Index

A

A (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) accelerator (matcha.utils.schemas.cli.Inference attribute) (matcha.utils.schemas.cli.PretrainTraining attribute) (matcha.utils.schemas.sklearn_api.TrainingInputModel attribute) act_fn (matcha.nn.layers.MultiMLP attribute) activation (matcha.torch.encoders.cnn.Conv1d attribute) (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.generic_models.MLPMixin attribute) ActivationRegistry (in module matcha.nn.activations) Adam (class in matcha.nn.optimizers) AdamW (class in matcha.nn.optimizers) AdaRMSN (class in matcha.nn.layers) add_dimension_glasso() (in module matcha.nn.deep_lasso) additional_mol_features_dim (matcha.torch.models.classic.base_classic_model.BaseClassicModel property) (matcha.torch.models.classic.BaseClassicModel property) (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ClassicMatchaModel attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) affinity_matrix (matcha.nn.multitask.TaskAffinityResult attribute) aggregate() (matcha.torch.encoders.gatedgcn.GatedGCNConv method) aggregate_scores() (in module matcha.cli.utils) aggregation (matcha.nn.readouts.PyGAggregationWrapper attribute) aggregator (matcha.torch.encoders.gps.MPNNPlusConv attribute) algorithm (matcha.utils.schemas.calibration.EMBaseInputModel attribute) (matcha.utils.schemas.cli.BaselineModel attribute) (matcha.utils.schemas.cli.CalibrationModelSettings attribute) (matcha.utils.schemas.EMBaseInputModel attribute) algorithm_params (matcha.utils.schemas.calibration.EMBaseInputModel attribute) (matcha.utils.schemas.EMBaseInputModel attribute) alpha (matcha.nn.layers.AdaRMSN attribute) (matcha.nn.losses.BCEFocalLoss attribute) ALPHA (matcha.nn.losses.GradNormLoss attribute) alpha (matcha.torch.models.finetuning.lora.LoRALinear attribute) (matcha.torch.models.finetuning.LoRALinear attribute) AnalogueGenerator (class in matcha.explainability) (class in matcha.explainability.analogue_generator) analogues (matcha.explainability.explainer.MatchaExplanation attribute) (matcha.explainability.MatchaExplanation attribute) annotate() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) apply_lora() (in module matcha.torch.models.finetuning) (in module matcha.torch.models.finetuning.lora) apply_sparse_scaling() (in module matcha.cli.prepare_sparse_dataset) architecture (matcha.utils.schemas.cli.EncoderPretrainModel attribute) (matcha.utils.schemas.cli.Model attribute) (matcha.utils.schemas.cli.PretrainMultitaskModel attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnEnsembleInputModel attribute) architecture_grid (matcha.utils.schemas.sklearn_api.TuningInputModel attribute) architecture_search (matcha.utils.schemas.cli.Tuning attribute)

architecture_search_budget (matcha.utils.schemas.sklearn_api.TuningInputModel attribute) ATOM_FEAT_DIM (in module matcha.datamodules.classic.graph_datamodule) atom_projection (matcha.torch.encoders.AttentiveFP attribute) (matcha.torch.encoders.attentivefp.AttentiveFP attribute) (matcha.torch.encoders.E3GNN attribute) (matcha.torch.encoders.e3gnn.E3GNN attribute) (matcha.torch.encoders.GPS attribute) (matcha.torch.encoders.gps.GPS attribute) (matcha.torch.encoders.GPS3D attribute) (matcha.torch.encoders.gps3d.GPS3D attribute) (matcha.torch.encoders.GT attribute) (matcha.torch.encoders.gt.GT attribute) (matcha.torch.encoders.gt3d.GT3D attribute) (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretrainingEncoder attribute) (matcha.torch.models.pretraining.gps_pretraining.GPSPretrainingEncoder attribute) (matcha.torch.models.pretraining.gt_pretraining.GTPretrainingEncoder attribute) att (matcha.torch.encoders.gps.GPSBlock attribute) att_l (matcha.torch.encoders.attentivefp.GATEConv attribute) att_r (matcha.torch.encoders.attentivefp.GATEConv attribute) attention (matcha.torch.encoders.CNN attribute) (matcha.torch.encoders.cnn.CNN attribute) (matcha.torch.encoders.RNN attribute) (matcha.torch.encoders.rnn.RNN attribute) AttentiveFP (class in matcha.torch.encoders) (class in matcha.torch.encoders.attentivefp) AttentiveFPClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.attentive_fp) AttentiveFPInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) AttentiveFPMixin (class in matcha.utils.schemas.generic_models) AttentiveFPModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.attentivefp_model) AttentiveFPPretraining (class in matcha.torch.models.pretraining) (class in matcha.torch.models.pretraining.attentivefp_pretraining) AttentiveFPPretrainingEncoder (class in matcha.torch.models.pretraining.attentivefp_pretraining) AttentiveFPRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.attentive_fp) AttentivePooling (class in matcha.nn.readouts) attn_dropout (matcha.nn.layers.BiasedMultiHeadAttention attribute) (matcha.torch.encoders.gt.GTConv attribute) augment() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) augment_resonance (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.cli.EncoderPretrainMLMDatamodule attribute) (matcha.utils.schemas.datamodules.BaseDataModuleFields attribute) autoload() (in module matcha.sklearn) (in module matcha.sklearn.autoload) automatic_optimization (matcha.torch.models.finetuning.Finetuner attribute) (matcha.torch.models.finetuning.finetuner.Finetuner attribute) AutotuneOptimum (class in matcha.utils.schemas.cli) AutotuneOutput (class in matcha.utils.schemas.cli)

B

B (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) BackwardTransformRegistry (class in matcha.datamodules.classic.label_transform) base (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule attribute) BaseCalibration (class in matcha.calibration) (class in matcha.calibration.base_calibration) BaseClassicModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.base_classic_model) BaseDataModel (class in matcha.utils.schemas.base) BaseDataModule (class in matcha.datamodules) (class in matcha.datamodules.base_datamodule) BaseDataModuleFields (class in matcha.utils.schemas.datamodules) BaseEncoder (class in matcha.torch.encoders.base_encoder) BaseEncoderInputModel (class in matcha.utils.schemas.label) BaseFinetuner (class in matcha.sklearn.finetuner) BaseGraphEncoder (class in matcha.torch.encoders.base_graph_encoder) BaseGraphPretrainingModel (class in matcha.torch.models.pretraining) (class in matcha.torch.models.pretraining.base_graph_pretraining) BaseLabelEncoder (class in matcha.datamodules) (class in matcha.datamodules.classic) (class in matcha.datamodules.classic.label_encoder) BaselineModel (class in matcha.utils.schemas.cli) BasePredictor (class in matcha.torch.predictors.base_predictor) BasePretrainingModel (class in matcha.torch.models.pretraining) (class in matcha.torch.models.pretraining.base_pretraining_model) BaseScikitLearnCLM (class in matcha.sklearn.clm.base_sklearn_clm) BaseScikitLearnGNN (class in matcha.sklearn.graph.base_sklearn_gnn) BaseScikitLearnGNN3D (class in matcha.sklearn.graph3d.base_sklearn_gnn3d) BaseScikitLearnModel (class in matcha.sklearn.base_sklearn_model) BaseScikitLearnTabular (class in matcha.sklearn.tabular.base_sklearn_tabular) batch_moltosmiles() (in module matcha.datamodules.classic.clm_datamodule) batch_size (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.cli.EncoderPretrainMLMDatamodule attribute) (matcha.utils.schemas.cli.Inference attribute) (matcha.utils.schemas.datamodules.BaseDataModuleFields attribute) (matcha.utils.schemas.sklearn_api.TrainingInputModel attribute)

batch_smiles_tokenize() (in module matcha.datamodules.classic.clm_datamodule) BatchNorm (class in matcha.nn.layers) BCEFocalLoss (class in matcha.nn.losses) BCELoss (class in matcha.nn.losses) beta (matcha.nn.layers.AdaRMSN attribute) beta_proj (matcha.nn.layers.SpatialEncoder3d attribute) bias (matcha.nn.layers.MultiBatchNorm attribute) (matcha.nn.layers.MultiLn attribute) (matcha.torch.encoders.attentivefp.GATEConv attribute) BiasedMultiHeadAttention (class in matcha.nn.layers) BinaryClassificationEncoderInputModel (class in matcha.utils.schemas.label) BinaryClassificationLabelEncoder (class in matcha.datamodules) (class in matcha.datamodules.classic) (class in matcha.datamodules.classic.label_encoder) BOND_FEAT_DIM (in module matcha.datamodules.classic.graph_datamodule) bond_projection (matcha.torch.encoders.GPS attribute) (matcha.torch.encoders.gps.GPS attribute) (matcha.torch.encoders.GPS3D attribute) (matcha.torch.encoders.gps3d.GPS3D attribute) (matcha.torch.encoders.GT attribute) (matcha.torch.encoders.gt.GT attribute) (matcha.torch.encoders.gt3d.GT3D attribute) (matcha.torch.models.pretraining.gps_pretraining.GPSPretrainingEncoder attribute) (matcha.torch.models.pretraining.gt_pretraining.GTPretrainingEncoder attribute) bootstrap_metrics() (in module matcha.cli.utils) BootstrapComparison (class in matcha.cli.statistical_tests) bound (matcha.utils.schemas.data.MolReadout attribute) (matcha.utils.schemas.MolReadout attribute) bound_mask (matcha.utils.schemas.data.MolDataset attribute) (matcha.utils.schemas.MolDataset attribute) BoundedHuberLoss (class in matcha.nn.losses) BoundedLoss (class in matcha.nn.losses) BoundedMAELoss (class in matcha.nn.losses) BoundedMSELoss (class in matcha.nn.losses) BoundedSmoothL1Loss (class in matcha.nn.losses) budget (matcha.utils.schemas.cli.Search attribute) build_callbacks() (matcha.sklearn.managers.training_manager.TrainingManager method) (matcha.sklearn.managers.TrainingManager method) build_comparison() (in module matcha.cli.statistical_tests)

C

C (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) calculate_feature_dim() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) calibrate() (matcha.sklearn.managers.ensemble_calibration_manager.EnsembleCalibrationManager method) (matcha.sklearn.managers.EnsembleCalibrationManager method) (matcha.sklearn.managers.uncertainty_manager.UncertaintyManager method) (matcha.sklearn.managers.UncertaintyManager method) calibrate_uncertainty() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) calibration (matcha.utils.schemas.cli.Dataset attribute) (matcha.utils.schemas.cli.Model attribute) (matcha.utils.schemas.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.ScikitLearnInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnInputModel attribute) CalibrationDataSettings (class in matcha.utils.schemas.cli) CalibrationModelSettings (class in matcha.utils.schemas.cli) CalibrationRegistry (in module matcha.calibration.base_calibration) calibrator (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel property) (matcha.sklearn.Ensemble property) (matcha.sklearn.ensemble.Ensemble property) (matcha.sklearn.managers.ensemble_calibration_manager.EnsembleCalibrationManager property) (matcha.sklearn.managers.EnsembleCalibrationManager property) (matcha.sklearn.managers.uncertainty_manager.UncertaintyManager property) (matcha.sklearn.managers.UncertaintyManager property) calibrator_type (matcha.utils.schemas.calibration.EMClassificationInputModel attribute) (matcha.utils.schemas.calibration.EMRegressionInputModel attribute) (matcha.utils.schemas.calibration.ICPClassificationInputModel attribute) (matcha.utils.schemas.calibration.ICPRegressionInputModel attribute) (matcha.utils.schemas.EMClassificationInputModel attribute) (matcha.utils.schemas.EMRegressionInputModel attribute) (matcha.utils.schemas.ICPClassificationInputModel attribute) (matcha.utils.schemas.ICPRegressionInputModel attribute) CalibratorModel (in module matcha.utils.schemas.calibration) CalibratorModels (class in matcha.utils.schemas.calibration) check_lengths() (matcha.utils.schemas.data.MolDataset method) (matcha.utils.schemas.MolDataset method) ChempropClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.chemprop) ChempropDataModule (class in matcha.datamodules.classic.chemprop_datamodule) ChempropDataModuleInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.datamodules) ChempropFinetuner (class in matcha.torch.models.finetuning) (class in matcha.torch.models.finetuning.chemprop_finetuner) ChempropFinetunerInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) ChempropFinetunerMixin (class in matcha.utils.schemas.generic_models) ChempropInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) ChempropMixin (class in matcha.sklearn.graph.chemprop) ChempropModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.chemprop_model) ChempropRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.chemprop) ChempropSchedulerConfig (class in matcha.nn.schedulers) class_labels (matcha.utils.schemas.label.BaseEncoderInputModel attribute) class_thresholds (matcha.utils.schemas.label.BaseEncoderInputModel attribute) ClassicMatchaModel (class in matcha.utils.schemas.generic_models) ClassicModelRegistry (in module matcha.torch.models.classic.base_classic_model) ClassRegistry (class in matcha.utils.registry) CLIAutotuneOutput (class in matcha.utils.schemas.cli) CLIBaselineInputModel (class in matcha.utils.schemas.cli) CLIEncoderPretrainInputModel (class in matcha.utils.schemas.cli) CLIEvaluationInputModel (class in matcha.utils.schemas.cli) clip (matcha.utils.schemas.datamodules.BaseDataModuleFields attribute) CLIPredictInputModel (class in matcha.utils.schemas.cli) CLIPrepareInputModel (class in matcha.utils.schemas.cli) CLIPretrainMultitaskInputModel (class in matcha.utils.schemas.cli) CLIStitcherInputModel (class in matcha.utils.schemas.cli) CLISummarizeInputModel (class in matcha.utils.schemas.cli) CLITrainInputModel (class in matcha.utils.schemas.cli) CLMDataModule (class in matcha.datamodules.classic.clm_datamodule) CLMDataModuleInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.datamodules) CLMMixin (class in matcha.utils.schemas.generic_models) CLMMLMDataModule (class in matcha.datamodules.pretraining) (class in matcha.datamodules.pretraining.clm_mlm_datamodule) CLMMLMDataModuleInputModel (class in matcha.utils.schemas.datamodules) CLMTrainingManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.training_manager) cluster_split() (in module matcha.utils.splitting) CNN (class in matcha.torch.encoders) (class in matcha.torch.encoders.cnn) CNNClassifier (class in matcha.sklearn) (class in matcha.sklearn.clm) (class in matcha.sklearn.clm.cnn) CNNInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) CNNMixin (class in matcha.utils.schemas.generic_models) CNNModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.cnn_model) CNNRegressor (class in matcha.sklearn) (class in matcha.sklearn.clm) (class in matcha.sklearn.clm.cnn) collate_fn() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.datamodules.classic.graph_datamodule.Graph3DDataModule method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) collate_fn_map (matcha.datamodules.base_datamodule.BaseDataModule attribute) (matcha.datamodules.BaseDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule attribute)

collate_fn_pyg_graph() (in module matcha.datamodules.utils) collate_fns (in module matcha.datamodules.utils) CombinedDataModule (class in matcha.datamodules.classic.combined_datamodule) CombinedDataModuleInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.datamodules) CombinedStackDataset (class in matcha.datamodules) (class in matcha.datamodules.utils) COMMANDS (in module matcha.cli) comparison (matcha.cli.summarize.ExperimentSummarizer attribute) compute() (matcha.sklearn.managers.uncertainty_manager.UncertaintyManager method) (matcha.sklearn.managers.UncertaintyManager method) compute_distances (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute) compute_learned_embedding() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.torch.models.classic.base_classic_model.BaseClassicModel method) (matcha.torch.models.classic.BaseClassicModel method) (matcha.torch.models.classic.chemprop_model.ChempropModel method) (matcha.torch.models.classic.ChempropModel method) (matcha.torch.models.finetuning.Finetuner method) (matcha.torch.models.finetuning.finetuner.Finetuner method) compute_p_values_both_classes() (matcha.calibration.ICPClassificationCalibration method) (matcha.calibration.inductive_conformal.ICPClassificationCalibration method) compute_sparse_scaling_stats() (in module matcha.cli.prepare_sparse_dataset) compute_task_affinity() (in module matcha.nn.multitask) compute_uncertainty() (matcha.calibration.base_calibration.BaseCalibration method) (matcha.calibration.BaseCalibration method) (matcha.calibration.EMCalibration method) (matcha.calibration.error_model.EMCalibration method) (matcha.calibration.ICPClassificationCalibration method) (matcha.calibration.ICPRegressionCalibration method) (matcha.calibration.inductive_conformal.ICPCalibration method) (matcha.calibration.inductive_conformal.ICPClassificationCalibration method) (matcha.calibration.inductive_conformal.ICPRegressionCalibration method) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.managers.ensemble_calibration_manager.EnsembleCalibrationManager method) (matcha.sklearn.managers.EnsembleCalibrationManager method) concat_tensors_merge_fn() (in module matcha.datamodules.utils) conclude_experiment() (matcha.utils.logging.MatchaLogger method) (matcha.utils.MatchaLogger method) confidence_alpha (matcha.utils.schemas.calibration.ICPBaseInputModel attribute) (matcha.utils.schemas.ICPBaseInputModel attribute) config (matcha.utils.schemas.cli.Search attribute) config_path (matcha.utils.schemas.cli.Model attribute) configure() (matcha.sklearn.managers.training_manager.TrainingManager method) (matcha.sklearn.managers.TrainingManager method) configure_label_encoder() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) configure_label_encoder_task() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) configure_optimizers() (matcha.torch.models.classic.base_classic_model.BaseClassicModel method) (matcha.torch.models.classic.BaseClassicModel method) (matcha.torch.models.finetuning.Finetuner method) (matcha.torch.models.finetuning.finetuner.Finetuner method) (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel method) (matcha.torch.models.pretraining.BasePretrainingModel method) Constant (class in matcha.nn.schedulers) conv (matcha.torch.encoders.cnn.Conv1d attribute) Conv1d (class in matcha.torch.encoders.cnn) coor_weights_clamp_value (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) coors_mlp (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) coors_norm (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) CoorsNorm (class in matcha.torch.encoders.e3gnn) correct_pairwise() (matcha.cli.statistical_tests.BootstrapComparison method) (matcha.cli.statistical_tests.NonParametricComparison method) (matcha.cli.statistical_tests.ParametricComparison method) correction_method (matcha.cli.statistical_tests.BootstrapComparison attribute) (matcha.cli.statistical_tests.NonParametricComparison attribute) (matcha.cli.statistical_tests.ParametricComparison attribute) cosine_steps (matcha.nn.schedulers.WarmupCosineAnnealingLR attribute) CosineAnnealing (class in matcha.nn.schedulers) CosineAnnealingCyclic (class in matcha.nn.schedulers) create_calibrator() (matcha.sklearn.managers.ensemble_calibration_manager.EnsembleCalibrationManager method) (matcha.sklearn.managers.EnsembleCalibrationManager method) (matcha.sklearn.managers.uncertainty_manager.UncertaintyManager method) (matcha.sklearn.managers.UncertaintyManager method) create_correlation_heatmaps() (matcha.cli.summarize.ExperimentSummarizer method) create_dataloader() (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule method) create_empty() (matcha.datamodules.BaseLabelEncoder class method) (matcha.datamodules.classic.BaseLabelEncoder class method) (matcha.datamodules.classic.label_encoder.BaseLabelEncoder class method) create_explainer() (matcha.sklearn.managers.explainability_manager.ExplainabilityManager method) (matcha.sklearn.managers.ExplainabilityManager method) create_logger() (matcha.sklearn.managers.mlflow_manager.MLFlowManager method) (matcha.sklearn.managers.MLFlowManager method) create_performance_plots() (matcha.cli.summarize.ExperimentSummarizer method) create_summary_statistics() (matcha.cli.summarize.ExperimentSummarizer method) create_validation_set_sparse() (in module matcha.cli.prepare_sparse_dataset) CrossEntropyLoss (class in matcha.nn.losses) current_step (matcha.nn.schedulers.WarmupCosineAnnealingLR attribute) (matcha.nn.schedulers.WarmupLinearDecayLR attribute) custom_mlflow_log() (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) cv_idx (matcha.sklearn.Ensemble property) (matcha.sklearn.ensemble.Ensemble property)

D

D (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) dataloader_num_workers (matcha.utils.schemas.cli.PretrainPipe attribute) datamodule (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel property) (matcha.sklearn.managers.datamodule_manager.DataModuleManager property) (matcha.sklearn.managers.DataModuleManager property) (matcha.utils.schemas.cli.EncoderPretrainModel attribute) (matcha.utils.schemas.cli.PretrainMultitaskModel attribute) (matcha.utils.schemas.ScikitLearnInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnInputModel attribute) datamodule_type (matcha.utils.schemas.ChempropDataModuleInputModel attribute) (matcha.utils.schemas.CLMDataModuleInputModel attribute) (matcha.utils.schemas.CombinedDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.ChempropDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CLMDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CLMMLMDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CombinedDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphPretrainingDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.TabularDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute) (matcha.utils.schemas.GraphPretrainingDataModuleInputModel attribute) (matcha.utils.schemas.TabularDataModuleInputModel attribute) DataModuleManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.datamodule_manager) DataModuleModel (in module matcha.utils.schemas.datamodules) DataModuleModels (class in matcha.utils.schemas.datamodules) (class in matcha.utils.schemas.label) DataModuleRegistry (in module matcha.datamodules) (in module matcha.datamodules.base_datamodule) datamodules (matcha.datamodules.classic.combined_datamodule.CombinedDataModule attribute) (matcha.utils.schemas.CombinedDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CombinedDataModuleInputModel attribute) Dataset (class in matcha.utils.schemas.cli) dataset (matcha.utils.schemas.cli.CLIAutotuneOutput attribute) (matcha.utils.schemas.cli.CLIBaselineInputModel attribute) (matcha.utils.schemas.cli.CLIEncoderPretrainInputModel attribute) (matcha.utils.schemas.cli.CLIEvaluationInputModel attribute) (matcha.utils.schemas.cli.CLIPredictInputModel attribute) (matcha.utils.schemas.cli.CLIPretrainMultitaskInputModel attribute) (matcha.utils.schemas.cli.CLITrainInputModel attribute) (matcha.utils.schemas.cli.Loss attribute) dataset_dir (matcha.utils.schemas.cli.MultitaskPretrainDataset attribute) dataset_names (matcha.utils.schemas.cli.StitcherInputModel attribute) dataset_predict (matcha.datamodules.base_datamodule.BaseDataModule property) (matcha.datamodules.BaseDataModule property) dataset_test (matcha.datamodules.base_datamodule.BaseDataModule property) (matcha.datamodules.BaseDataModule property) dataset_train (matcha.datamodules.base_datamodule.BaseDataModule property) (matcha.datamodules.BaseDataModule property) dataset_val (matcha.datamodules.base_datamodule.BaseDataModule property) (matcha.datamodules.BaseDataModule property) datasets (matcha.datamodules.CombinedStackDataset attribute) (matcha.datamodules.utils.CombinedStackDataset attribute) (matcha.utils.schemas.cli.CLIPrepareInputModel attribute) date (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) decay_steps (matcha.nn.schedulers.WarmupLinearDecayLR attribute) decompose() (matcha.explainability.analogue_generator.AnalogueGenerator class method) (matcha.explainability.AnalogueGenerator class method) (matcha.explainability.explainer.MatchaExplainer method) (matcha.explainability.MatchaExplainer method)

deep_lasso_regularizer() (in module matcha.nn.deep_lasso) deep_lasso_weight (matcha.torch.models.classic.mlp_model.MLPModel attribute) (matcha.torch.models.classic.MLPModel attribute) (matcha.torch.models.classic.snn_model.SNNModel attribute) (matcha.torch.models.classic.SNNModel attribute) (matcha.utils.schemas.generic_models.TabularMixin attribute) deepcopy_input() (in module matcha.utils.wrapper) DeepSetsPooling (class in matcha.nn.readouts) default_merge() (in module matcha.datamodules.classic.combined_datamodule) defaults (matcha.datamodules.classic.Engine property) (matcha.datamodules.classic.rdkit_engine.Engine property) (matcha.datamodules.Engine property) DegreeScalerPooling (class in matcha.nn.readouts) description (matcha.utils.schemas.cli.Metadata attribute) (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) descriptor_set (matcha.explainability.LIME property) (matcha.explainability.lime.LIME property) devices (matcha.utils.schemas.cli.Inference attribute) (matcha.utils.schemas.cli.PretrainTraining attribute) (matcha.utils.schemas.sklearn_api.TrainingInputModel attribute) df_desc (matcha.explainability.explainer.MatchaExplanation attribute) (matcha.explainability.MatchaExplanation attribute) dictionary (matcha.utils.schemas.CLMDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CLMDataModuleInputModel attribute) dim (matcha.nn.layers.AdaRMSN attribute) DirectoryExperimentSummarizer (class in matcha.cli.summarize) dist3d_encoder (matcha.torch.encoders.GPS3D attribute) (matcha.torch.encoders.gps3d.GPS3D attribute) (matcha.torch.encoders.gt3d.GT3D attribute) distmat_k (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute) distmat_pe() (matcha.datamodules.classic.graph_positional_encoder.GraphPE class method) dropout (matcha.nn.layers.MultiMLP attribute) (matcha.torch.encoders.AttentiveFP attribute) (matcha.torch.encoders.attentivefp.AttentiveFP attribute) (matcha.torch.encoders.attentivefp.GATEConv attribute) (matcha.torch.encoders.cnn.Conv1d attribute) (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretrainingEncoder attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.generic_models.TabularMixin attribute) dropout_layer (matcha.torch.encoders.E3GNN attribute) (matcha.torch.encoders.e3gnn.E3GNN attribute) (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) (matcha.torch.encoders.gt.GTConv attribute) dummy() (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule class method) (matcha.datamodules.classic.clm_datamodule.CLMDataModule class method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule class method) (matcha.datamodules.classic.graph_datamodule.GraphDataModule class method) (matcha.datamodules.classic.tabular_datamodule.TabularDataModule class method) (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule class method) (matcha.datamodules.pretraining.CLMMLMDataModule class method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule class method) (matcha.datamodules.pretraining.GraphPretrainingDataModule class method)

E

E (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) E3GNN (class in matcha.torch.encoders) (class in matcha.torch.encoders.e3gnn) E3GNNClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph3d) (class in matcha.sklearn.graph3d.e3gnn) E3GNNInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) E3GNNMixin (class in matcha.utils.schemas.generic_models) E3GNNModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.e3gnn_model) E3GNNRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph3d) (class in matcha.sklearn.graph3d.e3gnn) early_stopping (matcha.utils.schemas.cli.PretrainTraining attribute) (matcha.utils.schemas.sklearn_api.TrainingInputModel attribute) edge_in_dim (matcha.torch.encoders.gt.GTConv attribute) edge_input_dim (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) edge_mlp (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) edge_model (matcha.torch.encoders.gps.MPNNPlusConv attribute) edge_out (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) edge_update() (matcha.torch.encoders.attentivefp.GATEConv method) edge_weight (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) EGNN_Sparse (class in matcha.torch.encoders.e3gnn) elstatic_k (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute) elstatic_pe() (matcha.datamodules.classic.graph_positional_encoder.GraphPE class method) ELU (class in matcha.nn.activations) EM_REGISTRY (in module matcha.calibration.error_model) EMBaseInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.calibration) embed_dim (matcha.nn.layers.BiasedMultiHeadAttention attribute) embed_timeout (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) embedding (matcha.nn.layers.SpatialEncoder attribute) (matcha.torch.encoders.CNN attribute) (matcha.torch.encoders.cnn.CNN attribute) (matcha.torch.encoders.RNN attribute) (matcha.torch.encoders.rnn.RNN attribute) EMCalibration (class in matcha.calibration) (class in matcha.calibration.error_model) EMClassificationCalibration (class in matcha.calibration) (class in matcha.calibration.error_model) EMClassificationInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.calibration) EMRegressionCalibration (class in matcha.calibration) (class in matcha.calibration.error_model) EMRegressionInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.calibration) enc_activation (matcha.utils.schemas.AttentiveFPInputModel attribute) (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.GraphMixin attribute) (matcha.utils.schemas.torch_api.AttentiveFPInputModel attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) enc_aggregation (matcha.utils.schemas.generic_models.GINMixin attribute) (matcha.utils.schemas.generic_models.MPNNMixin attribute) enc_atom_hidden_dim (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.GraphMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) enc_atom_input_dim (matcha.utils.schemas.generic_models.GraphMixin attribute) enc_attention_dropout (matcha.utils.schemas.generic_models.RoFormerMixin attribute) enc_bidirectional (matcha.utils.schemas.generic_models.RNNMixin attribute) enc_bond_hidden_dim (matcha.utils.schemas.generic_models.MPNNMixin attribute) enc_bond_input_dim (matcha.utils.schemas.generic_models.AttentiveFPMixin attribute) (matcha.utils.schemas.generic_models.E3GNNMixin attribute) (matcha.utils.schemas.generic_models.GatedGCNMixin attribute) (matcha.utils.schemas.generic_models.GPS3DMixin attribute) (matcha.utils.schemas.generic_models.GPSMixin attribute) (matcha.utils.schemas.generic_models.GT3DMixin attribute) (matcha.utils.schemas.generic_models.GTMixin attribute) (matcha.utils.schemas.generic_models.MPNNMixin attribute) enc_distance_k (matcha.utils.schemas.generic_models.GPSMixin attribute) (matcha.utils.schemas.generic_models.GTMixin attribute) enc_distmat_k (matcha.utils.schemas.generic_models.GraphMixin attribute) enc_dropout (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.GraphMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) enc_elstatic_k (matcha.utils.schemas.generic_models.GraphMixin attribute) enc_embedding_dim (matcha.utils.schemas.generic_models.RNNMixin attribute) enc_expansion_dim (matcha.utils.schemas.generic_models.RoFormerMixin attribute) enc_expansion_k (matcha.utils.schemas.generic_models.GPS3DMixin attribute) (matcha.utils.schemas.generic_models.GPSMixin attribute) (matcha.utils.schemas.generic_models.GT3DMixin attribute) (matcha.utils.schemas.generic_models.GTMixin attribute) enc_fourier_features (matcha.utils.schemas.generic_models.E3GNNMixin attribute) enc_hidden_dim (matcha.utils.schemas.generic_models.CNNMixin attribute) (matcha.utils.schemas.generic_models.RNNMixin attribute) (matcha.utils.schemas.generic_models.RoFormerMixin attribute) enc_hidden_dropout (matcha.utils.schemas.generic_models.RoFormerMixin attribute) enc_jk (matcha.utils.schemas.generic_models.AttentiveFPMixin attribute) (matcha.utils.schemas.generic_models.E3GNNMixin attribute) (matcha.utils.schemas.generic_models.GatedGCNMixin attribute) (matcha.utils.schemas.generic_models.GINMixin attribute) (matcha.utils.schemas.generic_models.GPS3DMixin attribute) (matcha.utils.schemas.generic_models.GT3DMixin attribute) (matcha.utils.schemas.generic_models.GTMixin attribute) (matcha.utils.schemas.generic_models.MPNNMixin attribute) enc_kernel_dims (matcha.utils.schemas.generic_models.CNNMixin attribute) enc_laplacian_k (matcha.utils.schemas.generic_models.GraphMixin attribute) enc_m_dim (matcha.utils.schemas.generic_models.E3GNNMixin attribute) enc_norm (matcha.utils.schemas.generic_models.GatedGCNMixin attribute) (matcha.utils.schemas.generic_models.GINMixin attribute) (matcha.utils.schemas.generic_models.GPS3DMixin attribute) (matcha.utils.schemas.generic_models.GPSMixin attribute) enc_norm_coors (matcha.utils.schemas.generic_models.E3GNNMixin attribute) enc_norm_feats (matcha.utils.schemas.generic_models.E3GNNMixin attribute) enc_num_characters (matcha.utils.schemas.generic_models.CLMMixin attribute) enc_num_heads (matcha.utils.schemas.generic_models.CNNMixin attribute) (matcha.utils.schemas.generic_models.GPS3DMixin attribute) (matcha.utils.schemas.generic_models.GPSMixin attribute) (matcha.utils.schemas.generic_models.GT3DMixin attribute) (matcha.utils.schemas.generic_models.GTMixin attribute) (matcha.utils.schemas.generic_models.RNNMixin attribute) (matcha.utils.schemas.generic_models.RoFormerMixin attribute) enc_num_kernels (matcha.utils.schemas.generic_models.GPS3DMixin attribute) (matcha.utils.schemas.generic_models.GT3DMixin attribute) enc_num_layers (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.GraphMixin attribute) (matcha.utils.schemas.generic_models.RNNMixin attribute) (matcha.utils.schemas.generic_models.RoFormerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) enc_readout (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.GraphMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) enc_rnn_type (matcha.utils.schemas.generic_models.RNNMixin attribute) enc_rrwp_k (matcha.utils.schemas.generic_models.GraphMixin attribute) enc_rwse_k (matcha.utils.schemas.generic_models.GraphMixin attribute) enc_soft_edge (matcha.utils.schemas.generic_models.E3GNNMixin attribute) enc_update_coors (matcha.utils.schemas.generic_models.E3GNNMixin attribute) encode() (matcha.torch.models.classic.base_classic_model.BaseClassicModel method) (matcha.torch.models.classic.BaseClassicModel method) (matcha.torch.models.classic.chemprop_model.ChempropModel method) (matcha.torch.models.classic.ChempropModel method) (matcha.torch.models.finetuning.Finetuner method) (matcha.torch.models.finetuning.finetuner.Finetuner method) (matcha.torch.models.finetuning.pretrained_encoder_wrapper.PretrainedEncoderWrapper method) (matcha.torch.models.finetuning.PretrainedEncoderWrapper method) (matcha.torch.models.pretraining.base_graph_pretraining.BaseGraphPretrainingModel method) (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel method) (matcha.torch.models.pretraining.BaseGraphPretrainingModel method) (matcha.torch.models.pretraining.BasePretrainingModel method) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLM method) (matcha.torch.models.pretraining.RoFormerMLM method) (matcha.torch.predictors.base_predictor.BasePredictor method) (matcha.torch.predictors.SNN method) (matcha.torch.predictors.snn.SNN method)

encode_y() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.sklearn.base_sklearn_model.ScikitLearnClassifierMixin method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) encoder (matcha.torch.models.classic.attentivefp_model.AttentiveFPModel attribute) (matcha.torch.models.classic.AttentiveFPModel attribute) (matcha.torch.models.classic.base_classic_model.BaseClassicModel attribute) (matcha.torch.models.classic.BaseClassicModel attribute) (matcha.torch.models.classic.cnn_model.CNNModel attribute) (matcha.torch.models.classic.CNNModel attribute) (matcha.torch.models.classic.e3gnn_model.E3GNNModel attribute) (matcha.torch.models.classic.E3GNNModel attribute) (matcha.torch.models.classic.gatedcgn_model.GatedGCNModel attribute) (matcha.torch.models.classic.GatedGCNModel attribute) (matcha.torch.models.classic.gin_model.GINModel attribute) (matcha.torch.models.classic.GINModel attribute) (matcha.torch.models.classic.gps3d_model.GPS3DModel attribute) (matcha.torch.models.classic.GPS3DModel attribute) (matcha.torch.models.classic.gps_model.GPSModel attribute) (matcha.torch.models.classic.GPSModel attribute) (matcha.torch.models.classic.gt3d_model.GT3DModel attribute) (matcha.torch.models.classic.GT3DModel attribute) (matcha.torch.models.classic.gt_model.GTModel attribute) (matcha.torch.models.classic.GTModel attribute) (matcha.torch.models.classic.mlp_model.MLPModel attribute) (matcha.torch.models.classic.MLPModel attribute) (matcha.torch.models.classic.rnn_model.RNNModel attribute) (matcha.torch.models.classic.RNNModel attribute) (matcha.torch.models.classic.roformer_model.RoFormerModel attribute) (matcha.torch.models.classic.RoFormerModel attribute) (matcha.torch.models.classic.snn_model.SNNModel attribute) (matcha.torch.models.classic.SNNModel attribute) (matcha.torch.models.finetuning.pretrained_encoder_wrapper.PretrainedEncoderWrapper attribute) (matcha.torch.models.finetuning.PretrainedEncoderWrapper attribute) (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel attribute) (matcha.torch.models.pretraining.BasePretrainingModel attribute) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLM attribute) (matcha.torch.models.pretraining.RoFormerMLM attribute) encoder_type (matcha.utils.schemas.label.BinaryClassificationEncoderInputModel attribute) (matcha.utils.schemas.label.RegressionEncoderInputModel attribute) EncoderPretrainDataset (class in matcha.utils.schemas.cli) EncoderPretrainGraphDatamodule (class in matcha.utils.schemas.cli) EncoderPretrainMLMDatamodule (class in matcha.utils.schemas.cli) EncoderPretrainModel (class in matcha.utils.schemas.cli) EncoderPretrainPipe (in module matcha.utils.schemas.cli) EncoderPretrainTraining (in module matcha.utils.schemas.cli) EncoderRegistry (in module matcha.torch.encoders.base_encoder) Engine (class in matcha.datamodules) (class in matcha.datamodules.classic) (class in matcha.datamodules.classic.rdkit_engine) engine (matcha.calibration.EMCalibration attribute) (matcha.calibration.error_model.EMCalibration attribute) engine_params (matcha.utils.schemas.ChempropDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.ChempropDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.TabularDataModuleInputModel attribute) (matcha.utils.schemas.TabularDataModuleInputModel attribute) enrichment_factor_score() (in module matcha.utils.metrics) Ensemble (class in matcha.sklearn) (class in matcha.sklearn.ensemble) ensemble (matcha.utils.schemas.cli.Model attribute) EnsembleCalibrationManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.ensemble_calibration_manager) EnsembleMLFlowManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.ensemble_mlflow_manager) EnsembleSerializationManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.ensemble_serialization_manager) ensure_1d_array() (in module matcha.utils.sanitize) envs (matcha.explainability.explainer.MatchaExplanation attribute) (matcha.explainability.MatchaExplanation attribute) eps (matcha.nn.layers.MultiBatchNorm attribute) (matcha.nn.losses.BCEFocalLoss attribute) (matcha.nn.losses.Poly1BCELoss attribute) (matcha.torch.encoders.e3gnn.CoorsNorm attribute) (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) epsilon (matcha.nn.losses.Poly1BCELoss attribute) error_ratio (matcha.calibration.EMCalibration attribute) (matcha.calibration.error_model.EMCalibration attribute) error_threshold (matcha.utils.schemas.calibration.EMClassificationInputModel attribute) (matcha.utils.schemas.EMClassificationInputModel attribute) exists() (in module matcha.torch.encoders.e3gnn) expansion_k (matcha.torch.encoders.GT attribute) (matcha.torch.encoders.gt.GT attribute) (matcha.torch.encoders.gt3d.GT3D attribute) (matcha.torch.models.pretraining.gt_pretraining.GTPretrainingEncoder attribute) experiment (matcha.utils.schemas.sklearn_api.MLFlowInputModel attribute) experiment_name (matcha.cli.summarize.MLflowExperimentSummarizer attribute) (matcha.utils.schemas.cli.CLISummarizeInputModel attribute) (matcha.utils.schemas.cli.MLFlow attribute) ExperimentSummarizer (class in matcha.cli.summarize) explain() (matcha.explainability.explainer.MatchaExplainer method) (matcha.explainability.LIME method) (matcha.explainability.lime.LIME method) (matcha.explainability.MatchaExplainer method) (matcha.sklearn.managers.explainability_manager.ExplainabilityManager method) (matcha.sklearn.managers.ExplainabilityManager method) explain_prediction() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) ExplainabilityManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.explainability_manager) explainer (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel property) (matcha.sklearn.Ensemble property) (matcha.sklearn.ensemble.Ensemble property) (matcha.sklearn.managers.explainability_manager.ExplainabilityManager property) (matcha.sklearn.managers.ExplainabilityManager property) ExplainerInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.explainability) export_encoder_checkpoint() (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel method) (matcha.torch.models.pretraining.BasePretrainingModel method) export_to_classic() (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule method) (matcha.datamodules.pretraining.CLMMLMDataModule method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.GraphPretrainingDataModule method) export_to_yaml() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) (matcha.sklearn.managers.ensemble_serialization_manager.EnsembleSerializationManager method) (matcha.sklearn.managers.EnsembleSerializationManager method) (matcha.sklearn.managers.serialization_manager.SerializationManager method) (matcha.sklearn.managers.SerializationManager method) extra (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) extract_split_metrics() (matcha.cli.summarize.ExperimentSummarizer method)

F

feats_dim (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) feature_dimensionality (matcha.datamodules.classic.Engine property) (matcha.datamodules.classic.rdkit_engine.Engine property) (matcha.datamodules.Engine property) feature_list (matcha.utils.schemas.ChempropDataModuleInputModel attribute) (matcha.utils.schemas.cli.BaselineModel attribute) (matcha.utils.schemas.datamodules.ChempropDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.TabularDataModuleInputModel attribute) (matcha.utils.schemas.TabularDataModuleInputModel attribute) featurize() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule method) (matcha.datamodules.classic.clm_datamodule.CLMDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.datamodules.classic.graph_datamodule.GraphDataModule method) (matcha.datamodules.classic.tabular_datamodule.TabularDataModule method) (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule method) (matcha.datamodules.pretraining.CLMMLMDataModule method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) ffn (matcha.torch.encoders.gt.GTConv attribute) filename (matcha.utils.schemas.cli.AutotuneOptimum attribute) (matcha.utils.schemas.cli.StitcherOutputModel attribute) files (matcha.utils.schemas.cli.PrepareDatasets attribute) FILL (matcha.datamodules.utils.HandleMissing attribute) (matcha.utils.schemas.datamodules.HandleMissing attribute) final_lr (matcha.nn.schedulers.ChempropSchedulerConfig attribute) (matcha.torch.models.finetuning.chemprop_finetuner.ChempropFinetuner attribute) (matcha.torch.models.finetuning.ChempropFinetuner attribute) final_w (matcha.utils.schemas.cli.Loss attribute) finalize() (matcha.utils.logging.MatchaLogger method) (matcha.utils.MatchaLogger method) find_experiment_runs() (matcha.cli.summarize.DirectoryExperimentSummarizer method) (matcha.cli.summarize.ExperimentSummarizer method) (matcha.cli.summarize.MLflowExperimentSummarizer method) Finetuner (class in matcha.torch.models.finetuning) (class in matcha.torch.models.finetuning.finetuner) FinetunerInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) FinetunerMixin (class in matcha.utils.schemas.generic_models) FinetunerTrainingManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.training_manager) finetuning_strategy (matcha.utils.schemas.generic_models.FinetunerMixin attribute) FinetuningClassifier (class in matcha.sklearn) (class in matcha.sklearn.finetuner) FinetuningRegressor (class in matcha.sklearn) (class in matcha.sklearn.finetuner) fit() (matcha.calibration.base_calibration.BaseCalibration method) (matcha.calibration.BaseCalibration method) (matcha.calibration.EMCalibration method) (matcha.calibration.error_model.EMCalibration method) (matcha.calibration.ICPClassificationCalibration method) (matcha.calibration.inductive_conformal.ICPCalibration method) (matcha.calibration.inductive_conformal.ICPClassificationCalibration method) (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule method) (matcha.datamodules.classic.clm_datamodule.CLMDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.datamodules.classic.tabular_datamodule.TabularDataModule method) (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule method) (matcha.datamodules.pretraining.CLMMLMDataModule method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.GraphPretrainingDataModule method) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.clm.base_sklearn_clm.BaseScikitLearnCLM method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) fit_datamodule_size (matcha.utils.schemas.cli.PretrainPipe attribute) fit_dictionary() (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) flatten_performance_dict() (in module matcha.cli.evaluate) fold (matcha.utils.schemas.calibration.EMRegressionInputModel attribute) (matcha.utils.schemas.EMRegressionInputModel attribute) folder_path (matcha.utils.schemas.cli.StitcherInputModel attribute) (matcha.utils.schemas.cli.StitcherOutputModel attribute) forward() (matcha.nn.activations.GEGLU method) (matcha.nn.layers.AdaRMSN method) (matcha.nn.layers.BiasedMultiHeadAttention method) (matcha.nn.layers.LnBnDr method) (matcha.nn.layers.MultiBatchNorm method) (matcha.nn.layers.MultiLn method) (matcha.nn.layers.MultiMLP method) (matcha.nn.layers.SpatialEncoder method) (matcha.nn.layers.SpatialEncoder3d method) (matcha.nn.losses.BCEFocalLoss method) (matcha.nn.losses.BoundedLoss method) (matcha.nn.losses.GradNormLoss method) (matcha.nn.losses.MultiLoss method) (matcha.nn.losses.MultitaskLoss method) (matcha.nn.losses.Poly1BCELoss method) (matcha.nn.losses.WeightedBCELoss method) (matcha.nn.readouts.PyGAggregationWrapper method) (matcha.nn.readouts.VirtualNodePooling method) (matcha.torch.encoders.AttentiveFP method) (matcha.torch.encoders.attentivefp.AttentiveFP method) (matcha.torch.encoders.attentivefp.GATEConv method) (matcha.torch.encoders.base_encoder.BaseEncoder method) (matcha.torch.encoders.CNN method) (matcha.torch.encoders.cnn.CNN method) (matcha.torch.encoders.cnn.Conv1d method) (matcha.torch.encoders.E3GNN method) (matcha.torch.encoders.e3gnn.CoorsNorm method) (matcha.torch.encoders.e3gnn.E3GNN method) (matcha.torch.encoders.e3gnn.EGNN_Sparse method) (matcha.torch.encoders.e3gnn.SiLU method) (matcha.torch.encoders.GatedGCN method) (matcha.torch.encoders.gatedgcn.GatedGCN method) (matcha.torch.encoders.gatedgcn.GatedGCNConv method) (matcha.torch.encoders.GIN method) (matcha.torch.encoders.gin.GIN method) (matcha.torch.encoders.GPS method) (matcha.torch.encoders.gps.GPS method) (matcha.torch.encoders.gps.GPSBlock method) (matcha.torch.encoders.gps.MPNNPlusConv method) (matcha.torch.encoders.GPS3D method) (matcha.torch.encoders.gps3d.GPS3D method) (matcha.torch.encoders.GT method) (matcha.torch.encoders.gt.GT method) (matcha.torch.encoders.gt.GTConv method) (matcha.torch.encoders.gt3d.GT3D method) (matcha.torch.encoders.RNN method) (matcha.torch.encoders.rnn.RNN method) (matcha.torch.encoders.RoFormer method) (matcha.torch.encoders.roformer.RoFormer method) (matcha.torch.models.classic.base_classic_model.BaseClassicModel method) (matcha.torch.models.classic.BaseClassicModel method) (matcha.torch.models.finetuning.Finetuner method) (matcha.torch.models.finetuning.finetuner.Finetuner method) (matcha.torch.models.finetuning.lora.LoRALinear method) (matcha.torch.models.finetuning.LoRALinear method) (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretrainingEncoder method) (matcha.torch.models.pretraining.base_graph_pretraining.BaseGraphPretrainingModel method) (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel method) (matcha.torch.models.pretraining.BaseGraphPretrainingModel method) (matcha.torch.models.pretraining.BasePretrainingModel method) (matcha.torch.models.pretraining.gatedgcn_pretraining.GatedGCNPretrainingEncoder method) (matcha.torch.models.pretraining.gin_pretraining.GINPretrainingEncoder method) (matcha.torch.models.pretraining.gps_pretraining.GPSPretrainingEncoder method) (matcha.torch.models.pretraining.gt_pretraining.GTPretrainingEncoder method) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLM method) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLMEncoder method) (matcha.torch.models.pretraining.RoFormerMLM method) (matcha.torch.predictors.base_predictor.BasePredictor method) (matcha.torch.predictors.SNN method) (matcha.torch.predictors.snn.SNN method)

forward_nodes() (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretrainingEncoder method) (matcha.torch.models.pretraining.gatedgcn_pretraining.GatedGCNPretrainingEncoder method) (matcha.torch.models.pretraining.gin_pretraining.GINPretrainingEncoder method) (matcha.torch.models.pretraining.gps_pretraining.GPSPretrainingEncoder method) (matcha.torch.models.pretraining.gt_pretraining.GTPretrainingEncoder method) forward_nodes_per_layer() (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretrainingEncoder method) (matcha.torch.models.pretraining.gatedgcn_pretraining.GatedGCNPretrainingEncoder method) (matcha.torch.models.pretraining.gin_pretraining.GINPretrainingEncoder method) (matcha.torch.models.pretraining.gps_pretraining.GPSPretrainingEncoder method) (matcha.torch.models.pretraining.gt_pretraining.GTPretrainingEncoder method) ForwardTransformRegistry (class in matcha.datamodules.classic.label_transform) fourier_encode_dist() (in module matcha.torch.encoders.e3gnn) fourier_features (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) fp_dim (matcha.torch.encoders.base_encoder.BaseEncoder property) (matcha.torch.encoders.E3GNN property) (matcha.torch.encoders.e3gnn.E3GNN property) frac_bootstrap (matcha.utils.schemas.cli.Split attribute) from_config() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel class method) (matcha.sklearn.Ensemble class method) (matcha.sklearn.ensemble.Ensemble class method) from_dense_batch() (in module matcha.nn.layers) from_folder() (matcha.calibration.base_calibration.BaseCalibration class method) (matcha.calibration.BaseCalibration class method) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel class method) (matcha.sklearn.Ensemble class method) (matcha.sklearn.ensemble.Ensemble class method)

G

gamma (matcha.nn.losses.BCEFocalLoss attribute) gamma_proj (matcha.nn.layers.SpatialEncoder3d attribute) gate_conv (matcha.torch.encoders.AttentiveFP attribute) (matcha.torch.encoders.attentivefp.AttentiveFP attribute) (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretrainingEncoder attribute) GATEConv (class in matcha.torch.encoders.attentivefp) GatedGCN (class in matcha.torch.encoders) (class in matcha.torch.encoders.gatedgcn) GatedGCNClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.gatedgcn) GatedGCNConv (class in matcha.torch.encoders.gatedgcn) GatedGCNInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) GatedGCNMixin (class in matcha.utils.schemas.generic_models) GatedGCNModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.gatedcgn_model) GatedGCNPretraining (class in matcha.torch.models.pretraining) (class in matcha.torch.models.pretraining.gatedgcn_pretraining) GatedGCNPretrainingEncoder (class in matcha.torch.models.pretraining.gatedgcn_pretraining) GatedGCNRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.gatedgcn) GEGLU (class in matcha.nn.activations) GELU (class in matcha.nn.activations) generate_analogues() (matcha.explainability.analogue_generator.AnalogueGenerator class method) (matcha.explainability.AnalogueGenerator class method) (matcha.explainability.explainer.MatchaExplainer method) (matcha.explainability.MatchaExplainer method) generate_datacard_sparse() (in module matcha.cli.prepare_sparse_dataset) generate_features() (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule method) (matcha.datamodules.classic.clm_datamodule.CLMDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.datamodules.classic.graph_datamodule.Graph3DDataModule method) (matcha.datamodules.classic.graph_datamodule.GraphDataModule method) (matcha.datamodules.classic.tabular_datamodule.TabularDataModule method) (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule method) (matcha.datamodules.pretraining.CLMMLMDataModule method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) get_arbitrary_rdkit_descriptors() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_Avalon() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_default_logger() (in module matcha.utils.logging) get_ECFP() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_ECFP_count() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_envs_and_weights() (matcha.explainability.LIME method) (matcha.explainability.lime.LIME method) get_ERG() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_ESTATE() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_features() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_input_args() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.managers.serialization_manager.SerializationManager method) (matcha.sklearn.managers.SerializationManager method) get_lr() (matcha.nn.schedulers.WarmupCosineAnnealingLR method) (matcha.nn.schedulers.WarmupLinearDecayLR method) get_MAP4() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_MHFP() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_mordred() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_pubchem_fp() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_rdkit_all_descriptors() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_rdkit_fp() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) get_splits() (in module matcha.cli.utils) get_top_k() (matcha.nn.multitask.TaskAffinityResult method) GIN (class in matcha.torch.encoders) (class in matcha.torch.encoders.gin) GINClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.gin)

GINInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) GINMixin (class in matcha.utils.schemas.generic_models) GINModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.gin_model) GINPretraining (class in matcha.torch.models.pretraining) (class in matcha.torch.models.pretraining.gin_pretraining) GINPretrainingEncoder (class in matcha.torch.models.pretraining.gin_pretraining) GINRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.gin) GPS (class in matcha.torch.encoders) (class in matcha.torch.encoders.gps) GPS3D (class in matcha.torch.encoders) (class in matcha.torch.encoders.gps3d) GPS3DClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph3d) (class in matcha.sklearn.graph3d.gps3d) GPS3DInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) GPS3DMixin (class in matcha.utils.schemas.generic_models) GPS3DModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.gps3d_model) GPS3DRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph3d) (class in matcha.sklearn.graph3d.gps3d) GPSBlock (class in matcha.torch.encoders.gps) GPSClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.gps) GPSInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) GPSMixin (class in matcha.utils.schemas.generic_models) GPSModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.gps_model) GPSPretraining (class in matcha.torch.models.pretraining) (class in matcha.torch.models.pretraining.gps_pretraining) GPSPretrainingEncoder (class in matcha.torch.models.pretraining.gps_pretraining) GPSRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.gps) gradient_accumulation_steps (matcha.utils.schemas.cli.PretrainPipe attribute) gradient_clip_val (matcha.utils.schemas.cli.PretrainPipe attribute) GradNormLoss (class in matcha.nn.losses) Graph3DDataModule (class in matcha.datamodules.classic.graph_datamodule) Graph3DDataModuleInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.datamodules) graph_head (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretraining attribute) (matcha.torch.models.pretraining.AttentiveFPPretraining attribute) (matcha.torch.models.pretraining.gatedgcn_pretraining.GatedGCNPretraining attribute) (matcha.torch.models.pretraining.GatedGCNPretraining attribute) (matcha.torch.models.pretraining.gin_pretraining.GINPretraining attribute) (matcha.torch.models.pretraining.GINPretraining attribute) (matcha.torch.models.pretraining.gps_pretraining.GPSPretraining attribute) (matcha.torch.models.pretraining.GPSPretraining attribute) (matcha.torch.models.pretraining.gt_pretraining.GTPretraining attribute) (matcha.torch.models.pretraining.GTPretraining attribute) GraphDataModule (class in matcha.datamodules.classic.graph_datamodule) GraphDataModuleInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.datamodules) GraphMixin (class in matcha.utils.schemas.generic_models) GraphMultisetTransformerPooling (class in matcha.nn.readouts) GraphNorm (class in matcha.nn.layers) GraphPE (class in matcha.datamodules.classic.graph_positional_encoder) GraphPretrainingDataModule (class in matcha.datamodules.pretraining) (class in matcha.datamodules.pretraining.graph_pretraining_datamodule) GraphPretrainingDataModuleInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.datamodules) gru (matcha.torch.encoders.AttentiveFP attribute) (matcha.torch.encoders.attentivefp.AttentiveFP attribute) (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretrainingEncoder attribute) GRUPooling (class in matcha.nn.readouts) GT (class in matcha.torch.encoders) (class in matcha.torch.encoders.gt) GT3D (class in matcha.torch.encoders.gt3d) GT3DClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph3d) (class in matcha.sklearn.graph3d.gt3d) GT3DInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) GT3DMixin (class in matcha.utils.schemas.generic_models) GT3DModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.gt3d_model) GT3DRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph3d) (class in matcha.sklearn.graph3d.gt3d) GTClassifier (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.gt) GTConv (class in matcha.torch.encoders.gt) GTInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) GTMixin (class in matcha.utils.schemas.generic_models) GTModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.gt_model) GTPretraining (class in matcha.torch.models.pretraining) (class in matcha.torch.models.pretraining.gt_pretraining) GTPretrainingEncoder (class in matcha.torch.models.pretraining.gt_pretraining) GTRegressor (class in matcha.sklearn) (class in matcha.sklearn.graph) (class in matcha.sklearn.graph.gt)

H

HandleMissing (class in matcha.datamodules.utils) (class in matcha.utils.schemas.datamodules) has_class_labels() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method)

head_dim (matcha.nn.layers.BiasedMultiHeadAttention attribute) (matcha.torch.encoders.gt.GTConv attribute) hidden_dim (matcha.torch.encoders.gt.GTConv attribute) hidden_dims (matcha.utils.schemas.generic_models.MLPMixin attribute) (matcha.utils.schemas.generic_models.SNNMixin attribute) HPOManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.hpo_manager) HuberLoss (class in matcha.nn.losses)

I

ICPBaseInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.calibration) ICPCalibration (class in matcha.calibration.inductive_conformal) ICPClassificationCalibration (class in matcha.calibration) (class in matcha.calibration.inductive_conformal) ICPClassificationInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.calibration) ICPRegressionCalibration (class in matcha.calibration) (class in matcha.calibration.inductive_conformal) ICPRegressionInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.calibration) in_features (matcha.nn.layers.LnBnDr attribute) include_canonical (matcha.utils.schemas.cli.EncoderPretrainMLMDatamodule attribute) (matcha.utils.schemas.CLMDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CLMDataModuleInputModel attribute) index_key (matcha.utils.schemas.cli.StitcherInputModel attribute) Inference (class in matcha.utils.schemas.cli) inference (matcha.utils.schemas.cli.PredictModel attribute) init_fn (matcha.nn.layers.MultiLn attribute) init_lr (matcha.torch.models.finetuning.chemprop_finetuner.ChempropFinetuner attribute) (matcha.torch.models.finetuning.ChempropFinetuner attribute) init_virtual_nodes (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute) init_w (matcha.utils.schemas.cli.Loss attribute) initial_losses (matcha.nn.losses.GradNormLoss attribute) input (matcha.utils.schemas.cli.CLIStitcherInputModel attribute) input_dim (matcha.utils.schemas.ChempropDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.ChempropDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.TabularDataModuleInputModel attribute) (matcha.utils.schemas.TabularDataModuleInputModel attribute) inputmodels (matcha.utils.schemas.calibration.CalibratorModels attribute) (matcha.utils.schemas.datamodules.DataModuleModels attribute) (matcha.utils.schemas.label.DataModuleModels attribute) (matcha.utils.schemas.torch_api.TorchModels attribute)

InstanceNorm (class in matcha.nn.layers) inv_ln() (in module matcha.datamodules.classic.label_transform) inv_log10() (in module matcha.datamodules.classic.label_transform) inv_log10p() (in module matcha.datamodules.classic.label_transform) inv_log1p() (in module matcha.datamodules.classic.label_transform) inv_log2() (in module matcha.datamodules.classic.label_transform) inv_logk100() (in module matcha.datamodules.classic.label_transform) invert_y() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) is_active (matcha.sklearn.managers.ensemble_mlflow_manager.EnsembleMLFlowManager property) (matcha.sklearn.managers.EnsembleMLFlowManager property) (matcha.sklearn.managers.mlflow_manager.MLFlowManager property) (matcha.sklearn.managers.MLFlowManager property) is_classification (matcha.utils.schemas.datamodules.BaseDataModuleFields attribute) is_classifier (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel property) (matcha.sklearn.Ensemble property) (matcha.sklearn.ensemble.Ensemble property) is_fitted (matcha.calibration.base_calibration.BaseCalibration property) (matcha.calibration.BaseCalibration property) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel property) (matcha.sklearn.managers.training_manager.TrainingManager property) (matcha.sklearn.managers.TrainingManager property) is_set() (matcha.datamodules.BaseLabelEncoder method) (matcha.datamodules.BinaryClassificationLabelEncoder method) (matcha.datamodules.classic.BaseLabelEncoder method) (matcha.datamodules.classic.BinaryClassificationLabelEncoder method) (matcha.datamodules.classic.label_encoder.BaseLabelEncoder method) (matcha.datamodules.classic.label_encoder.BinaryClassificationLabelEncoder method)

J

jk (matcha.torch.encoders.base_graph_encoder.BaseGraphEncoder property)

K

k_proj (matcha.nn.layers.BiasedMultiHeadAttention attribute)

keep_cols (matcha.utils.schemas.cli.PredictDataset attribute)

L

L1Loss (class in matcha.nn.losses) label_encoder (matcha.datamodules.base_datamodule.BaseDataModule property) (matcha.datamodules.BaseDataModule property) label_encoder_params (matcha.utils.schemas.cli.BaselineModel attribute) (matcha.utils.schemas.datamodules.BaseDataModuleFields attribute) label_key (matcha.utils.schemas.cli.Dataset attribute) (matcha.utils.schemas.cli.PredictDataset attribute) label_keys (matcha.utils.schemas.cli.StitcherInputModel attribute) label_names (matcha.datamodules.BaseLabelEncoder property) (matcha.datamodules.classic.BaseLabelEncoder property) (matcha.datamodules.classic.label_encoder.BaseLabelEncoder property) label_transform (matcha.datamodules.base_datamodule.BaseDataModule property) (matcha.datamodules.BaseDataModule property) (matcha.utils.schemas.cli.BaselineModel attribute) label_transform_params (matcha.utils.schemas.datamodules.BaseDataModuleFields attribute) LabelEncoderModel (in module matcha.utils.schemas.label) LabelEncoderRegistry (in module matcha.datamodules) (in module matcha.datamodules.classic) (in module matcha.datamodules.classic.label_encoder) LabelTransform (class in matcha.datamodules) (class in matcha.datamodules.classic) (class in matcha.datamodules.classic.label_transform) LabelTransformInputModel (class in matcha.utils.schemas.label) lap_pe() (matcha.datamodules.classic.graph_positional_encoder.GraphPE class method) laplacian_k (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute) last_epoch (matcha.nn.schedulers.WarmupCosineAnnealingLR attribute) (matcha.nn.schedulers.WarmupLinearDecayLR attribute) latent_dim (matcha.torch.models.classic.base_classic_model.BaseClassicModel property) (matcha.torch.models.classic.BaseClassicModel property) (matcha.torch.models.finetuning.Finetuner property) (matcha.torch.models.finetuning.finetuner.Finetuner property) (matcha.torch.models.finetuning.pretrained_encoder_wrapper.PretrainedEncoderWrapper property) (matcha.torch.models.finetuning.PretrainedEncoderWrapper property) (matcha.torch.predictors.base_predictor.BasePredictor property) layer_weights (matcha.torch.encoders.CNN attribute) (matcha.torch.encoders.cnn.CNN attribute) LayerNorm (class in matcha.nn.layers) LayerRegistry (in module matcha.nn.layers) layers (matcha.nn.layers.LnBnDr attribute) (matcha.torch.encoders.AttentiveFP attribute) (matcha.torch.encoders.attentivefp.AttentiveFP attribute) (matcha.torch.encoders.CNN attribute) (matcha.torch.encoders.cnn.CNN attribute) (matcha.torch.encoders.E3GNN attribute) (matcha.torch.encoders.e3gnn.E3GNN attribute) (matcha.torch.encoders.GatedGCN attribute) (matcha.torch.encoders.gatedgcn.GatedGCN attribute) (matcha.torch.encoders.GIN attribute) (matcha.torch.encoders.gin.GIN attribute) (matcha.torch.encoders.GPS attribute) (matcha.torch.encoders.gps.GPS attribute) (matcha.torch.encoders.GPS3D attribute) (matcha.torch.encoders.gps3d.GPS3D attribute) (matcha.torch.encoders.GT attribute) (matcha.torch.encoders.gt.GT attribute) (matcha.torch.encoders.gt3d.GT3D attribute) (matcha.torch.encoders.RNN attribute) (matcha.torch.encoders.rnn.RNN attribute) (matcha.torch.encoders.RoFormer attribute) (matcha.torch.encoders.roformer.RoFormer attribute) (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretrainingEncoder attribute) (matcha.torch.models.pretraining.gatedgcn_pretraining.GatedGCNPretrainingEncoder attribute) (matcha.torch.models.pretraining.gin_pretraining.GINPretrainingEncoder attribute) (matcha.torch.models.pretraining.gps_pretraining.GPSPretrainingEncoder attribute) (matcha.torch.models.pretraining.gt_pretraining.GTPretrainingEncoder attribute) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLMEncoder attribute) LCMPooling (class in matcha.nn.readouts) LeakyReLU (class in matcha.nn.activations) learner (matcha.utils.schemas.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnEnsembleInputModel attribute) LIME (class in matcha.explainability) (class in matcha.explainability.lime) lime_descriptor_set (matcha.utils.schemas.explainability.ExplainerInputModel attribute) (matcha.utils.schemas.ExplainerInputModel attribute) lime_fingerprint_params (matcha.utils.schemas.explainability.ExplainerInputModel attribute) (matcha.utils.schemas.ExplainerInputModel attribute) lime_remove_noise (matcha.utils.schemas.explainability.ExplainerInputModel attribute) (matcha.utils.schemas.ExplainerInputModel attribute) lime_scale_coeff (matcha.utils.schemas.explainability.ExplainerInputModel attribute) (matcha.utils.schemas.ExplainerInputModel attribute) lin1 (matcha.torch.encoders.attentivefp.GATEConv attribute) lin2 (matcha.torch.encoders.attentivefp.GATEConv attribute) Linear (class in matcha.nn.schedulers) linear_layer_1 (matcha.nn.layers.SpatialEncoder3d attribute) linear_layer_2 (matcha.nn.layers.SpatialEncoder3d attribute) linear_layers (matcha.nn.layers.MultiMLP attribute) LnBnDr (class in matcha.nn.layers) load_dataset() (in module matcha.cli.utils) load_default_architecture_grid() (in module matcha.torch.tuning.routine) load_default_optimizer_grid() (in module matcha.torch.tuning.routine) load_default_scheduler_grid() (in module matcha.torch.tuning.routine) load_from_config() (matcha.sklearn.managers.ensemble_serialization_manager.EnsembleSerializationManager static method) (matcha.sklearn.managers.EnsembleSerializationManager static method) (matcha.sklearn.managers.serialization_manager.SerializationManager static method) (matcha.sklearn.managers.SerializationManager static method) load_from_folder() (matcha.sklearn.managers.ensemble_serialization_manager.EnsembleSerializationManager static method) (matcha.sklearn.managers.EnsembleSerializationManager static method) (matcha.sklearn.managers.serialization_manager.SerializationManager static method) (matcha.sklearn.managers.SerializationManager static method)

load_json() (in module matcha.utils) (in module matcha.utils.serialization) load_performance_artifacts() (matcha.cli.summarize.ExperimentSummarizer method) load_pickle() (in module matcha.utils) (in module matcha.utils.serialization) load_predictions_artifacts() (matcha.cli.summarize.ExperimentSummarizer method) load_state_dict() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.BaseLabelEncoder method) (matcha.datamodules.classic.BaseLabelEncoder method) (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule method) (matcha.datamodules.classic.clm_datamodule.CLMDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.datamodules.classic.graph_datamodule.Graph3DDataModule method) (matcha.datamodules.classic.graph_datamodule.GraphDataModule method) (matcha.datamodules.classic.label_encoder.BaseLabelEncoder method) (matcha.datamodules.classic.label_transform.LabelTransform method) (matcha.datamodules.classic.LabelTransform method) (matcha.datamodules.classic.tabular_datamodule.TabularDataModule method) (matcha.datamodules.LabelTransform method) (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule method) (matcha.datamodules.pretraining.CLMMLMDataModule method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) (matcha.nn.schedulers.ChempropSchedulerConfig method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) load_yaml() (in module matcha.utils) (in module matcha.utils.serialization) log10 (matcha.utils.schemas.calibration.EMRegressionInputModel attribute) (matcha.utils.schemas.EMRegressionInputModel attribute) log10p() (in module matcha.datamodules.classic.label_transform) log_artifact() (matcha.sklearn.managers.ensemble_mlflow_manager.EnsembleMLFlowManager method) (matcha.sklearn.managers.EnsembleMLFlowManager method) log_calibrator() (matcha.sklearn.managers.ensemble_mlflow_manager.EnsembleMLFlowManager method) (matcha.sklearn.managers.EnsembleMLFlowManager method) (matcha.sklearn.managers.mlflow_manager.MLFlowManager method) (matcha.sklearn.managers.MLFlowManager method) log_dir (matcha.utils.schemas.cli.MLFlow attribute) (matcha.utils.schemas.sklearn_api.MLFlowInputModel attribute) log_ensemble_params() (matcha.sklearn.managers.ensemble_mlflow_manager.EnsembleMLFlowManager method) (matcha.sklearn.managers.EnsembleMLFlowManager method) log_hyperparams() (matcha.utils.logging.MatchaLogger method) (matcha.utils.MatchaLogger method) log_matcha_artifacts() (matcha.utils.logging.MatchaLogger method) (matcha.utils.MatchaLogger method) log_training() (matcha.sklearn.managers.mlflow_manager.MLFlowManager method) (matcha.sklearn.managers.MLFlowManager method) logger (in module matcha.explainability.explainer) (in module matcha.explainability.lime) (in module matcha.torch.tuning.routine) (matcha.cli.summarize.ExperimentSummarizer attribute) (matcha.sklearn.managers.datamodule_manager.DataModuleManager attribute) (matcha.sklearn.managers.DataModuleManager attribute) (matcha.sklearn.managers.ensemble_calibration_manager.EnsembleCalibrationManager attribute) (matcha.sklearn.managers.ensemble_mlflow_manager.EnsembleMLFlowManager attribute) (matcha.sklearn.managers.ensemble_serialization_manager.EnsembleSerializationManager attribute) (matcha.sklearn.managers.EnsembleCalibrationManager attribute) (matcha.sklearn.managers.EnsembleMLFlowManager attribute) (matcha.sklearn.managers.EnsembleSerializationManager attribute) (matcha.sklearn.managers.explainability_manager.ExplainabilityManager attribute) (matcha.sklearn.managers.ExplainabilityManager attribute) (matcha.sklearn.managers.hpo_manager.HPOManager attribute) (matcha.sklearn.managers.HPOManager attribute) (matcha.sklearn.managers.mlflow_manager.MLFlowManager attribute) (matcha.sklearn.managers.MLFlowManager attribute) (matcha.sklearn.managers.serialization_manager.SerializationManager attribute) (matcha.sklearn.managers.SerializationManager attribute) (matcha.sklearn.managers.training_manager.TrainingManager attribute) (matcha.sklearn.managers.TrainingManager attribute) (matcha.sklearn.managers.uncertainty_manager.UncertaintyManager attribute) (matcha.sklearn.managers.UncertaintyManager attribute) lora_A (matcha.torch.models.finetuning.lora.LoRALinear attribute) (matcha.torch.models.finetuning.LoRALinear attribute) lora_alpha (matcha.utils.schemas.generic_models.FinetunerMixin attribute) lora_B (matcha.torch.models.finetuning.lora.LoRALinear attribute) (matcha.torch.models.finetuning.LoRALinear attribute) lora_min_dim (matcha.utils.schemas.generic_models.FinetunerMixin attribute) lora_rank (matcha.utils.schemas.generic_models.FinetunerMixin attribute) LoRALinear (class in matcha.torch.models.finetuning) (class in matcha.torch.models.finetuning.lora) Loss (class in matcha.utils.schemas.cli) loss (matcha.nn.losses.BoundedLoss attribute) (matcha.nn.losses.GradNormLoss attribute) (matcha.nn.losses.MultitaskLoss attribute) (matcha.utils.schemas.cli.CLIPretrainMultitaskInputModel attribute) loss_args (matcha.utils.schemas.cli.Loss attribute) (matcha.utils.schemas.generic_models.ClassicMatchaModel attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) loss_configs (matcha.nn.losses.MultiLoss attribute) loss_fn (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.cli.Loss attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.generic_models.ClassicMatchaModel attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) losses (matcha.nn.losses.MultiLoss attribute) LossRegistry (in module matcha.nn.losses) LSTMPooling (class in matcha.nn.readouts)

M

m_dim (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) magic (matcha.utils.schemas.cli.CLIAutotuneOutput attribute) (matcha.utils.schemas.cli.CLIBaselineInputModel attribute) (matcha.utils.schemas.cli.CLIEncoderPretrainInputModel attribute) (matcha.utils.schemas.cli.CLIEvaluationInputModel attribute) (matcha.utils.schemas.cli.CLIPredictInputModel attribute) (matcha.utils.schemas.cli.CLIPrepareInputModel attribute) (matcha.utils.schemas.cli.CLIPretrainMultitaskInputModel attribute) (matcha.utils.schemas.cli.CLIStitcherInputModel attribute) (matcha.utils.schemas.cli.CLISummarizeInputModel attribute) (matcha.utils.schemas.cli.CLITrainInputModel attribute) main() (in module matcha.cli) (in module matcha.cli.autotune) (in module matcha.cli.baseline) (in module matcha.cli.evaluate) (in module matcha.cli.predict) (in module matcha.cli.prepare_sparse_dataset) (in module matcha.cli.pretrain_encoder) (in module matcha.cli.pretrain_multitask) (in module matcha.cli.stitch) (in module matcha.cli.summarize) (in module matcha.cli.train) mapping (matcha.datamodules.classic.label_transform.BackwardTransformRegistry attribute) (matcha.datamodules.classic.label_transform.ForwardTransformRegistry attribute) mask_rate (matcha.utils.schemas.cli.EncoderPretrainMLMDatamodule attribute) (matcha.utils.schemas.datamodules.CLMMLMDataModuleInputModel attribute) matcha module matcha.calibration module matcha.calibration.base_calibration module matcha.calibration.error_model module matcha.calibration.inductive_conformal module matcha.cli module matcha.cli.autotune module matcha.cli.baseline module matcha.cli.evaluate module matcha.cli.predict module matcha.cli.prepare_sparse_dataset module matcha.cli.pretrain_encoder module matcha.cli.pretrain_multitask module matcha.cli.statistical_tests module matcha.cli.stitch module matcha.cli.summarize module matcha.cli.train module matcha.cli.utils module matcha.datamodules module matcha.datamodules.base_datamodule module matcha.datamodules.classic module matcha.datamodules.classic.chemprop_datamodule module matcha.datamodules.classic.clm_datamodule module matcha.datamodules.classic.combined_datamodule module matcha.datamodules.classic.graph_datamodule module matcha.datamodules.classic.graph_positional_encoder module matcha.datamodules.classic.label_encoder module matcha.datamodules.classic.label_transform module matcha.datamodules.classic.rdkit_engine module matcha.datamodules.classic.tabular_datamodule module matcha.datamodules.pretraining module matcha.datamodules.pretraining.clm_mlm_datamodule module matcha.datamodules.pretraining.graph_pretraining_datamodule module matcha.datamodules.pretraining.on_the_fly_datamodule module matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule module matcha.datamodules.pretraining.on_the_fly_mlm_datamodule module matcha.datamodules.utils module matcha.explainability module matcha.explainability.analogue_generator module matcha.explainability.explainer module matcha.explainability.lime module matcha.nn module matcha.nn.activations module matcha.nn.deep_lasso module matcha.nn.layers module matcha.nn.losses module matcha.nn.multitask module matcha.nn.optimizers module matcha.nn.readouts module matcha.nn.schedulers module matcha.sklearn module matcha.sklearn.autoload module matcha.sklearn.base_sklearn_model module matcha.sklearn.clm module matcha.sklearn.clm.base_sklearn_clm module matcha.sklearn.clm.cnn module matcha.sklearn.clm.rnn module matcha.sklearn.clm.roformer module matcha.sklearn.ensemble module matcha.sklearn.finetuner module matcha.sklearn.graph module matcha.sklearn.graph.attentive_fp module matcha.sklearn.graph.base_sklearn_gnn module matcha.sklearn.graph.chemprop module matcha.sklearn.graph.gatedgcn module matcha.sklearn.graph.gin module matcha.sklearn.graph.gps module matcha.sklearn.graph.gt module matcha.sklearn.graph3d module matcha.sklearn.graph3d.base_sklearn_gnn3d module matcha.sklearn.graph3d.e3gnn module matcha.sklearn.graph3d.gps3d module matcha.sklearn.graph3d.gt3d module matcha.sklearn.managers module matcha.sklearn.managers.datamodule_manager module matcha.sklearn.managers.ensemble_calibration_manager module matcha.sklearn.managers.ensemble_mlflow_manager module matcha.sklearn.managers.ensemble_serialization_manager module matcha.sklearn.managers.explainability_manager module matcha.sklearn.managers.hpo_manager module matcha.sklearn.managers.mlflow_manager module matcha.sklearn.managers.serialization_manager module matcha.sklearn.managers.training_manager module matcha.sklearn.managers.uncertainty_manager module matcha.sklearn.tabular module matcha.sklearn.tabular.base_sklearn_tabular module matcha.sklearn.tabular.mlp module matcha.sklearn.tabular.snn module matcha.sklearn.utils module matcha.torch module matcha.torch.encoders module matcha.torch.encoders.attentivefp module matcha.torch.encoders.base_encoder module matcha.torch.encoders.base_graph_encoder module matcha.torch.encoders.cnn module matcha.torch.encoders.e3gnn module matcha.torch.encoders.gatedgcn module matcha.torch.encoders.gin module matcha.torch.encoders.gps module matcha.torch.encoders.gps3d module matcha.torch.encoders.gt module matcha.torch.encoders.gt3d module matcha.torch.encoders.rnn module matcha.torch.encoders.roformer module matcha.torch.models module matcha.torch.models.classic module matcha.torch.models.classic.attentivefp_model module matcha.torch.models.classic.base_classic_model module matcha.torch.models.classic.chemprop_model module matcha.torch.models.classic.cnn_model module matcha.torch.models.classic.e3gnn_model module matcha.torch.models.classic.gatedcgn_model module matcha.torch.models.classic.gin_model module matcha.torch.models.classic.gps3d_model module matcha.torch.models.classic.gps_model module matcha.torch.models.classic.gt3d_model module matcha.torch.models.classic.gt_model module matcha.torch.models.classic.mlp_model module matcha.torch.models.classic.rnn_model module matcha.torch.models.classic.roformer_model module matcha.torch.models.classic.snn_model module matcha.torch.models.finetuning module matcha.torch.models.finetuning.chemprop_finetuner module matcha.torch.models.finetuning.finetuner module matcha.torch.models.finetuning.lora module matcha.torch.models.finetuning.pretrained_encoder_wrapper module matcha.torch.models.mixin module matcha.torch.models.pretraining module matcha.torch.models.pretraining.attentivefp_pretraining module matcha.torch.models.pretraining.base_graph_pretraining module matcha.torch.models.pretraining.base_pretraining_model module matcha.torch.models.pretraining.gatedgcn_pretraining module matcha.torch.models.pretraining.gin_pretraining module matcha.torch.models.pretraining.gps_pretraining module matcha.torch.models.pretraining.gt_pretraining module matcha.torch.models.pretraining.roformer_mlm module matcha.torch.predictors module matcha.torch.predictors.base_predictor module matcha.torch.predictors.mlp module matcha.torch.predictors.snn module matcha.torch.tuning module matcha.torch.tuning.routine module matcha.utils module matcha.utils.logging module matcha.utils.metrics module matcha.utils.plotting module matcha.utils.registry module matcha.utils.sanitize module matcha.utils.schemas module matcha.utils.schemas.base module matcha.utils.schemas.calibration module

matcha.utils.schemas.cli module matcha.utils.schemas.data module matcha.utils.schemas.datamodules module matcha.utils.schemas.explainability module matcha.utils.schemas.generic_models module matcha.utils.schemas.label module matcha.utils.schemas.sklearn_api module matcha.utils.schemas.torch_api module matcha.utils.serialization module matcha.utils.splitting module matcha.utils.warnings module matcha.utils.wrapper module matcha_version (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) MatchaExplainer (class in matcha.explainability) (class in matcha.explainability.explainer) MatchaExplanation (class in matcha.explainability) (class in matcha.explainability.explainer) MatchaLogger (class in matcha.utils) (class in matcha.utils.logging) max_dist (matcha.nn.layers.SpatialEncoder attribute) max_length (matcha.utils.schemas.cli.EncoderPretrainMLMDatamodule attribute) (matcha.utils.schemas.CLMDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CLMDataModuleInputModel attribute) max_lr (matcha.nn.schedulers.ChempropSchedulerConfig attribute) (matcha.torch.models.finetuning.chemprop_finetuner.ChempropFinetuner attribute) (matcha.torch.models.finetuning.ChempropFinetuner attribute) MaxPooling (class in matcha.nn.readouts) mc_dropout_flag (matcha.torch.models.mixin.ModelMixin property) MeanPooling (class in matcha.nn.readouts) means (matcha.nn.layers.SpatialEncoder3d attribute) MedianPooling (class in matcha.nn.readouts) merge_col (matcha.utils.schemas.cli.PrepareMetadata attribute) merge_datasets_streaming_sparse() (in module matcha.cli.prepare_sparse_dataset) merge_fn (matcha.datamodules.CombinedStackDataset attribute) (matcha.datamodules.utils.CombinedStackDataset attribute) (matcha.utils.schemas.CombinedDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CombinedDataModuleInputModel attribute) message() (matcha.torch.encoders.attentivefp.GATEConv method) (matcha.torch.encoders.e3gnn.EGNN_Sparse method) (matcha.torch.encoders.gatedgcn.GatedGCNConv method) Metadata (class in matcha.utils.schemas.cli) metadata (matcha.utils.schemas.cli.CLIPrepareInputModel attribute) (matcha.utils.schemas.cli.Model attribute) (matcha.utils.schemas.cli.ModelEvaluation attribute) (matcha.utils.schemas.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.ScikitLearnInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnInputModel attribute) MetadataInputModel (class in matcha.utils.schemas.sklearn_api) method (matcha.utils.schemas.cli.Split attribute) (matcha.utils.Wrapper property) (matcha.utils.wrapper.Wrapper property) method_name (matcha.utils.Wrapper attribute) (matcha.utils.wrapper.Wrapper attribute) method_params (matcha.utils.schemas.cli.Split attribute) min_compounds (matcha.utils.schemas.calibration.EMBaseInputModel attribute) (matcha.utils.schemas.cli.PrepareValidation attribute) (matcha.utils.schemas.EMBaseInputModel attribute) min_lr (matcha.nn.schedulers.WarmupCosineAnnealingLR attribute) (matcha.nn.schedulers.WarmupLinearDecayLR attribute) MinPooling (class in matcha.nn.readouts) Mish (class in matcha.nn.activations) MLFlow (class in matcha.utils.schemas.cli) mlflow (matcha.utils.schemas.cli.Output attribute) (matcha.utils.schemas.cli.PretrainOutput attribute) (matcha.utils.schemas.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.ScikitLearnInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnInputModel attribute) MLflowExperimentSummarizer (class in matcha.cli.summarize) MLFlowInputModel (class in matcha.utils.schemas.sklearn_api) MLFlowManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.mlflow_manager) MLP (class in matcha.torch.predictors) (class in matcha.torch.predictors.mlp) mlp (matcha.torch.encoders.gps.GPSBlock attribute) MLPClassifier (class in matcha.sklearn) (class in matcha.sklearn.tabular) (class in matcha.sklearn.tabular.mlp) MLPInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) MLPMixin (class in matcha.utils.schemas.generic_models) MLPModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.mlp_model) MLPPooling (class in matcha.nn.readouts) MLPRegressor (class in matcha.sklearn) (class in matcha.sklearn.tabular) (class in matcha.sklearn.tabular.mlp) mlruns_path (matcha.cli.summarize.MLflowExperimentSummarizer attribute) (matcha.utils.schemas.cli.CLISummarizeInputModel attribute) Model (class in matcha.utils.schemas.cli) model (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel property) (matcha.torch.encoders.RoFormer attribute) (matcha.torch.encoders.roformer.RoFormer attribute) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLMEncoder attribute) (matcha.utils.schemas.cli.CLIAutotuneOutput attribute) (matcha.utils.schemas.cli.CLIBaselineInputModel attribute) (matcha.utils.schemas.cli.CLIEncoderPretrainInputModel attribute) (matcha.utils.schemas.cli.CLIEvaluationInputModel attribute) (matcha.utils.schemas.cli.CLIPredictInputModel attribute) (matcha.utils.schemas.cli.CLIPretrainMultitaskInputModel attribute) (matcha.utils.schemas.cli.CLITrainInputModel attribute) (matcha.utils.schemas.ScikitLearnInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnInputModel attribute) model_box (matcha.calibration.EMCalibration attribute) (matcha.calibration.error_model.EMCalibration attribute) (matcha.sklearn.Ensemble property) (matcha.sklearn.ensemble.Ensemble property) model_config (matcha.torch.encoders.RoFormer attribute) (matcha.torch.encoders.roformer.RoFormer attribute) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLMEncoder attribute) (matcha.utils.schemas.base.BaseDataModel attribute) (matcha.utils.schemas.CombinedDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CombinedDataModuleInputModel attribute) model_name (matcha.utils.schemas.cli.Metadata attribute) (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) model_owner (matcha.utils.schemas.cli.Metadata attribute) (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) model_registry (in module matcha.cli.baseline) model_scope (matcha.utils.schemas.cli.Metadata attribute) (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) model_type (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) model_version (matcha.utils.schemas.cli.Metadata attribute) (matcha.utils.schemas.sklearn_api.MetadataInputModel attribute) ModelEvaluation (class in matcha.utils.schemas.cli) ModelMixin (class in matcha.torch.models.mixin) module matcha matcha.calibration matcha.calibration.base_calibration matcha.calibration.error_model matcha.calibration.inductive_conformal matcha.cli matcha.cli.autotune matcha.cli.baseline matcha.cli.evaluate matcha.cli.predict matcha.cli.prepare_sparse_dataset matcha.cli.pretrain_encoder matcha.cli.pretrain_multitask matcha.cli.statistical_tests matcha.cli.stitch matcha.cli.summarize matcha.cli.train matcha.cli.utils matcha.datamodules matcha.datamodules.base_datamodule matcha.datamodules.classic matcha.datamodules.classic.chemprop_datamodule matcha.datamodules.classic.clm_datamodule matcha.datamodules.classic.combined_datamodule matcha.datamodules.classic.graph_datamodule matcha.datamodules.classic.graph_positional_encoder matcha.datamodules.classic.label_encoder matcha.datamodules.classic.label_transform matcha.datamodules.classic.rdkit_engine matcha.datamodules.classic.tabular_datamodule matcha.datamodules.pretraining matcha.datamodules.pretraining.clm_mlm_datamodule matcha.datamodules.pretraining.graph_pretraining_datamodule matcha.datamodules.pretraining.on_the_fly_datamodule matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule matcha.datamodules.pretraining.on_the_fly_mlm_datamodule matcha.datamodules.utils matcha.explainability matcha.explainability.analogue_generator matcha.explainability.explainer matcha.explainability.lime matcha.nn matcha.nn.activations matcha.nn.deep_lasso matcha.nn.layers matcha.nn.losses matcha.nn.multitask matcha.nn.optimizers matcha.nn.readouts matcha.nn.schedulers matcha.sklearn matcha.sklearn.autoload matcha.sklearn.base_sklearn_model matcha.sklearn.clm matcha.sklearn.clm.base_sklearn_clm matcha.sklearn.clm.cnn matcha.sklearn.clm.rnn matcha.sklearn.clm.roformer matcha.sklearn.ensemble matcha.sklearn.finetuner matcha.sklearn.graph matcha.sklearn.graph.attentive_fp matcha.sklearn.graph.base_sklearn_gnn matcha.sklearn.graph.chemprop matcha.sklearn.graph.gatedgcn matcha.sklearn.graph.gin matcha.sklearn.graph.gps matcha.sklearn.graph.gt matcha.sklearn.graph3d matcha.sklearn.graph3d.base_sklearn_gnn3d matcha.sklearn.graph3d.e3gnn matcha.sklearn.graph3d.gps3d matcha.sklearn.graph3d.gt3d matcha.sklearn.managers matcha.sklearn.managers.datamodule_manager matcha.sklearn.managers.ensemble_calibration_manager matcha.sklearn.managers.ensemble_mlflow_manager matcha.sklearn.managers.ensemble_serialization_manager matcha.sklearn.managers.explainability_manager matcha.sklearn.managers.hpo_manager matcha.sklearn.managers.mlflow_manager matcha.sklearn.managers.serialization_manager matcha.sklearn.managers.training_manager matcha.sklearn.managers.uncertainty_manager matcha.sklearn.tabular matcha.sklearn.tabular.base_sklearn_tabular matcha.sklearn.tabular.mlp matcha.sklearn.tabular.snn matcha.sklearn.utils matcha.torch matcha.torch.encoders matcha.torch.encoders.attentivefp matcha.torch.encoders.base_encoder matcha.torch.encoders.base_graph_encoder matcha.torch.encoders.cnn matcha.torch.encoders.e3gnn matcha.torch.encoders.gatedgcn matcha.torch.encoders.gin matcha.torch.encoders.gps matcha.torch.encoders.gps3d matcha.torch.encoders.gt matcha.torch.encoders.gt3d matcha.torch.encoders.rnn matcha.torch.encoders.roformer matcha.torch.models matcha.torch.models.classic matcha.torch.models.classic.attentivefp_model matcha.torch.models.classic.base_classic_model matcha.torch.models.classic.chemprop_model matcha.torch.models.classic.cnn_model matcha.torch.models.classic.e3gnn_model matcha.torch.models.classic.gatedcgn_model matcha.torch.models.classic.gin_model matcha.torch.models.classic.gps3d_model matcha.torch.models.classic.gps_model matcha.torch.models.classic.gt3d_model matcha.torch.models.classic.gt_model matcha.torch.models.classic.mlp_model matcha.torch.models.classic.rnn_model matcha.torch.models.classic.roformer_model matcha.torch.models.classic.snn_model matcha.torch.models.finetuning matcha.torch.models.finetuning.chemprop_finetuner matcha.torch.models.finetuning.finetuner matcha.torch.models.finetuning.lora matcha.torch.models.finetuning.pretrained_encoder_wrapper matcha.torch.models.mixin matcha.torch.models.pretraining matcha.torch.models.pretraining.attentivefp_pretraining matcha.torch.models.pretraining.base_graph_pretraining matcha.torch.models.pretraining.base_pretraining_model matcha.torch.models.pretraining.gatedgcn_pretraining matcha.torch.models.pretraining.gin_pretraining matcha.torch.models.pretraining.gps_pretraining matcha.torch.models.pretraining.gt_pretraining matcha.torch.models.pretraining.roformer_mlm matcha.torch.predictors matcha.torch.predictors.base_predictor matcha.torch.predictors.mlp matcha.torch.predictors.snn matcha.torch.tuning matcha.torch.tuning.routine matcha.utils matcha.utils.logging matcha.utils.metrics matcha.utils.plotting matcha.utils.registry matcha.utils.sanitize matcha.utils.schemas matcha.utils.schemas.base matcha.utils.schemas.calibration matcha.utils.schemas.cli matcha.utils.schemas.data matcha.utils.schemas.datamodules matcha.utils.schemas.explainability matcha.utils.schemas.generic_models matcha.utils.schemas.label matcha.utils.schemas.sklearn_api matcha.utils.schemas.torch_api matcha.utils.serialization matcha.utils.splitting matcha.utils.warnings matcha.utils.wrapper module (matcha.utils.Wrapper attribute) (matcha.utils.wrapper.Wrapper attribute) mol (matcha.utils.schemas.data.MolReadout attribute) (matcha.utils.schemas.MolReadout attribute) MolDataset (class in matcha.utils.schemas) (class in matcha.utils.schemas.data) MolReadout (class in matcha.utils.schemas) (class in matcha.utils.schemas.data) mols (matcha.utils.schemas.data.MolDataset attribute) (matcha.utils.schemas.MolDataset attribute) momentum (matcha.nn.layers.MultiBatchNorm attribute) mp (matcha.torch.encoders.gps.GPSBlock attribute) MPNNInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) MPNNMixin (class in matcha.utils.schemas.generic_models) MPNNPlusConv (class in matcha.torch.encoders.gps) MSELoss (class in matcha.nn.losses) MulPooling (class in matcha.nn.readouts) MultiBatchNorm (class in matcha.nn.layers) MultiLn (class in matcha.nn.layers) MultiLoss (class in matcha.nn.losses) MultiMLP (class in matcha.nn.layers) MultiPooling (class in matcha.nn.readouts) MultitaskLoss (class in matcha.nn.losses) MultitaskPretrainDataset (class in matcha.utils.schemas.cli)

N

n_bootstrap (matcha.utils.schemas.cli.Split attribute) n_compounds (matcha.calibration.EMCalibration attribute) (matcha.calibration.error_model.EMCalibration attribute) n_jobs (matcha.datamodules.classic.Engine property) (matcha.datamodules.classic.rdkit_engine.Engine property) (matcha.datamodules.Engine property) (matcha.utils.schemas.cli.BaselineModel attribute) n_models (matcha.utils.schemas.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnEnsembleInputModel attribute) n_subset (matcha.utils.schemas.cli.Split attribute) nitrogen_walk() (matcha.explainability.analogue_generator.AnalogueGenerator class method) (matcha.explainability.AnalogueGenerator class method) nitrogen_walk_params (matcha.utils.schemas.explainability.ExplainerInputModel attribute) (matcha.utils.schemas.ExplainerInputModel attribute) no_scale() (in module matcha.datamodules.classic.label_transform) node_head (matcha.torch.models.pretraining.attentivefp_pretraining.AttentiveFPPretraining attribute) (matcha.torch.models.pretraining.AttentiveFPPretraining attribute) (matcha.torch.models.pretraining.gatedgcn_pretraining.GatedGCNPretraining attribute) (matcha.torch.models.pretraining.GatedGCNPretraining attribute) (matcha.torch.models.pretraining.gin_pretraining.GINPretraining attribute) (matcha.torch.models.pretraining.GINPretraining attribute) (matcha.torch.models.pretraining.gps_pretraining.GPSPretraining attribute) (matcha.torch.models.pretraining.GPSPretraining attribute) (matcha.torch.models.pretraining.gt_pretraining.GTPretraining attribute) (matcha.torch.models.pretraining.GTPretraining attribute) node_in_dim (matcha.torch.encoders.gt.GTConv attribute) node_mlp (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) node_model (matcha.torch.encoders.gps.MPNNPlusConv attribute) node_norm (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) NonParametricComparison (class in matcha.cli.statistical_tests) norm1 (matcha.torch.encoders.gt.GTConv attribute) norm1_global (matcha.torch.encoders.gps.GPSBlock attribute) norm1_local (matcha.torch.encoders.gps.GPSBlock attribute) norm2 (matcha.torch.encoders.gps.GPSBlock attribute) (matcha.torch.encoders.gt.GTConv attribute) norm_coors (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) norm_feats (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) norm_in (matcha.torch.encoders.RNN attribute) (matcha.torch.encoders.rnn.RNN attribute) norm_layers (matcha.nn.layers.MultiMLP attribute) norm_ln() (in module matcha.datamodules.classic.label_transform) norm_log10() (in module matcha.datamodules.classic.label_transform) norm_log1p() (in module matcha.datamodules.classic.label_transform) norm_log2() (in module matcha.datamodules.classic.label_transform) norm_logk100() (in module matcha.datamodules.classic.label_transform) norm_out (matcha.torch.encoders.RNN attribute) (matcha.torch.encoders.rnn.RNN attribute) norm_type (matcha.torch.encoders.GatedGCN attribute) (matcha.torch.encoders.gatedgcn.GatedGCN attribute) (matcha.torch.encoders.gatedgcn.GatedGCNConv attribute) (matcha.torch.encoders.GIN attribute) (matcha.torch.encoders.gin.GIN attribute) (matcha.torch.models.pretraining.gatedgcn_pretraining.GatedGCNPretrainingEncoder attribute) (matcha.torch.models.pretraining.gin_pretraining.GINPretrainingEncoder attribute)

norms (matcha.torch.encoders.GIN attribute) (matcha.torch.encoders.gin.GIN attribute) (matcha.torch.models.pretraining.gin_pretraining.GINPretrainingEncoder attribute) num_augmentations (matcha.utils.schemas.cli.EncoderPretrainMLMDatamodule attribute) (matcha.utils.schemas.CLMDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CLMDataModuleInputModel attribute) num_classes (matcha.utils.schemas.label.BaseEncoderInputModel attribute) num_endpoints (matcha.nn.losses.GradNormLoss attribute) (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.generic_models.ClassicMatchaModel attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) num_epochs (matcha.nn.multitask.TaskAffinityResult attribute) (matcha.utils.schemas.cli.PretrainTraining attribute) (matcha.utils.schemas.sklearn_api.TrainingInputModel attribute) num_features (matcha.nn.layers.MultiBatchNorm attribute) num_graph_targets (matcha.torch.models.pretraining.base_graph_pretraining.BaseGraphPretrainingModel property) (matcha.torch.models.pretraining.BaseGraphPretrainingModel property) num_heads (matcha.nn.layers.BiasedMultiHeadAttention attribute) (matcha.nn.layers.SpatialEncoder attribute) (matcha.nn.layers.SpatialEncoder3d attribute) (matcha.torch.encoders.GT attribute) (matcha.torch.encoders.gt.GT attribute) (matcha.torch.encoders.gt.GTConv attribute) (matcha.torch.encoders.gt3d.GT3D attribute) (matcha.torch.models.pretraining.gt_pretraining.GTPretrainingEncoder attribute) num_kernels (matcha.nn.layers.SpatialEncoder3d attribute) num_layers (matcha.nn.layers.MultiMLP attribute) num_node_targets (matcha.torch.models.pretraining.base_graph_pretraining.BaseGraphPretrainingModel property) (matcha.torch.models.pretraining.BaseGraphPretrainingModel property) num_parallel (matcha.nn.layers.MultiBatchNorm attribute) (matcha.torch.predictors.SNN attribute) (matcha.torch.predictors.snn.SNN attribute) (matcha.utils.schemas.generic_models.SNNMixin attribute) num_test_augmentations (matcha.utils.schemas.cli.EncoderPretrainMLMDatamodule attribute) (matcha.utils.schemas.CLMDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CLMDataModuleInputModel attribute) num_tokens (matcha.utils.schemas.CLMDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.CLMDataModuleInputModel attribute) num_virtual_nodes (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute) num_workers (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule attribute) (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.cli.EncoderPretrainMLMDatamodule attribute) (matcha.utils.schemas.datamodules.BaseDataModuleFields attribute)

O

omnibus_method (matcha.cli.statistical_tests.BootstrapComparison attribute) (matcha.cli.statistical_tests.NonParametricComparison attribute) (matcha.cli.statistical_tests.ParametricComparison attribute) omnibus_name (matcha.cli.statistical_tests.BootstrapComparison attribute) (matcha.cli.statistical_tests.NonParametricComparison attribute) (matcha.cli.statistical_tests.ParametricComparison attribute) OneCycleLR (class in matcha.nn.schedulers) OnTheFlyDataModule (class in matcha.datamodules.pretraining) (class in matcha.datamodules.pretraining.on_the_fly_datamodule) OnTheFlyDataset (class in matcha.datamodules.pretraining) (class in matcha.datamodules.pretraining.on_the_fly_datamodule) OnTheFlyGraphPretrainingDataModule (class in matcha.datamodules.pretraining) (class in matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule) OnTheFlyGraphPretrainingDataset (class in matcha.datamodules.pretraining) (class in matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule) OnTheFlyMLMDataModule (class in matcha.datamodules.pretraining) (class in matcha.datamodules.pretraining.on_the_fly_mlm_datamodule) OnTheFlyMLMDataset (class in matcha.datamodules.pretraining) (class in matcha.datamodules.pretraining.on_the_fly_mlm_datamodule) operator_key (matcha.utils.schemas.cli.Dataset attribute) (matcha.utils.schemas.cli.StitcherInputModel attribute) optimizer (matcha.nn.schedulers.WarmupCosineAnnealingLR attribute) (matcha.nn.schedulers.WarmupLinearDecayLR attribute) (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.generic_models.ClassicMatchaModel attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute)

optimizer_args (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.generic_models.ClassicMatchaModel attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) optimizer_grid (matcha.utils.schemas.sklearn_api.TuningInputModel attribute) optimizer_search (matcha.utils.schemas.cli.Tuning attribute) optimizer_search_budget (matcha.utils.schemas.sklearn_api.TuningInputModel attribute) OptimizerRegistry (in module matcha.nn.optimizers) optimum (matcha.utils.schemas.cli.AutotuneOutput attribute) original_linear (matcha.torch.models.finetuning.lora.LoRALinear attribute) (matcha.torch.models.finetuning.LoRALinear attribute) out_features (matcha.nn.layers.LnBnDr attribute) out_proj (matcha.nn.layers.BiasedMultiHeadAttention attribute) Output (class in matcha.utils.schemas.cli) output (matcha.utils.schemas.cli.CLIAutotuneOutput attribute) (matcha.utils.schemas.cli.CLIBaselineInputModel attribute) (matcha.utils.schemas.cli.CLIEncoderPretrainInputModel attribute) (matcha.utils.schemas.cli.CLIEvaluationInputModel attribute) (matcha.utils.schemas.cli.CLIPredictInputModel attribute) (matcha.utils.schemas.cli.CLIPrepareInputModel attribute) (matcha.utils.schemas.cli.CLIPretrainMultitaskInputModel attribute) (matcha.utils.schemas.cli.CLIStitcherInputModel attribute) (matcha.utils.schemas.cli.CLITrainInputModel attribute) output_path (matcha.cli.summarize.DirectoryExperimentSummarizer attribute) (matcha.utils.schemas.cli.CLISummarizeInputModel attribute)

P

pairwise_method (matcha.cli.statistical_tests.BootstrapComparison attribute) (matcha.cli.statistical_tests.NonParametricComparison attribute) (matcha.cli.statistical_tests.ParametricComparison attribute) parallelize() (in module matcha.utils.wrapper) ParametricComparison (class in matcha.cli.statistical_tests) params (matcha.calibration.EMClassificationCalibration attribute) (matcha.calibration.EMRegressionCalibration attribute) (matcha.calibration.error_model.EMClassificationCalibration attribute) (matcha.calibration.error_model.EMRegressionCalibration attribute) (matcha.calibration.ICPClassificationCalibration attribute) (matcha.calibration.ICPRegressionCalibration attribute) (matcha.calibration.inductive_conformal.ICPClassificationCalibration attribute) (matcha.calibration.inductive_conformal.ICPRegressionCalibration attribute) (matcha.datamodules.BinaryClassificationLabelEncoder attribute) (matcha.datamodules.classic.BinaryClassificationLabelEncoder attribute) (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule attribute) (matcha.datamodules.classic.clm_datamodule.CLMDataModule attribute) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule attribute) (matcha.datamodules.classic.graph_datamodule.Graph3DDataModule attribute) (matcha.datamodules.classic.graph_datamodule.GraphDataModule attribute) (matcha.datamodules.classic.label_encoder.BinaryClassificationLabelEncoder attribute) (matcha.datamodules.classic.label_encoder.RegressionLabelEncoder attribute) (matcha.datamodules.classic.label_transform.LabelTransform attribute) (matcha.datamodules.classic.LabelTransform attribute) (matcha.datamodules.classic.RegressionLabelEncoder attribute) (matcha.datamodules.classic.tabular_datamodule.TabularDataModule attribute) (matcha.datamodules.LabelTransform attribute) (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule attribute) (matcha.datamodules.pretraining.CLMMLMDataModule attribute) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule attribute) (matcha.datamodules.pretraining.GraphPretrainingDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule attribute) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule attribute) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule attribute) (matcha.datamodules.RegressionLabelEncoder attribute) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel property) (matcha.sklearn.Ensemble attribute) (matcha.sklearn.ensemble.Ensemble attribute) (matcha.sklearn.managers.datamodule_manager.DataModuleManager property) (matcha.sklearn.managers.DataModuleManager property) (matcha.sklearn.managers.ensemble_calibration_manager.EnsembleCalibrationManager property) (matcha.sklearn.managers.ensemble_mlflow_manager.EnsembleMLFlowManager attribute) (matcha.sklearn.managers.EnsembleCalibrationManager property) (matcha.sklearn.managers.EnsembleMLFlowManager attribute) (matcha.sklearn.managers.hpo_manager.HPOManager property) (matcha.sklearn.managers.HPOManager property) (matcha.sklearn.managers.mlflow_manager.MLFlowManager attribute) (matcha.sklearn.managers.MLFlowManager attribute) (matcha.sklearn.managers.training_manager.TrainingManager property) (matcha.sklearn.managers.TrainingManager property) (matcha.sklearn.managers.uncertainty_manager.UncertaintyManager property) (matcha.sklearn.managers.UncertaintyManager property) (matcha.torch.models.classic.attentivefp_model.AttentiveFPModel attribute) (matcha.torch.models.classic.AttentiveFPModel attribute) (matcha.torch.models.classic.chemprop_model.ChempropModel attribute) (matcha.torch.models.classic.ChempropModel attribute) (matcha.torch.models.classic.cnn_model.CNNModel attribute) (matcha.torch.models.classic.CNNModel attribute) (matcha.torch.models.classic.e3gnn_model.E3GNNModel attribute) (matcha.torch.models.classic.E3GNNModel attribute) (matcha.torch.models.classic.gatedcgn_model.GatedGCNModel attribute) (matcha.torch.models.classic.GatedGCNModel attribute) (matcha.torch.models.classic.gin_model.GINModel attribute) (matcha.torch.models.classic.GINModel attribute) (matcha.torch.models.classic.gps3d_model.GPS3DModel attribute) (matcha.torch.models.classic.GPS3DModel attribute) (matcha.torch.models.classic.gps_model.GPSModel attribute) (matcha.torch.models.classic.GPSModel attribute) (matcha.torch.models.classic.gt3d_model.GT3DModel attribute) (matcha.torch.models.classic.GT3DModel attribute) (matcha.torch.models.classic.gt_model.GTModel attribute) (matcha.torch.models.classic.GTModel attribute) (matcha.torch.models.classic.mlp_model.MLPModel attribute) (matcha.torch.models.classic.MLPModel attribute) (matcha.torch.models.classic.rnn_model.RNNModel attribute) (matcha.torch.models.classic.RNNModel attribute) (matcha.torch.models.classic.roformer_model.RoFormerModel attribute) (matcha.torch.models.classic.RoFormerModel attribute) (matcha.torch.models.classic.snn_model.SNNModel attribute) (matcha.torch.models.classic.SNNModel attribute) (matcha.torch.models.finetuning.chemprop_finetuner.ChempropFinetuner attribute) (matcha.torch.models.finetuning.ChempropFinetuner attribute) (matcha.torch.models.finetuning.Finetuner attribute) (matcha.torch.models.finetuning.finetuner.Finetuner attribute) (matcha.utils.schemas.cli.BaselineModel attribute) (matcha.utils.schemas.cli.CalibrationModelSettings attribute) (matcha.utils.schemas.cli.EncoderPretrainModel attribute) (matcha.utils.schemas.cli.Model attribute) (matcha.utils.schemas.cli.PretrainMultitaskModel attribute) parse_betas() (in module matcha.torch.tuning.routine) parse_config() (in module matcha.torch.tuning.routine) parse_df() (in module matcha.utils.serialization) parse_num_heads() (in module matcha.torch.tuning.routine) parse_output() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) parse_params() (in module matcha.sklearn.utils) path (matcha.utils.schemas.cli.AutotuneOptimum attribute) (matcha.utils.schemas.cli.Dataset attribute) (matcha.utils.schemas.cli.PredictModel attribute) (matcha.utils.schemas.cli.Serialization attribute) path_to_pretrained (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) patience (matcha.utils.schemas.cli.PretrainTraining attribute) (matcha.utils.schemas.sklearn_api.TrainingInputModel attribute) peak_lr_factor (matcha.nn.schedulers.WarmupCosineAnnealingLR attribute) (matcha.nn.schedulers.WarmupLinearDecayLR attribute) Pipe (in module matcha.utils.schemas.cli) pipe (matcha.utils.schemas.cli.CLIEncoderPretrainInputModel attribute) (matcha.utils.schemas.cli.CLIPretrainMultitaskInputModel attribute)

plot_affinity_matrix() (matcha.nn.multitask.TaskAffinityResult method) plot_classification() (in module matcha.utils.plotting) plot_coefficients() (matcha.explainability.explainer.MatchaExplanation method) (matcha.explainability.MatchaExplanation method) plot_heatmap() (matcha.explainability.explainer.MatchaExplanation method) (matcha.explainability.MatchaExplanation method) plot_regression() (in module matcha.utils.plotting) Poly1BCELoss (class in matcha.nn.losses) positional_analogue_scanning() (matcha.explainability.analogue_generator.AnalogueGenerator class method) (matcha.explainability.AnalogueGenerator class method) positional_analogue_scanning_params (matcha.utils.schemas.explainability.ExplainerInputModel attribute) (matcha.utils.schemas.ExplainerInputModel attribute) post_norm (matcha.torch.encoders.CNN attribute) (matcha.torch.encoders.cnn.CNN attribute) PowerMeanPooling (class in matcha.nn.readouts) pre_norm (matcha.torch.encoders.CNN attribute) (matcha.torch.encoders.cnn.CNN attribute) pred_activation (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.generic_models.GraphMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) pred_dropout (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.generic_models.GraphMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) pred_hidden_dim (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) pred_hidden_dims (matcha.utils.schemas.generic_models.CLMMixin attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.generic_models.GraphMixin attribute) pred_num_layers (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) pred_task_head_dims (matcha.utils.schemas.generic_models.GraphMixin attribute) predict() (matcha.sklearn.base_sklearn_model.ScikitLearnClassifierMixin method) (matcha.sklearn.base_sklearn_model.ScikitLearnRegressorMixin method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) predict_dataloader() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) predict_proba() (matcha.sklearn.base_sklearn_model.ScikitLearnClassifierMixin method) (matcha.sklearn.ChempropClassifier method) (matcha.sklearn.finetuner.FinetuningClassifier method) (matcha.sklearn.FinetuningClassifier method) (matcha.sklearn.graph.chemprop.ChempropClassifier method) (matcha.sklearn.graph.ChempropClassifier method) predict_sets() (matcha.calibration.ICPClassificationCalibration method) (matcha.calibration.inductive_conformal.ICPClassificationCalibration method) predict_step() (matcha.torch.models.classic.base_classic_model.BaseClassicModel method) (matcha.torch.models.classic.BaseClassicModel method) (matcha.torch.models.finetuning.Finetuner method) (matcha.torch.models.finetuning.finetuner.Finetuner method) (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel method) (matcha.torch.models.pretraining.BasePretrainingModel method) PredictDataset (class in matcha.utils.schemas.cli) prediction_head (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel attribute) (matcha.torch.models.pretraining.BasePretrainingModel attribute) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLM attribute) (matcha.torch.models.pretraining.RoFormerMLM attribute) PredictModel (class in matcha.utils.schemas.cli) predictor (matcha.torch.models.classic.base_classic_model.BaseClassicModel attribute) (matcha.torch.models.classic.BaseClassicModel attribute) (matcha.torch.models.classic.mlp_model.MLPModel attribute) (matcha.torch.models.classic.MLPModel attribute) (matcha.torch.models.classic.snn_model.SNNModel attribute) (matcha.torch.models.classic.SNNModel attribute) (matcha.torch.models.finetuning.Finetuner attribute) (matcha.torch.models.finetuning.finetuner.Finetuner attribute) (matcha.torch.models.finetuning.pretrained_encoder_wrapper.PretrainedEncoderWrapper attribute) (matcha.torch.models.finetuning.PretrainedEncoderWrapper attribute) PredictorRegistry (in module matcha.torch.predictors.base_predictor) PReLU (class in matcha.nn.activations) prepare_fit_datasets() (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) PrepareDatasets (class in matcha.utils.schemas.cli) PrepareMetadata (class in matcha.utils.schemas.cli) PrepareValidation (class in matcha.utils.schemas.cli) pretrain_decay (matcha.utils.schemas.generic_models.FinetunerMixin attribute) pretrain_lr (matcha.utils.schemas.generic_models.FinetunerMixin attribute) pretrain_output_dim (matcha.torch.models.finetuning.Finetuner attribute) (matcha.torch.models.finetuning.finetuner.Finetuner attribute) pretrained_model_dir (matcha.datamodules.classic.Engine property) (matcha.datamodules.classic.rdkit_engine.Engine property) (matcha.datamodules.Engine property) PretrainedEncoderWrapper (class in matcha.torch.models.finetuning) (class in matcha.torch.models.finetuning.pretrained_encoder_wrapper) PretrainingModelRegistry (in module matcha.torch.models.pretraining) (in module matcha.torch.models.pretraining.base_pretraining_model) PretrainMultitaskModel (class in matcha.utils.schemas.cli) PretrainMultitaskOutput (in module matcha.utils.schemas.cli) PretrainOutput (class in matcha.utils.schemas.cli) PretrainPipe (class in matcha.utils.schemas.cli) PretrainTraining (class in matcha.utils.schemas.cli) process() (matcha.datamodules.BinaryClassificationLabelEncoder method) (matcha.datamodules.classic.BinaryClassificationLabelEncoder method) (matcha.datamodules.classic.label_encoder.BinaryClassificationLabelEncoder method) (matcha.datamodules.classic.label_encoder.RegressionLabelEncoder method) (matcha.datamodules.classic.label_transform.LabelTransform method) (matcha.datamodules.classic.LabelTransform method) (matcha.datamodules.classic.RegressionLabelEncoder method) (matcha.datamodules.LabelTransform method) (matcha.datamodules.RegressionLabelEncoder method) process_censor() (in module matcha.utils.metrics) process_classification() (in module matcha.utils.metrics) process_regression() (in module matcha.utils.metrics) propagate() (matcha.torch.encoders.e3gnn.EGNN_Sparse method) PyGAggregationWrapper (class in matcha.nn.readouts)

Q

q_proj (matcha.nn.layers.BiasedMultiHeadAttention attribute) quantile (matcha.utils.schemas.calibration.ICPBaseInputModel attribute) (matcha.utils.schemas.ICPBaseInputModel attribute) QuantilePooling (class in matcha.nn.readouts)

quantize (matcha.utils.schemas.cli.CLIEvaluationInputModel attribute) (matcha.utils.schemas.cli.Serialization attribute) quantize() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.managers.serialization_manager.SerializationManager method) (matcha.sklearn.managers.SerializationManager method)

R

r2_box (matcha.explainability.LIME property) (matcha.explainability.lime.LIME property) RAISE (matcha.datamodules.utils.HandleMissing attribute) (matcha.utils.schemas.datamodules.HandleMissing attribute) random_split() (in module matcha.sklearn.utils) (in module matcha.utils.splitting) rank (matcha.torch.models.finetuning.lora.LoRALinear attribute) (matcha.torch.models.finetuning.LoRALinear attribute) rdkit_all_descriptors (matcha.datamodules.classic.Engine property) (matcha.datamodules.classic.rdkit_engine.Engine property) (matcha.datamodules.Engine property) rdkit_common_descriptors (matcha.datamodules.classic.Engine property) (matcha.datamodules.classic.rdkit_engine.Engine property) (matcha.datamodules.Engine property) rdkit_custom_descriptors (matcha.datamodules.classic.Engine property) (matcha.datamodules.classic.rdkit_engine.Engine property) (matcha.datamodules.Engine property) RDKIT_FEATURES (in module matcha.datamodules.classic.tabular_datamodule) ReadoutRegistry (in module matcha.nn.readouts) reduction (matcha.nn.losses.BCEFocalLoss attribute) (matcha.nn.losses.Poly1BCELoss attribute) (matcha.nn.losses.WeightedBCELoss attribute) register() (matcha.utils.registry.ClassRegistry method) RegressionEncoderInputModel (class in matcha.utils.schemas.label) RegressionInputModel (class in matcha.utils.schemas.sklearn_api) RegressionLabelEncoder (class in matcha.datamodules) (class in matcha.datamodules.classic) (class in matcha.datamodules.classic.label_encoder) reload_pretrained() (matcha.sklearn.finetuner.BaseFinetuner method) ReLU (class in matcha.nn.activations) reset_initial_losses() (matcha.nn.losses.GradNormLoss method) reset_parameters() (matcha.nn.layers.MultiLn method) (matcha.torch.encoders.attentivefp.GATEConv method) RNN (class in matcha.torch.encoders) (class in matcha.torch.encoders.rnn) rnn (matcha.torch.encoders.RNN attribute) (matcha.torch.encoders.rnn.RNN attribute) RNNClassifier (class in matcha.sklearn) (class in matcha.sklearn.clm) (class in matcha.sklearn.clm.rnn) RNNInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) RNNMixin (class in matcha.utils.schemas.generic_models) RNNModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.rnn_model)

RNNRegressor (class in matcha.sklearn) (class in matcha.sklearn.clm) (class in matcha.sklearn.clm.rnn) RoFormer (class in matcha.torch.encoders) (class in matcha.torch.encoders.roformer) RoFormerClassifier (class in matcha.sklearn) (class in matcha.sklearn.clm) (class in matcha.sklearn.clm.roformer) RoFormerInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) RoFormerMixin (class in matcha.utils.schemas.generic_models) RoFormerMLM (class in matcha.torch.models.pretraining) (class in matcha.torch.models.pretraining.roformer_mlm) RoFormerMLMEncoder (class in matcha.torch.models.pretraining.roformer_mlm) RoFormerModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.roformer_model) RoFormerRegressor (class in matcha.sklearn) (class in matcha.sklearn.clm) (class in matcha.sklearn.clm.roformer) root_dir (matcha.cli.summarize.DirectoryExperimentSummarizer attribute) (matcha.utils.schemas.cli.CLISummarizeInputModel attribute) rrwp_k (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute) rrwp_re() (matcha.datamodules.classic.graph_positional_encoder.GraphPE class method) run (matcha.utils.schemas.sklearn_api.MLFlowInputModel attribute) run() (matcha.sklearn.managers.CLMTrainingManager method) (matcha.sklearn.managers.training_manager.CLMTrainingManager method) (matcha.sklearn.managers.training_manager.TrainingManager method) (matcha.sklearn.managers.TrainingManager method) run_hparam_tuning() (in module matcha.torch.tuning) (in module matcha.torch.tuning.routine) run_name (matcha.utils.schemas.cli.MLFlow attribute) run_omnibus() (matcha.cli.statistical_tests.BootstrapComparison method) run_pairwise() (matcha.cli.statistical_tests.BootstrapComparison method) (matcha.cli.statistical_tests.NonParametricComparison method) (matcha.cli.statistical_tests.ParametricComparison method) runs (matcha.utils.schemas.cli.CLISummarizeInputModel attribute) rw_se() (matcha.datamodules.classic.graph_positional_encoder.GraphPE class method) rwse_k (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.datamodules.GraphDataModuleInputModel attribute) (matcha.utils.schemas.Graph3DDataModuleInputModel attribute) (matcha.utils.schemas.GraphDataModuleInputModel attribute)

S

sampling_rate (matcha.utils.schemas.cli.PrepareValidation attribute) save() (matcha.sklearn.managers.ensemble_serialization_manager.EnsembleSerializationManager method) (matcha.sklearn.managers.EnsembleSerializationManager method) (matcha.sklearn.managers.serialization_manager.SerializationManager method) (matcha.sklearn.managers.SerializationManager method) save_calibrator() (matcha.calibration.base_calibration.BaseCalibration method) (matcha.calibration.BaseCalibration method) save_checkpoint() (matcha.sklearn.managers.training_manager.TrainingManager method) (matcha.sklearn.managers.TrainingManager method) save_config_as_yaml() (in module matcha.cli.utils) save_json() (in module matcha.utils) (in module matcha.utils.serialization) save_model() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) save_pickle() (in module matcha.utils) (in module matcha.utils.serialization) save_plot() (in module matcha.utils.plotting) save_summary_to_backend() (matcha.cli.summarize.DirectoryExperimentSummarizer method) (matcha.cli.summarize.ExperimentSummarizer method) (matcha.cli.summarize.MLflowExperimentSummarizer method) save_yaml() (in module matcha.utils) (in module matcha.utils.serialization) scale (matcha.nn.layers.BiasedMultiHeadAttention attribute) (matcha.torch.encoders.e3gnn.CoorsNorm attribute) (matcha.torch.encoders.gt.GTConv attribute) scale() (matcha.datamodules.classic.label_transform.BackwardTransformRegistry class method) (matcha.datamodules.classic.label_transform.ForwardTransformRegistry class method) scale_coeff (matcha.explainability.LIME property) (matcha.explainability.lime.LIME property) scale_y_graph (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.GraphPretrainingDataModuleInputModel attribute) (matcha.utils.schemas.GraphPretrainingDataModuleInputModel attribute) scale_y_node (matcha.utils.schemas.cli.EncoderPretrainGraphDatamodule attribute) (matcha.utils.schemas.datamodules.GraphPretrainingDataModuleInputModel attribute) (matcha.utils.schemas.GraphPretrainingDataModuleInputModel attribute) scaler_box (matcha.calibration.EMCalibration attribute) (matcha.calibration.error_model.EMCalibration attribute) scaler_type (matcha.utils.schemas.datamodules.BaseDataModuleFields attribute) scaling (matcha.torch.models.finetuning.lora.LoRALinear attribute) (matcha.torch.models.finetuning.LoRALinear attribute) scheduler (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ClassicMatchaModel attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) scheduler_args (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.generic_models.ChempropFinetunerMixin attribute) (matcha.utils.schemas.generic_models.ClassicMatchaModel attribute) (matcha.utils.schemas.generic_models.FinetunerMixin attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) scheduler_grid (matcha.utils.schemas.sklearn_api.TuningInputModel attribute) SchedulerRegistry (in module matcha.nn.schedulers) ScikitLearnClassifierMixin (class in matcha.sklearn.base_sklearn_model) ScikitLearnEnsembleInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.sklearn_api) ScikitLearnInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.sklearn_api) ScikitLearnModelRegistry (in module matcha.sklearn) (in module matcha.sklearn.base_sklearn_model) ScikitLearnRegressorMixin (class in matcha.sklearn.base_sklearn_model) Search (class in matcha.utils.schemas.cli) seed (matcha.utils.schemas.cli.PrepareValidation attribute) (matcha.utils.schemas.cli.PretrainTraining attribute) (matcha.utils.schemas.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnEnsembleInputModel attribute) (matcha.utils.schemas.sklearn_api.TrainingInputModel attribute) SELU (class in matcha.nn.activations) Sequential (class in matcha.nn.schedulers) Serialization (class in matcha.utils.schemas.cli) serialization (matcha.utils.schemas.cli.Output attribute) (matcha.utils.schemas.cli.PretrainOutput attribute) SerializationManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.serialization_manager) server_uri (matcha.utils.schemas.cli.MLFlow attribute) (matcha.utils.schemas.sklearn_api.MLFlowInputModel attribute) Set2SetPooling (class in matcha.nn.readouts) set_batch_size() (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) set_clipping_bounds() (matcha.datamodules.classic.label_transform.LabelTransform method) (matcha.datamodules.classic.LabelTransform method) (matcha.datamodules.LabelTransform method) set_data() (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) set_defaults() (matcha.datamodules.classic.Engine method) (matcha.datamodules.classic.rdkit_engine.Engine method) (matcha.datamodules.Engine method) set_label_names() (matcha.torch.models.classic.chemprop_model.ChempropModel method) (matcha.torch.models.classic.ChempropModel method) (matcha.torch.models.mixin.ModelMixin method) set_mlflow_experiment() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) set_predict_dataset() (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) set_train_dataset() (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) set_val_dataset() (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) SetTransformerPooling (class in matcha.nn.readouts) setup() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method)

setup_experiment() (matcha.sklearn.managers.ensemble_mlflow_manager.EnsembleMLFlowManager method) (matcha.sklearn.managers.EnsembleMLFlowManager method) (matcha.sklearn.managers.mlflow_manager.MLFlowManager method) (matcha.sklearn.managers.MLFlowManager method) setup_member_mlflow() (matcha.sklearn.managers.ensemble_mlflow_manager.EnsembleMLFlowManager method) (matcha.sklearn.managers.EnsembleMLFlowManager method) SGD (class in matcha.nn.optimizers) show_help() (in module matcha.cli) Sigmoid (class in matcha.nn.activations) silence_nuisance_warnings() (in module matcha.utils) (in module matcha.utils.warnings) SILU (class in matcha.nn.activations) SiLU (class in matcha.torch.encoders.e3gnn) smiles (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataset attribute) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataset attribute) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataset attribute) (matcha.datamodules.pretraining.OnTheFlyDataset attribute) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataset attribute) (matcha.datamodules.pretraining.OnTheFlyMLMDataset attribute) smiles_key (matcha.utils.schemas.cli.Dataset attribute) (matcha.utils.schemas.cli.StitcherInputModel attribute) SMILES_REGEX (in module matcha.datamodules.classic.clm_datamodule) SmoothL1Loss (class in matcha.nn.losses) SNN (class in matcha.torch.predictors) (class in matcha.torch.predictors.snn) SNNClassifier (class in matcha.sklearn) (class in matcha.sklearn.tabular) (class in matcha.sklearn.tabular.snn) SNNInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.torch_api) SNNMixin (class in matcha.utils.schemas.generic_models) SNNModel (class in matcha.torch.models.classic) (class in matcha.torch.models.classic.snn_model) SNNRegressor (class in matcha.sklearn) (class in matcha.sklearn.tabular) (class in matcha.sklearn.tabular.snn) soft_edge (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) Softmax (class in matcha.nn.activations) SoftmaxPooling (class in matcha.nn.readouts) SortPooling (class in matcha.nn.readouts) source_identifier (matcha.cli.summarize.DirectoryExperimentSummarizer attribute) (matcha.cli.summarize.ExperimentSummarizer attribute) (matcha.cli.summarize.MLflowExperimentSummarizer attribute) source_identifier_key (matcha.cli.summarize.DirectoryExperimentSummarizer attribute) (matcha.cli.summarize.ExperimentSummarizer attribute) (matcha.cli.summarize.MLflowExperimentSummarizer attribute) SpatialEncoder (class in matcha.nn.layers) SpatialEncoder3d (class in matcha.nn.layers) Split (class in matcha.utils.schemas.cli) split (matcha.utils.schemas.cli.CLIAutotuneOutput attribute) (matcha.utils.schemas.cli.CLIBaselineInputModel attribute) (matcha.utils.schemas.cli.CLIEvaluationInputModel attribute) split_column (matcha.utils.schemas.cli.CalibrationDataSettings attribute) split_ratio (matcha.utils.schemas.cli.CalibrationDataSettings attribute) start_lr (matcha.nn.schedulers.WarmupCosineAnnealingLR attribute) (matcha.nn.schedulers.WarmupLinearDecayLR attribute) state_dict() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.BaseLabelEncoder method) (matcha.datamodules.classic.BaseLabelEncoder method) (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule method) (matcha.datamodules.classic.clm_datamodule.CLMDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.datamodules.classic.graph_datamodule.Graph3DDataModule method) (matcha.datamodules.classic.graph_datamodule.GraphDataModule method) (matcha.datamodules.classic.label_encoder.BaseLabelEncoder method) (matcha.datamodules.classic.label_transform.LabelTransform method) (matcha.datamodules.classic.LabelTransform method) (matcha.datamodules.classic.tabular_datamodule.TabularDataModule method) (matcha.datamodules.LabelTransform method) (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule method) (matcha.datamodules.pretraining.CLMMLMDataModule method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) (matcha.nn.schedulers.ChempropSchedulerConfig method) (matcha.sklearn.managers.datamodule_manager.DataModuleManager method) (matcha.sklearn.managers.DataModuleManager method) statistical_test (matcha.cli.summarize.ExperimentSummarizer attribute) (matcha.utils.schemas.cli.CLISummarizeInputModel attribute) statistics (matcha.utils.schemas.cli.Dataset attribute) StdPooling (class in matcha.nn.readouts) stds (matcha.nn.layers.SpatialEncoder3d attribute) Step (class in matcha.nn.schedulers) step() (matcha.nn.schedulers.ChempropSchedulerConfig method) stitch_datasets() (in module matcha.nn.multitask) StitcherInputModel (class in matcha.utils.schemas.cli) StitcherOutputModel (class in matcha.utils.schemas.cli) stochastic_weight_averaging (matcha.utils.schemas.sklearn_api.TrainingInputModel attribute) store (matcha.utils.logging.MatchaLogger property) (matcha.utils.MatchaLogger property) store_split_scores() (in module matcha.cli.utils) strategy (matcha.utils.schemas.cli.PretrainPipe attribute) SumPooling (class in matcha.nn.readouts) switch_mc_dropout() (matcha.torch.models.classic.chemprop_model.ChempropModel method) (matcha.torch.models.classic.ChempropModel method) (matcha.torch.models.mixin.ModelMixin method)

T

T (in module matcha.utils.registry) (matcha.utils.schemas.cli.Loss attribute) TabularDataModule (class in matcha.datamodules.classic.tabular_datamodule) TabularDataModuleInputModel (class in matcha.utils.schemas) (class in matcha.utils.schemas.datamodules) TabularMixin (class in matcha.utils.schemas.generic_models) tag (matcha.utils.schemas.cli.StitcherInputModel attribute) (matcha.utils.schemas.sklearn_api.MLFlowInputModel attribute) tag_to_add (matcha.utils.schemas.cli.PrepareMetadata attribute) tags (matcha.utils.schemas.cli.MLFlow attribute) Tanh (class in matcha.nn.activations) task_head_dims (matcha.utils.schemas.generic_models.MLPMixin attribute) task_labels (matcha.utils.schemas.label.BaseEncoderInputModel attribute) (matcha.utils.schemas.label.RegressionEncoderInputModel attribute) task_metadata (matcha.utils.schemas.cli.MultitaskPretrainDataset attribute) task_names (matcha.nn.multitask.TaskAffinityResult attribute) task_type (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel property) (matcha.sklearn.Ensemble property) (matcha.sklearn.ensemble.Ensemble property) (matcha.utils.schemas.cli.EncoderPretrainDataset attribute) (matcha.utils.schemas.cli.PrepareDatasets attribute) (matcha.utils.schemas.ScikitLearnInputModel attribute) (matcha.utils.schemas.sklearn_api.RegressionInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnInputModel attribute) TaskAffinityResult (class in matcha.nn.multitask) test_dataloader() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) time_split() (in module matcha.utils.splitting) tolerance (in module matcha.datamodules.classic.label_transform) torch_type (matcha.utils.schemas.AttentiveFPInputModel attribute) (matcha.utils.schemas.ChempropFinetunerInputModel attribute) (matcha.utils.schemas.ChempropInputModel attribute) (matcha.utils.schemas.CNNInputModel attribute) (matcha.utils.schemas.E3GNNInputModel attribute) (matcha.utils.schemas.FinetunerInputModel attribute) (matcha.utils.schemas.GatedGCNInputModel attribute) (matcha.utils.schemas.GINInputModel attribute) (matcha.utils.schemas.GPS3DInputModel attribute) (matcha.utils.schemas.GPSInputModel attribute) (matcha.utils.schemas.GT3DInputModel attribute) (matcha.utils.schemas.GTInputModel attribute) (matcha.utils.schemas.MLPInputModel attribute) (matcha.utils.schemas.MPNNInputModel attribute) (matcha.utils.schemas.RNNInputModel attribute) (matcha.utils.schemas.RoFormerInputModel attribute) (matcha.utils.schemas.SNNInputModel attribute) (matcha.utils.schemas.torch_api.AttentiveFPInputModel attribute) (matcha.utils.schemas.torch_api.ChempropFinetunerInputModel attribute) (matcha.utils.schemas.torch_api.ChempropInputModel attribute) (matcha.utils.schemas.torch_api.CNNInputModel attribute) (matcha.utils.schemas.torch_api.E3GNNInputModel attribute) (matcha.utils.schemas.torch_api.FinetunerInputModel attribute) (matcha.utils.schemas.torch_api.GatedGCNInputModel attribute) (matcha.utils.schemas.torch_api.GINInputModel attribute) (matcha.utils.schemas.torch_api.GPS3DInputModel attribute) (matcha.utils.schemas.torch_api.GPSInputModel attribute) (matcha.utils.schemas.torch_api.GT3DInputModel attribute) (matcha.utils.schemas.torch_api.GTInputModel attribute) (matcha.utils.schemas.torch_api.MLPInputModel attribute) (matcha.utils.schemas.torch_api.MPNNInputModel attribute) (matcha.utils.schemas.torch_api.RNNInputModel attribute) (matcha.utils.schemas.torch_api.RoFormerInputModel attribute) (matcha.utils.schemas.torch_api.SNNInputModel attribute)

TorchModel (in module matcha.utils.schemas.torch_api) TorchModels (class in matcha.utils.schemas.torch_api) total_steps (matcha.nn.schedulers.WarmupCosineAnnealingLR attribute) (matcha.nn.schedulers.WarmupLinearDecayLR attribute) train_dataloader() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) train_smiles (matcha.utils.schemas.cli.EncoderPretrainDataset attribute) (matcha.utils.schemas.cli.MultitaskPretrainDataset attribute) train_tasks (matcha.utils.schemas.cli.MultitaskPretrainDataset attribute) train_y_graph (matcha.utils.schemas.cli.EncoderPretrainDataset attribute) train_y_node (matcha.utils.schemas.cli.EncoderPretrainDataset attribute) trainer (matcha.sklearn.managers.training_manager.TrainingManager property) (matcha.sklearn.managers.TrainingManager property) training (matcha.utils.schemas.cli.EncoderPretrainModel attribute) (matcha.utils.schemas.cli.PretrainMultitaskModel attribute) (matcha.utils.schemas.ScikitLearnInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnInputModel attribute) training_step() (matcha.torch.models.classic.base_classic_model.BaseClassicModel method) (matcha.torch.models.classic.BaseClassicModel method) (matcha.torch.models.classic.mlp_model.MLPModel method) (matcha.torch.models.classic.MLPModel method) (matcha.torch.models.classic.snn_model.SNNModel method) (matcha.torch.models.classic.SNNModel method) (matcha.torch.models.finetuning.Finetuner method) (matcha.torch.models.finetuning.finetuner.Finetuner method) (matcha.torch.models.pretraining.base_graph_pretraining.BaseGraphPretrainingModel method) (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel method) (matcha.torch.models.pretraining.BaseGraphPretrainingModel method) (matcha.torch.models.pretraining.BasePretrainingModel method) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLM method) (matcha.torch.models.pretraining.RoFormerMLM method) TrainingInputModel (class in matcha.utils.schemas.sklearn_api) TrainingManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.training_manager) transform() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule method) (matcha.datamodules.classic.clm_datamodule.CLMDataModule method) (matcha.datamodules.classic.combined_datamodule.CombinedDataModule method) (matcha.datamodules.classic.tabular_datamodule.TabularDataModule method) (matcha.datamodules.pretraining.clm_mlm_datamodule.CLMMLMDataModule method) (matcha.datamodules.pretraining.CLMMLMDataModule method) (matcha.datamodules.pretraining.graph_pretraining_datamodule.GraphPretrainingDataModule method) (matcha.datamodules.pretraining.GraphPretrainingDataModule method) (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.Ensemble method) (matcha.sklearn.ensemble.Ensemble method) transform_map (matcha.utils.schemas.label.LabelTransformInputModel attribute) tune() (matcha.sklearn.base_sklearn_model.BaseScikitLearnModel method) (matcha.sklearn.managers.hpo_manager.HPOManager method) (matcha.sklearn.managers.HPOManager method) Tuning (class in matcha.utils.schemas.cli) tuning (matcha.utils.schemas.cli.CLIAutotuneOutput attribute) (matcha.utils.schemas.ScikitLearnInputModel attribute) (matcha.utils.schemas.sklearn_api.ScikitLearnInputModel attribute) TuningInputModel (class in matcha.utils.schemas.sklearn_api)

U

UncertaintyManager (class in matcha.sklearn.managers) (class in matcha.sklearn.managers.uncertainty_manager) update() (matcha.torch.encoders.gatedgcn.GatedGCNConv method) update_coors (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute) update_feats (matcha.torch.encoders.e3gnn.EGNN_Sparse attribute)

use_ecfp (matcha.utils.schemas.calibration.EMBaseInputModel attribute) (matcha.utils.schemas.EMBaseInputModel attribute) use_features (matcha.datamodules.classic.chemprop_datamodule.ChempropDataModule property) use_interaction (matcha.utils.schemas.calibration.EMBaseInputModel attribute) (matcha.utils.schemas.EMBaseInputModel attribute)

V

v_proj (matcha.nn.layers.BiasedMultiHeadAttention attribute) val_dataloader() (matcha.datamodules.base_datamodule.BaseDataModule method) (matcha.datamodules.BaseDataModule method) (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataModule method) (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.on_the_fly_mlm_datamodule.OnTheFlyMLMDataModule method) (matcha.datamodules.pretraining.OnTheFlyDataModule method) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataModule method) (matcha.datamodules.pretraining.OnTheFlyMLMDataModule method) val_smiles (matcha.utils.schemas.cli.EncoderPretrainDataset attribute) (matcha.utils.schemas.cli.MultitaskPretrainDataset attribute) val_tasks (matcha.utils.schemas.cli.MultitaskPretrainDataset attribute) val_y_graph (matcha.utils.schemas.cli.EncoderPretrainDataset attribute) val_y_node (matcha.utils.schemas.cli.EncoderPretrainDataset attribute) validate_bound_mask() (matcha.utils.schemas.data.MolDataset method) (matcha.utils.schemas.MolDataset method) validate_merge_fn() (matcha.utils.schemas.CombinedDataModuleInputModel class method) (matcha.utils.schemas.datamodules.CombinedDataModuleInputModel class method)

validate_mols() (matcha.utils.schemas.data.MolDataset method) (matcha.utils.schemas.MolDataset method) validate_y() (matcha.utils.schemas.data.MolDataset method) (matcha.utils.schemas.MolDataset method) validation (matcha.utils.schemas.cli.CLIPrepareInputModel attribute) validation_step() (matcha.torch.models.classic.base_classic_model.BaseClassicModel method) (matcha.torch.models.classic.BaseClassicModel method) (matcha.torch.models.mixin.ModelMixin method) (matcha.torch.models.pretraining.base_graph_pretraining.BaseGraphPretrainingModel method) (matcha.torch.models.pretraining.base_pretraining_model.BasePretrainingModel method) (matcha.torch.models.pretraining.BaseGraphPretrainingModel method) (matcha.torch.models.pretraining.BasePretrainingModel method) (matcha.torch.models.pretraining.roformer_mlm.RoFormerMLM method) (matcha.torch.models.pretraining.RoFormerMLM method) VariancePreservingPooling (class in matcha.nn.readouts) VarPooling (class in matcha.nn.readouts) VirtualNodePooling (class in matcha.nn.readouts) visible_devices (matcha.utils.schemas.cli.PretrainPipe attribute)

W

w0 (matcha.nn.losses.WeightedBCELoss attribute) w1 (matcha.nn.losses.WeightedBCELoss attribute) warmup (matcha.utils.schemas.cli.Loss attribute) warmup_epochs (matcha.nn.schedulers.ChempropSchedulerConfig attribute) (matcha.torch.models.finetuning.chemprop_finetuner.ChempropFinetuner attribute) (matcha.torch.models.finetuning.ChempropFinetuner attribute) WarmupCosineAnnealingLR (class in matcha.nn.schedulers) WarmupLinearDecayLR (class in matcha.nn.schedulers) weight (matcha.nn.layers.MultiBatchNorm attribute) (matcha.nn.layers.MultiLn attribute)

weight_lr (matcha.nn.losses.GradNormLoss attribute) WeightedBCELoss (class in matcha.nn.losses) weights (matcha.explainability.explainer.MatchaExplanation attribute) (matcha.explainability.MatchaExplanation attribute) WK (matcha.torch.encoders.gt.GTConv attribute) WO (matcha.torch.encoders.gt.GTConv attribute) WQ (matcha.torch.encoders.gt.GTConv attribute) wrapped_MolToSmiles (in module matcha.datamodules.classic.clm_datamodule) Wrapper (class in matcha.utils) (class in matcha.utils.wrapper) WV (matcha.torch.encoders.gt.GTConv attribute)

X

x_scaler (matcha.datamodules.classic.tabular_datamodule.TabularDataModule property)

Y

y (matcha.datamodules.pretraining.on_the_fly_datamodule.OnTheFlyDataset attribute) (matcha.datamodules.pretraining.OnTheFlyDataset attribute) (matcha.utils.schemas.data.MolDataset attribute) (matcha.utils.schemas.data.MolReadout attribute) (matcha.utils.schemas.MolDataset attribute) (matcha.utils.schemas.MolReadout attribute)

y_clip (matcha.utils.schemas.label.LabelTransformInputModel attribute) y_graph (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataset attribute) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataset attribute) y_node (matcha.datamodules.pretraining.on_the_fly_graph_pretraining_datamodule.OnTheFlyGraphPretrainingDataset attribute) (matcha.datamodules.pretraining.OnTheFlyGraphPretrainingDataset attribute) y_scaler (matcha.datamodules.base_datamodule.BaseDataModule property) (matcha.datamodules.BaseDataModule property)