Index

A

Accuracy (biofefi.options.enums.Metrics attribute) Adam (biofefi.options.enums.OptimiserTypes attribute) angle_rotate_xaxis_labels (biofefi.options.plotting.PlottingOptions attribute)

angle_rotate_yaxis_labels (biofefi.options.plotting.PlottingOptions attribute) Auto (biofefi.options.enums.ProblemTypes attribute) AxisFontSize (biofefi.options.enums.PlotOptionKeys attribute) AxisTickSize (biofefi.options.enums.PlotOptionKeys attribute)

B

batch_size (biofefi.options.ml.BrnnOptions attribute) BinaryClassification (biofefi.options.enums.ProblemTypes attribute) biofefi module biofefi.components module biofefi.components.configuration module biofefi.components.experiments module biofefi.components.forms module biofefi.components.images module biofefi.components.images.logos module biofefi.components.logs module biofefi.components.plots module biofefi.components.preprocessing module biofefi.Home module biofefi.launch module biofefi.options module biofefi.options.choices module biofefi.options.choices.metrics module biofefi.options.choices.ml_models module biofefi.options.choices.ui module biofefi.options.enums module biofefi.options.execution module biofefi.options.fi module biofefi.options.file_paths module biofefi.options.fuzzy module biofefi.options.ml module biofefi.options.plotting module biofefi.options.preprocessing module biofefi.options.search_grids module

biofefi.pages module biofefi.pages.1_New_Experiment module biofefi.pages.2_Data_Preprocessing module biofefi.pages.3_Data_Visualisation module biofefi.pages.4_Train_Models module biofefi.pages.5_Feature_Importance module biofefi.pages.6_View_Experiments module biofefi.services module biofefi.services.configuration module biofefi.services.experiments module biofefi.services.feature_importance module biofefi.services.feature_importance.ensemble_methods module biofefi.services.feature_importance.global_methods module biofefi.services.feature_importance.local_methods module biofefi.services.feature_importance.results module biofefi.services.logs module biofefi.services.machine_learning module biofefi.services.machine_learning.results module biofefi.services.metrics module biofefi.services.ml_models module biofefi.services.plotting module biofefi.services.preprocessing module biofefi.services.weights_init module biofefi_experiments_base_dir() (in module biofefi.options.file_paths) BRNNClassifier (biofefi.options.enums.ModelNames attribute) BrnnOptions (class in biofefi.options.ml) BRNNRegressor (biofefi.options.enums.ModelNames attribute) build_config() (in module biofefi.pages.2_Data_Preprocessing) build_configuration() (in module biofefi.pages.4_Train_Models) (in module biofefi.pages.5_Feature_Importance)

C

calculate_ensemble_fuzzy() (in module biofefi.services.feature_importance.ensemble_methods) calculate_ensemble_majorityvote() (in module biofefi.services.feature_importance.ensemble_methods) calculate_ensemble_mean() (in module biofefi.services.feature_importance.ensemble_methods) calculate_global_shap_values() (in module biofefi.services.feature_importance.global_methods) calculate_lime_values() (in module biofefi.services.feature_importance.local_methods) calculate_local_shap_values() (in module biofefi.services.feature_importance.local_methods) calculate_permutation_importance() (in module biofefi.services.feature_importance.global_methods) Classification (biofefi.options.enums.ProblemTypes attribute) classification_cutoff (biofefi.options.ml.BrnnOptions attribute)

cluster_names (biofefi.options.fuzzy.FuzzyOptions attribute) ClusterNames (biofefi.options.enums.FuzzyStateKeys attribute) ColourMap (biofefi.options.enums.PlotOptionKeys attribute) ColourScheme (biofefi.options.enums.PlotOptionKeys attribute) correlation_heatmap_form() (in module biofefi.components.forms) correlation_threshold (biofefi.options.preprocessing.PreprocessingOptions attribute) CorrelationHeatmap (biofefi.options.enums.DataAnalysisStateKeys attribute) CorrelationThreshold (biofefi.options.enums.DataPreprocessingStateKeys attribute) create_experiment() (in module biofefi.services.experiments)

D

data_analysis_plots_dir() (in module biofefi.options.file_paths) data_is_preprocessed (biofefi.options.preprocessing.PreprocessingOptions attribute) data_path (biofefi.options.execution.ExecutionOptions attribute) data_preprocessing_options_path() (in module biofefi.options.file_paths) data_selector() (in module biofefi.components.experiments) data_split (biofefi.options.execution.ExecutionOptions attribute) DataAnalysisStateKeys (class in biofefi.options.enums) DataPreprocessingStateKeys (class in biofefi.options.enums) DataSplit (biofefi.options.enums.ExecutionStateKeys attribute)

DataSplitMethods (class in biofefi.options.enums) delete_previous_fi_results() (in module biofefi.services.experiments) dependent_variable (biofefi.options.execution.ExecutionOptions attribute) dependent_variable_transformation (biofefi.options.preprocessing.PreprocessingOptions attribute) DependentNormalisation (biofefi.options.enums.DataPreprocessingStateKeys attribute) DependentVariableName (biofefi.options.enums.ExecutionStateKeys attribute) DescriptorCorrelation (biofefi.options.enums.DataAnalysisStateKeys attribute) DescriptorPairPlot (biofefi.options.enums.DataAnalysisStateKeys attribute) display_metrics_table() (in module biofefi.components.plots)

E

EnsembleMethods (biofefi.options.enums.FeatureImportanceStateKeys attribute) epochs (biofefi.options.ml.BrnnOptions attribute) execution_options_box_auto() (in module biofefi.components.configuration) execution_options_box_manual() (in module biofefi.components.configuration) execution_options_path() (in module biofefi.options.file_paths) ExecutionOptions (class in biofefi.options.execution)

ExecutionStateKeys (class in biofefi.options.enums) experiment_name (biofefi.options.execution.ExecutionOptions attribute) experiment_selector() (in module biofefi.components.experiments) ExperimentName (biofefi.options.enums.ExecutionStateKeys attribute) (biofefi.options.enums.ViewExperimentKeys attribute) ExplainAllModels (biofefi.options.enums.FeatureImportanceStateKeys attribute) ExplainModels (biofefi.options.enums.FeatureImportanceStateKeys attribute)

F

F1Score (biofefi.options.enums.Metrics attribute) feature_importance_ensemble (biofefi.options.fi.FeatureImportanceOptions attribute) feature_selection_methods (biofefi.options.preprocessing.PreprocessingOptions attribute) FeatureImportanceOptions (class in biofefi.options.fi) FeatureImportanceStateKeys (class in biofefi.options.enums) fi_log_dir (biofefi.options.fi.FeatureImportanceOptions attribute) fi_options_dir() (in module biofefi.options.file_paths) fi_options_form() (in module biofefi.components.forms) fi_options_path() (in module biofefi.options.file_paths) fi_plot_dir() (in module biofefi.options.file_paths) fi_result_dir() (in module biofefi.options.file_paths) FILogBox (biofefi.options.enums.FeatureImportanceStateKeys attribute)

find_non_numeric_columns() (in module biofefi.services.preprocessing) find_previous_fi_results() (in module biofefi.services.experiments) FontFamily (biofefi.options.enums.PlotOptionKeys attribute) fuzzy_feature_selection (biofefi.options.fuzzy.FuzzyOptions attribute) fuzzy_log_dir (biofefi.options.fuzzy.FuzzyOptions attribute) fuzzy_options_path() (in module biofefi.options.file_paths) fuzzy_plot_dir() (in module biofefi.options.file_paths) fuzzy_result_dir() (in module biofefi.options.file_paths) FuzzyFeatureSelection (biofefi.options.enums.FuzzyStateKeys attribute) FuzzyLogBox (biofefi.options.enums.FuzzyStateKeys attribute) FuzzyOptions (class in biofefi.options.fuzzy) FuzzyStateKeys (class in biofefi.options.enums)

G

get_experiments() (in module biofefi.services.experiments) get_logs() (in module biofefi.services.logs) get_metrics() (in module biofefi.services.metrics) get_model() (in module biofefi.services.ml_models)

get_model_type() (in module biofefi.services.ml_models) global_importance_methods (biofefi.options.fi.FeatureImportanceOptions attribute) GlobalFeatureImportanceMethods (biofefi.options.enums.FeatureImportanceStateKeys attribute) granular_features (biofefi.options.fuzzy.FuzzyOptions attribute) GranularFeatures (biofefi.options.enums.FuzzyStateKeys attribute)

H

header_logo() (in module biofefi.components.images.logos)

hidden_dim (biofefi.options.ml.BrnnOptions attribute) Holdout (biofefi.options.enums.DataSplitMethods attribute)

I

independent_variable_normalisation (biofefi.options.preprocessing.PreprocessingOptions attribute)

IndependentNormalisation (biofefi.options.enums.DataPreprocessingStateKeys attribute)

K

kaiming_init() (in module biofefi.services.weights_init)

KFold (biofefi.options.enums.DataSplitMethods attribute)

L

lambda_reg (biofefi.options.ml.BrnnOptions attribute) lasso_regularisation_term (biofefi.options.preprocessing.PreprocessingOptions attribute) LassoFeatureSelection (biofefi.options.enums.DataPreprocessingStateKeys attribute) Linear (biofefi.options.enums.SvmKernels attribute) LinearModel (biofefi.options.enums.ModelNames attribute) load_data_preprocessing_options() (in module biofefi.services.configuration) load_execution_options() (in module biofefi.services.configuration) load_fi_options() (in module biofefi.services.configuration)

load_models() (in module biofefi.services.ml_models) load_models_to_explain() (in module biofefi.services.ml_models) load_plot_options() (in module biofefi.services.configuration) local_importance_methods (biofefi.options.fi.FeatureImportanceOptions attribute) LocalImportanceFeatures (biofefi.options.enums.FeatureImportanceStateKeys attribute) Log (biofefi.options.enums.TransformationsY attribute) log_box() (in module biofefi.components.logs) log_dir() (in module biofefi.options.file_paths) lr (biofefi.options.ml.BrnnOptions attribute)

M

MachineLearningOptions (class in biofefi.options.ml) MachineLearningStateKeys (class in biofefi.options.enums) MAE (biofefi.options.enums.Metrics attribute) main() (in module biofefi.launch) Metrics (class in biofefi.options.enums) MinMax (biofefi.options.enums.Normalisations attribute) MinMaxNormalisation (biofefi.options.enums.TransformationsY attribute) ml_log_dir (biofefi.options.ml.MachineLearningOptions attribute) ml_metrics_path() (in module biofefi.options.file_paths) ml_model_dir() (in module biofefi.options.file_paths) ml_options_form() (in module biofefi.components.forms) ml_options_path() (in module biofefi.options.file_paths) ml_plot_dir (biofefi.options.ml.MachineLearningOptions attribute) ml_plot_dir() (in module biofefi.options.file_paths) MLLogBox (biofefi.options.enums.MachineLearningStateKeys attribute) model_selector() (in module biofefi.components.experiments) model_types (biofefi.options.ml.MachineLearningOptions attribute) ModelNames (class in biofefi.options.enums) models_exist() (in module biofefi.services.ml_models) ModelTypes (biofefi.options.enums.MachineLearningStateKeys attribute) module biofefi biofefi.components biofefi.components.configuration biofefi.components.experiments biofefi.components.forms biofefi.components.images biofefi.components.images.logos biofefi.components.logs biofefi.components.plots biofefi.components.preprocessing biofefi.Home biofefi.launch biofefi.options biofefi.options.choices biofefi.options.choices.metrics biofefi.options.choices.ml_models biofefi.options.choices.ui biofefi.options.enums biofefi.options.execution biofefi.options.fi biofefi.options.file_paths biofefi.options.fuzzy biofefi.options.ml biofefi.options.plotting biofefi.options.preprocessing biofefi.options.search_grids biofefi.pages biofefi.pages.1_New_Experiment biofefi.pages.2_Data_Preprocessing biofefi.pages.3_Data_Visualisation biofefi.pages.4_Train_Models biofefi.pages.5_Feature_Importance biofefi.pages.6_View_Experiments biofefi.services biofefi.services.configuration biofefi.services.experiments biofefi.services.feature_importance biofefi.services.feature_importance.ensemble_methods biofefi.services.feature_importance.global_methods biofefi.services.feature_importance.local_methods biofefi.services.feature_importance.results biofefi.services.logs biofefi.services.machine_learning biofefi.services.machine_learning.results biofefi.services.metrics biofefi.services.ml_models biofefi.services.plotting biofefi.services.preprocessing biofefi.services.weights_init

MultiClassification (biofefi.options.enums.ProblemTypes attribute)

N

n_bootstraps (biofefi.options.execution.ExecutionOptions attribute) NBins (biofefi.options.enums.DataAnalysisStateKeys attribute) NoNormalisation (biofefi.options.enums.Normalisations attribute) normal_init() (in module biofefi.services.weights_init) Normalisation (biofefi.options.enums.ExecutionStateKeys attribute) Normalisations (class in biofefi.options.enums) normalise_independent_variables() (in module biofefi.services.preprocessing) normalization (biofefi.options.execution.ExecutionOptions attribute) NoSplit (biofefi.options.enums.DataSplitMethods attribute) NoTransformation (biofefi.options.enums.TransformationsY attribute)

num_features_to_plot (biofefi.options.fi.FeatureImportanceOptions attribute) number_clusters (biofefi.options.fuzzy.FuzzyOptions attribute) number_fuzzy_features (biofefi.options.fuzzy.FuzzyOptions attribute) number_rules (biofefi.options.fuzzy.FuzzyOptions attribute) NumberOfBootstraps (biofefi.options.enums.ExecutionStateKeys attribute) NumberOfClusters (biofefi.options.enums.FuzzyStateKeys attribute) NumberOfFuzzyFeatures (biofefi.options.enums.FuzzyStateKeys attribute) NumberOfImportantFeatures (biofefi.options.enums.FeatureImportanceStateKeys attribute) NumberOfRepetitions (biofefi.options.enums.FeatureImportanceStateKeys attribute) NumberOfTopRules (biofefi.options.enums.FuzzyStateKeys attribute)

O

OptimiserTypes (class in biofefi.options.enums)

original_view() (in module biofefi.components.preprocessing) output_dim (biofefi.options.ml.BrnnOptions attribute)

P

PairPlot (biofefi.options.enums.DataAnalysisStateKeys attribute) pairplot_form() (in module biofefi.components.forms) permutation_importance_repeat (biofefi.options.fi.FeatureImportanceOptions attribute) permutation_importance_scoring (biofefi.options.fi.FeatureImportanceOptions attribute) Perplexity (biofefi.options.enums.DataAnalysisStateKeys attribute) pipeline() (in module biofefi.pages.4_Train_Models) (in module biofefi.pages.5_Feature_Importance) plot_auc_roc() (in module biofefi.services.plotting) plot_axis_font_size (biofefi.options.plotting.PlottingOptions attribute) plot_axis_tick_size (biofefi.options.plotting.PlottingOptions attribute) plot_box() (in module biofefi.components.plots) plot_colour_map (biofefi.options.plotting.PlottingOptions attribute) plot_colour_scheme (biofefi.options.plotting.PlottingOptions attribute) plot_confusion_matrix() (in module biofefi.services.plotting) plot_font_family (biofefi.options.plotting.PlottingOptions attribute) plot_global_shap_importance() (in module biofefi.services.plotting) plot_lime_importance() (in module biofefi.services.plotting) plot_local_shap_importance() (in module biofefi.services.plotting)

plot_options_box() (in module biofefi.components.configuration) plot_options_path() (in module biofefi.options.file_paths) plot_scatter() (in module biofefi.services.plotting) plot_title_font_size (biofefi.options.plotting.PlottingOptions attribute) PlotOptionKeys (class in biofefi.options.enums) PlottingOptions (class in biofefi.options.plotting) Poly (biofefi.options.enums.SvmKernels attribute) Precision (biofefi.options.enums.Metrics attribute) Precomputed (biofefi.options.enums.SvmKernels attribute) preprocessed_data_path() (in module biofefi.options.file_paths) preprocessed_view() (in module biofefi.components.preprocessing) preprocessing_opts_form() (in module biofefi.components.forms) PreprocessingOptions (class in biofefi.options.preprocessing) prior_mu (biofefi.options.ml.BrnnOptions attribute) prior_sigma (biofefi.options.ml.BrnnOptions attribute) problem_type (biofefi.options.execution.ExecutionOptions attribute) ProblemType (biofefi.options.enums.ExecutionStateKeys attribute) ProblemTypes (class in biofefi.options.enums) ProceedTransformation (biofefi.options.enums.DataPreprocessingStateKeys attribute)

R

R2 (biofefi.options.enums.Metrics attribute) random_state (biofefi.options.execution.ExecutionOptions attribute) RandomForest (biofefi.options.enums.ModelNames attribute) RandomSeed (biofefi.options.enums.ExecutionStateKeys attribute) RBF (biofefi.options.enums.SvmKernels attribute) Recall (biofefi.options.enums.Metrics attribute) Regression (biofefi.options.enums.ProblemTypes attribute) RegularisationTerm (biofefi.options.enums.DataPreprocessingStateKeys attribute)

RerunFI (biofefi.options.enums.FuzzyStateKeys attribute) RerunML (biofefi.options.enums.MachineLearningStateKeys attribute) RMSE (biofefi.options.enums.Metrics attribute) RMSprop (biofefi.options.enums.OptimiserTypes attribute) ROC_AUC (biofefi.options.enums.Metrics attribute) RotateXAxisLabels (biofefi.options.enums.PlotOptionKeys attribute) RotateYAxisLabels (biofefi.options.enums.PlotOptionKeys attribute) run_feature_selection() (in module biofefi.services.preprocessing) run_preprocessing() (in module biofefi.services.preprocessing)

S

save_actual_pred_plots (biofefi.options.ml.MachineLearningOptions attribute) save_actual_pred_plots() (in module biofefi.services.machine_learning.results) save_feature_importance_options (biofefi.options.fi.FeatureImportanceOptions attribute) save_feature_importance_plots (biofefi.options.fi.FeatureImportanceOptions attribute) save_feature_importance_results (biofefi.options.fi.FeatureImportanceOptions attribute) save_fuzzy_set_plots (biofefi.options.fuzzy.FuzzyOptions attribute) save_fuzzy_sets_plots() (in module biofefi.services.feature_importance.results) save_importance_results() (in module biofefi.services.feature_importance.results) save_model() (in module biofefi.services.ml_models) save_models (biofefi.options.ml.MachineLearningOptions attribute) save_models_metrics() (in module biofefi.services.ml_models) save_options() (in module biofefi.services.configuration) save_plots (biofefi.options.plotting.PlottingOptions attribute) save_target_clusters_plots() (in module biofefi.services.feature_importance.results) SaveFeatureImportanceOptions (biofefi.options.enums.FeatureImportanceStateKeys attribute) SaveFeatureImportanceResults (biofefi.options.enums.FeatureImportanceStateKeys attribute) SaveHeatmap (biofefi.options.enums.DataAnalysisStateKeys attribute) SaveModels (biofefi.options.enums.MachineLearningStateKeys attribute)

SavePairPlot (biofefi.options.enums.DataAnalysisStateKeys attribute) SavePlots (biofefi.options.enums.PlotOptionKeys attribute) SaveTargetVarDistribution (biofefi.options.enums.DataAnalysisStateKeys attribute) SaveTSNEPlot (biofefi.options.enums.DataAnalysisStateKeys attribute) ScoringFunction (biofefi.options.enums.FeatureImportanceStateKeys attribute) SelectAllDescriptorsCorrelation (biofefi.options.enums.DataAnalysisStateKeys attribute) SelectAllDescriptorsPairPlot (biofefi.options.enums.DataAnalysisStateKeys attribute) SelectNormTsne (biofefi.options.enums.DataAnalysisStateKeys attribute) SGD (biofefi.options.enums.OptimiserTypes attribute) shap_reduce_data (biofefi.options.fi.FeatureImportanceOptions attribute) ShapDataPercentage (biofefi.options.enums.FeatureImportanceStateKeys attribute) ShowKDE (biofefi.options.enums.DataAnalysisStateKeys attribute) sidebar_logo() (in module biofefi.components.images.logos) Sigmoid (biofefi.options.enums.SvmKernels attribute) Sqrt (biofefi.options.enums.TransformationsY attribute) StandardisationNormalisation (biofefi.options.enums.TransformationsY attribute) Standardization (biofefi.options.enums.Normalisations attribute) SVM (biofefi.options.enums.ModelNames attribute) SvmKernels (class in biofefi.options.enums)

T

target_variable_dist_form() (in module biofefi.components.forms) TargetVarDistribution (biofefi.options.enums.DataAnalysisStateKeys attribute) ThresholdCorrelation (biofefi.options.enums.DataPreprocessingStateKeys attribute) ThresholdVariance (biofefi.options.enums.DataPreprocessingStateKeys attribute)

TitleFontSize (biofefi.options.enums.PlotOptionKeys attribute) transform_dependent_variable() (in module biofefi.services.preprocessing) TransformationsY (class in biofefi.options.enums) tSNE_plot_form() (in module biofefi.components.forms) TSNEPlot (biofefi.options.enums.DataAnalysisStateKeys attribute)

U

uploaded_file_path() (in module biofefi.options.file_paths) UploadedFileName (biofefi.options.enums.ExecutionStateKeys attribute)

use_hyperparam_search (biofefi.options.execution.ExecutionOptions attribute) UseHyperParamSearch (biofefi.options.enums.ExecutionStateKeys attribute)

V

variance_threshold (biofefi.options.preprocessing.PreprocessingOptions attribute)

VarianceThreshold (biofefi.options.enums.DataPreprocessingStateKeys attribute) ViewExperimentKeys (class in biofefi.options.enums)

X

xavier_init() (in module biofefi.services.weights_init)

XGBoost (biofefi.options.enums.ModelNames attribute)