Index

_

__init__() (pgsui.data_processing.transformers.SimMissingTransformer method) (pgsui.impute.unsupervised.callbacks.EarlyStopping method) (pgsui.impute.unsupervised.imputers.autoencoder.ImputeAutoencoder method) (pgsui.impute.unsupervised.imputers.nlpca.ImputeNLPCA method) (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP method) (pgsui.impute.unsupervised.imputers.vae.ImputeVAE method) (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.UBPModel method) (pgsui.impute.unsupervised.models.vae_model.VAEModel method) (pgsui.utils.plotting.Plotting method) (pgsui.utils.scorers.Scorer method)

_X_train_work_init_ (pgsui.impute.unsupervised.imputers.nlpca.ImputeNLPCA attribute)

A

accuracy() (pgsui.utils.scorers.Scorer method) all_missing_mask_ (pgsui.data_processing.transformers.SimMissingTransformer attribute)

apply_dot_overrides() (in module pgsui.data_processing.config) AutoencoderModel (class in pgsui.impute.unsupervised.models.autoencoder_model) average_precision() (pgsui.utils.scorers.Scorer method)

B

best_params_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

C

class_weights_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

count() (pgsui.utils.misc.OptunaParamSpec method)

D

dataclass_to_yaml() (in module pgsui.data_processing.config) Decoder (class in pgsui.impute.unsupervised.models.autoencoder_model) (class in pgsui.impute.unsupervised.models.vae_model)

detect_computing_device() (in module pgsui.utils.misc)

E

EarlyStopping (class in pgsui.impute.unsupervised.callbacks) Encoder (class in pgsui.impute.unsupervised.models.autoencoder_model) (class in pgsui.impute.unsupervised.models.vae_model) ensure_2d() (in module pgsui.utils.misc) ensure_autoencoder_config() (in module pgsui.impute.unsupervised.imputers.autoencoder) ensure_hgb_config() (in module pgsui.impute.supervised.imputers.hist_gradient_boosting) ensure_nlpca_config() (in module pgsui.impute.unsupervised.imputers.nlpca)

ensure_rf_config() (in module pgsui.impute.supervised.imputers.random_forest) ensure_ubp_config() (in module pgsui.impute.unsupervised.imputers.ubp) ensure_vae_config() (in module pgsui.impute.unsupervised.imputers.vae) eval_mask_test_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) eval_mask_train_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) eval_mask_val_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) evaluate() (pgsui.utils.scorers.Scorer method)

F

f1() (pgsui.utils.scorers.Scorer method) fit() (pgsui.data_processing.transformers.SimGenotypeDataTransformer method) (pgsui.data_processing.transformers.SimMissingTransformer method) (pgsui.impute.supervised.imputers.hist_gradient_boosting.ImputeHistGradientBoosting method) (pgsui.impute.supervised.imputers.random_forest.ImputeRandomForest method) (pgsui.impute.unsupervised.imputers.autoencoder.ImputeAutoencoder method) (pgsui.impute.unsupervised.imputers.nlpca.ImputeNLPCA method) (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP method) (pgsui.impute.unsupervised.imputers.vae.ImputeVAE method)

flatten_1d() (in module pgsui.utils.misc) forward() (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.UBPModel 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)

G

get_missing_mask() (in module pgsui.utils.misc)

ground_truth_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

I

ImputeAutoencoder (class in pgsui.impute.unsupervised.imputers.autoencoder) ImputeHistGradientBoosting (class in pgsui.impute.supervised.imputers.hist_gradient_boosting) ImputeNLPCA (class in pgsui.impute.unsupervised.imputers.nlpca) ImputeRandomForest (class in pgsui.impute.supervised.imputers.random_forest)

ImputeUBP (class in pgsui.impute.unsupervised.imputers.ubp) ImputeVAE (class in pgsui.impute.unsupervised.imputers.vae) is_fit_ (pgsui.impute.unsupervised.imputers.nlpca.ImputeNLPCA attribute) (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) is_haploid_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

J

jaccard() (pgsui.utils.scorers.Scorer method)

K

keys (pgsui.utils.misc.OptunaParamSpec attribute), [1]

L

load_yaml_to_dataclass() (in module pgsui.data_processing.config)

logger (pgsui.utils.plotting.Plotting attribute)

M

mcc() (pgsui.utils.scorers.Scorer method) missing_count (pgsui.data_processing.transformers.SimMissingTransformer property) model_ (pgsui.impute.unsupervised.imputers.nlpca.ImputeNLPCA attribute) (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) model_name (pgsui.utils.plotting.Plotting attribute) model_params (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) model_tuned_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) module pgsui.data_processing pgsui.data_processing.config pgsui.data_processing.transformers pgsui.impute pgsui.impute.supervised pgsui.impute.supervised.imputers pgsui.impute.supervised.imputers.hist_gradient_boosting pgsui.impute.supervised.imputers.random_forest pgsui.impute.unsupervised pgsui.impute.unsupervised.callbacks pgsui.impute.unsupervised.imputers pgsui.impute.unsupervised.imputers.autoencoder pgsui.impute.unsupervised.imputers.nlpca pgsui.impute.unsupervised.imputers.ubp pgsui.impute.unsupervised.imputers.vae 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.utils pgsui.utils.misc pgsui.utils.plotting pgsui.utils.scorers

N

NLPCAModel (class in pgsui.impute.unsupervised.models.nlpca_model) num_classes_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

num_features_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) num_tuned_params_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

O

OptunaParamSpec (class in pgsui.utils.misc) orig_mask_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) orig_mask_test_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

orig_mask_train_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) orig_mask_val_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) original_missing_mask_ (pgsui.data_processing.transformers.SimMissingTransformer attribute) output_dir (pgsui.utils.plotting.Plotting attribute)

P

pgsui.data_processing module pgsui.data_processing.config module pgsui.data_processing.transformers module pgsui.impute module pgsui.impute.supervised module pgsui.impute.supervised.imputers module pgsui.impute.supervised.imputers.hist_gradient_boosting module pgsui.impute.supervised.imputers.random_forest module pgsui.impute.unsupervised module pgsui.impute.unsupervised.callbacks module pgsui.impute.unsupervised.imputers module pgsui.impute.unsupervised.imputers.autoencoder module pgsui.impute.unsupervised.imputers.nlpca module pgsui.impute.unsupervised.imputers.ubp module pgsui.impute.unsupervised.imputers.vae 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.utils module pgsui.utils.misc module pgsui.utils.plotting module pgsui.utils.scorers module plot_confusion_matrix() (pgsui.utils.plotting.Plotting method) plot_dpi (pgsui.utils.plotting.Plotting attribute) plot_fontsize (pgsui.utils.plotting.Plotting attribute) plot_format (pgsui.utils.plotting.Plotting attribute) plot_gt_distribution() (pgsui.utils.plotting.Plotting method) plot_history() (pgsui.utils.plotting.Plotting method) plot_metrics() (pgsui.utils.plotting.Plotting method) plot_tuning() (pgsui.utils.plotting.Plotting method) plotter_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) Plotting (class in pgsui.utils.plotting) pr_macro() (pgsui.utils.scorers.Scorer method) precision() (pgsui.utils.scorers.Scorer method) prefix (pgsui.utils.plotting.Plotting attribute) prop_missing_real (pgsui.data_processing.transformers.SimMissingTransformer property)

R

random_weighted_missing_data() (pgsui.data_processing.transformers.SimMissingTransformer method) read_mask() (pgsui.data_processing.transformers.SimMissingTransformer method)

recall() (pgsui.utils.scorers.Scorer method) roc_auc() (pgsui.utils.scorers.Scorer method)

S

safe_shape() (in module pgsui.utils.misc) Sampling (class in pgsui.impute.unsupervised.models.vae_model) save_dataclass_yaml() (in module pgsui.data_processing.config) Scorer (class in pgsui.utils.scorers) scorers_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) show_plots (pgsui.utils.plotting.Plotting attribute) sim_mask_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

sim_mask_test_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) sim_mask_train_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) sim_mask_val_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) sim_missing_mask_ (pgsui.data_processing.transformers.SimMissingTransformer attribute) SimGenotypeDataTransformer (class in pgsui.data_processing.transformers) SimMissingTransformer (class in pgsui.data_processing.transformers) sqrt_transform() (pgsui.data_processing.transformers.SimMissingTransformer method)

T

T (class in pgsui.data_processing.config) test_idx_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) title_fontsize (pgsui.utils.plotting.Plotting attribute) total_samples_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) train_idx_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) train_loader_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) transform() (pgsui.data_processing.transformers.SimGenotypeDataTransformer method) (pgsui.data_processing.transformers.SimMissingTransformer method) (pgsui.impute.supervised.imputers.hist_gradient_boosting.ImputeHistGradientBoosting method) (pgsui.impute.supervised.imputers.random_forest.ImputeRandomForest method) (pgsui.impute.unsupervised.imputers.autoencoder.ImputeAutoencoder method) (pgsui.impute.unsupervised.imputers.nlpca.ImputeNLPCA method) (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP method) (pgsui.impute.unsupervised.imputers.vae.ImputeVAE method)

tuned_params_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

U

UBPModel (class in pgsui.impute.unsupervised.models.ubp_model)

V

v_init_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) VAEModel (class in pgsui.impute.unsupervised.models.vae_model) val_idx_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

val_loader_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) validate() (pgsui.utils.misc.OptunaParamSpec method) validate_input_type() (in module pgsui.utils.misc)

W

write_mask() (pgsui.data_processing.transformers.SimMissingTransformer method)

X

X_test_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) X_test_clean_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) X_test_corrupted_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) X_train_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) X_train_clean_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

X_train_corrupted_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) X_train_work_ (pgsui.impute.unsupervised.imputers.nlpca.ImputeNLPCA attribute) X_val_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) X_val_clean_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) X_val_corrupted_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

Y

y_test_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)

y_train_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute) y_val_ (pgsui.impute.unsupervised.imputers.ubp.ImputeUBP attribute)