Index

_

__init__() (pathforge.adapters.losses.TorchClassificationLoss method) (pathforge.adapters.losses.TorchRegressionLoss method) (pathforge.adapters.losses.TorchSurvivalLoss method) (pathforge.adapters.metrics.classification.ClassificationMetricsBackend method) (pathforge.adapters.metrics.classification.TorchMetricsClassificationBackend method) (pathforge.adapters.metrics.survival.SurvivalLossBackend method) (pathforge.adapters.metrics.survival.SurvivalMetricsBackend method) (pathforge.adapters.metrics.survival.TorchSurvBackend method) (pathforge.adapters.mil_lab.backend.MILLabBackendModel method) (pathforge.adapters.mil_lab.backend.MILLabModelSpec method) (pathforge.adapters.torchmil.backend.MILBackendModelProtocol method) (pathforge.adapters.torchmil.backend.TorchMILBackendModel method) (pathforge.adapters.torchmil.backend.TorchMILModelSpec method) (pathforge.adapters.torchmil.heatmap_explainer.HeatMap method) (pathforge.config.config.BenchmarkParamEntry method) (pathforge.core.annotations.csv.CSVAnnotations method) (pathforge.core.base.CoreRegistries method) (pathforge.core.datasets.bag_dataset.BagDataset method) (pathforge.core.datasets.bag_dataset.BagSample method) (pathforge.core.datasets.bag_dataset.SlideRetrievalBagDataset method) (pathforge.core.datasets.bag_dataset.SlideRetrievalDatasetItem method) (pathforge.core.datasets.wsi_dataset.WSI method) (pathforge.core.datasets.wsi_dataset.WSIDataset method) (pathforge.core.evaluation.base.TaskEvaluationAdapterBase method) (pathforge.core.evaluation.orchestrator.EvaluationOrchestrator method) (pathforge.core.evaluation.registry.EvaluationMetricSpec method) (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationData method) (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationHit method) (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationQuery method) (pathforge.core.evaluation.types.EvaluationRunContext method) (pathforge.core.evaluation.types.EvaluationSummary method) (pathforge.core.evaluation.types.MetricRequest method) (pathforge.core.experiments.base.ComboConfig method) (pathforge.core.experiments.base.Experiment method) (pathforge.core.experiments.combinations.ComboConfig method) (pathforge.core.io.h5.base.FileHandleH5 method) (pathforge.core.io.h5.layout.H5Layout method) (pathforge.core.io.slide_artifacts.base.FileHandleH5 method) (pathforge.core.io.slide_artifacts.layout.H5Layout method) (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) (pathforge.core.losses.base.BaseLoss method) (pathforge.core.losses.base.ClassificationLoss method) (pathforge.core.losses.base.RegressionLoss method) (pathforge.core.losses.base.SurvivalContinuousLoss method) (pathforge.core.losses.base.SurvivalDiscreteLoss method) (pathforge.core.models.base.TorchModelBase method) (pathforge.core.models.layers.GlobalAttention method) (pathforge.core.models.layers.GlobalGatedAttention method) (pathforge.core.models.layers.NystromAttention method) (pathforge.core.models.layers.PPEG method) (pathforge.core.models.layers.StandardTransformerBlock method) (pathforge.core.models.layers.TransLayer method) (pathforge.core.models.mil_base.MILModelBase method) (pathforge.core.models.mil_ens.EnsembleMILModel method) (pathforge.core.models.mil_graph.GraphMILModel method) (pathforge.core.models.perceiver_mil.PerceiverMIL method) (pathforge.core.models.prototype_mil.PrototypeMIL method) (pathforge.core.models.sklearn_slide.SklearnCoxnet method) (pathforge.core.models.sklearn_slide.SklearnCoxPH method) (pathforge.core.models.sklearn_slide.SklearnElasticNetRegressor method) (pathforge.core.models.sklearn_slide.SklearnGradientBoostingClassifier method) (pathforge.core.models.sklearn_slide.SklearnGradientBoostingRegressor method) (pathforge.core.models.sklearn_slide.SklearnHingeLossSurvivalSVM method) (pathforge.core.models.sklearn_slide.SklearnIPCRidge method) (pathforge.core.models.sklearn_slide.SklearnLinearRegressor method) (pathforge.core.models.sklearn_slide.SklearnLogisticRegressionClassifier method) (pathforge.core.models.sklearn_slide.SklearnNaiveSurvivalSVM method) (pathforge.core.models.sklearn_slide.SklearnRandomForestClassifier method) (pathforge.core.models.sklearn_slide.SklearnRandomForestRegressor method) (pathforge.core.models.sklearn_slide.SklearnRandomSurvivalForest method) (pathforge.core.models.sklearn_slide.SklearnRidgeRegressor method) (pathforge.core.models.sklearn_slide.SklearnSlideClassifier method) (pathforge.core.models.sklearn_slide.SklearnSlideRegressor method) (pathforge.core.models.sklearn_slide.SklearnSlideSurvival method) (pathforge.core.models.sklearn_slide.SklearnSurvivalTree method) (pathforge.core.models.sklearn_slide.SklearnSVMClassifier method) (pathforge.core.models.sklearn_slide.SklearnSVMRegressor method) (pathforge.core.models.slide_base.SlideLevelModel method) (pathforge.core.models.slide_mlp.SlideVectorMLP method) (pathforge.core.models.var_mil.VarMIL method) (pathforge.core.reports.base.Report method) (pathforge.core.reports.tiles_report_pdf.TilesOverviewEntry method) (pathforge.core.reports.tiles_report_pdf.TilesReportCollection method) (pathforge.core.reports.tiles_report_pdf.TilesReportStats method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) (pathforge.core.tasks.base.TaskBase method) (pathforge.core.visualization.base.TaskVisualizationAdapterBase method) (pathforge.core.visualization.orchestrator.VisualizationOrchestrator method) (pathforge.core.visualization.tiles_overview.TilesOverviewRenderResult method) (pathforge.core.visualization.types.VisualizationRunContext method) (pathforge.core.visualization.types.VisualizationSummary method) (pathforge.inference.heatmaps.InferenceHeatmapResult method) (pathforge.inference.model_package.LoadedModelPackage method) (pathforge.policy.base.PolicyBase method) (pathforge.policy.benchmarking.BenchmarkingPolicy method) (pathforge.policy.feature_extraction.FeatureExtractionPolicy method) (pathforge.policy.inference.InferencePolicy method) (pathforge.policy.optimization.OptimizationPolicy method) (pathforge.policy.utils.ComboConfig method) (pathforge.slide_retrieval.hyperparams.HyperParam method) (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy method) (pathforge.slide_retrieval.representation_strategies.types.RetrievalRepresentation method) (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) (pathforge.slide_retrieval.search_strategies.types.SearchDatabaseItem method) (pathforge.slide_retrieval.search_strategies.types.SearchHit method) (pathforge.slide_retrieval.search_strategies.types.SearchResult method) (pathforge.slide_retrieval.types.RetrievalItemIdentity method) (pathforge.slide_retrieval.types.RetrievalItemMetadata method) (pathforge.slide_retrieval.types.SlideRetrievalManifest method) (pathforge.slide_retrieval.visualization.service.SlideRetrievalVisualizationService method) (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset method) (pathforge.training.base.MILTrainer method) (pathforge.training.lightning.LightningModuleAdapter method) (pathforge.training.lightning.LightningTrainer method) (pathforge.training.metrics.TaskEvaluationArtifacts method) (pathforge.training.sklearn_trainer.SklearnSlideTrainer method) (pathforge.utils.optional.mil_lab.MILLabModules method) (pathforge.utils.optional.torchmil.TorchMILModules method) (pathforge.utils.registries.BackendCatalogEntry method) (pathforge.utils.registry.Registry method)

A

account (pathforge.config.config.SlurmExecutionConfig attribute) accumulate_grad_batches (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) activation_function (pathforge.config.config.BenchmarkParameters attribute) add_config_argument() (in module pathforge.cli.base) add_log_level_argument() (in module pathforge.cli.base) additional_data (pathforge.slide_retrieval.representation_strategies.types.RetrievalRepresentation attribute) (pathforge.slide_retrieval.search_strategies.types.SearchDatabaseItem attribute) additional_retrieval_representation_data_exists() (in module pathforge.core.io.slide_retrieval.retrieval_representations) adj (pathforge.core.datasets.bag_schema.BagBatch attribute) aggregate_command() (in module pathforge.cli.execution) aggregate_plan() (in module pathforge.execution.distributed) aggregation (pathforge.config.config.ExecutionResourcesConfig attribute) aggregation_level (pathforge.config.config.ExperimentConfig attribute) (pathforge.core.datasets.bag_dataset.BagDataset attribute) (pathforge.core.evaluation.types.EvaluationRunContext attribute) (pathforge.core.visualization.types.VisualizationRunContext attribute) (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) all_feature_extractor_names() (in module pathforge.utils.registries) allowed_dataset_uses (pathforge.core.tasks.base.TaskBase attribute) (pathforge.core.tasks.slide_retrieval.SlideRetrievalTask attribute)

amp (pathforge.config.config.FeatureExtractionRuntimeConfig attribute) annotation_file (pathforge.config.config.ExperimentConfig attribute) annotations_df (pathforge.core.datasets.bag_dataset.BagDataset attribute) AnnotationsBase (class in pathforge.core.annotations.base) apply_search_params() (in module pathforge.policy.utils) artifact_path (pathforge.core.datasets.wsi_dataset.WSI attribute) (pathforge.core.reports.tiles_report_pdf.TilesOverviewEntry attribute) (pathforge.inference.heatmaps.InferenceHeatmapResult attribute) (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset attribute) artifact_paths (pathforge.core.datasets.bag_dataset.BagSample attribute) artifacts_dir (pathforge.config.config.DatasetEntry attribute) (pathforge.core.datasets.bag_dataset.BagDataset attribute) (pathforge.core.datasets.wsi_dataset.WSIDataset property) as_bag_batch() (in module pathforge.core.datasets.bag_schema) as_numpy_feature_matrix() (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy static method) assert_bag_schema() (in module pathforge.core.datasets.bag_schema) atomic_slide_artifact_write() (in module pathforge.core.io.slide_artifacts.atomic) Attn_Net_Gated (in module pathforge.core.models.layers) augmentation_methods (pathforge.core.base.CoreRegistries attribute) available (pathforge.utils.registries.BackendCatalogEntry attribute) available_feature_extractor_names() (in module pathforge.utils.registries)

B

backend (pathforge.config.config.ExecutionConfig attribute) (pathforge.config.config.MILConfig attribute) (pathforge.config.config.SlideProcessingConfig attribute) (pathforge.utils.registries.BackendCatalogEntry attribute) BACKEND_NAME (pathforge.core.slide_processing.lazyslide.LazySlideProcessor attribute) BackendCatalogEntry (class in pathforge.utils.registries) bag_group() (pathforge.core.io.h5.layout.H5Layout method) (pathforge.core.io.slide_artifacts.layout.H5Layout method) bag_id (pathforge.core.reports.tiles_report_pdf.TilesReportCollection attribute) (pathforge.inference.heatmaps.InferenceHeatmapResult attribute) bag_size (pathforge.adapters.mil_lab.backend.MILLabBackendModel property) (pathforge.adapters.torchmil.backend.TorchMILBackendModel property) (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) (pathforge.core.datasets.bag_dataset.BagDataset attribute) (pathforge.core.models.mil_base.MILModelBase property) (pathforge.core.models.mil_ens.EnsembleMILModel property) (pathforge.core.models.mil_graph.GraphMILModel property) (pathforge.core.models.perceiver_mil.PerceiverMIL property) (pathforge.core.models.prototype_mil.PrototypeMIL property) (pathforge.core.models.slide_mlp.SlideVectorMLP property) (pathforge.core.models.var_mil.VarMIL property) BagBatch (class in pathforge.core.datasets.bag_schema) BagDataset (class in pathforge.core.datasets.bag_dataset) BagDatasetBase (class in pathforge.core.datasets.base) bags_group (pathforge.core.io.h5.layout.H5Layout attribute) (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) BagSample (class in pathforge.core.datasets.bag_dataset) balancing (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) BaseLoss (class in pathforge.core.losses.base) BaseRetrievalRepresentationStrategy (class in pathforge.slide_retrieval.representation_strategies.base) BaseSearchStrategy (class in pathforge.slide_retrieval.search_strategies.base) batch_size (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.FeatureExtractionRuntimeConfig attribute) (pathforge.config.config.MILConfig attribute) benchmark_manifest (pathforge.execution.distributed.ExecutionPlan attribute) benchmark_parameters (pathforge.config.config.Config attribute) benchmark_search_space() (in module pathforge.policy.utils) benchmarking (pathforge.config.config.ExecutionResourcesConfig attribute)

BenchmarkingPolicy (class in pathforge.policy.benchmarking) BenchmarkParamEntry (class in pathforge.config.config) BenchmarkParameters (class in pathforge.config.config) best_epoch_based_on (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) bin_times() (in module pathforge.core.annotations.binning) bind_sample_loader() (pathforge.core.datasets.bag_dataset.SlideRetrievalBagDataset method) build_aggregated_reference_pool() (in module pathforge.core.evaluation.slide_retrieval.pool) build_bag_dataset() (in module pathforge.core.datasets.factory) build_bag_dataset_for_task() (in module pathforge.policy.utils) build_bag_datasets() (in module pathforge.core.datasets.factory) build_bag_datasets_for_combo() (pathforge.policy.benchmarking.BenchmarkingPolicy method) build_bag_id() (in module pathforge.core.experiments.combo_ids) build_combinations() (in module pathforge.core.experiments.combinations) (pathforge.core.experiments.base.Experiment method) build_combos() (pathforge.policy.feature_extraction.FeatureExtractionPolicy method) build_database() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) build_database_item() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) build_exclusion_key_from_row() (in module pathforge.core.evaluation.slide_retrieval.pool) build_feature_name() (in module pathforge.core.experiments.combo_ids) build_index() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) build_kwargs (pathforge.adapters.mil_lab.backend.MILLabModelSpec attribute) (pathforge.adapters.torchmil.backend.TorchMILModelSpec attribute) build_mil_lab_model() (in module pathforge.adapters.mil_lab.backend) build_mil_model_for_config() (in module pathforge.policy.utils) build_representation_strategy() (in module pathforge.slide_retrieval.representation_strategies.registry) build_retrieval_representation_artifact_path() (in module pathforge.slide_retrieval.representation_strategies.storage) build_retrieval_representation_entry_id() (in module pathforge.slide_retrieval.representation_strategies.storage) build_retrieval_representation_id() (in module pathforge.slide_retrieval.representation_strategies.storage) build_run_hash() (pathforge.slide_retrieval.types.SlideRetrievalManifest method) build_search_strategy() (in module pathforge.slide_retrieval.search_strategies.registry) build_slide_retrieval_inference_output_root() (in module pathforge.slide_retrieval.io) build_slide_retrieval_output_root() (in module pathforge.slide_retrieval.io) build_slide_retrieval_representation_root() (in module pathforge.slide_retrieval.io) build_task() (in module pathforge.core.tasks.registry) build_task_evaluation_adapter() (in module pathforge.core.evaluation.registry) build_task_visualization_adapter() (in module pathforge.core.visualization.registry) build_tiling_id() (in module pathforge.core.experiments.combo_ids) build_torchmil_model() (in module pathforge.adapters.torchmil.backend) build_wsi_dataset() (in module pathforge.core.datasets.factory) build_wsi_datasets() (in module pathforge.core.datasets.factory) builder (pathforge.utils.optional.mil_lab.MILLabModules attribute)

C

calculate_combinations() (in module pathforge.policy.utils) calculate_loss() (pathforge.core.losses.base.ClassificationLoss method) (pathforge.core.losses.base.RegressionLoss method) (pathforge.core.losses.base.SurvivalContinuousLoss method) (pathforge.core.losses.base.SurvivalDiscreteLoss method) canonical_name (pathforge.core.evaluation.registry.EvaluationMetricSpec attribute) (pathforge.core.evaluation.types.MetricRequest attribute) case_id (pathforge.core.datasets.bag_dataset.BagSample attribute) (pathforge.slide_retrieval.types.RetrievalItemMetadata attribute) category (pathforge.core.datasets.bag_dataset.BagSample attribute) (pathforge.core.datasets.wsi_dataset.WSI attribute) (pathforge.slide_retrieval.types.RetrievalItemMetadata attribute) (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset attribute) cfg (pathforge.core.experiments.base.Experiment attribute) choices (pathforge.config.config.SearchSpaceParameter attribute) (pathforge.slide_retrieval.hyperparams.HyperParam attribute) class_weighting (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) classification (pathforge.config.config.Config attribute) classification_backend (pathforge.config.config.MetricsConfig attribute) classification_metrics (pathforge.config.config.MetricsConfig attribute) ClassificationConfig (class in pathforge.config.config) ClassificationLoss (class in pathforge.core.losses.base) ClassificationMetricsBackend (class in pathforge.adapters.metrics.classification) ClassificationMilTask (class in pathforge.core.tasks.mil) clear_sample_loader() (pathforge.core.datasets.bag_dataset.SlideRetrievalBagDataset method) close_wsi() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) collect_hyperparams() (in module pathforge.slide_retrieval.hyperparams) collect_run_summary_row() (in module pathforge.policy.utils) collect_tiles_overview_entries() (in module pathforge.core.reports.tiles_report_pdf) color_norm (pathforge.config.config.BenchmarkParameters attribute) combo_cfg (pathforge.core.datasets.bag_dataset.BagDataset attribute) (pathforge.core.evaluation.types.EvaluationRunContext attribute) (pathforge.core.visualization.types.VisualizationRunContext attribute) (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) combo_keys (pathforge.policy.feature_extraction.FeatureExtractionPolicy attribute) ComboConfig (class in pathforge.core.experiments.base) (class in pathforge.core.experiments.combinations) (class in pathforge.policy.utils) compute() (pathforge.adapters.metrics.classification.ClassificationMetricsBackend method) (pathforge.adapters.metrics.classification.TorchMetricsClassificationBackend method) compute_dcg() (in module pathforge.core.evaluation.slide_retrieval.pool) compute_fn (pathforge.core.evaluation.registry.EvaluationMetricSpec attribute)

compute_hit_at_k() (in module pathforge.core.evaluation.slide_retrieval.metrics.hit) compute_macro_f1_at_k() (in module pathforge.core.evaluation.slide_retrieval.metrics.f1) compute_map_at_k() (in module pathforge.core.evaluation.slide_retrieval.metrics.map) compute_mmv_at_k() (in module pathforge.core.evaluation.slide_retrieval.metrics.mmv) compute_ndcg_at_k() (in module pathforge.core.evaluation.slide_retrieval.metrics.ndcg) compute_precision_at_k() (in module pathforge.core.evaluation.slide_retrieval.metrics.precision) compute_retrieval_representations() (pathforge.core.tasks.slide_retrieval.SlideRetrievalTask method) compute_task_metrics() (in module pathforge.training.metrics) concordance_index() (pathforge.adapters.metrics.survival.SurvivalMetricsBackend method) (pathforge.adapters.metrics.survival.TorchSurvBackend method) Config (class in pathforge.config.config) config (pathforge.inference.model_package.LoadedModelPackage attribute) config_field (pathforge.utils.registries.BackendCatalogEntry attribute) config_path (pathforge.execution.distributed.ExecutionPlan attribute) (pathforge.execution.distributed.WorkRecord attribute) configure_logging() (in module pathforge.cli.base) (in module pathforge.cli.common) configure_optimizers() (pathforge.training.lightning.LightningModuleAdapter method) constraint (pathforge.config.config.SlurmExecutionConfig attribute) COORD_SPACE (pathforge.core.slide_processing.lazyslide.LazySlideProcessor attribute) coords (pathforge.adapters.torchmil.heatmap_explainer.HeatMap attribute) (pathforge.core.datasets.bag_schema.BagBatch attribute) coords_dataset() (pathforge.core.io.h5.layout.H5Layout method) (pathforge.core.io.slide_artifacts.layout.H5Layout method) coords_exist() (in module pathforge.core.io.slide_artifacts.tiles) coords_name (pathforge.core.io.h5.layout.H5Layout attribute) (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) coords_num_rows() (in module pathforge.core.io.slide_artifacts.tiles) CoreRegistries (class in pathforge.core.base) corrupt_overview (pathforge.core.reports.tiles_report_pdf.TilesReportStats attribute) count_relevant_reference_items_by_query() (in module pathforge.core.evaluation.slide_retrieval.pool) count_relevant_reference_items_for_query() (in module pathforge.core.evaluation.slide_retrieval.pool) cpus (pathforge.config.config.StageResourceConfig attribute) create_execution_plan() (in module pathforge.execution.distributed) create_inference_heatmap() (in module pathforge.inference.heatmaps) create_mlp() (in module pathforge.core.models.layers) create_tiles_report_pdf() (in module pathforge.core.reports.tiles_report_pdf) created_at (pathforge.execution.distributed.ExecutionPlan attribute) created_files (pathforge.core.visualization.types.VisualizationSummary attribute) crop_thumbnail_background() (in module pathforge.core.visualization.thumbnail) crop_thumbnail_to_tissue_bounds() (in module pathforge.core.visualization.thumbnail) CSVAnnotations (class in pathforge.core.annotations.csv) curve_data_path (pathforge.training.metrics.TaskEvaluationArtifacts attribute) custom_metrics (pathforge.config.config.ExperimentConfig attribute)

D

data (pathforge.slide_retrieval.representation_strategies.types.RetrievalRepresentation attribute) (pathforge.slide_retrieval.search_strategies.types.SearchDatabaseItem attribute) (pathforge.utils.optional.torchmil.TorchMILModules attribute) dataset_name (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset attribute) dataset_train (pathforge.training.base.MILTrainer attribute) dataset_val (pathforge.training.base.MILTrainer attribute) DatasetBase (class in pathforge.core.datasets.base) DatasetEntry (class in pathforge.config.config) datasets (pathforge.config.config.Config attribute) (pathforge.core.base.CoreRegistries attribute) (pathforge.utils.optional.torchmil.TorchMILModules attribute) DebugReport (class in pathforge.core.reports.base) decode_thumbnail_image() (in module pathforge.core.visualization.thumbnail) default (pathforge.slide_retrieval.hyperparams.HyperParam attribute) delete_all_features_for_bag() (in module pathforge.core.io.slide_artifacts.features) delete_all_retrieval_representations_for_bag() (in module pathforge.core.io.slide_retrieval.retrieval_representations) delete_all_retrieval_representations_for_representation() (in module pathforge.core.io.slide_retrieval.retrieval_representations) delete_if_exists() (in module pathforge.core.io.slide_artifacts.base)

delete_retrieval_representation() (in module pathforge.core.io.slide_retrieval.retrieval_representations) dependencies (pathforge.execution.distributed.WorkRecord attribute) describe_all_representations_strategies() (in module pathforge.slide_retrieval.representation_strategies.registry) describe_all_search_strategies() (in module pathforge.slide_retrieval.search_strategies.registry) descriptor() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) descriptor_exists() (in module pathforge.core.io.slide_retrieval.descriptors) descriptors_group() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) descriptors_group_name (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout attribute) discover_runs() (pathforge.core.evaluation.base.TaskEvaluationAdapterBase method) (pathforge.core.evaluation.slide_retrieval.adapter.SlideRetrievalEvaluationAdapter method) (pathforge.core.visualization.base.TaskVisualizationAdapterBase method) (pathforge.core.visualization.tasks.slide_retrieval.SlideRetrievalVisualizationAdapter method) downscale_x (pathforge.core.visualization.tiles_overview.TilesOverviewRenderResult attribute) downscale_y (pathforge.core.visualization.tiles_overview.TilesOverviewRenderResult attribute) dropout_p (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) ds_cfg (pathforge.core.datasets.bag_dataset.BagDataset attribute)

E

enable_dask_query_planning() (in module pathforge.cli.base) (in module pathforge.cli.common) encoder_layers (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) EnsembleMILModel (class in pathforge.core.models.mil_ens) ensure_artifact_readable_or_quarantine() (in module pathforge.core.io.slide_artifacts.atomic) ensure_bag_features_exist() (pathforge.policy.benchmarking.BenchmarkingPolicy method) ensure_group() (in module pathforge.core.io.slide_artifacts.base) entries (pathforge.core.reports.tiles_report_pdf.TilesReportCollection attribute) epochs (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) error (pathforge.execution.distributed.WorkStatus attribute) evaluate() (pathforge.core.evaluation.orchestrator.EvaluationOrchestrator method) evaluation (pathforge.config.config.Config attribute) (pathforge.config.config.ExperimentConfig attribute) evaluation_metric() (in module pathforge.core.evaluation.registry) evaluation_task_adapter() (in module pathforge.core.evaluation.registry) EvaluationConfig (class in pathforge.config.config) EvaluationMetricSpec (class in pathforge.core.evaluation.registry) EvaluationOrchestrator (class in pathforge.core.evaluation.orchestrator) EvaluationRunContext (class in pathforge.core.evaluation.types) EvaluationSummary (class in pathforge.core.evaluation.types) event_column (pathforge.core.datasets.bag_dataset.BagDataset attribute) exclusion_key (pathforge.slide_retrieval.representation_strategies.types.RetrievalRepresentation attribute) (pathforge.slide_retrieval.search_strategies.types.SearchDatabaseItem attribute) (pathforge.slide_retrieval.types.RetrievalItemIdentity attribute) exclusion_level (pathforge.config.config.SlideRetrievalConfig attribute) (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) execute() (pathforge.core.tasks.base.TaskBase method) (pathforge.core.tasks.slide_retrieval.SlideRetrievalTask method) (pathforge.policy.base.PolicyBase method) (pathforge.policy.benchmarking.BenchmarkingPolicy method) (pathforge.policy.feature_extraction.FeatureExtractionPolicy method) (pathforge.policy.inference.InferencePolicy method) (pathforge.policy.optimization.OptimizationPolicy method)

execute_combination() (pathforge.policy.benchmarking.BenchmarkingPolicy method) execute_combo() (pathforge.policy.feature_extraction.FeatureExtractionPolicy method) execute_dataset() (pathforge.policy.feature_extraction.FeatureExtractionPolicy method) execute_stage() (in module pathforge.execution.distributed) execute_work_record() (in module pathforge.execution.distributed) execution (pathforge.config.config.Config attribute) ExecutionConfig (class in pathforge.config.config) ExecutionPlan (class in pathforge.execution.distributed) ExecutionResourcesConfig (class in pathforge.config.config) exists() (in module pathforge.core.io.slide_artifacts.base) Experiment (class in pathforge.core.experiments.base) experiment (pathforge.config.config.Config attribute) experiment_output_root() (in module pathforge.policy.utils) ExperimentConfig (class in pathforge.config.config) explain() (pathforge.adapters.torchmil.heatmap_explainer.TorchMILHeatmapExplainer method) (pathforge.core.explainer_base.ExplainerBase method) explainability (pathforge.config.config.Config attribute) ExplainabilityConfig (class in pathforge.config.config) ExplainerBase (class in pathforge.core.explainer_base) explainers (pathforge.core.base.CoreRegistries attribute) extra (pathforge.slide_retrieval.types.RetrievalItemMetadata attribute) extra_directives (pathforge.config.config.SlurmExecutionConfig attribute) extract_cells() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) extract_features() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) extract_patches() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) extractor_name (pathforge.core.datasets.bag_dataset.BagDataset attribute)

F

fallback_mpp (pathforge.core.datasets.wsi_dataset.WSI attribute) (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset attribute) feature_dim (pathforge.core.datasets.bag_dataset.BagDataset property) feature_extraction (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ExecutionResourcesConfig attribute) (pathforge.config.config.SlideProcessingConfig attribute) (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) feature_extractors (pathforge.core.base.CoreRegistries attribute) feature_manifest (pathforge.execution.distributed.ExecutionPlan attribute) feature_path (pathforge.core.datasets.bag_dataset.BagDataset attribute) feature_policy (pathforge.policy.benchmarking.BenchmarkingPolicy property) FeatureExtractionPolicy (class in pathforge.policy.feature_extraction) FeatureExtractionRuntimeConfig (class in pathforge.config.config) features_dataset() (pathforge.core.io.h5.layout.H5Layout method) (pathforge.core.io.slide_artifacts.layout.H5Layout method) features_dir (pathforge.config.config.DatasetEntry attribute) features_exist() (in module pathforge.core.io.slide_artifacts.features) features_group() (pathforge.core.io.h5.layout.H5Layout method) (pathforge.core.io.slide_artifacts.layout.H5Layout method) features_group_name (pathforge.core.io.h5.layout.H5Layout attribute) (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) figure_paths (pathforge.training.metrics.TaskEvaluationArtifacts attribute) FileHandleH5 (class in pathforge.core.io.h5.base) (class in pathforge.core.io.slide_artifacts.base) filter_database_by_exclusion_key() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) filter_query_self_hits() (in module pathforge.core.evaluation.slide_retrieval.voting) finalize_command() (in module pathforge.cli.optimize_run) find_slides_with_missing_features() (in module pathforge.core.features.utils) finished_at (pathforge.execution.distributed.WorkStatus attribute) fit() (pathforge.core.models.base.ScikitBase method) (pathforge.core.models.sklearn_slide.SklearnSlideClassifier method) (pathforge.core.models.sklearn_slide.SklearnSlideRegressor method) (pathforge.core.models.sklearn_slide.SklearnSlideSurvival method) (pathforge.training.base.TrainerBase method) (pathforge.training.lightning.LightningTrainer method) (pathforge.training.sklearn_trainer.SklearnSlideTrainer method)

fit_image_to_canvas() (in module pathforge.core.visualization.thumbnail) forward() (pathforge.adapters.losses.TorchClassificationLoss method) (pathforge.adapters.losses.TorchRegressionLoss method) (pathforge.adapters.losses.TorchSurvivalLoss method) (pathforge.core.losses.base.BaseLoss method) (pathforge.core.losses.base.ClassificationLoss method) (pathforge.core.losses.base.RegressionLoss method) (pathforge.core.losses.base.SurvivalContinuousLoss method) (pathforge.core.losses.base.SurvivalDiscreteLoss method) (pathforge.core.models.layers.GlobalAttention method) (pathforge.core.models.layers.GlobalGatedAttention method) (pathforge.core.models.layers.NystromAttention method) (pathforge.core.models.layers.PPEG method) (pathforge.core.models.layers.StandardTransformerBlock method) (pathforge.core.models.layers.TransLayer method) (pathforge.core.models.mil_base.MILModelBase method) (pathforge.core.models.slide_base.SlideLevelModel method) (pathforge.training.lightning.LightningModuleAdapter method) forward_bag() (pathforge.adapters.mil_lab.backend.MILLabBackendModel method) (pathforge.adapters.torchmil.backend.MILBackendModelProtocol method) (pathforge.adapters.torchmil.backend.TorchMILBackendModel method) (pathforge.core.models.mil_base.MILModelBase method) (pathforge.core.models.mil_ens.EnsembleMILModel method) (pathforge.core.models.mil_graph.GraphMILModel method) (pathforge.core.models.perceiver_mil.PerceiverMIL method) (pathforge.core.models.prototype_mil.PrototypeMIL method) (pathforge.core.models.slide_mlp.SlideVectorMLP method) (pathforge.core.models.var_mil.VarMIL method) forward_slide() (pathforge.core.models.slide_base.SlideLevelModel method) (pathforge.core.models.slide_mlp.SlideVectorMLP method) from_dict() (pathforge.slide_retrieval.types.RetrievalItemIdentity class method) from_keys_values() (pathforge.core.experiments.base.ComboConfig class method) (pathforge.core.experiments.combinations.ComboConfig class method) (pathforge.policy.utils.ComboConfig class method) from_yaml() (pathforge.config.config.Config class method)

G

get() (pathforge.core.base.RegistryBase method) (pathforge.core.experiments.base.ComboConfig method) (pathforge.core.experiments.combinations.ComboConfig method) (pathforge.policy.utils.ComboConfig method) (pathforge.utils.registry.Registry method) get_allowed_dataset_uses() (pathforge.core.tasks.base.TaskBase class method) get_bag_sample() (pathforge.core.datasets.bag_dataset.BagDataset method) get_base_mpp() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) get_dataset() (in module pathforge.core.io.slide_artifacts.base) get_discovery_keys() (pathforge.core.evaluation.base.TaskEvaluationAdapterBase class method) (pathforge.core.evaluation.slide_retrieval.adapter.SlideRetrievalEvaluationAdapter class method) (pathforge.core.visualization.tasks.slide_retrieval.SlideRetrievalVisualizationAdapter class method) get_entries() (pathforge.config.config.BenchmarkParameters method) get_feature_level() (pathforge.core.datasets.bag_dataset.BagDataset method) get_feature_level_reason() (pathforge.core.datasets.bag_dataset.BagDataset method) get_grid_keys() (pathforge.core.tasks.base.TaskBase class method) get_hyperparams() (pathforge.core.experiments.base.ComboConfig method) (pathforge.core.experiments.combinations.ComboConfig method) (pathforge.policy.utils.ComboConfig method) get_inference_dataset_uses() (pathforge.core.tasks.base.TaskBase class method) get_inference_grid_keys() (pathforge.core.tasks.base.TaskBase class method) get_inference_input_use() (pathforge.core.tasks.base.TaskBase class method) get_learnable_parameters() (pathforge.adapters.mil_lab.backend.MILLabBackendModel method) (pathforge.adapters.torchmil.backend.TorchMILBackendModel method) (pathforge.core.models.base.ModelBase method) (pathforge.core.models.base.TorchModelBase method) (pathforge.core.models.sklearn_slide.SklearnSlideClassifier method) (pathforge.core.models.sklearn_slide.SklearnSlideRegressor method) (pathforge.core.models.sklearn_slide.SklearnSlideSurvival method)

get_representation_strategy() (in module pathforge.slide_retrieval.representation_strategies.registry) get_representation_strategy_defaults() (in module pathforge.slide_retrieval.representation_strategies.registry) get_representation_strategy_hyperparams() (in module pathforge.slide_retrieval.representation_strategies.registry) get_representation_strategy_output_kind() (in module pathforge.slide_retrieval.representation_strategies.registry) get_representation_strategy_supported_feature_levels() (in module pathforge.slide_retrieval.representation_strategies.registry) get_representation_strategy_values() (in module pathforge.slide_retrieval.representation_strategies.registry) get_sample() (pathforge.core.datasets.bag_dataset.BagDataset method) get_search_strategy() (in module pathforge.slide_retrieval.search_strategies.registry) get_search_strategy_defaults() (in module pathforge.slide_retrieval.search_strategies.registry) get_search_strategy_hyperparams() (in module pathforge.slide_retrieval.search_strategies.registry) get_search_strategy_supported_representation_kinds() (in module pathforge.slide_retrieval.search_strategies.registry) get_search_strategy_supports() (in module pathforge.slide_retrieval.search_strategies.registry) get_search_strategy_values() (in module pathforge.slide_retrieval.search_strategies.registry) get_status() (in module pathforge.core.io.slide_artifacts.base) get_task() (in module pathforge.core.tasks.registry) get_task_allowed_dataset_uses() (in module pathforge.core.tasks.registry) get_task_evaluation_adapter() (in module pathforge.core.evaluation.registry) get_thumbnail() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) get_top_k_hits() (in module pathforge.core.evaluation.slide_retrieval.voting) get_values() (pathforge.config.config.BenchmarkParameters method) GlobalAttention (class in pathforge.core.models.layers) GlobalGatedAttention (class in pathforge.core.models.layers) gpus (pathforge.config.config.StageResourceConfig attribute) gradient_clip_val (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) GraphMILModel (class in pathforge.core.models.mil_graph) grid_keys (pathforge.core.tasks.base.TaskBase attribute) (pathforge.core.tasks.slide_retrieval.SlideRetrievalTask attribute) group_bag_datasets_by_use() (pathforge.policy.benchmarking.BenchmarkingPolicy method) group_datasets_by_use() (in module pathforge.core.datasets.utils)

H

h5 (pathforge.core.io.h5.base.FileHandleH5 property) (pathforge.core.io.slide_artifacts.base.FileHandleH5 property) H5Layout (class in pathforge.core.io.h5.layout) (class in pathforge.core.io.slide_artifacts.layout) heartbeat_interval (pathforge.config.config.OptimizationConfig attribute) HeatMap (class in pathforge.adapters.torchmil.heatmap_explainer) heatmap_backend (pathforge.config.config.ExplainabilityConfig attribute) heatmap_colormap (pathforge.config.config.ExplainabilityConfig attribute) heatmap_coords_name (pathforge.core.io.h5.layout.H5Layout attribute) heatmap_metadata_name (pathforge.core.io.h5.layout.H5Layout attribute) heatmap_name (pathforge.inference.heatmaps.InferenceHeatmapResult attribute) heatmap_scores_name (pathforge.core.io.h5.layout.H5Layout attribute) heatmap_smoothed_alpha (pathforge.config.config.ExplainabilityConfig attribute) heatmap_smoothing_sigma_scale (pathforge.config.config.ExplainabilityConfig attribute) heatmap_tile_alpha (pathforge.config.config.ExplainabilityConfig attribute)

heatmap_top_k_tiles (pathforge.config.config.ExplainabilityConfig attribute) heatmaps_group_name (pathforge.core.io.h5.layout.H5Layout attribute) help (pathforge.slide_retrieval.hyperparams.HyperParam attribute) hf_key (pathforge.config.config.Config attribute) high (pathforge.config.config.SearchSpaceParameter attribute) hits (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationQuery attribute) (pathforge.slide_retrieval.search_strategies.types.SearchResult attribute) hostname (pathforge.execution.distributed.WorkStatus attribute) hp_type (pathforge.slide_retrieval.hyperparams.HyperParam attribute) HyperParam (class in pathforge.slide_retrieval.hyperparams) hyperparam_spec() (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy class method) (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy class method) hyperparam_values() (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy method) (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) hyperparams (pathforge.config.config.BenchmarkParamEntry attribute)

I

image_bytes (pathforge.core.reports.tiles_report_pdf.TilesOverviewEntry attribute) (pathforge.core.visualization.tiles_overview.TilesOverviewRenderResult attribute) image_height_px (pathforge.core.visualization.tiles_overview.TilesOverviewRenderResult attribute) image_output_path (pathforge.inference.heatmaps.InferenceHeatmapResult attribute) image_width_px (pathforge.core.visualization.tiles_overview.TilesOverviewRenderResult attribute) import_evaluation_metric_modules() (in module pathforge.core.evaluation.registry) import_representation_strategy_modules() (in module pathforge.slide_retrieval.representation_strategies.registry) import_search_strategy_modules() (in module pathforge.slide_retrieval.search_strategies.registry) import_task_evaluation_adapter_modules() (in module pathforge.core.evaluation.registry) import_task_modules() (in module pathforge.core.tasks.registry) import_task_visualization_adapter_modules() (in module pathforge.core.visualization.registry) included_slides (pathforge.core.reports.tiles_report_pdf.TilesReportStats attribute) index (pathforge.core.datasets.bag_dataset.SlideRetrievalDatasetItem attribute) infer_feature_level() (in module pathforge.core.io.slide_artifacts.features) infer_model_dimensions() (in module pathforge.policy.utils) inference() (pathforge.core.tasks.base.TaskBase method) (pathforge.core.tasks.slide_retrieval.SlideRetrievalTask method) inference_dataset_uses (pathforge.core.tasks.base.TaskBase attribute) (pathforge.core.tasks.slide_retrieval.SlideRetrievalTask attribute) inference_input_use (pathforge.core.tasks.base.TaskBase attribute) (pathforge.core.tasks.slide_retrieval.SlideRetrievalTask attribute) inference_metadata (pathforge.inference.model_package.LoadedModelPackage property) InferenceHeatmapResult (class in pathforge.inference.heatmaps) InferencePolicy (class in pathforge.policy.inference) initialize() (pathforge.adapters.torchmil.heatmap_explainer.TorchMILHeatmapExplainer method) (pathforge.core.explainer_base.ExplainerBase method) (pathforge.core.models.base.ModelBase method) (pathforge.core.models.base.TorchModelBase method) (pathforge.core.models.sklearn_slide.SklearnSlideClassifier method) (pathforge.core.models.sklearn_slide.SklearnSlideRegressor method) (pathforge.core.models.sklearn_slide.SklearnSlideSurvival method)

inputs (pathforge.core.datasets.bag_dataset.SlideRetrievalDatasetItem attribute) inspect_annotations() (pathforge.core.annotations.base.AnnotationsBase method) (pathforge.core.annotations.csv.CSVAnnotations method) inspect_slide() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) instance_scores() (pathforge.core.models.mil_base.MILModelBase method) is_available() (pathforge.core.base.RegistryBase method) (pathforge.utils.registry.Registry method) is_complete() (in module pathforge.core.io.slide_artifacts.base) is_feature_extractor_available() (in module pathforge.utils.registries) is_loaded (pathforge.core.datasets.wsi_dataset.WSI property) is_mil_lab_available() (in module pathforge.utils.optional.mil_lab) is_representation_strategy_available() (in module pathforge.slide_retrieval.representation_strategies.registry) is_search_strategy_available() (in module pathforge.slide_retrieval.search_strategies.registry) is_task_available() (in module pathforge.core.tasks.registry) is_torchmetrics_available() (in module pathforge.utils.optional.torchmil) is_torchmil_available() (in module pathforge.utils.optional.torchmil) is_torchsurv_available() (in module pathforge.utils.optional.torchmil) item_id (pathforge.slide_retrieval.search_strategies.types.SearchDatabaseItem property) (pathforge.slide_retrieval.search_strategies.types.SearchHit property)

K

k (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute)

kind (pathforge.config.config.SearchSpaceParameter attribute)

L

label (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationHit attribute) label_column (pathforge.config.config.EvaluationConfig attribute) (pathforge.config.config.ExperimentConfig attribute) (pathforge.core.evaluation.types.EvaluationRunContext attribute) lazyslide_model_names() (in module pathforge.utils.registries) LazySlideProcessor (class in pathforge.core.slide_processing.lazyslide) LightningModuleAdapter (class in pathforge.training.lightning) LightningTrainer (class in pathforge.training.lightning) list_evaluation_metrics() (in module pathforge.core.evaluation.registry) list_feature_extractors() (in module pathforge.utils.registries) list_mil_models() (in module pathforge.utils.registries) list_plugins() (pathforge.core.base.RegistryBase method) (pathforge.utils.registry.Registry method) list_representation_strategies() (in module pathforge.slide_retrieval.representation_strategies.registry) list_search_strategies() (in module pathforge.slide_retrieval.search_strategies.registry) list_sklearn_slide_models() (in module pathforge.core.models.sklearn_slide) list_task_evaluation_adapters() (in module pathforge.core.evaluation.registry) list_tasks() (in module pathforge.core.tasks.registry) load() (pathforge.core.models.base.ModelBase method) (pathforge.core.models.base.ScikitBase method) (pathforge.core.models.base.TorchModelBase method) load_annotations() (pathforge.core.annotations.base.AnnotationsBase method) (pathforge.core.annotations.csv.CSVAnnotations method) (pathforge.core.experiments.base.Experiment method) load_bag() (pathforge.core.datasets.bag_dataset.BagDataset method) load_bag_from_input() (in module pathforge.inference.model_package)

load_config() (in module pathforge.cli.base) load_experiment() (in module pathforge.cli.base) load_external_tissue_polygons() (in module pathforge.core.io.slide_artifacts.tissue) load_mil_lab_modules() (in module pathforge.utils.optional.mil_lab) load_or_create_slide_patch_mean_rgb() (in module pathforge.slide_retrieval.representation_strategies.mean_rgb) load_packaged_model() (in module pathforge.inference.model_package) load_patch_dicts_pickle() (in module pathforge.slide_retrieval.search_strategies.utils) load_plan() (in module pathforge.execution.distributed) load_run_data() (pathforge.core.evaluation.base.TaskEvaluationAdapterBase method) (pathforge.core.evaluation.slide_retrieval.adapter.SlideRetrievalEvaluationAdapter method) load_sample() (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy method) load_sample_patch_coords() (in module pathforge.slide_retrieval.io) load_slide_retrieval_representation() (in module pathforge.slide_retrieval.io) load_study (pathforge.config.config.OptimizationConfig attribute) load_torchmil_modules() (in module pathforge.utils.optional.torchmil) load_wsi() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) LoadedModelPackage (class in pathforge.inference.model_package) log (pathforge.config.config.SearchSpaceParameter attribute) loss (pathforge.config.config.BenchmarkParameters attribute) (pathforge.training.base.MILTrainer attribute) losses (pathforge.core.base.CoreRegistries attribute) low (pathforge.config.config.SearchSpaceParameter attribute) lr (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute)

M

main() (in module pathforge.cli.app) (in module pathforge.cli.benchmark_run) (in module pathforge.cli.evaluate_run) (in module pathforge.cli.features_run) (in module pathforge.cli.features_slide) (in module pathforge.cli.infer_run) (in module pathforge.cli.inference) (in module pathforge.cli.optimize_run) (in module pathforge.cli.report_tiles) (in module pathforge.cli.retrieval_mean_rgb) (in module pathforge.cli.retrieval_representations) (in module pathforge.cli.retrieval_sish_vqvae) (in module pathforge.cli.visualize_run) make_sklearn_slide_model() (in module pathforge.core.models.sklearn_slide) make_survival_structured_array() (in module pathforge.core.models.sklearn_slide) manifest (pathforge.core.evaluation.types.EvaluationRunContext attribute) (pathforge.core.visualization.types.VisualizationRunContext attribute) mask (pathforge.core.datasets.bag_schema.BagBatch attribute) max (pathforge.slide_retrieval.hyperparams.HyperParam attribute) max_concurrent (pathforge.config.config.SlurmExecutionConfig attribute) max_workers (pathforge.config.config.ExecutionConfig attribute) member_ids (pathforge.slide_retrieval.types.RetrievalItemMetadata attribute) memory_gb (pathforge.config.config.StageResourceConfig attribute) metadata (pathforge.core.datasets.bag_dataset.BagSample attribute) (pathforge.slide_retrieval.representation_strategies.types.RetrievalRepresentation attribute) (pathforge.slide_retrieval.search_strategies.types.SearchDatabaseItem attribute) (pathforge.slide_retrieval.search_strategies.types.SearchHit attribute) (pathforge.slide_retrieval.search_strategies.types.SearchResult attribute) (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset attribute) metric_should_minimize() (in module pathforge.policy.utils) MetricRequest (class in pathforge.core.evaluation.types) metrics (pathforge.config.config.Config attribute) (pathforge.config.config.EvaluationConfig attribute) (pathforge.core.evaluation.types.EvaluationSummary attribute) metrics_for_task() (pathforge.config.config.MetricsConfig method) metrics_path (pathforge.training.metrics.TaskEvaluationArtifacts attribute) MetricsConfig (class in pathforge.config.config) mil (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.Config attribute) mil_lab_from_pretrained (pathforge.config.config.MILConfig attribute) mil_lab_model (pathforge.config.config.MILConfig attribute) mil_lab_model_kwargs (pathforge.config.config.MILConfig attribute) MILBackendModelProtocol (class in pathforge.adapters.torchmil.backend) MILBagDataset (class in pathforge.core.datasets.bag_dataset) MILConfig (class in pathforge.config.config) MILLabBackendModel (class in pathforge.adapters.mil_lab.backend) MILLabModelSpec (class in pathforge.adapters.mil_lab.backend) MILLabModules (class in pathforge.utils.optional.mil_lab) MILModelBase (class in pathforge.core.models.mil_base) MILTrainer (class in pathforge.training.base) min (pathforge.slide_retrieval.hyperparams.HyperParam attribute) missing_coords (pathforge.core.reports.tiles_report_pdf.TilesReportStats attribute) missing_overview (pathforge.core.reports.tiles_report_pdf.TilesReportStats attribute) mixed_precision (pathforge.config.config.ExperimentConfig attribute) mode (pathforge.config.config.ExperimentConfig attribute) (pathforge.core.io.h5.base.FileHandleH5 attribute) (pathforge.core.io.slide_artifacts.base.FileHandleH5 attribute) model (pathforge.inference.model_package.LoadedModelPackage attribute) (pathforge.training.base.MILTrainer attribute) model_config (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.Config attribute) (pathforge.config.config.DatasetEntry attribute) (pathforge.config.config.EvaluationConfig attribute) (pathforge.config.config.ExecutionConfig attribute) (pathforge.config.config.ExecutionResourcesConfig attribute) (pathforge.config.config.ExperimentConfig attribute) (pathforge.config.config.ExplainabilityConfig attribute) (pathforge.config.config.FeatureExtractionRuntimeConfig attribute) (pathforge.config.config.MetricsConfig attribute) (pathforge.config.config.MILConfig attribute) (pathforge.config.config.OptimizationConfig attribute) (pathforge.config.config.SearchSpaceParameter attribute) (pathforge.config.config.SlideProcessingConfig attribute) (pathforge.config.config.SlideRetrievalConfig attribute) (pathforge.config.config.SlurmExecutionConfig attribute) (pathforge.config.config.StageResourceConfig attribute) (pathforge.execution.distributed.ExecutionPlan attribute) (pathforge.execution.distributed.WorkRecord attribute) (pathforge.execution.distributed.WorkStatus attribute) model_name (pathforge.inference.model_package.LoadedModelPackage property) ModelBase (class in pathforge.core.models.base) models (pathforge.core.base.CoreRegistries attribute) (pathforge.utils.optional.torchmil.TorchMILModules attribute) module pathforge.adapters.losses pathforge.adapters.metrics.classification pathforge.adapters.metrics.survival pathforge.adapters.mil_lab.backend pathforge.adapters.tcga_tools pathforge.adapters.torchmil.backend pathforge.adapters.torchmil.collate pathforge.adapters.torchmil.heatmap_explainer pathforge.adapters.torchmil.task_output pathforge.cli.app pathforge.cli.base pathforge.cli.benchmark_run pathforge.cli.common pathforge.cli.evaluate_run pathforge.cli.execution pathforge.cli.features_run pathforge.cli.features_slide pathforge.cli.infer_run pathforge.cli.inference pathforge.cli.optimize_run pathforge.cli.report_tiles pathforge.cli.retrieval_mean_rgb pathforge.cli.retrieval_representations pathforge.cli.retrieval_sish_vqvae pathforge.cli.visualize_run pathforge.config.config pathforge.core.annotations.base pathforge.core.annotations.binning pathforge.core.annotations.csv pathforge.core.base pathforge.core.datasets.bag_dataset pathforge.core.datasets.bag_schema pathforge.core.datasets.factory pathforge.core.datasets.samplers pathforge.core.datasets.utils pathforge.core.evaluation.base pathforge.core.evaluation.orchestrator pathforge.core.evaluation.registry pathforge.core.evaluation.slide_retrieval.adapter pathforge.core.evaluation.slide_retrieval.data pathforge.core.evaluation.slide_retrieval.metrics.f1 pathforge.core.evaluation.slide_retrieval.metrics.hit pathforge.core.evaluation.slide_retrieval.metrics.map pathforge.core.evaluation.slide_retrieval.metrics.mmv pathforge.core.evaluation.slide_retrieval.metrics.ndcg pathforge.core.evaluation.slide_retrieval.metrics.precision pathforge.core.evaluation.slide_retrieval.pool pathforge.core.evaluation.slide_retrieval.voting pathforge.core.evaluation.types pathforge.core.experiments.combinations pathforge.core.experiments.combo_ids pathforge.core.features.utils pathforge.core.io.h5.descriptors pathforge.core.io.h5.features pathforge.core.io.h5.heatmaps pathforge.core.io.h5.layout pathforge.core.io.h5.tiles pathforge.core.io.h5.tissue pathforge.core.io.slide_artifacts.atomic pathforge.core.io.slide_artifacts.base pathforge.core.io.slide_artifacts.features pathforge.core.io.slide_artifacts.layout pathforge.core.io.slide_artifacts.thumbnail pathforge.core.io.slide_artifacts.tiles pathforge.core.io.slide_artifacts.tissue pathforge.core.io.slide_retrieval.descriptors pathforge.core.io.slide_retrieval.layout pathforge.core.io.slide_retrieval.retrieval_representations pathforge.core.models.layers pathforge.core.models.mil_ens pathforge.core.models.mil_graph pathforge.core.models.perceiver_mil pathforge.core.models.prototype_mil pathforge.core.models.sklearn_slide pathforge.core.models.slide_mlp pathforge.core.models.utils pathforge.core.models.var_mil pathforge.core.registry pathforge.core.reports.base pathforge.core.reports.tiles_report_pdf pathforge.core.slide_processing.lazyslide pathforge.core.tasks.mil pathforge.core.tasks.registry pathforge.core.visualization.base pathforge.core.visualization.orchestrator pathforge.core.visualization.registry pathforge.core.visualization.tasks.slide_retrieval pathforge.core.visualization.thumbnail pathforge.core.visualization.tiles_overview pathforge.core.visualization.types pathforge.execution.distributed pathforge.inference.heatmaps pathforge.inference.model_package pathforge.policy.inference pathforge.policy.utils pathforge.slide_retrieval.hyperparams pathforge.slide_retrieval.io pathforge.slide_retrieval.representation_strategies.base pathforge.slide_retrieval.representation_strategies.mean_rgb pathforge.slide_retrieval.representation_strategies.registry pathforge.slide_retrieval.representation_strategies.storage pathforge.slide_retrieval.representation_strategies.types pathforge.slide_retrieval.search_strategies.base pathforge.slide_retrieval.search_strategies.registry pathforge.slide_retrieval.search_strategies.types pathforge.slide_retrieval.search_strategies.utils pathforge.slide_retrieval.types pathforge.slide_retrieval.visualization.renderers pathforge.slide_retrieval.visualization.service pathforge.training.callbacks pathforge.training.lightning pathforge.training.metrics pathforge.training.sklearn_trainer pathforge.utils.constants pathforge.utils.io pathforge.utils.logging pathforge.utils.optional.mil_lab pathforge.utils.optional.torchmil pathforge.utils.registries pathforge.utils.registry pathforge.utils.serialization

N

name (pathforge.adapters.mil_lab.backend.MILLabModelSpec attribute) (pathforge.adapters.torchmil.backend.TorchMILModelSpec attribute) (pathforge.config.config.DatasetEntry attribute) (pathforge.core.datasets.bag_dataset.BagDataset property) (pathforge.core.datasets.base.DatasetBase property) (pathforge.core.datasets.wsi_dataset.WSIDataset property) (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy attribute) (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy attribute) (pathforge.utils.registries.BackendCatalogEntry attribute) neg_partial_log_likelihood() (pathforge.adapters.metrics.survival.SurvivalLossBackend method) (pathforge.adapters.metrics.survival.TorchSurvBackend method) normalize_log_level() (in module pathforge.cli.common) normalize_mil_lab_output() (in module pathforge.adapters.mil_lab.backend) normalize_text_id() (in module pathforge.core.evaluation.slide_retrieval.pool) normalize_torchmil_output() (in module pathforge.adapters.torchmil.task_output) normalizers (pathforge.core.base.CoreRegistries attribute)

num_bags (pathforge.core.datasets.bag_dataset.BagDataset property) (pathforge.core.datasets.base.BagDatasetBase property) num_benchmark_jobs (pathforge.execution.distributed.ExecutionPlan attribute) num_feature_jobs (pathforge.execution.distributed.ExecutionPlan attribute) num_optimization_workers (pathforge.execution.distributed.ExecutionPlan attribute) num_points (pathforge.inference.heatmaps.InferenceHeatmapResult attribute) num_queries (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) num_reference_items (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) num_samples (pathforge.core.datasets.base.BagDatasetBase property) (pathforge.core.datasets.base.DatasetBase property) (pathforge.core.datasets.wsi_dataset.WSIDataset property) num_tiles (pathforge.core.datasets.base.TileDatasetBase property) (pathforge.core.reports.tiles_report_pdf.TilesOverviewEntry attribute) num_workers (pathforge.config.config.ExperimentConfig attribute) (pathforge.config.config.FeatureExtractionRuntimeConfig attribute) NystromAttention (class in pathforge.core.models.layers)

O

obj (pathforge.core.datasets.wsi_dataset.WSI property) objective() (pathforge.policy.optimization.OptimizationPolicy method) objective_dataset (pathforge.config.config.OptimizationConfig attribute) objective_metric (pathforge.config.config.OptimizationConfig attribute) objective_mode (pathforge.config.config.OptimizationConfig attribute) on_validation_epoch_end() (pathforge.training.lightning.LightningModuleAdapter method) on_validation_epoch_start() (pathforge.training.lightning.LightningModuleAdapter method) optimization (pathforge.config.config.Config attribute) (pathforge.config.config.ExecutionResourcesConfig attribute)

optimization_search_space() (in module pathforge.policy.utils) OptimizationConfig (class in pathforge.config.config) OptimizationPolicy (class in pathforge.policy.optimization) optimizer (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.MILConfig attribute) output_dim() (pathforge.core.datasets.bag_dataset.BagDataset method) output_path (pathforge.inference.heatmaps.InferenceHeatmapResult attribute) output_representation_kind (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy attribute)

P

package_path_from_checkpoint() (in module pathforge.inference.model_package) package_payload (pathforge.inference.model_package.LoadedModelPackage attribute) params (pathforge.core.evaluation.types.MetricRequest attribute) parser (pathforge.core.evaluation.registry.EvaluationMetricSpec attribute) partition (pathforge.config.config.SlurmExecutionConfig attribute) path (pathforge.core.datasets.wsi_dataset.WSI attribute) (pathforge.core.io.h5.base.FileHandleH5 attribute) (pathforge.core.io.slide_artifacts.base.FileHandleH5 attribute) pathforge.adapters.losses module pathforge.adapters.metrics.classification module pathforge.adapters.metrics.survival module pathforge.adapters.mil_lab.backend module pathforge.adapters.tcga_tools module pathforge.adapters.torchmil.backend module pathforge.adapters.torchmil.collate module pathforge.adapters.torchmil.heatmap_explainer module pathforge.adapters.torchmil.task_output module pathforge.cli.app module pathforge.cli.base module pathforge.cli.benchmark_run module pathforge.cli.common module pathforge.cli.evaluate_run module pathforge.cli.execution module pathforge.cli.features_run module pathforge.cli.features_slide module pathforge.cli.infer_run module pathforge.cli.inference module pathforge.cli.optimize_run module pathforge.cli.report_tiles module pathforge.cli.retrieval_mean_rgb module pathforge.cli.retrieval_representations module pathforge.cli.retrieval_sish_vqvae module pathforge.cli.visualize_run module pathforge.config.config module pathforge.core.annotations.base module pathforge.core.annotations.binning module pathforge.core.annotations.csv module pathforge.core.base module pathforge.core.datasets.bag_dataset module pathforge.core.datasets.bag_schema module pathforge.core.datasets.factory module pathforge.core.datasets.samplers module pathforge.core.datasets.utils module pathforge.core.evaluation.base module pathforge.core.evaluation.orchestrator module pathforge.core.evaluation.registry module pathforge.core.evaluation.slide_retrieval.adapter module pathforge.core.evaluation.slide_retrieval.data module pathforge.core.evaluation.slide_retrieval.metrics.f1 module pathforge.core.evaluation.slide_retrieval.metrics.hit module pathforge.core.evaluation.slide_retrieval.metrics.map module pathforge.core.evaluation.slide_retrieval.metrics.mmv module pathforge.core.evaluation.slide_retrieval.metrics.ndcg module pathforge.core.evaluation.slide_retrieval.metrics.precision module pathforge.core.evaluation.slide_retrieval.pool module pathforge.core.evaluation.slide_retrieval.voting module pathforge.core.evaluation.types module pathforge.core.experiments.combinations module pathforge.core.experiments.combo_ids module pathforge.core.features.utils module pathforge.core.io.h5.descriptors module pathforge.core.io.h5.features module pathforge.core.io.h5.heatmaps module pathforge.core.io.h5.layout module pathforge.core.io.h5.tiles module pathforge.core.io.h5.tissue module pathforge.core.io.slide_artifacts.atomic module pathforge.core.io.slide_artifacts.base module pathforge.core.io.slide_artifacts.features module pathforge.core.io.slide_artifacts.layout module pathforge.core.io.slide_artifacts.thumbnail module pathforge.core.io.slide_artifacts.tiles module pathforge.core.io.slide_artifacts.tissue module pathforge.core.io.slide_retrieval.descriptors module pathforge.core.io.slide_retrieval.layout module pathforge.core.io.slide_retrieval.retrieval_representations module pathforge.core.models.layers module pathforge.core.models.mil_ens module pathforge.core.models.mil_graph module pathforge.core.models.perceiver_mil module

pathforge.core.models.prototype_mil module pathforge.core.models.sklearn_slide module pathforge.core.models.slide_mlp module pathforge.core.models.utils module pathforge.core.models.var_mil module pathforge.core.registry module pathforge.core.reports.base module pathforge.core.reports.tiles_report_pdf module pathforge.core.slide_processing.lazyslide module pathforge.core.tasks.mil module pathforge.core.tasks.registry module pathforge.core.visualization.base module pathforge.core.visualization.orchestrator module pathforge.core.visualization.registry module pathforge.core.visualization.tasks.slide_retrieval module pathforge.core.visualization.thumbnail module pathforge.core.visualization.tiles_overview module pathforge.core.visualization.types module pathforge.execution.distributed module pathforge.inference.heatmaps module pathforge.inference.model_package module pathforge.policy.inference module pathforge.policy.utils module pathforge.slide_retrieval.hyperparams module pathforge.slide_retrieval.io module pathforge.slide_retrieval.representation_strategies.base module pathforge.slide_retrieval.representation_strategies.mean_rgb module pathforge.slide_retrieval.representation_strategies.registry module pathforge.slide_retrieval.representation_strategies.storage module pathforge.slide_retrieval.representation_strategies.types module pathforge.slide_retrieval.search_strategies.base module pathforge.slide_retrieval.search_strategies.registry module pathforge.slide_retrieval.search_strategies.types module pathforge.slide_retrieval.search_strategies.utils module pathforge.slide_retrieval.types module pathforge.slide_retrieval.visualization.renderers module pathforge.slide_retrieval.visualization.service module pathforge.training.callbacks module pathforge.training.lightning module pathforge.training.metrics module pathforge.training.sklearn_trainer module pathforge.utils.constants module pathforge.utils.io module pathforge.utils.logging module pathforge.utils.optional.mil_lab module pathforge.utils.optional.torchmil module pathforge.utils.registries module pathforge.utils.registry module pathforge.utils.serialization module pathforge_collate() (in module pathforge.adapters.torchmil.collate) patience (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) patient (pathforge.core.datasets.wsi_dataset.WSI attribute) patient_id (pathforge.core.datasets.bag_dataset.BagSample attribute) (pathforge.slide_retrieval.types.RetrievalItemMetadata attribute) (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset attribute) payload (pathforge.core.reports.base.DebugReport attribute) (pathforge.core.reports.base.PredictionReport attribute) (pathforge.core.reports.base.ProcessingReport attribute) (pathforge.core.reports.base.Report attribute) (pathforge.execution.distributed.WorkRecord attribute) PerceiverMIL (class in pathforge.core.models.perceiver_mil) perform_kmeans() (in module pathforge.core.models.utils) pid (pathforge.execution.distributed.WorkStatus attribute) plan_command() (in module pathforge.cli.execution) plan_dir (pathforge.execution.distributed.ExecutionPlan attribute) plan_id (pathforge.execution.distributed.ExecutionPlan attribute) PolicyBase (class in pathforge.policy.base) populate_dynamic_registries() (in module pathforge.utils.registries) PPEG (class in pathforge.core.models.layers) predict() (pathforge.core.models.sklearn_slide.SklearnSlideClassifier method) (pathforge.core.models.sklearn_slide.SklearnSlideRegressor method) (pathforge.core.models.sklearn_slide.SklearnSlideSurvival method) (pathforge.training.base.TrainerBase method) (pathforge.training.lightning.LightningTrainer method) (pathforge.training.sklearn_trainer.SklearnSlideTrainer method) predict_as_tensor() (pathforge.core.models.base.ScikitBase method) (pathforge.core.models.sklearn_slide.SklearnSlideClassifier method) (pathforge.core.models.sklearn_slide.SklearnSlideRegressor method) (pathforge.core.models.sklearn_slide.SklearnSlideSurvival method) predict_bag() (in module pathforge.inference.model_package) predict_label_from_top_k() (in module pathforge.core.evaluation.slide_retrieval.voting) predict_proba() (pathforge.core.models.sklearn_slide.SklearnSlideClassifier method) predict_step() (pathforge.training.lightning.LightningModuleAdapter method) prediction_heatmap_coords_dataset() (pathforge.core.io.h5.layout.H5Layout method) prediction_heatmap_exists() (in module pathforge.core.io.h5.heatmaps) prediction_heatmap_group() (pathforge.core.io.h5.layout.H5Layout method) prediction_heatmap_metadata_dataset() (pathforge.core.io.h5.layout.H5Layout method) prediction_heatmap_scores_dataset() (pathforge.core.io.h5.layout.H5Layout method) prediction_heatmaps_group() (pathforge.core.io.h5.layout.H5Layout method) prediction_level (pathforge.config.config.ExperimentConfig attribute) PredictionReport (class in pathforge.core.reports.base) predictions_group_name (pathforge.core.io.h5.layout.H5Layout attribute) prepare_query() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) process_slide() (pathforge.policy.feature_extraction.FeatureExtractionPolicy method) ProcessingReport (class in pathforge.core.reports.base) project_level0_to_thumbnail() (in module pathforge.core.visualization.thumbnail) project_name (pathforge.config.config.ExperimentConfig attribute) project_root (pathforge.config.config.ExperimentConfig attribute) (pathforge.core.experiments.base.Experiment attribute) PrototypeMIL (class in pathforge.core.models.prototype_mil) pruner (pathforge.config.config.OptimizationConfig attribute) push_to_hub() (in module pathforge.utils.serialization)

Q

qc_filters (pathforge.config.config.SlideProcessingConfig attribute) qos (pathforge.config.config.SlurmExecutionConfig attribute) quarantine_corrupt_artifact() (in module pathforge.core.io.slide_artifacts.atomic) queries (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationData attribute)

query_id (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationQuery attribute) (pathforge.slide_retrieval.search_strategies.types.SearchResult property) query_label (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationQuery attribute) query_sample_id (pathforge.slide_retrieval.search_strategies.types.SearchResult attribute) query_sample_ids (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute)

R

rank (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationHit attribute) (pathforge.slide_retrieval.search_strategies.types.SearchHit attribute) rank() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) raw_name (pathforge.core.evaluation.types.MetricRequest attribute) read_additional_retrieval_representation_data() (in module pathforge.core.io.slide_retrieval.retrieval_representations) read_array_dataset() (in module pathforge.core.io.slide_artifacts.base) read_coords() (in module pathforge.core.io.slide_artifacts.tiles) read_descriptor() (in module pathforge.core.io.slide_retrieval.descriptors) read_features() (in module pathforge.core.io.slide_artifacts.features) read_json_dataset() (in module pathforge.core.io.slide_artifacts.base) read_patch_region() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) read_prediction_heatmap() (in module pathforge.core.io.h5.heatmaps) read_retrieval_representation() (in module pathforge.core.io.slide_retrieval.retrieval_representations) read_retrieval_representation_entry() (in module pathforge.core.io.slide_retrieval.retrieval_representations) read_retrieval_representation_metadata() (in module pathforge.core.io.slide_retrieval.retrieval_representations) read_retrieval_representation_params() (in module pathforge.core.io.slide_retrieval.retrieval_representations) read_retrieval_representation_type() (in module pathforge.core.io.slide_retrieval.retrieval_representations) read_slide_retrieval_results_csv() (in module pathforge.slide_retrieval.io) read_thumbnail_image() (in module pathforge.core.io.slide_artifacts.thumbnail) read_thumbnail_spec() (in module pathforge.core.io.slide_artifacts.thumbnail) read_tiles_overview() (in module pathforge.core.io.slide_artifacts.tiles) read_tiling_spec() (in module pathforge.core.io.slide_artifacts.tiles) read_tissue() (in module pathforge.core.io.slide_artifacts.tissue) read_work_record() (in module pathforge.execution.distributed) reference_sample_ids (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) register() (pathforge.core.base.RegistryBase method) (pathforge.utils.registry.Registry method) register_builtin_loss_factories() (in module pathforge.adapters.losses) register_external_tissue_loader() (in module pathforge.core.io.slide_artifacts.tissue) register_mil_lab_backend() (in module pathforge.adapters.mil_lab.backend) register_representation_strategy() (in module pathforge.slide_retrieval.representation_strategies.registry) register_search_strategy() (in module pathforge.slide_retrieval.search_strategies.registry) register_task() (in module pathforge.core.tasks.registry) register_torchmil_backend() (in module pathforge.adapters.torchmil.backend) register_torchmil_fallback_aliases() (in module pathforge.adapters.mil_lab.backend) register_torchmil_heatmap_explainer() (in module pathforge.adapters.torchmil.heatmap_explainer) registered_feature_extractor_names() (in module pathforge.utils.registries) Registry (class in pathforge.utils.registry) registry_namespace (pathforge.config.config.MetricsConfig attribute) RegistryBase (class in pathforge.core.base) regression_metrics (pathforge.config.config.MetricsConfig attribute) RegressionLoss (class in pathforge.core.losses.base) RegressionMilTask (class in pathforge.core.tasks.mil) render_requested_visualizations() (pathforge.slide_retrieval.visualization.service.SlideRetrievalVisualizationService method) render_retrieval_representation_image() (in module pathforge.slide_retrieval.visualization.renderers) render_retrieval_results_image() (in module pathforge.slide_retrieval.visualization.renderers) render_run() (pathforge.core.visualization.base.TaskVisualizationAdapterBase method) (pathforge.core.visualization.tasks.slide_retrieval.SlideRetrievalVisualizationAdapter method) render_thumbnail_image() (in module pathforge.core.visualization.thumbnail) render_tiles_overview() (in module pathforge.core.visualization.tiles_overview) render_tiles_overview_image() (in module pathforge.core.visualization.tiles_overview) Report (class in pathforge.core.reports.base) report (pathforge.config.config.ExperimentConfig attribute) representation_id (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) representation_loader_workers (pathforge.config.config.SlideRetrievalConfig attribute) representation_type (pathforge.slide_retrieval.representation_strategies.types.RetrievalRepresentation attribute) representation_workers (pathforge.config.config.SlideRetrievalConfig attribute) representative_tiling_spec (pathforge.core.reports.tiles_report_pdf.TilesReportCollection attribute) require_mil_lab() (in module pathforge.utils.optional.mil_lab) require_torchmetrics() (in module pathforge.utils.optional.torchmil) require_torchmil() (in module pathforge.utils.optional.torchmil) require_torchsurv() (in module pathforge.utils.optional.torchmil) required_keys (pathforge.adapters.torchmil.backend.TorchMILModelSpec attribute) resolve_config_path() (in module pathforge.cli.common) resolve_dataset_feature_dir() (in module pathforge.policy.utils)

resolve_external_dataset_sources() (in module pathforge.adapters.tcga_tools) resolve_hyperparam() (in module pathforge.slide_retrieval.hyperparams) resolve_id_column_for_aggregation() (in module pathforge.core.evaluation.slide_retrieval.pool) resolve_metric_request() (in module pathforge.core.evaluation.registry) resolve_mil_model_backend() (in module pathforge.utils.registries) resolve_project_root_from_run_context() (in module pathforge.core.evaluation.slide_retrieval.pool) resolve_sample_patch_mean_rgb() (in module pathforge.slide_retrieval.representation_strategies.mean_rgb) resolve_slide_retrieval_results_path() (in module pathforge.slide_retrieval.io) resolve_torchmil_model_spec() (in module pathforge.adapters.torchmil.backend) resources (pathforge.config.config.ExecutionConfig attribute) result (pathforge.execution.distributed.WorkStatus attribute) results_dir (pathforge.execution.distributed.ExecutionPlan attribute) resume (pathforge.config.config.ExecutionConfig attribute) retrieval_representation (pathforge.config.config.BenchmarkParameters attribute) retrieval_representation_additional_data() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representation_additional_data_group() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representation_additional_data_group_name (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout attribute) retrieval_representation_embedding() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representation_embedding_name (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout attribute) retrieval_representation_entry_exists() (in module pathforge.core.io.slide_retrieval.retrieval_representations) retrieval_representation_entry_group() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representation_exists() (in module pathforge.core.io.slide_retrieval.retrieval_representations) retrieval_representation_group() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representation_item_exists() (in module pathforge.core.io.slide_retrieval.retrieval_representations) retrieval_representation_metadata() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representation_metadata_name (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout attribute) retrieval_representation_params() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representation_params_name (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout attribute) retrieval_representation_type() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representation_type_name (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout attribute) retrieval_representations_group() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) retrieval_representations_group_name (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout attribute) RetrievalH5Layout (class in pathforge.core.io.slide_retrieval.layout) RetrievalItemIdentity (class in pathforge.slide_retrieval.types) RetrievalItemMetadata (class in pathforge.slide_retrieval.types) RetrievalRepresentation (class in pathforge.slide_retrieval.representation_strategies.types) root (pathforge.utils.optional.torchmil.TorchMILModules attribute) row_count (pathforge.slide_retrieval.representation_strategies.types.RetrievalRepresentation property) run() (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy method) (pathforge.training.base.MILTrainer method) run_benchmark() (in module pathforge.cli.benchmark_run) run_command() (in module pathforge.cli.benchmark_run) (in module pathforge.cli.evaluate_run) (in module pathforge.cli.execution) (in module pathforge.cli.features_run) (in module pathforge.cli.features_slide) (in module pathforge.cli.infer_run) (in module pathforge.cli.optimize_run) (in module pathforge.cli.report_tiles) (in module pathforge.cli.retrieval_mean_rgb) (in module pathforge.cli.retrieval_representations) (in module pathforge.cli.retrieval_sish_vqvae) (in module pathforge.cli.visualize_run) run_context (pathforge.core.evaluation.types.EvaluationSummary attribute) run_dir (pathforge.core.evaluation.types.EvaluationRunContext attribute) (pathforge.core.visualization.types.VisualizationRunContext attribute) run_dirs (pathforge.core.visualization.types.VisualizationSummary attribute) run_evaluation() (in module pathforge.cli.evaluate_run) run_feature_extraction() (in module pathforge.cli.features_run) run_feature_extraction_single_slide() (in module pathforge.cli.features_slide) run_inference() (in module pathforge.cli.infer_run) run_mean_rgb() (in module pathforge.cli.retrieval_mean_rgb) run_optimization() (in module pathforge.cli.optimize_run) run_sish_vqvae() (in module pathforge.cli.retrieval_sish_vqvae) run_slide_retrieval_representations() (in module pathforge.cli.retrieval_representations) run_tiles_report() (in module pathforge.cli.report_tiles) run_visualization() (in module pathforge.cli.visualize_run)

S

sample (pathforge.core.datasets.bag_dataset.SlideRetrievalDatasetItem attribute) sample_id (pathforge.core.datasets.bag_dataset.BagSample attribute) (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationHit attribute) (pathforge.slide_retrieval.representation_strategies.types.RetrievalRepresentation attribute) (pathforge.slide_retrieval.search_strategies.types.SearchDatabaseItem attribute) (pathforge.slide_retrieval.search_strategies.types.SearchHit attribute) (pathforge.slide_retrieval.types.RetrievalItemIdentity attribute) sample_loader (pathforge.core.datasets.bag_dataset.SlideRetrievalBagDataset attribute) sampler (pathforge.config.config.OptimizationConfig attribute) samples (pathforge.core.datasets.bag_dataset.BagDataset attribute) save() (pathforge.core.models.base.ModelBase method) (pathforge.core.models.base.ScikitBase method) (pathforge.core.models.base.TorchModelBase method) save_annotations() (pathforge.core.annotations.base.AnnotationsBase method) (pathforge.core.annotations.csv.CSVAnnotations method) save_benchmark_visualizations() (in module pathforge.policy.utils) save_global_summary_visualizations() (in module pathforge.policy.utils) save_optuna_visualizations() (in module pathforge.policy.utils) save_packaged_model() (in module pathforge.inference.model_package) save_slide_retrieval_representation() (in module pathforge.slide_retrieval.io) save_task_evaluation_artifacts() (in module pathforge.training.metrics) save_tiles (pathforge.config.config.SlideProcessingConfig attribute) save_yaml() (pathforge.config.config.Config method) scheduler (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) scheduler_monitor (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) schema_version (pathforge.execution.distributed.ExecutionPlan attribute) (pathforge.execution.distributed.WorkRecord attribute) (pathforge.execution.distributed.WorkStatus attribute) ScikitBase (class in pathforge.core.models.base) score (pathforge.core.evaluation.slide_retrieval.data.SlideRetrievalEvaluationHit attribute) (pathforge.slide_retrieval.search_strategies.types.SearchHit attribute) scores (pathforge.adapters.torchmil.heatmap_explainer.HeatMap attribute) search() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) search_method (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) search_params (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) search_space (pathforge.config.config.OptimizationConfig attribute) search_strategy (pathforge.config.config.BenchmarkParameters attribute) search_workers (pathforge.config.config.SlideRetrievalConfig attribute) SearchDatabaseItem (class in pathforge.slide_retrieval.search_strategies.types) SearchHit (class in pathforge.slide_retrieval.search_strategies.types) SearchResult (class in pathforge.slide_retrieval.search_strategies.types) SearchSpaceParameter (class in pathforge.config.config) seeds (pathforge.config.config.BenchmarkParameters attribute) segment_tissue() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) segmentation_method (pathforge.config.config.SlideProcessingConfig attribute) select_inference_feature_metadata() (in module pathforge.inference.model_package) skip_extracted (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) skip_feature_extraction (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) SklearnCoxnet (class in pathforge.core.models.sklearn_slide) SklearnCoxPH (class in pathforge.core.models.sklearn_slide) SklearnElasticNetRegressor (class in pathforge.core.models.sklearn_slide) SklearnGradientBoostingClassifier (class in pathforge.core.models.sklearn_slide) SklearnGradientBoostingRegressor (class in pathforge.core.models.sklearn_slide) SklearnHingeLossSurvivalSVM (class in pathforge.core.models.sklearn_slide) SklearnIPCRidge (class in pathforge.core.models.sklearn_slide) SklearnLinearRegressor (class in pathforge.core.models.sklearn_slide) SklearnLogisticRegressionClassifier (class in pathforge.core.models.sklearn_slide) SklearnNaiveSurvivalSVM (class in pathforge.core.models.sklearn_slide) SklearnRandomForestClassifier (class in pathforge.core.models.sklearn_slide) SklearnRandomForestRegressor (class in pathforge.core.models.sklearn_slide) SklearnRandomSurvivalForest (class in pathforge.core.models.sklearn_slide) SklearnRidgeRegressor (class in pathforge.core.models.sklearn_slide) SklearnSlideClassifier (class in pathforge.core.models.sklearn_slide) SklearnSlideRegressor (class in pathforge.core.models.sklearn_slide) SklearnSlideSurvival (class in pathforge.core.models.sklearn_slide) SklearnSlideTrainer (class in pathforge.training.sklearn_trainer)

SklearnSurvivalTree (class in pathforge.core.models.sklearn_slide) SklearnSVMClassifier (class in pathforge.core.models.sklearn_slide) SklearnSVMRegressor (class in pathforge.core.models.sklearn_slide) slide (pathforge.core.datasets.wsi_dataset.WSI attribute) slide_aggregation (pathforge.config.config.BenchmarkParameters attribute) slide_artifact_path() (pathforge.core.datasets.wsi_dataset.WSIDataset method) slide_column (pathforge.config.config.ExperimentConfig attribute) (pathforge.core.datasets.bag_dataset.BagDataset attribute) slide_id (pathforge.core.reports.tiles_report_pdf.TilesOverviewEntry attribute) (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset attribute) slide_ids (pathforge.core.datasets.bag_dataset.BagSample attribute) slide_level_models (pathforge.config.config.BenchmarkParameters attribute) slide_path (pathforge.slide_retrieval.visualization.service.SlideVisualizationAsset attribute) slide_processing (pathforge.config.config.Config attribute) slide_representation (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) slide_representation_params (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) slide_retrieval (pathforge.config.config.Config attribute) SlideLevelModel (class in pathforge.core.models.slide_base) SlideProcessingConfig (class in pathforge.config.config) SlideProcessorBase (class in pathforge.core.slide_processing.base) SlideRetrievalBagDataset (class in pathforge.core.datasets.bag_dataset) SlideRetrievalConfig (class in pathforge.config.config) SlideRetrievalDatasetItem (class in pathforge.core.datasets.bag_dataset) SlideRetrievalEvaluationAdapter (class in pathforge.core.evaluation.slide_retrieval.adapter) SlideRetrievalEvaluationData (class in pathforge.core.evaluation.slide_retrieval.data) SlideRetrievalEvaluationHit (class in pathforge.core.evaluation.slide_retrieval.data) SlideRetrievalEvaluationQuery (class in pathforge.core.evaluation.slide_retrieval.data) SlideRetrievalManifest (class in pathforge.slide_retrieval.types) SlideRetrievalTask (class in pathforge.core.tasks.slide_retrieval) SlideRetrievalVisualizationAdapter (class in pathforge.core.visualization.tasks.slide_retrieval) SlideRetrievalVisualizationService (class in pathforge.slide_retrieval.visualization.service) slides_dir (pathforge.config.config.DatasetEntry attribute) (pathforge.core.datasets.wsi_dataset.WSIDataset property) SlideVectorMLP (class in pathforge.core.models.slide_mlp) SlideVisualizationAsset (class in pathforge.slide_retrieval.visualization.service) slurm (pathforge.config.config.ExecutionConfig attribute) slurm_array_task_id (pathforge.execution.distributed.WorkStatus attribute) slurm_job_id (pathforge.execution.distributed.WorkStatus attribute) SlurmExecutionConfig (class in pathforge.config.config) smoothed_image_output_path (pathforge.inference.heatmaps.InferenceHeatmapResult attribute) source (pathforge.utils.registries.BackendCatalogEntry attribute) split_technique (pathforge.config.config.ClassificationConfig attribute) stage (pathforge.execution.distributed.WorkRecord attribute) (pathforge.execution.distributed.WorkStatus attribute) StageResourceConfig (class in pathforge.config.config) stale_trial_timeout (pathforge.config.config.OptimizationConfig attribute) StandardTransformerBlock (class in pathforge.core.models.layers) started_at (pathforge.execution.distributed.WorkStatus attribute) state (pathforge.execution.distributed.WorkStatus attribute) stats (pathforge.core.reports.tiles_report_pdf.TilesReportCollection attribute) status_command() (in module pathforge.cli.execution) status_dir (pathforge.execution.distributed.ExecutionPlan attribute) step (pathforge.config.config.SearchSpaceParameter attribute) storage (pathforge.config.config.OptimizationConfig attribute) study_name (pathforge.config.config.OptimizationConfig attribute) suggest_parameter() (in module pathforge.policy.utils) summary_command() (in module pathforge.cli.visualize_run) supported_feature_levels (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy attribute) supported_representation_kinds (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy attribute) supported_tasks (pathforge.core.evaluation.registry.EvaluationMetricSpec attribute) supports_feature_level() (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy method) supports_representation_kind() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) survival_continuous_backend (pathforge.config.config.MetricsConfig attribute) survival_event_column (pathforge.config.config.ExperimentConfig attribute) survival_metrics (pathforge.config.config.MetricsConfig attribute) survival_time_column (pathforge.config.config.ExperimentConfig attribute) SurvivalContinuousLoss (class in pathforge.core.losses.base) SurvivalDiscreteLoss (class in pathforge.core.losses.base) SurvivalDiscreteMilTask (class in pathforge.core.tasks.mil) SurvivalLossBackend (class in pathforge.adapters.metrics.survival) SurvivalMetricsBackend (class in pathforge.adapters.metrics.survival) SurvivalMilTask (class in pathforge.core.tasks.mil)

T

target_column (pathforge.core.datasets.bag_dataset.BagDataset attribute) task (pathforge.config.config.ExperimentConfig attribute) (pathforge.core.datasets.bag_dataset.BagDataset attribute) (pathforge.inference.model_package.LoadedModelPackage property) task_name (pathforge.core.evaluation.base.TaskEvaluationAdapterBase attribute) (pathforge.core.evaluation.slide_retrieval.adapter.SlideRetrievalEvaluationAdapter attribute) (pathforge.core.evaluation.types.EvaluationRunContext attribute) (pathforge.core.visualization.base.TaskVisualizationAdapterBase attribute) (pathforge.core.visualization.tasks.slide_retrieval.SlideRetrievalVisualizationAdapter attribute) (pathforge.core.visualization.types.VisualizationRunContext attribute) (pathforge.core.visualization.types.VisualizationSummary attribute) task_types (pathforge.adapters.mil_lab.backend.MILLabModelSpec attribute) (pathforge.adapters.torchmil.backend.TorchMILModelSpec attribute) task_visualization_adapter() (in module pathforge.core.visualization.registry) TaskBase (class in pathforge.core.tasks.base) TaskEvaluationAdapterBase (class in pathforge.core.evaluation.base) TaskEvaluationArtifacts (class in pathforge.training.metrics) tasks (pathforge.core.base.CoreRegistries attribute) TaskVisualizationAdapterBase (class in pathforge.core.visualization.base) thumbnail (pathforge.config.config.ExperimentConfig attribute) thumbnail_group (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) thumbnail_image_dataset() (pathforge.core.io.slide_artifacts.layout.H5Layout method) thumbnail_image_exists() (in module pathforge.core.io.slide_artifacts.thumbnail) thumbnail_image_name (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) thumbnail_spec_dataset() (pathforge.core.io.slide_artifacts.layout.H5Layout method) thumbnail_spec_exists() (in module pathforge.core.io.slide_artifacts.thumbnail) thumbnail_spec_name (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) tile_group() (pathforge.core.io.slide_retrieval.layout.RetrievalH5Layout method) tile_mpp (pathforge.config.config.BenchmarkParameters attribute) tile_px (pathforge.config.config.BenchmarkParameters attribute) TileDatasetBase (class in pathforge.core.datasets.base) tiles_overview_dataset() (pathforge.core.io.h5.layout.H5Layout method) (pathforge.core.io.slide_artifacts.layout.H5Layout method) tiles_overview_exists() (in module pathforge.core.io.slide_artifacts.tiles) tiles_overview_name (pathforge.core.io.h5.layout.H5Layout attribute) (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) TilesOverviewEntry (class in pathforge.core.reports.tiles_report_pdf) TilesOverviewRenderResult (class in pathforge.core.visualization.tiles_overview) TilesReportCollection (class in pathforge.core.reports.tiles_report_pdf) TilesReportStats (class in pathforge.core.reports.tiles_report_pdf) tiling_id (pathforge.core.datasets.bag_dataset.BagDataset attribute) (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) tiling_spec (pathforge.core.reports.tiles_report_pdf.TilesOverviewEntry attribute)

tiling_spec_dataset() (pathforge.core.io.h5.layout.H5Layout method) (pathforge.core.io.slide_artifacts.layout.H5Layout method) tiling_spec_exists() (in module pathforge.core.io.slide_artifacts.tiles) tiling_spec_matches() (in module pathforge.core.io.slide_artifacts.tiles) tiling_spec_name (pathforge.core.io.h5.layout.H5Layout attribute) (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) time (pathforge.config.config.StageResourceConfig attribute) time_column (pathforge.core.datasets.bag_dataset.BagDataset attribute) timm_model_names() (in module pathforge.utils.registries) tissue_annotations_dir (pathforge.config.config.DatasetEntry attribute) (pathforge.core.datasets.wsi_dataset.WSIDataset property) tissue_dataset (pathforge.core.io.h5.layout.H5Layout attribute) (pathforge.core.io.slide_artifacts.layout.H5Layout attribute) tissue_exists() (in module pathforge.core.io.slide_artifacts.tissue) to_dict() (pathforge.core.evaluation.types.EvaluationRunContext method) (pathforge.core.evaluation.types.EvaluationSummary method) (pathforge.core.experiments.base.ComboConfig method) (pathforge.core.experiments.combinations.ComboConfig method) (pathforge.policy.utils.ComboConfig method) (pathforge.slide_retrieval.types.RetrievalItemIdentity method) (pathforge.slide_retrieval.types.SlideRetrievalManifest method) to_spec() (pathforge.slide_retrieval.hyperparams.HyperParam method) top_k_saved (pathforge.slide_retrieval.types.SlideRetrievalManifest attribute) top_tiles_output_path (pathforge.inference.heatmaps.InferenceHeatmapResult attribute) TorchClassificationLoss (class in pathforge.adapters.losses) TorchMetricsClassificationBackend (class in pathforge.adapters.metrics.classification) torchmil_model (pathforge.config.config.MILConfig attribute) torchmil_model_kwargs (pathforge.config.config.MILConfig attribute) torchmil_or_pathforge_collate() (in module pathforge.adapters.torchmil.collate) TorchMILBackendModel (class in pathforge.adapters.torchmil.backend) TorchMILHeatmapExplainer (class in pathforge.adapters.torchmil.heatmap_explainer) TorchMILModelSpec (class in pathforge.adapters.torchmil.backend) TorchMILModules (class in pathforge.utils.optional.torchmil) TorchModelBase (class in pathforge.core.models.base) TorchRegressionLoss (class in pathforge.adapters.losses) TorchSurvBackend (class in pathforge.adapters.metrics.survival) TorchSurvivalLoss (class in pathforge.adapters.losses) total_slides_expected (pathforge.core.reports.tiles_report_pdf.TilesReportStats attribute) trainer (pathforge.training.base.MILTrainer attribute) TrainerBase (class in pathforge.training.base) training_step() (pathforge.training.lightning.LightningModuleAdapter method) TransLayer (class in pathforge.core.models.layers) trials (pathforge.config.config.OptimizationConfig attribute) trials_per_worker (pathforge.config.config.OptimizationConfig attribute)

U

unreadable_h5 (pathforge.core.reports.tiles_report_pdf.TilesReportStats attribute) use_torchmil_collate (pathforge.config.config.MILConfig attribute)

used_for (pathforge.config.config.DatasetEntry attribute) (pathforge.core.datasets.wsi_dataset.WSIDataset property)

V

val_fraction (pathforge.config.config.ClassificationConfig attribute) validate_activations() (pathforge.config.config.BenchmarkParameters class method) validate_annotations() (pathforge.core.annotations.base.AnnotationsBase method) (pathforge.core.annotations.csv.CSVAnnotations method) validate_backend_constraints() (pathforge.config.config.Config method) validate_batch_sizes() (pathforge.config.config.BenchmarkParameters class method) validate_classification_metrics() (pathforge.config.config.MetricsConfig class method) validate_color_norm() (pathforge.config.config.BenchmarkParameters class method) validate_dropouts() (pathforge.config.config.BenchmarkParameters class method) validate_epochs() (pathforge.config.config.BenchmarkParameters class method) validate_feature_extractors() (pathforge.config.config.BenchmarkParameters class method) validate_feature_level() (pathforge.slide_retrieval.representation_strategies.base.BaseRetrievalRepresentationStrategy method) validate_h5_artifact() (in module pathforge.core.io.slide_artifacts.atomic) validate_label_column() (pathforge.config.config.EvaluationConfig class method) validate_learning_rates() (pathforge.config.config.BenchmarkParameters class method) validate_mil_models() (pathforge.config.config.BenchmarkParameters class method) validate_num_workers() (pathforge.config.config.ExperimentConfig class method) validate_optimizers() (pathforge.config.config.BenchmarkParameters class method) validate_positive_int_lists() (pathforge.config.config.BenchmarkParameters class method) validate_regression_metrics() (pathforge.config.config.MetricsConfig class method) validate_representation_kind() (pathforge.slide_retrieval.search_strategies.base.BaseSearchStrategy method) validate_shape() (pathforge.config.config.SearchSpaceParameter method) validate_slide_level_models() (pathforge.config.config.BenchmarkParameters class method)

validate_strategy_hyperparams() (pathforge.config.config.BenchmarkParameters method) validate_survival_metrics() (pathforge.config.config.MetricsConfig class method) validate_task_for_mode() (pathforge.config.config.ExperimentConfig method) validate_tile_mpp() (pathforge.config.config.BenchmarkParameters class method) validate_tile_px() (pathforge.config.config.BenchmarkParameters class method) validate_tile_spec() (pathforge.core.slide_processing.base.SlideProcessorBase method) (pathforge.core.slide_processing.lazyslide.LazySlideProcessor method) validate_used_for() (pathforge.config.config.DatasetEntry class method) validate_visualization_metadata_columns() (pathforge.config.config.SlideRetrievalConfig class method) validate_visualization_subset_file() (pathforge.config.config.EvaluationConfig class method) validate_weight_decay() (pathforge.config.config.BenchmarkParameters class method) validation_step() (pathforge.training.lightning.LightningModuleAdapter method) value (pathforge.config.config.BenchmarkParamEntry attribute) VarMIL (class in pathforge.core.models.var_mil) visualization (pathforge.config.config.EvaluationConfig attribute) (pathforge.config.config.ExperimentConfig attribute) visualization_metadata_columns (pathforge.config.config.SlideRetrievalConfig attribute) visualization_subset_file (pathforge.config.config.EvaluationConfig attribute) visualization_top_k (pathforge.config.config.SlideRetrievalConfig attribute) VisualizationOrchestrator (class in pathforge.core.visualization.orchestrator) VisualizationRunContext (class in pathforge.core.visualization.types) VisualizationSummary (class in pathforge.core.visualization.types) visualize() (pathforge.core.visualization.orchestrator.VisualizationOrchestrator method)

W

weight_decay (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute) weights_dir (pathforge.config.config.Config attribute) (pathforge.config.config.SlideRetrievalConfig attribute) work_dir (pathforge.config.config.ExecutionConfig attribute) work_id (pathforge.execution.distributed.WorkRecord attribute) (pathforge.execution.distributed.WorkStatus attribute) worker_command() (in module pathforge.cli.execution) (in module pathforge.cli.optimize_run) WorkRecord (class in pathforge.execution.distributed) WorkStatus (class in pathforge.execution.distributed) write_additional_retrieval_representation_data() (in module pathforge.core.io.slide_retrieval.retrieval_representations) write_array_dataset() (in module pathforge.core.io.slide_artifacts.base) write_coords() (in module pathforge.core.io.slide_artifacts.tiles) write_descriptor() (in module pathforge.core.io.slide_retrieval.descriptors) write_experiment_summary_csv() (in module pathforge.policy.utils) write_features() (in module pathforge.core.io.slide_artifacts.features)

write_json_dataset() (in module pathforge.core.io.slide_artifacts.base) write_metrics_csv() (in module pathforge.slide_retrieval.io) write_prediction_heatmap() (in module pathforge.core.io.h5.heatmaps) write_retrieval_representation() (in module pathforge.core.io.slide_retrieval.retrieval_representations) write_retrieval_representation_entry() (in module pathforge.core.io.slide_retrieval.retrieval_representations) write_retrieval_representation_metadata() (in module pathforge.core.io.slide_retrieval.retrieval_representations) write_retrieval_representation_params() (in module pathforge.core.io.slide_retrieval.retrieval_representations) write_retrieval_representation_type() (in module pathforge.core.io.slide_retrieval.retrieval_representations) write_slide_retrieval_manifest() (in module pathforge.slide_retrieval.io) write_slide_retrieval_results_csv() (in module pathforge.slide_retrieval.io) write_slide_retrieval_results_xlsx() (in module pathforge.slide_retrieval.io) write_thumbnail_image() (in module pathforge.core.io.slide_artifacts.thumbnail) write_thumbnail_spec() (in module pathforge.core.io.slide_artifacts.thumbnail) write_tiles_overview() (in module pathforge.core.io.slide_artifacts.tiles) write_tiling_spec() (in module pathforge.core.io.slide_artifacts.tiles) write_tissue() (in module pathforge.core.io.slide_artifacts.tissue) WSI (class in pathforge.core.datasets.wsi_dataset) WSIDataset (class in pathforge.core.datasets.wsi_dataset)

X

X (pathforge.core.datasets.bag_schema.BagBatch attribute)

Y

Y (pathforge.core.datasets.bag_schema.BagBatch attribute)

y_inst (pathforge.core.datasets.bag_schema.BagBatch attribute)

Z

z_dim (pathforge.config.config.BenchmarkParameters attribute) (pathforge.config.config.ClassificationConfig attribute) (pathforge.config.config.MILConfig attribute)