Index

_

__init__() (biomedical_data_generator.BatchEffectsConfig method) (biomedical_data_generator.ClassConfig method) (biomedical_data_generator.config.BatchEffectsConfig method) (biomedical_data_generator.config.ClassConfig method) (biomedical_data_generator.config.CorrClusterConfig method) (biomedical_data_generator.config.CovarianceChannel method) (biomedical_data_generator.config.DatasetConfig method) (biomedical_data_generator.config.MeanChannel method) (biomedical_data_generator.config.StandaloneInformativeGroup method) (biomedical_data_generator.CorrClusterConfig method) (biomedical_data_generator.DatasetConfig method) (biomedical_data_generator.DatasetMeta method) (biomedical_data_generator.meta.DatasetMeta method) (biomedical_data_generator.meta.FeatureRoles method) (biomedical_data_generator.meta.FeatureStrengths method)

A

anchor_index (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute)

apply_batch_effects() (in module biomedical_data_generator.effects.batch) apply_batch_effects_from_config() (in module biomedical_data_generator.effects.batch) assess_correlation_quality() (in module biomedical_data_generator.utils.correlation_tools)

B

baseline_correlation (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute) batch_effects (biomedical_data_generator.DatasetMeta property) (biomedical_data_generator.meta.DatasetMeta property) batch_labels (biomedical_data_generator.DatasetMeta property) (biomedical_data_generator.meta.DatasetMeta property) BatchEffectsConfig (class in biomedical_data_generator) (class in biomedical_data_generator.config) biomedical_data_generator.effects.batch module biomedical_data_generator.features.correlated module biomedical_data_generator.features.informative module

biomedical_data_generator.utils.correlation_tools module biomedical_data_generator.utils.export_utils module biomedical_data_generator.utils.sampling module biomedical_data_generator.utils.sklearn_compat module biomedical_data_generator.utils.visualization module breakdown() (biomedical_data_generator.config.DatasetConfig method), [1] (biomedical_data_generator.DatasetConfig method), [1] build_correlation_matrix() (in module biomedical_data_generator.features.correlated)

C

class_counts (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) class_labels (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) class_sep (biomedical_data_generator.config.StandaloneInformativeGroup attribute) ClassConfig (class in biomedical_data_generator) (class in biomedical_data_generator.config) cluster_column_informative_flags() (biomedical_data_generator.config.DatasetConfig method) (biomedical_data_generator.DatasetConfig method) cluster_informative_flags() (biomedical_data_generator.config.DatasetConfig method), [1] (biomedical_data_generator.DatasetConfig method), [1] cluster_membership (biomedical_data_generator.meta.FeatureRoles attribute) compute_correlation_matrix() (in module biomedical_data_generator.utils.correlation_tools)

compute_correlation_matrix_for_cluster() (in module biomedical_data_generator.utils.correlation_tools) compute_correlation_metrics() (in module biomedical_data_generator.utils.correlation_tools) compute_feature_roles() (in module biomedical_data_generator.meta) compute_feature_strengths() (in module biomedical_data_generator.meta) confounded_batch_assignment() (in module biomedical_data_generator.effects.batch) CorrClusterConfig (class in biomedical_data_generator) (class in biomedical_data_generator.config) correlation_structure (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute) covariance_channel (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute) covariance_strength (biomedical_data_generator.meta.FeatureStrengths attribute) CovarianceChannel (class in biomedical_data_generator.config)

D

DatasetConfig (class in biomedical_data_generator) (class in biomedical_data_generator.config)

DatasetMeta (class in biomedical_data_generator) (class in biomedical_data_generator.meta)

E

effective_correlation_for_class() (biomedical_data_generator.config.CorrClusterConfig method) (biomedical_data_generator.CorrClusterConfig method)

F

FeatureRoles (class in biomedical_data_generator.meta) FeatureStrengths (class in biomedical_data_generator.meta) find_best_seed_for_correlation() (in module biomedical_data_generator.utils.correlation_tools) find_seed_for_correlation() (in module biomedical_data_generator.utils.correlation_tools)

from_yaml() (biomedical_data_generator.config.DatasetConfig class method) (biomedical_data_generator.config.DatasetConfig method) (biomedical_data_generator.DatasetConfig class method) (biomedical_data_generator.DatasetConfig method)

G

generate_batch_assignments() (in module biomedical_data_generator.effects.batch) generate_dataset() (in module biomedical_data_generator)

generate_informative_features() (in module biomedical_data_generator.features.informative) get_cluster_column_names() (in module biomedical_data_generator.utils.correlation_tools) get_cluster_frame() (in module biomedical_data_generator.utils.correlation_tools)

I

informative_anchor_indices (biomedical_data_generator.meta.FeatureRoles attribute)

informative_proxy_indices (biomedical_data_generator.meta.FeatureRoles attribute)

L

label (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute)

M

make_biomedical_dataset() (in module biomedical_data_generator.utils.sklearn_compat) mean_channel (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute) mean_effect_for_class() (biomedical_data_generator.config.CorrClusterConfig method) (biomedical_data_generator.CorrClusterConfig method) mean_strength (biomedical_data_generator.meta.FeatureStrengths attribute) MeanChannel (class in biomedical_data_generator.config) model_config (biomedical_data_generator.BatchEffectsConfig attribute) (biomedical_data_generator.ClassConfig attribute) (biomedical_data_generator.config.BatchEffectsConfig attribute) (biomedical_data_generator.config.ClassConfig attribute) (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.config.CovarianceChannel attribute) (biomedical_data_generator.config.DatasetConfig attribute) (biomedical_data_generator.config.MeanChannel attribute) (biomedical_data_generator.config.StandaloneInformativeGroup attribute) (biomedical_data_generator.CorrClusterConfig attribute) (biomedical_data_generator.DatasetConfig attribute)

module biomedical_data_generator.effects.batch biomedical_data_generator.features.correlated biomedical_data_generator.features.informative biomedical_data_generator.utils.correlation_tools biomedical_data_generator.utils.export_utils biomedical_data_generator.utils.sampling biomedical_data_generator.utils.sklearn_compat biomedical_data_generator.utils.visualization

N

n_classes (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) n_cluster_features (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute) n_features (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.config.StandaloneInformativeGroup attribute) (biomedical_data_generator.DatasetConfig property) n_informative (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property)

n_noise (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) n_samples (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) n_standalone_informative (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) noise_anchor_indices (biomedical_data_generator.meta.FeatureRoles attribute) noise_proxy_indices (biomedical_data_generator.meta.FeatureRoles attribute)

P

parse_cluster_id() (in module biomedical_data_generator.utils.correlation_tools) pc1_share() (in module biomedical_data_generator.utils.correlation_tools) pc1_share_from_corr() (in module biomedical_data_generator.utils.correlation_tools) per_class_correlation (biomedical_data_generator.config.CovarianceChannel attribute) per_class_effect (biomedical_data_generator.config.MeanChannel attribute)

plot_all_correlation_clusters() (in module biomedical_data_generator.utils.visualization) plot_correlation_matrices_per_cluster() (in module biomedical_data_generator.utils.visualization) plot_correlation_matrix() (in module biomedical_data_generator.utils.visualization) plot_correlation_matrix_for_cluster() (in module biomedical_data_generator.utils.visualization) proxy_attenuation (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute)

R

random_batch_assignment() (in module biomedical_data_generator.effects.batch)

resolve_standalone_groups() (in module biomedical_data_generator.features.informative)

S

sample_all_correlated_clusters() (in module biomedical_data_generator.features.correlated) sample_correlated_data() (in module biomedical_data_generator.features.correlated) sample_distribution() (in module biomedical_data_generator.utils.sampling)

signal_channels (biomedical_data_generator.meta.FeatureStrengths attribute) standalone_informative_indices (biomedical_data_generator.meta.FeatureRoles attribute) standalone_noise_indices (biomedical_data_generator.meta.FeatureRoles attribute) StandaloneInformativeGroup (class in biomedical_data_generator.config)

T

to_csv() (in module biomedical_data_generator.utils.export_utils) to_dict() (biomedical_data_generator.DatasetMeta method) (biomedical_data_generator.meta.DatasetMeta method)

to_labeled_dataframe() (in module biomedical_data_generator.utils.export_utils) to_parquet() (in module biomedical_data_generator.utils.export_utils)

V

validate_proportions() (biomedical_data_generator.BatchEffectsConfig class method) (biomedical_data_generator.config.BatchEffectsConfig class method)

variance_partition_pc1() (in module biomedical_data_generator.utils.correlation_tools)