelBase attribute) 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)

using_train_test (openadmet.models.anvil.specification.DataSpec property)

V

val_resource (openadmet.models.anvil.specification.DataSpec attribute) 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)

version (openadmet.models.anvil.specification.Metadata 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)