immuneML.hyperparameter_optimization package

Subpackages

• immuneML.hyperparameter_optimization.config package
  • Submodules
  • immuneML.hyperparameter_optimization.config.LeaveOneOutConfig module
    • LeaveOneOutConfig
      • LeaveOneOutConfig.min_count
      • LeaveOneOutConfig.parameter
  • immuneML.hyperparameter_optimization.config.ManualSplitConfig module
    • ManualSplitConfig
      • ManualSplitConfig.test_metadata_path
      • ManualSplitConfig.train_metadata_path
  • immuneML.hyperparameter_optimization.config.ReportConfig module
    • ReportConfig
      • ReportConfig.get_documentation()
  • immuneML.hyperparameter_optimization.config.SplitConfig module
    • SplitConfig
      • SplitConfig.get_documentation()
  • immuneML.hyperparameter_optimization.config.SplitType module
    • SplitType
      • SplitType.K_FOLD
      • SplitType.LEAVE_ONE_OUT_STRATIFICATION
      • SplitType.LOOCV
      • SplitType.MANUAL
      • SplitType.RANDOM
      • SplitType.STRATIFIED_K_FOLD
  • Module contents
• immuneML.hyperparameter_optimization.core package
  • Submodules
  • immuneML.hyperparameter_optimization.core.HPAssessment module
    • HPAssessment
      • HPAssessment.create_assessment_path()
      • HPAssessment.reeval_on_assessment_split()
      • HPAssessment.run_assessment()
      • HPAssessment.run_assessment_split()
      • HPAssessment.run_assessment_split_per_label()
      • HPAssessment.update_hp_setting_for_assessment()
  • immuneML.hyperparameter_optimization.core.HPSelection module
    • HPSelection
      • HPSelection.create_selection_path()
      • HPSelection.evaluate_hp_setting()
      • HPSelection.run_selection()
      • HPSelection.run_setting()
      • HPSelection.update_split_count()
  • immuneML.hyperparameter_optimization.core.HPUtil module
    • HPUtil
      • HPUtil.assess_performance()
      • HPUtil.encode_dataset()
      • HPUtil.get_average_performance()
      • HPUtil.preprocess_dataset()
      • HPUtil.run_hyperparameter_reports()
      • HPUtil.run_selection_reports()
      • HPUtil.split_data()
      • HPUtil.weight_examples()
  • Module contents
• immuneML.hyperparameter_optimization.states package
  • Submodules
  • immuneML.hyperparameter_optimization.states.HPAssessmentState module
    • HPAssessmentState
  • immuneML.hyperparameter_optimization.states.HPItem module
    • HPItem
      • HPItem.encoder
      • HPItem.encoding_test_results
      • HPItem.encoding_train_results
      • HPItem.hp_setting
      • HPItem.method
      • HPItem.ml_settings_export_path
      • HPItem.model_report_results
      • HPItem.performance
      • HPItem.split_index
      • HPItem.test_dataset
      • HPItem.test_predictions_path
      • HPItem.train_dataset
      • HPItem.train_predictions_path
  • immuneML.hyperparameter_optimization.states.HPLabelState module
    • HPLabelState
      • HPLabelState.optimal_assessment_item
      • HPLabelState.optimal_hp_setting
  • immuneML.hyperparameter_optimization.states.HPSelectionState module
    • HPSelectionState
      • HPSelectionState.optimal_hp_setting
  • immuneML.hyperparameter_optimization.states.TrainMLModelState module
    • TrainMLModelState
      • TrainMLModelState.assessment
      • TrainMLModelState.assessment_states
      • TrainMLModelState.context
      • TrainMLModelState.dataset
      • TrainMLModelState.example_weighting
      • TrainMLModelState.export_all_ml_settings
      • TrainMLModelState.hp_settings
      • TrainMLModelState.hp_strategy
      • TrainMLModelState.label_configuration
      • TrainMLModelState.metrics
      • TrainMLModelState.name
      • TrainMLModelState.number_of_processes
      • TrainMLModelState.optimal_hp_item_paths
      • TrainMLModelState.optimal_hp_items
      • TrainMLModelState.optimization_metric
      • TrainMLModelState.path
      • TrainMLModelState.refit_optimal_model
      • TrainMLModelState.region_type
      • TrainMLModelState.report_results
      • TrainMLModelState.reports
      • TrainMLModelState.selection
      • TrainMLModelState.sequence_type
  • Module contents
• immuneML.hyperparameter_optimization.strategy package
  • Submodules
  • immuneML.hyperparameter_optimization.strategy.GridSearch module
    • GridSearch
      • GridSearch.clone()
      • GridSearch.generate_next_setting()
      • GridSearch.get_all_hps()
      • GridSearch.get_optimal_hps()
      • GridSearch.get_performance()
  • immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy module
    • HPOptimizationStrategy
      • HPOptimizationStrategy.clone()
      • HPOptimizationStrategy.generate_next_setting()
      • HPOptimizationStrategy.get_all_hps()
      • HPOptimizationStrategy.get_optimal_hps()
  • Module contents

Submodules

immuneML.hyperparameter_optimization.HPSetting module

class immuneML.hyperparameter_optimization.HPSetting.HPSetting(encoder: DatasetEncoder, encoder_params: dict, ml_method: MLMethod, ml_params: dict, preproc_sequence: list, encoder_name: str = None, ml_method_name: str = None, preproc_sequence_name: str = None)

Bases: object

get_key()

immuneML.hyperparameter_optimization.HPSettingResult module

class immuneML.hyperparameter_optimization.HPSettingResult.HPSettingResult(optimal_setting: HPSetting, all_settings: dict)

Bases: object

HPSettingResult encapsulates the results from evaluating a set of different hyperparameter settings (e.g. on one train/test split in the outer loop of nested cross-validation) - it stores the optimal setting which can be used to assess the performance on the task, and all settings if needed for downstream analysis.

Module contents