Index

A

accuracy() (pgsui.data_processing.transformers.SimGenotypeDataTransformer method) (pgsui.impute.simple_imputers.ImputeMF method) accuracy_scorer() (pgsui.utils.scorers.Scorers static method) alignment (pgsui.impute.simple_imputers.ImputeAlleleFreq property) (pgsui.impute.simple_imputers.ImputeMF property) (pgsui.impute.simple_imputers.ImputePhylo property) (pgsui.impute.simple_imputers.ImputeRefAllele property)

all_missing_mask_ (pgsui.data_processing.transformers.SimGenotypeDataTransformer attribute) all_zero() (in module pgsui.utils.misc) auc_roc_pr_ap() (pgsui.data_processing.transformers.SimGenotypeDataTransformer method) AutoEncoderFeatureTransformer (class in pgsui.data_processing.transformers) AutoEncoderModel (class in pgsui.impute.unsupervised.models.autoencoder_model)

B

BaseNNImputer (class in pgsui.impute.unsupervised.neural_network_imputers) batch_idx (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel property) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 property) (pgsui.impute.unsupervised.models.vae_model.VAEModel property) batch_size (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel property) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 property) (pgsui.impute.unsupervised.models.vae_model.VAEModel property)

best_params (pgsui.impute.estimators.SupervisedImputer attribute) (pgsui.impute.estimators.UnsupervisedImputer attribute) blacklist_maf() (in module pgsui.utils.sequence_tools) blacklist_missing() (in module pgsui.utils.sequence_tools)

C

call() (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel method) (pgsui.impute.unsupervised.models.autoencoder_model.Decoder method) (pgsui.impute.unsupervised.models.autoencoder_model.Encoder method) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 method) (pgsui.impute.unsupervised.models.vae_model.Decoder method) (pgsui.impute.unsupervised.models.vae_model.Encoder method) (pgsui.impute.unsupervised.models.vae_model.Sampling method) (pgsui.impute.unsupervised.models.vae_model.VAEModel method)

check_if_tuple() (pgsui.utils.scorers.Scorers static method) clf_kwargs (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) clf_type (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) compute_metric() (pgsui.utils.scorers.Scorers static method) compute_pr() (pgsui.utils.scorers.Scorers static method) compute_roc_auc_micro_macro() (pgsui.utils.scorers.Scorers static method) compute_score() (pgsui.utils.scorers.Scorers static method) count_alleles() (in module pgsui.utils.sequence_tools) countSlidingWindow() (in module pgsui.utils.sequence_tools) CyclicalAnnealingCallback (class in pgsui.impute.unsupervised.callbacks)

D

decode_binary_multilab() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods class method) decode_masked() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods class method) decode_multiclass() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods class method) decode_multilab() (pgsui.data_processing.transformers.AutoEncoderFeatureTransformer method) Decoder (class in pgsui.impute.unsupervised.models.autoencoder_model) (class in pgsui.impute.unsupervised.models.vae_model) deprecated() (in module pgsui.data_processing.transformers) (in module pgsui.impute.unsupervised.models.autoencoder_model) (in module pgsui.impute.unsupervised.models.nlpca_model) (in module pgsui.impute.unsupervised.models.ubp_model) (in module pgsui.impute.unsupervised.models.vae_model) (in module pgsui.impute.unsupervised.neural_network_imputers) (in module pgsui.impute.unsupervised.neural_network_methods)

disable_progressbar (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) DisabledCV (class in pgsui.impute.unsupervised.neural_network_methods)

E

encode_012() (pgsui.data_processing.transformers.AutoEncoderFeatureTransformer method) encode_categorical() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) encode_multiclass() (pgsui.data_processing.transformers.AutoEncoderFeatureTransformer method) (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) encode_multilab() (pgsui.data_processing.transformers.AutoEncoderFeatureTransformer method) (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method)

encode_onehot() (in module pgsui.data_processing.transformers) Encoder (class in pgsui.impute.unsupervised.models.autoencoder_model) (class in pgsui.impute.unsupervised.models.vae_model) estimator (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) expand012() (in module pgsui.utils.sequence_tools) expandAmbiquousDNA() (in module pgsui.utils.sequence_tools) expandLoci() (in module pgsui.utils.sequence_tools)

F

feature_encoder (pgsui.impute.unsupervised.keras_classifiers.MLPClassifier property) (pgsui.impute.unsupervised.keras_classifiers.SAEClassifier property) (pgsui.impute.unsupervised.keras_classifiers.VAEClassifier property) fit() (pgsui.data_processing.transformers.AutoEncoderFeatureTransformer method) (pgsui.data_processing.transformers.MLPTargetTransformer method) (pgsui.data_processing.transformers.SimGenotypeDataTransformer method) (pgsui.data_processing.transformers.UBPInputTransformer method) (pgsui.data_processing.transformers.UBPTargetTransformer method) (pgsui.impute.unsupervised.neural_network_imputers.BaseNNImputer method)

fit_predict() (pgsui.impute.impute.Impute method) (pgsui.impute.simple_imputers.ImputeAlleleFreq method) (pgsui.impute.simple_imputers.ImputeMF method) (pgsui.impute.simple_imputers.ImputeRefAllele method) fit_transform() (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams method) (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch method) flatten_bin_encodings() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods class method) flush() (pgsui.utils.misc.StreamToLogger method)

G

gc_content() (in module pgsui.utils.sequence_tools) gc_counts() (in module pgsui.utils.sequence_tools) generate_012_genotypes() (in module pgsui.utils.misc) generate_random_dataset() (in module pgsui.utils.misc) genotype_data (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch attribute) genotypes_012 (pgsui.impute.simple_imputers.ImputeAlleleFreq property) (pgsui.impute.simple_imputers.ImputeMF property) (pgsui.impute.simple_imputers.ImputePhylo property) (pgsui.impute.simple_imputers.ImputeRefAllele property) get_class_weights() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods class method) get_hidden_layer_sizes() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods method)

get_indices() (in module pgsui.utils.misc) get_iupac_caseless() (in module pgsui.utils.sequence_tools) get_iupac_full() (in module pgsui.utils.sequence_tools) get_major_allele() (in module pgsui.utils.sequence_tools) get_metadata() (pgsui.impute.unsupervised.keras_classifiers.MLPClassifier method) (pgsui.impute.unsupervised.keras_classifiers.SAEClassifier method) (pgsui.impute.unsupervised.keras_classifiers.VAEClassifier method) get_n_splits() (pgsui.impute.unsupervised.neural_network_methods.DisabledCV method) get_optimal_threshold() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods class method) get_processor_name() (in module pgsui.utils.misc) get_revComp_caseless() (in module pgsui.utils.sequence_tools) getFlankCounts() (in module pgsui.utils.sequence_tools)

H

hamming_scorer() (pgsui.utils.scorers.Scorers static method)

HiddenPrints (class in pgsui.utils.misc)

I

imputation_order (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) imputation_sequence_ (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch attribute) Impute (class in pgsui.impute.impute) impute_phylo() (pgsui.impute.simple_imputers.ImputePhylo method) ImputeAlleleFreq (class in pgsui.impute.simple_imputers) imputed (pgsui.impute.estimators.SupervisedImputer attribute) (pgsui.impute.estimators.UnsupervisedImputer attribute) (pgsui.impute.simple_imputers.ImputeAlleleFreq attribute) (pgsui.impute.simple_imputers.ImputeMF attribute) (pgsui.impute.simple_imputers.ImputePhylo attribute) (pgsui.impute.simple_imputers.ImputeRefAllele attribute) ImputeKNN (class in pgsui.impute.estimators) ImputeMF (class in pgsui.impute.simple_imputers) ImputeNLPCA (class in pgsui.impute.estimators) ImputePhylo (class in pgsui.impute.simple_imputers) ImputeRandomForest (class in pgsui.impute.estimators)

ImputeRefAllele (class in pgsui.impute.simple_imputers) ImputeStandardAutoEncoder (class in pgsui.impute.estimators) ImputeUBP (class in pgsui.impute.estimators) ImputeVAE (class in pgsui.impute.estimators) ImputeXGBoost (class in pgsui.impute.estimators) indicator_ (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch attribute) init_weights() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) initial_imputer_ (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch attribute) initial_strategy (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) inverse_transform() (pgsui.data_processing.transformers.AutoEncoderFeatureTransformer method) (pgsui.data_processing.transformers.MLPTargetTransformer method) (pgsui.data_processing.transformers.UBPTargetTransformer method) isnotebook() (in module pgsui.utils.misc) IterativeImputerFixedParams (class in pgsui.impute.supervised.iterative_imputer_fixedparams) IterativeImputerGridSearch (class in pgsui.impute.supervised.iterative_imputer_gridsearch)

K

kl_divergence() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method)

L

listToSortUniqueString() (in module pgsui.utils.sequence_tools)

logfilepath (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute)

M

make_masked_binary_accuracy() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) make_masked_binary_crossentropy() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) make_masked_categorical_accuracy() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) make_masked_categorical_crossentropy() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) make_multimetric_scorer() (pgsui.utils.scorers.Scorers class method) make_reconstruction_loss() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods method) mask_content() (in module pgsui.utils.sequence_tools) mask_counts() (in module pgsui.utils.sequence_tools) masked_mse() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) max_iter (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) max_value (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) metrics (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel property) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 property) (pgsui.impute.unsupervised.models.vae_model.VAEModel property) min_value (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) missing_count (pgsui.data_processing.transformers.SimGenotypeDataTransformer property) missing_mask (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel property) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 property) (pgsui.impute.unsupervised.models.vae_model.VAEModel property) mle() (in module pgsui.data_processing.transformers) (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) MLPClassifier (class in pgsui.impute.unsupervised.keras_classifiers) MLPTargetTransformer (class in pgsui.data_processing.transformers) model() (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel method) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 method) (pgsui.impute.unsupervised.models.vae_model.VAEModel method)

module pgsui.data_processing pgsui.data_processing.transformers pgsui.impute pgsui.impute.estimators pgsui.impute.impute pgsui.impute.simple_imputers pgsui.impute.supervised pgsui.impute.supervised.iterative_imputer_fixedparams pgsui.impute.supervised.iterative_imputer_gridsearch pgsui.impute.unsupervised pgsui.impute.unsupervised.callbacks pgsui.impute.unsupervised.keras_classifiers pgsui.impute.unsupervised.models pgsui.impute.unsupervised.models.autoencoder_model pgsui.impute.unsupervised.models.nlpca_model pgsui.impute.unsupervised.models.ubp_model pgsui.impute.unsupervised.models.vae_model pgsui.impute.unsupervised.neural_network_imputers pgsui.impute.unsupervised.neural_network_methods pgsui.utils pgsui.utils.misc pgsui.utils.plotting pgsui.utils.scorers pgsui.utils.sequence_tools

N

n_features_with_missing_ (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch attribute) n_iter_ (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch attribute) n_lower_chars() (in module pgsui.utils.sequence_tools)

n_nearest_features (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) nbiallelic() (pgsui.impute.simple_imputers.ImputePhylo method) NeuralNetworkMethods (class in pgsui.impute.unsupervised.neural_network_methods) NLPCAModel (class in pgsui.impute.unsupervised.models.nlpca_model) normalize_data() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) normalize_sum_to_1() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method)

O

on_epoch_begin() (pgsui.impute.unsupervised.callbacks.CyclicalAnnealingCallback method) (pgsui.impute.unsupervised.callbacks.UBPCallbacks method) (pgsui.impute.unsupervised.callbacks.VAECallbacks method) on_epoch_end() (pgsui.impute.unsupervised.callbacks.UBPCallbacks method) (pgsui.impute.unsupervised.callbacks.UBPEarlyStopping method) (pgsui.impute.unsupervised.callbacks.VAECallbacks method)

on_train_batch_begin() (pgsui.impute.unsupervised.callbacks.UBPCallbacks method) (pgsui.impute.unsupervised.callbacks.VAECallbacks method) on_train_begin() (pgsui.impute.unsupervised.callbacks.CyclicalAnnealingCallback method) (pgsui.impute.unsupervised.callbacks.UBPEarlyStopping method) original_missing_mask_ (pgsui.data_processing.transformers.SimGenotypeDataTransformer attribute)

P

pgsui.data_processing module pgsui.data_processing.transformers module pgsui.impute module pgsui.impute.estimators module pgsui.impute.impute module pgsui.impute.simple_imputers module pgsui.impute.supervised module pgsui.impute.supervised.iterative_imputer_fixedparams module pgsui.impute.supervised.iterative_imputer_gridsearch module pgsui.impute.unsupervised module pgsui.impute.unsupervised.callbacks module pgsui.impute.unsupervised.keras_classifiers module pgsui.impute.unsupervised.models module pgsui.impute.unsupervised.models.autoencoder_model module pgsui.impute.unsupervised.models.nlpca_model module pgsui.impute.unsupervised.models.ubp_model module pgsui.impute.unsupervised.models.vae_model module

pgsui.impute.unsupervised.neural_network_imputers module pgsui.impute.unsupervised.neural_network_methods module pgsui.utils module pgsui.utils.misc module pgsui.utils.plotting module pgsui.utils.scorers module pgsui.utils.sequence_tools module plot_certainty_heatmap() (pgsui.utils.plotting.Plotting static method) plot_confusion_matrix() (pgsui.utils.plotting.Plotting static method) plot_grid_search() (pgsui.utils.plotting.Plotting static method) plot_gt_distribution() (pgsui.utils.plotting.Plotting static method) plot_heatmap() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) plot_history() (pgsui.utils.plotting.Plotting static method) plot_label_clusters() (pgsui.utils.plotting.Plotting static method) plot_metrics() (pgsui.utils.plotting.Plotting static method) plot_search_space() (pgsui.utils.plotting.Plotting static method) Plotting (class in pgsui.utils.plotting) pops (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) predict() (pgsui.impute.unsupervised.keras_classifiers.MLPClassifier method) (pgsui.impute.unsupervised.keras_classifiers.SAEClassifier method) (pgsui.impute.unsupervised.keras_classifiers.VAEClassifier method) (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods class method) prefix (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) prepare_training_batches() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods method) progress_update_percent (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) progressbar() (in module pgsui.utils.misc) prop_missing_real (pgsui.data_processing.transformers.SimGenotypeDataTransformer property)

R

random_state_ (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch attribute) random_weighted_missing_data() (pgsui.data_processing.transformers.SimGenotypeDataTransformer method) read_mask() (pgsui.data_processing.transformers.SimGenotypeDataTransformer method) remove_items() (in module pgsui.utils.sequence_tools) remove_single_unique_val_cols() (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch method) reset_seeds() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods method)

reverseComplement() (in module pgsui.utils.sequence_tools) run_and_plot_pca() (pgsui.utils.plotting.Plotting static method) run_clf() (pgsui.impute.unsupervised.neural_network_imputers.BaseNNImputer method) run_nlpca() (pgsui.impute.unsupervised.neural_network_imputers.UBP method) run_sae() (pgsui.impute.unsupervised.neural_network_imputers.SAE method) run_ubp() (pgsui.impute.unsupervised.neural_network_imputers.UBP method) run_vae() (pgsui.impute.unsupervised.neural_network_imputers.VAE method)

S

SAE (class in pgsui.impute.unsupervised.neural_network_imputers) SAEClassifier (class in pgsui.impute.unsupervised.keras_classifiers) sample_posterior (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) sample_weight (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel property) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 property) (pgsui.impute.unsupervised.models.vae_model.VAEModel property) Sampling (class in pgsui.impute.unsupervised.models.vae_model) scorer() (pgsui.impute.unsupervised.keras_classifiers.MLPClassifier static method) (pgsui.impute.unsupervised.keras_classifiers.SAEClassifier static method) (pgsui.impute.unsupervised.keras_classifiers.VAEClassifier static method) (pgsui.utils.scorers.Scorers static method) Scorers (class in pgsui.utils.scorers) seqCounter() (in module pgsui.utils.sequence_tools) seqCounterSimple() (in module pgsui.utils.sequence_tools) seqSlidingWindow() (in module pgsui.utils.sequence_tools) seqSlidingWindowString() (in module pgsui.utils.sequence_tools) set_compile_params() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods method) set_fit_request() (pgsui.impute.unsupervised.keras_classifiers.MLPClassifier method) (pgsui.impute.unsupervised.keras_classifiers.SAEClassifier method) (pgsui.impute.unsupervised.keras_classifiers.VAEClassifier method) set_inverse_transform_request() (pgsui.data_processing.transformers.AutoEncoderFeatureTransformer method) set_model_outputs() (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel method) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 method) (pgsui.impute.unsupervised.models.vae_model.VAEModel method)

set_partial_fit_request() (pgsui.impute.unsupervised.keras_classifiers.MLPClassifier method) (pgsui.impute.unsupervised.keras_classifiers.SAEClassifier method) (pgsui.impute.unsupervised.keras_classifiers.VAEClassifier method) set_score_request() (pgsui.impute.unsupervised.keras_classifiers.MLPClassifier method) (pgsui.impute.unsupervised.keras_classifiers.SAEClassifier method) (pgsui.impute.unsupervised.keras_classifiers.VAEClassifier method) SimGenotypeDataTransformer (class in pgsui.data_processing.transformers) simplifySeq() (in module pgsui.utils.sequence_tools) simulated_missing_mask_ (pgsui.data_processing.transformers.SimGenotypeDataTransformer attribute) skip_complete (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) slidingWindowGenerator (class in pgsui.utils.sequence_tools) smooth_weights() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) snp_data (pgsui.impute.simple_imputers.ImputeAlleleFreq property) (pgsui.impute.simple_imputers.ImputeMF property) (pgsui.impute.simple_imputers.ImputePhylo property) (pgsui.impute.simple_imputers.ImputeRefAllele property) split() (pgsui.impute.unsupervised.neural_network_methods.DisabledCV method) status_printer() (pgsui.utils.misc.tqdm_linux static method) str_encodings (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) (pgsui.impute.supervised.iterative_imputer_gridsearch.IterativeImputerGridSearch attribute) StreamToLogger (class in pgsui.utils.misc) stringSubstitute() (in module pgsui.utils.sequence_tools) SupervisedImputer (class in pgsui.impute.estimators)

T

target_encoder (pgsui.impute.unsupervised.keras_classifiers.MLPClassifier property) (pgsui.impute.unsupervised.keras_classifiers.SAEClassifier property) (pgsui.impute.unsupervised.keras_classifiers.VAEClassifier property) test_step() (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel method) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 method) (pgsui.impute.unsupervised.models.vae_model.VAEModel method) timer() (in module pgsui.utils.misc) tol (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) tqdm_linux (class in pgsui.utils.misc)

train_step() (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel method) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 method) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 method) (pgsui.impute.unsupervised.models.vae_model.VAEModel method) transform() (pgsui.data_processing.transformers.AutoEncoderFeatureTransformer method) (pgsui.data_processing.transformers.MLPTargetTransformer method) (pgsui.data_processing.transformers.SimGenotypeDataTransformer method) (pgsui.data_processing.transformers.UBPInputTransformer method) (pgsui.data_processing.transformers.UBPTargetTransformer method) (pgsui.impute.simple_imputers.ImputeMF method) (pgsui.impute.unsupervised.neural_network_imputers.BaseNNImputer method)

U

UBP (class in pgsui.impute.unsupervised.neural_network_imputers) UBPCallbacks (class in pgsui.impute.unsupervised.callbacks) UBPEarlyStopping (class in pgsui.impute.unsupervised.callbacks) UBPInputTransformer (class in pgsui.data_processing.transformers) UBPPhase1 (class in pgsui.impute.unsupervised.models.ubp_model)

UBPPhase2 (class in pgsui.impute.unsupervised.models.ubp_model) UBPPhase3 (class in pgsui.impute.unsupervised.models.ubp_model) UBPTargetTransformer (class in pgsui.data_processing.transformers) unique2D_subarray() (in module pgsui.utils.misc) UnsupervisedImputer (class in pgsui.impute.estimators)

V

V_latent (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 property) VAE (class in pgsui.impute.unsupervised.neural_network_imputers) VAECallbacks (class in pgsui.impute.unsupervised.callbacks) VAEClassifier (class in pgsui.impute.unsupervised.keras_classifiers)

VAEModel (class in pgsui.impute.unsupervised.models.vae_model) validate_batch_size() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods method) validate_hidden_layers() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods method) validate_input_type() (in module pgsui.utils.misc) validate_model_inputs() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods method) verbose (pgsui.impute.supervised.iterative_imputer_fixedparams.IterativeImputerFixedParams attribute) visualize_missingness() (pgsui.utils.plotting.Plotting static method)

W

weighted_draw() (in module pgsui.utils.misc) write() (pgsui.utils.misc.StreamToLogger method) write2file() (pgsui.impute.simple_imputers.ImputeAlleleFreq method) (pgsui.impute.simple_imputers.ImputeMF method) (pgsui.impute.simple_imputers.ImputeRefAllele method)

write_gt_state_probs() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method) write_mask() (pgsui.data_processing.transformers.SimGenotypeDataTransformer method)

Y

y (pgsui.impute.unsupervised.models.autoencoder_model.AutoEncoderModel property) (pgsui.impute.unsupervised.models.nlpca_model.NLPCAModel property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase1 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase2 property) (pgsui.impute.unsupervised.models.ubp_model.UBPPhase3 property) (pgsui.impute.unsupervised.models.vae_model.VAEModel property)

Z

zero_extra_categories() (pgsui.impute.unsupervised.neural_network_methods.NeuralNetworkMethods static method)