OCDocker.OCScore.Optimization package

Module contents

Optimization routines and hyperparameter search utilities.

Usage:

import OCDocker.OCScore.Optimization as ocopt

Modules

• Protocol: Current minimal staged protocol abstractions.

• StagedOptuna: Current task-separated PDBbind/DUDEz Optuna protocol.

• archived: Previous mixed-metric Optuna protocol family.

Staged Optuna orchestration (StagedOptuna), model export (ModelExport), and cross-validation (ModelCrossValidation).

Submodules

• OCDocker.OCScore.Optimization.ModelCrossValidation module
  • CrossValidationConfig
  • CrossValidationFoldResult
  • CrossValidationResult
  • build_scorer_comparison_summary()
  • diagnose_entity_overlap()
  • evaluate_scoring_function_baselines_on_fold()
  • identify_scoring_function_columns()
  • infer_higher_is_better()
  • iter_receptor_group_kfold_indices()
  • iter_row_kfold_indices()
  • run_cross_validation_from_export()
  • save_cross_validation_result()
  • validate_fold_indices()
  • validate_fold_split()
  • validate_receptor_group_split()
• OCDocker.OCScore.Optimization.ModelExport module
  • export_best_model_bundle()
  • load_exported_model()
  • predict_from_export()
  • retrain_from_export()
  • transform_export_features()
  • validate_export_bundle()
  • validate_export_features()
• OCDocker.OCScore.Optimization.OptunaSearchSpace module
  • OptimizerSearchSpace
  • EncoderSearchSpace
  • ProjectionSearchSpace
  • DecoderSearchSpace
  • PDBbindHeadSearchSpace
  • DUDEzHeadSearchSpace
  • SharedNeuralSearchSpace
  • PDBbindSearchSpaceConfig
  • DUDEzSearchSpaceConfig
  • validate_pdbbind_search_phase()
  • pdbbind_search_space_for_phase()
  • available_activation_options()
  • activation_is_available()
  • build_activation_module()
  • search_space_to_summary()
• OCDocker.OCScore.Optimization.OptunaStorage module
  • configure_sqlite_wal()
  • resolve_optuna_storage()
• OCDocker.OCScore.Optimization.Protocol module
  • ProtocolContext
  • ProtocolStage
  • ReplicaResult
  • ReplicatedProtocolConfig
  • ReplicatedProtocolResult
  • ReplicatedStagedProtocol
  • StagedProtocol
• OCDocker.OCScore.Optimization.StagedOptuna module
  • DUDEzOptunaConfig
  • DUDEzOptunaStage
  • DUDEzScreeningModel
  • FeatureExtractor
  • PDBbindOptunaConfig
  • PDBbindOptunaStage
  • PDBbindRegressionModel
  • TransferFeatureExtractorStage
  • apply_fine_tuning_mode()
  • build_dudez_model()
  • build_pdbbind_model()
  • compute_regression_reconstruction_loss()
  • derive_dudez_labels()
  • dudez_search_space_summary()
  • evaluate_regression_metrics()
  • pdbbind_phase1_experiment_config()
  • pdbbind_search_space_summary()
  • prepare_dudez_screening_data()
  • summarize_dudez_split_diagnostics()
  • prepare_pdbbind_regression_data()
  • resolve_dudez_primary_metric()
  • run_staged_ocscore_optuna_protocol()
  • suggest_decoder_hidden_sizes()
  • suggest_dudez_trial_params()
  • suggest_encoder_architecture()
  • suggest_pdbbind_trial_params()
• OCDocker.OCScore.Optimization.StagedTrainProtocol module
  • AblationProtocolSection
  • StagedTrainProtocol
  • bundled_protocol_names()
  • load_staged_train_protocol()
  • normalize_ablation_variant_name()
  • resolve_protocol_path()