Index

A

AdaBoostDecisionTree (class in drevalpy.models.baselines.sklearn_models) add_features() (drevalpy.datasets.dataset.FeatureDataset method) add_meta_info() (drevalpy.datasets.dataset.FeatureDataset method)

add_rows() (drevalpy.datasets.dataset.DrugResponseDataset method) apply() (drevalpy.datasets.dataset.FeatureDataset method) AttentionLayer (class in drevalpy.models.DIPK.model_utils)

B

build_model() (drevalpy.models.baselines.naive_pred.NaiveModel method) (drevalpy.models.baselines.singledrug_baselines.SingleDrugElasticNet method) (drevalpy.models.baselines.singledrug_baselines.SingleDrugRandomForest method) (drevalpy.models.baselines.sklearn_models.AdaBoostDecisionTree method) (drevalpy.models.baselines.sklearn_models.ElasticNetModel method) (drevalpy.models.baselines.sklearn_models.GradientBoosting method) (drevalpy.models.baselines.sklearn_models.KNNRegressor method) (drevalpy.models.baselines.sklearn_models.LassoModel method) (drevalpy.models.baselines.sklearn_models.RandomForest method) (drevalpy.models.baselines.sklearn_models.SklearnModel method) (drevalpy.models.baselines.sklearn_models.SVMRegressor method) (drevalpy.models.DIPK.dipk.DIPKModel method) (drevalpy.models.drp_model.DRPModel method) (drevalpy.models.DrugGNN.drug_gnn.DrugGNN method) (drevalpy.models.MOLIR.molir.MOLIR method) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel method) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork method) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork method) (drevalpy.models.SRMF.srmf.SRMF method) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR method)

C

cell_line_ids (drevalpy.datasets.dataset.DrugResponseDataset property) cell_line_views (drevalpy.models.baselines.multi_view_random_forest.MultiViewRandomForest attribute) (drevalpy.models.baselines.naive_pred.NaiveCellLineMeanPredictor attribute) (drevalpy.models.baselines.naive_pred.NaiveDrugMeanPredictor attribute) (drevalpy.models.baselines.naive_pred.NaiveMeanEffectsPredictor attribute) (drevalpy.models.baselines.naive_pred.NaivePredictor attribute) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor attribute) (drevalpy.models.baselines.naive_pred.NaiveTissueMeanPredictor attribute) (drevalpy.models.baselines.sklearn_models.SklearnModel attribute) (drevalpy.models.DIPK.dipk.DIPKModel attribute) (drevalpy.models.drp_model.DRPModel property) (drevalpy.models.DrugGNN.drug_gnn.DrugGNN property) (drevalpy.models.MOLIR.molir.MOLIR attribute) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel attribute) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork attribute) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork attribute) (drevalpy.models.SRMF.srmf.SRMF attribute) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR attribute) check_arguments() (in module drevalpy.utils) check_measure() (in module drevalpy.datasets.loader) CollateFn (class in drevalpy.models.DIPK.data_utils) (class in drevalpy.models.DIPK.gene_expression_encoder)

CombinedModel (class in drevalpy.models.PharmaFormer.model_utils) ComparisonScatter (class in drevalpy.visualization.comp_scatter) compute_and_log_final_metrics() (drevalpy.models.drp_model.DRPModel method) compute_evaluation() (in module drevalpy.visualization.utils) compute_performance_metrics() (drevalpy.models.drp_model.DRPModel method) configure_optimizers() (drevalpy.models.DrugGNN.drug_gnn.DrugGNNModule method) (drevalpy.models.MOLIR.utils.MOLIModel method) (drevalpy.models.SimpleNeuralNetwork.utils.FeedForwardNetwork method) (drevalpy.models.SuperFELTR.utils.SuperFELTEncoder method) (drevalpy.models.SuperFELTR.utils.SuperFELTRegressor method) consolidate_single_drug_model_predictions() (in module drevalpy.experiment) copy() (drevalpy.datasets.dataset.DrugResponseDataset method) (drevalpy.datasets.dataset.FeatureDataset method) create_dataset_and_loaders() (in module drevalpy.models.MOLIR.utils) create_html() (in module drevalpy.visualization.utils) create_index_html() (in module drevalpy.visualization.utils) create_output_directories() (in module drevalpy.visualization.utils) CriticalDifferencePlot (class in drevalpy.visualization.critical_difference_plot) cross_study_prediction() (in module drevalpy.experiment) CrossStudyTables (class in drevalpy.visualization.cross_study_tables) cv_splits (drevalpy.datasets.dataset.DrugResponseDataset property)

D

DataSet (class in drevalpy.models.DIPK.gene_expression_encoder) dataset_name (drevalpy.datasets.dataset.DrugResponseDataset property) DenseLayers (class in drevalpy.models.DIPK.model_utils) DIPKDataset (class in drevalpy.models.DIPK.data_utils) DIPKModel (class in drevalpy.models.DIPK.dipk) download_dataset() (in module drevalpy.datasets.utils) download_from_url() (in module drevalpy.datasets.utils) draw() (drevalpy.visualization.cross_study_tables.CrossStudyTables method) draw_algorithm_plots() (in module drevalpy.visualization.utils) draw_and_save() (drevalpy.visualization.comp_scatter.ComparisonScatter method) (drevalpy.visualization.critical_difference_plot.CriticalDifferencePlot method) (drevalpy.visualization.cross_study_tables.CrossStudyTables method) (drevalpy.visualization.heatmap.Heatmap method) (drevalpy.visualization.outplot.OutPlot method) (drevalpy.visualization.regression_slider_plot.RegressionSliderPlot method) (drevalpy.visualization.vioheat.VioHeat method) (drevalpy.visualization.violin.Violin method) draw_test_mode_plots() (in module drevalpy.visualization.utils) drevalpy.datasets.curvecurator module drevalpy.datasets.dataset module drevalpy.datasets.loader module drevalpy.datasets.utils module drevalpy.evaluation module drevalpy.experiment module drevalpy.models.baselines.multi_view_random_forest module drevalpy.models.baselines.naive_pred module drevalpy.models.baselines.singledrug_baselines module drevalpy.models.baselines.sklearn_models module drevalpy.models.DIPK.attention_utils module drevalpy.models.DIPK.data_utils module drevalpy.models.DIPK.dipk module drevalpy.models.DIPK.gene_expression_encoder module drevalpy.models.DIPK.model_utils module drevalpy.models.drp_model module drevalpy.models.DrugGNN.drug_gnn module drevalpy.models.MOLIR.molir module drevalpy.models.MOLIR.utils module drevalpy.models.PharmaFormer.model_utils module drevalpy.models.PharmaFormer.pharmaformer module

drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network module drevalpy.models.SimpleNeuralNetwork.simple_neural_network module drevalpy.models.SimpleNeuralNetwork.utils module drevalpy.models.SRMF.srmf module drevalpy.models.SuperFELTR.superfeltr module drevalpy.models.SuperFELTR.utils module drevalpy.models.utils module drevalpy.pipeline_function module drevalpy.utils module drevalpy.visualization.comp_scatter module drevalpy.visualization.critical_difference_plot module drevalpy.visualization.cross_study_tables module drevalpy.visualization.heatmap module drevalpy.visualization.outplot module drevalpy.visualization.regression_slider_plot module drevalpy.visualization.utils module drevalpy.visualization.vioheat module drevalpy.visualization.violin module DRPModel (class in drevalpy.models.drp_model) drug_ids (drevalpy.datasets.dataset.DrugResponseDataset property) drug_response_experiment() (in module drevalpy.experiment) drug_views (drevalpy.models.baselines.naive_pred.NaiveCellLineMeanPredictor attribute) (drevalpy.models.baselines.naive_pred.NaiveDrugMeanPredictor attribute) (drevalpy.models.baselines.naive_pred.NaiveMeanEffectsPredictor attribute) (drevalpy.models.baselines.naive_pred.NaivePredictor attribute) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor attribute) (drevalpy.models.baselines.naive_pred.NaiveTissueMeanPredictor attribute) (drevalpy.models.baselines.singledrug_baselines.SingleDrugElasticNet attribute) (drevalpy.models.baselines.singledrug_baselines.SingleDrugRandomForest attribute) (drevalpy.models.baselines.sklearn_models.SklearnModel attribute) (drevalpy.models.DIPK.dipk.DIPKModel attribute) (drevalpy.models.drp_model.DRPModel property) (drevalpy.models.DrugGNN.drug_gnn.DrugGNN property) (drevalpy.models.MOLIR.molir.MOLIR attribute) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel attribute) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork attribute) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork attribute) (drevalpy.models.SRMF.srmf.SRMF attribute) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR attribute) DrugGNN (class in drevalpy.models.DrugGNN.drug_gnn) DrugGNNModule (class in drevalpy.models.DrugGNN.drug_gnn) DrugGraphNet (class in drevalpy.models.DrugGNN.drug_gnn) DrugResponseDataset (class in drevalpy.datasets.dataset)

E

early_stopping (drevalpy.models.baselines.singledrug_baselines.SingleDrugElasticNet attribute) (drevalpy.models.baselines.singledrug_baselines.SingleDrugRandomForest attribute) (drevalpy.models.DIPK.dipk.DIPKModel attribute) (drevalpy.models.drp_model.DRPModel attribute) (drevalpy.models.MOLIR.molir.MOLIR attribute) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel attribute) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork attribute) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork attribute) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR attribute)

ElasticNetModel (class in drevalpy.models.baselines.sklearn_models) encode_gene_expression() (in module drevalpy.models.DIPK.gene_expression_encoder) evaluate() (in module drevalpy.evaluation) evaluate_file() (in module drevalpy.visualization.utils)

F

FeatureDataset (class in drevalpy.datasets.dataset) FeatureExtractor (class in drevalpy.models.PharmaFormer.model_utils) features (drevalpy.datasets.dataset.FeatureDataset property) FeedForwardNetwork (class in drevalpy.models.SimpleNeuralNetwork.utils) filter_and_sort_omics() (in module drevalpy.models.MOLIR.utils) finish_wandb() (drevalpy.models.drp_model.DRPModel method) fit() (drevalpy.models.MOLIR.utils.MOLIModel method) (drevalpy.models.SimpleNeuralNetwork.utils.FeedForwardNetwork method) (drevalpy.models.utils.ProteomicsMedianCenterAndImputeTransformer method) (drevalpy.models.utils.VarianceFeatureSelector method) fit_curves() (in module drevalpy.datasets.curvecurator) fit_transform() (drevalpy.datasets.dataset.DrugResponseDataset method) fit_transform_features() (drevalpy.datasets.dataset.FeatureDataset method) forward() (drevalpy.models.DIPK.attention_utils.MultiHeadAttentionLayer method) (drevalpy.models.DIPK.gene_expression_encoder.GeneExpressionDecoder method) (drevalpy.models.DIPK.gene_expression_encoder.GeneExpressionEncoder method) (drevalpy.models.DIPK.model_utils.AttentionLayer method) (drevalpy.models.DIPK.model_utils.DenseLayers method) (drevalpy.models.DIPK.model_utils.Predictor method) (drevalpy.models.DrugGNN.drug_gnn.DrugGNNModule method) (drevalpy.models.DrugGNN.drug_gnn.DrugGraphNet method) (drevalpy.models.MOLIR.utils.MOLIEncoder method) (drevalpy.models.MOLIR.utils.MOLIModel method) (drevalpy.models.MOLIR.utils.MOLIRegressor method) (drevalpy.models.PharmaFormer.model_utils.CombinedModel method) (drevalpy.models.PharmaFormer.model_utils.FeatureExtractor method) (drevalpy.models.PharmaFormer.model_utils.TransModel method) (drevalpy.models.SimpleNeuralNetwork.utils.FeedForwardNetwork method) (drevalpy.models.SuperFELTR.utils.SuperFELTEncoder method) (drevalpy.models.SuperFELTR.utils.SuperFELTRegressor method)

from_csv() (drevalpy.datasets.dataset.DrugResponseDataset class method) (drevalpy.datasets.dataset.FeatureDataset class method)

G

GeneExpressionDecoder (class in drevalpy.models.DIPK.gene_expression_encoder) GeneExpressionEncoder (class in drevalpy.models.DIPK.gene_expression_encoder) generate_data_saving_path() (in module drevalpy.experiment) generate_triplets_indices() (in module drevalpy.models.MOLIR.utils) get_concatenated_features() (drevalpy.models.drp_model.DRPModel method) get_data() (in module drevalpy.models.DIPK.data_utils) get_datasets() (in module drevalpy.utils) get_datasets_from_cv_split() (in module drevalpy.experiment) get_dimensions_of_omics_data() (in module drevalpy.models.MOLIR.utils) get_feature_matrices() (drevalpy.models.drp_model.DRPModel method) get_feature_matrix() (drevalpy.datasets.dataset.FeatureDataset method) get_hyperparameter_set() (drevalpy.models.drp_model.DRPModel class method) get_mode() (in module drevalpy.evaluation) get_model_name() (drevalpy.models.baselines.multi_view_random_forest.MultiViewRandomForest class method) (drevalpy.models.baselines.naive_pred.NaiveCellLineMeanPredictor class method) (drevalpy.models.baselines.naive_pred.NaiveDrugMeanPredictor class method) (drevalpy.models.baselines.naive_pred.NaiveMeanEffectsPredictor class method) (drevalpy.models.baselines.naive_pred.NaivePredictor class method) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor class method) (drevalpy.models.baselines.naive_pred.NaiveTissueMeanPredictor class method) (drevalpy.models.baselines.singledrug_baselines.SingleDrugElasticNet class method) (drevalpy.models.baselines.singledrug_baselines.SingleDrugRandomForest class method) (drevalpy.models.baselines.sklearn_models.AdaBoostDecisionTree class method) (drevalpy.models.baselines.sklearn_models.ElasticNetModel class method) (drevalpy.models.baselines.sklearn_models.GradientBoosting class method) (drevalpy.models.baselines.sklearn_models.KNNRegressor class method) (drevalpy.models.baselines.sklearn_models.LassoModel class method) (drevalpy.models.baselines.sklearn_models.RandomForest class method) (drevalpy.models.baselines.sklearn_models.SklearnModel class method) (drevalpy.models.baselines.sklearn_models.SVMRegressor class method) (drevalpy.models.DIPK.dipk.DIPKModel class method) (drevalpy.models.drp_model.DRPModel class method) (drevalpy.models.DrugGNN.drug_gnn.DrugGNN class method) (drevalpy.models.MOLIR.molir.MOLIR class method) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel class method) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork class method) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork class method) (drevalpy.models.SRMF.srmf.SRMF class method) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR class method)

get_model_name_and_drug_id() (in module drevalpy.experiment) get_multiomics_feature_dataset() (in module drevalpy.models.utils) get_randomization_test_views() (in module drevalpy.experiment) get_response_transformation() (in module drevalpy.utils) get_wandb_logger() (drevalpy.models.drp_model.DRPModel method) GradientBoosting (class in drevalpy.models.baselines.sklearn_models)

H

Heatmap (class in drevalpy.visualization.heatmap)

hpam_tune() (in module drevalpy.experiment) hpam_tune_raytune() (in module drevalpy.experiment)

I

identifiers (drevalpy.datasets.dataset.FeatureDataset property) init_wandb() (drevalpy.models.drp_model.DRPModel method) inverse_transform() (drevalpy.datasets.dataset.DrugResponseDataset method) is_single_drug_model (drevalpy.models.baselines.singledrug_baselines.SingleDrugElasticNet attribute) (drevalpy.models.baselines.singledrug_baselines.SingleDrugRandomForest attribute) (drevalpy.models.drp_model.DRPModel attribute) (drevalpy.models.MOLIR.molir.MOLIR attribute) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR attribute)

is_wandb_enabled() (drevalpy.models.drp_model.DRPModel method) iterate_features() (in module drevalpy.models.utils)

K

kendall() (in module drevalpy.evaluation)

KNNRegressor (class in drevalpy.models.baselines.sklearn_models)

L

LassoModel (class in drevalpy.models.baselines.sklearn_models) load() (drevalpy.models.baselines.multi_view_random_forest.MultiViewRandomForest class method) (drevalpy.models.baselines.naive_pred.NaiveModel class method) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor class method) (drevalpy.models.baselines.sklearn_models.SklearnModel class method) (drevalpy.models.DIPK.dipk.DIPKModel class method) (drevalpy.models.drp_model.DRPModel class method) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel class method) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork class method) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork class method) (drevalpy.models.SRMF.srmf.SRMF class method) load_and_select_gene_features() (in module drevalpy.models.utils) load_beataml2() (in module drevalpy.datasets.loader) load_bionic_features() (in module drevalpy.models.DIPK.data_utils) load_ccle() (in module drevalpy.datasets.loader) load_cell_line_features() (drevalpy.models.baselines.multi_view_random_forest.MultiViewRandomForest method) (drevalpy.models.baselines.naive_pred.NaiveCellLineMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveDrugMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveMeanEffectsPredictor method) (drevalpy.models.baselines.naive_pred.NaivePredictor method) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveTissueMeanPredictor method) (drevalpy.models.baselines.sklearn_models.SklearnModel method) (drevalpy.models.DIPK.dipk.DIPKModel method) (drevalpy.models.drp_model.DRPModel method) (drevalpy.models.DrugGNN.drug_gnn.DrugGNN method) (drevalpy.models.MOLIR.molir.MOLIR method) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel method) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork method) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork method) (drevalpy.models.SRMF.srmf.SRMF method) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR method) load_cl_ids_from_csv() (in module drevalpy.models.utils) load_ctrpv1() (in module drevalpy.datasets.loader) load_ctrpv2() (in module drevalpy.datasets.loader) load_custom() (in module drevalpy.datasets.loader) load_dataset() (in module drevalpy.datasets.loader)

load_drug_features() (drevalpy.models.baselines.naive_pred.NaiveCellLineMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveDrugMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveMeanEffectsPredictor method) (drevalpy.models.baselines.naive_pred.NaivePredictor method) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveTissueMeanPredictor method) (drevalpy.models.baselines.singledrug_baselines.SingleDrugElasticNet method) (drevalpy.models.baselines.singledrug_baselines.SingleDrugRandomForest method) (drevalpy.models.baselines.sklearn_models.SklearnModel method) (drevalpy.models.DIPK.dipk.DIPKModel method) (drevalpy.models.drp_model.DRPModel method) (drevalpy.models.DrugGNN.drug_gnn.DrugGNN method) (drevalpy.models.MOLIR.molir.MOLIR method) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel method) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork method) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork method) (drevalpy.models.SRMF.srmf.SRMF method) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR method) load_drug_fingerprint_features() (in module drevalpy.models.utils) load_drug_ids_from_csv() (in module drevalpy.models.utils) load_features() (in module drevalpy.experiment) load_gdsc1() (in module drevalpy.datasets.loader) load_gdsc2() (in module drevalpy.datasets.loader) load_generic_csv() (in module drevalpy.models.utils) load_model() (drevalpy.models.DrugGNN.drug_gnn.DrugGNN method) load_multi_cell_line_view() (in module drevalpy.models.utils) load_pdx_bruna() (in module drevalpy.datasets.loader) load_single_cell_line_view() (in module drevalpy.models.utils) load_single_drug_view() (in module drevalpy.models.utils) load_splits() (drevalpy.datasets.dataset.DrugResponseDataset method) load_tissues_from_csv() (in module drevalpy.models.utils) load_toyv1() (in module drevalpy.datasets.loader) load_toyv2() (in module drevalpy.datasets.loader) log10_and_set_na() (in module drevalpy.models.utils) log_final_metrics() (drevalpy.models.drp_model.DRPModel method) log_hyperparameters() (drevalpy.models.drp_model.DRPModel method) log_metrics() (drevalpy.models.drp_model.DRPModel method)

M

main() (in module drevalpy.utils) make_model_list() (in module drevalpy.experiment) make_ranges() (in module drevalpy.models.MOLIR.utils) make_train_val_split() (in module drevalpy.experiment) mask() (drevalpy.datasets.dataset.DrugResponseDataset method) meta_info (drevalpy.datasets.dataset.FeatureDataset property) module drevalpy.datasets.curvecurator drevalpy.datasets.dataset drevalpy.datasets.loader drevalpy.datasets.utils drevalpy.evaluation drevalpy.experiment drevalpy.models.baselines.multi_view_random_forest drevalpy.models.baselines.naive_pred drevalpy.models.baselines.singledrug_baselines drevalpy.models.baselines.sklearn_models drevalpy.models.DIPK.attention_utils drevalpy.models.DIPK.data_utils drevalpy.models.DIPK.dipk drevalpy.models.DIPK.gene_expression_encoder drevalpy.models.DIPK.model_utils drevalpy.models.drp_model drevalpy.models.DrugGNN.drug_gnn drevalpy.models.MOLIR.molir drevalpy.models.MOLIR.utils drevalpy.models.PharmaFormer.model_utils drevalpy.models.PharmaFormer.pharmaformer drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network drevalpy.models.SimpleNeuralNetwork.simple_neural_network drevalpy.models.SimpleNeuralNetwork.utils drevalpy.models.SRMF.srmf drevalpy.models.SuperFELTR.superfeltr drevalpy.models.SuperFELTR.utils drevalpy.models.utils drevalpy.pipeline_function drevalpy.utils drevalpy.visualization.comp_scatter drevalpy.visualization.critical_difference_plot drevalpy.visualization.cross_study_tables drevalpy.visualization.heatmap drevalpy.visualization.outplot drevalpy.visualization.regression_slider_plot drevalpy.visualization.utils drevalpy.visualization.vioheat drevalpy.visualization.violin

MOLIEncoder (class in drevalpy.models.MOLIR.utils) MOLIModel (class in drevalpy.models.MOLIR.utils) MOLIR (class in drevalpy.models.MOLIR.molir) MOLIRegressor (class in drevalpy.models.MOLIR.utils) MultiHeadAttentionLayer (class in drevalpy.models.DIPK.attention_utils) MultiViewNeuralNetwork (class in drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network) MultiViewRandomForest (class in drevalpy.models.baselines.multi_view_random_forest)

N

NaiveCellLineMeanPredictor (class in drevalpy.models.baselines.naive_pred) NaiveDrugMeanPredictor (class in drevalpy.models.baselines.naive_pred) NaiveMeanEffectsPredictor (class in drevalpy.models.baselines.naive_pred)

NaiveModel (class in drevalpy.models.baselines.naive_pred) NaivePredictor (class in drevalpy.models.baselines.naive_pred) NaiveTissueDrugMeanPredictor (class in drevalpy.models.baselines.naive_pred) NaiveTissueMeanPredictor (class in drevalpy.models.baselines.naive_pred)

O

OutPlot (class in drevalpy.visualization.outplot)

P

parse_results() (in module drevalpy.visualization.utils) pearson() (in module drevalpy.evaluation) permute_features() (in module drevalpy.datasets.utils) PharmaFormerModel (class in drevalpy.models.PharmaFormer.pharmaformer) pipeline_function() (in module drevalpy.pipeline_function) postprocess() (in module drevalpy.datasets.curvecurator) predict() (drevalpy.models.baselines.multi_view_random_forest.MultiViewRandomForest method) (drevalpy.models.baselines.naive_pred.NaiveCellLineMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveDrugMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveMeanEffectsPredictor method) (drevalpy.models.baselines.naive_pred.NaivePredictor method) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveTissueMeanPredictor method) (drevalpy.models.baselines.sklearn_models.SklearnModel method) (drevalpy.models.DIPK.dipk.DIPKModel method) (drevalpy.models.drp_model.DRPModel method) (drevalpy.models.DrugGNN.drug_gnn.DrugGNN method) (drevalpy.models.MOLIR.molir.MOLIR method) (drevalpy.models.MOLIR.utils.MOLIModel method) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel method) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork method) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork method) (drevalpy.models.SimpleNeuralNetwork.utils.FeedForwardNetwork method) (drevalpy.models.SRMF.srmf.SRMF method) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR method) (drevalpy.models.SuperFELTR.utils.SuperFELTRegressor method)

predict_cl() (drevalpy.models.baselines.naive_pred.NaiveCellLineMeanPredictor method) predict_drug() (drevalpy.models.baselines.naive_pred.NaiveDrugMeanPredictor method) predict_step() (drevalpy.models.DrugGNN.drug_gnn.DrugGNNModule method) predictions (drevalpy.datasets.dataset.DrugResponseDataset property) Predictor (class in drevalpy.models.DIPK.model_utils) prep_results() (in module drevalpy.visualization.utils) prepare_expression_and_methylation() (in module drevalpy.models.utils) prepare_proteomics() (in module drevalpy.models.utils) preprocess() (in module drevalpy.datasets.curvecurator) ProteomicsMedianCenterAndImputeTransformer (class in drevalpy.models.utils)

R

RandomForest (class in drevalpy.models.baselines.sklearn_models) randomization_test() (in module drevalpy.experiment) randomize_features() (drevalpy.datasets.dataset.FeatureDataset method) randomize_graph() (in module drevalpy.datasets.utils) randomize_train_predict() (in module drevalpy.experiment) reduce_to() (drevalpy.datasets.dataset.DrugResponseDataset method) RegressionDataset (class in drevalpy.models.MOLIR.utils) (class in drevalpy.models.SimpleNeuralNetwork.utils)

RegressionSliderPlot (class in drevalpy.visualization.regression_slider_plot) remove_nan_responses() (drevalpy.datasets.dataset.DrugResponseDataset method) remove_rows() (drevalpy.datasets.dataset.DrugResponseDataset method) response (drevalpy.datasets.dataset.DrugResponseDataset property) robustness_test() (in module drevalpy.experiment) robustness_train_predict() (in module drevalpy.experiment)

S

save() (drevalpy.models.baselines.multi_view_random_forest.MultiViewRandomForest method) (drevalpy.models.baselines.naive_pred.NaiveModel method) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor method) (drevalpy.models.baselines.sklearn_models.SklearnModel method) (drevalpy.models.DIPK.dipk.DIPKModel method) (drevalpy.models.drp_model.DRPModel method) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel method) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork method) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork method) (drevalpy.models.SRMF.srmf.SRMF method) save_model() (drevalpy.models.DrugGNN.drug_gnn.DrugGNN method) save_splits() (drevalpy.datasets.dataset.DrugResponseDataset method) scale_gene_expression() (in module drevalpy.models.utils) seed_everything() (in module drevalpy.experiment)

shuffle() (drevalpy.datasets.dataset.DrugResponseDataset method) SimpleNeuralNetwork (class in drevalpy.models.SimpleNeuralNetwork.simple_neural_network) SingleDrugElasticNet (class in drevalpy.models.baselines.singledrug_baselines) SingleDrugRandomForest (class in drevalpy.models.baselines.singledrug_baselines) SklearnModel (class in drevalpy.models.baselines.sklearn_models) spearman() (in module drevalpy.evaluation) split_dataset() (drevalpy.datasets.dataset.DrugResponseDataset method) split_early_stopping() (in module drevalpy.experiment) split_early_stopping_data() (in module drevalpy.datasets.dataset) SRMF (class in drevalpy.models.SRMF.srmf) SuperFELTEncoder (class in drevalpy.models.SuperFELTR.utils) SuperFELTR (class in drevalpy.models.SuperFELTR.superfeltr) SuperFELTRegressor (class in drevalpy.models.SuperFELTR.utils) SVMRegressor (class in drevalpy.models.baselines.sklearn_models)

T

tissue (drevalpy.datasets.dataset.DrugResponseDataset property) to_csv() (drevalpy.datasets.dataset.DrugResponseDataset method) (drevalpy.datasets.dataset.FeatureDataset method) to_dataframe() (drevalpy.datasets.dataset.DrugResponseDataset method) train() (drevalpy.models.baselines.multi_view_random_forest.MultiViewRandomForest method) (drevalpy.models.baselines.naive_pred.NaiveCellLineMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveDrugMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveMeanEffectsPredictor method) (drevalpy.models.baselines.naive_pred.NaivePredictor method) (drevalpy.models.baselines.naive_pred.NaiveTissueDrugMeanPredictor method) (drevalpy.models.baselines.naive_pred.NaiveTissueMeanPredictor method) (drevalpy.models.baselines.sklearn_models.SklearnModel method) (drevalpy.models.DIPK.dipk.DIPKModel method) (drevalpy.models.drp_model.DRPModel method) (drevalpy.models.DrugGNN.drug_gnn.DrugGNN method) (drevalpy.models.MOLIR.molir.MOLIR method) (drevalpy.models.PharmaFormer.pharmaformer.PharmaFormerModel method) (drevalpy.models.SimpleNeuralNetwork.multi_view_neural_network.MultiViewNeuralNetwork method) (drevalpy.models.SimpleNeuralNetwork.simple_neural_network.SimpleNeuralNetwork method) (drevalpy.models.SRMF.srmf.SRMF method) (drevalpy.models.SuperFELTR.superfeltr.SuperFELTR method)

train_and_evaluate() (in module drevalpy.experiment) train_and_predict() (in module drevalpy.experiment) train_final_model() (in module drevalpy.experiment) train_gene_expession_autoencoder() (in module drevalpy.models.DIPK.gene_expression_encoder) train_superfeltr_model() (in module drevalpy.models.SuperFELTR.utils) training_step() (drevalpy.models.DrugGNN.drug_gnn.DrugGNNModule method) (drevalpy.models.MOLIR.utils.MOLIModel method) (drevalpy.models.SimpleNeuralNetwork.utils.FeedForwardNetwork method) (drevalpy.models.SuperFELTR.utils.SuperFELTEncoder method) (drevalpy.models.SuperFELTR.utils.SuperFELTRegressor method) transform() (drevalpy.datasets.dataset.DrugResponseDataset method) (drevalpy.models.utils.ProteomicsMedianCenterAndImputeTransformer method) (drevalpy.models.utils.VarianceFeatureSelector method) transform_features() (drevalpy.datasets.dataset.FeatureDataset method) TransModel (class in drevalpy.models.PharmaFormer.model_utils)

U

unique() (in module drevalpy.models.utils)

unzip_data() (in module drevalpy.datasets.utils)

V

validation_step() (drevalpy.models.DrugGNN.drug_gnn.DrugGNNModule method) (drevalpy.models.MOLIR.utils.MOLIModel method) (drevalpy.models.SimpleNeuralNetwork.utils.FeedForwardNetwork method) (drevalpy.models.SuperFELTR.utils.SuperFELTEncoder method) (drevalpy.models.SuperFELTR.utils.SuperFELTRegressor method)

VarianceFeatureSelector (class in drevalpy.models.utils) view_names (drevalpy.datasets.dataset.FeatureDataset property) VioHeat (class in drevalpy.visualization.vioheat) Violin (class in drevalpy.visualization.violin)

W

write_results() (in module drevalpy.visualization.utils) write_to_html() (drevalpy.visualization.comp_scatter.ComparisonScatter static method) (drevalpy.visualization.critical_difference_plot.CriticalDifferencePlot static method) (drevalpy.visualization.cross_study_tables.CrossStudyTables static method) (drevalpy.visualization.outplot.OutPlot static method) (drevalpy.visualization.regression_slider_plot.RegressionSliderPlot static method) (drevalpy.visualization.vioheat.VioHeat static method)