Index

A

ablation_study.leakage_ablation module ablation_study.multi_seed_synthesis module analysis.build_summary_tables module analysis.clustering_evaluation module analysis.distribution_metrics module

analysis.marker_clustering_grid module analysis.mmd_analysis module analysis.sc_specific_benchmark module analysis.swd_analysis module

B

biological_analysis.biological_validation module biological_analysis.marker_gene_clustering module

biological_analysis.rare_cell_utility module

C

cluster_and_evaluate() (in module analysis.clustering_evaluation) (in module data_validation.data_validation) compute_ari_nmi() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering) config module

Critic (class in ablation_study.multi_seed_synthesis) cv2() (in module analysis.clustering_evaluation) cv2_selection() (in module data_validation.data_validation) (in module data_validation.feature_selection)

D

data_generation.garage module data_generation.wasserstein_distance module data_validation.data_validation module

data_validation.feature_selection module DATASET_CONFIG (in module config) Discriminator (class in ablation_study.leakage_ablation) (class in data_generation.garage)

E

enrichment_analysis() (in module biological_analysis.biological_validation) evaluate_ari() (in module analysis.sc_specific_benchmark) evaluate_baseline() (in module analysis.clustering_evaluation) (in module biological_analysis.marker_gene_clustering) evaluate_classifier() (in module biological_analysis.rare_cell_utility) evaluate_classifier_downgraded() (in module biological_analysis.rare_cell_utility)

evaluate_clustering() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering) evaluate_real_reference() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering) evaluate_sweep() (in module analysis.clustering_evaluation) (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering)

F

fano_selection() (in module analysis.sc_specific_benchmark) (in module data_validation.feature_selection) FDiscriminator (class in ablation_study.multi_seed_synthesis) FGenerator (class in ablation_study.multi_seed_synthesis) fisher_ratio() (in module ablation_study.multi_seed_synthesis) fmt_mean_std() (in module analysis.build_summary_tables) forward() (ablation_study.leakage_ablation.Discriminator method) (ablation_study.leakage_ablation.Generator method) (ablation_study.multi_seed_synthesis.Critic method) (ablation_study.multi_seed_synthesis.FDiscriminator method) (ablation_study.multi_seed_synthesis.FGenerator method) (ablation_study.multi_seed_synthesis.GATG_Discriminator method) (ablation_study.multi_seed_synthesis.GATG_Generator method) (ablation_study.multi_seed_synthesis.LSHDiscriminator method) (ablation_study.multi_seed_synthesis.LSHGenerator method) (ablation_study.multi_seed_synthesis.VanillaDiscriminator method) (ablation_study.multi_seed_synthesis.VanillaGenerator method) (ablation_study.multi_seed_synthesis.WGenerator method) (biological_analysis.rare_cell_utility.GarageDiscriminator method) (biological_analysis.rare_cell_utility.GarageGenerator method) (biological_analysis.rare_cell_utility.GATClassifier method) (biological_analysis.rare_cell_utility.LSHDiscriminator method) (biological_analysis.rare_cell_utility.LSHGenerator method) (biological_analysis.rare_cell_utility.VanillaDiscriminator method) (biological_analysis.rare_cell_utility.VanillaGenerator method) (data_generation.garage.Discriminator method) (data_generation.garage.GATClassifier method) (data_generation.garage.Generator method)

G

GARAGE_DEFAULTS (in module config) garage_gat_seeds() (in module biological_analysis.rare_cell_utility) GarageDiscriminator (class in biological_analysis.rare_cell_utility) GarageGenerator (class in biological_analysis.rare_cell_utility) gat_subsample() (in module ablation_study.leakage_ablation) (in module ablation_study.multi_seed_synthesis) (in module data_generation.garage) GATClassifier (class in biological_analysis.rare_cell_utility) (class in data_generation.garage)

GATG_Discriminator (class in ablation_study.multi_seed_synthesis) GATG_Generator (class in ablation_study.multi_seed_synthesis) generate_data() (in module data_generation.garage) generate_garage() (in module biological_analysis.rare_cell_utility) generate_lsh_gan() (in module biological_analysis.rare_cell_utility) generate_vanilla_gan() (in module biological_analysis.rare_cell_utility) Generator (class in ablation_study.leakage_ablation) (class in data_generation.garage) get_pseudo_labels() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering)

K

knn_subsample() (in module ablation_study.multi_seed_synthesis) (in module biological_analysis.rare_cell_utility)

L

load_cbmc() (in module ablation_study.leakage_ablation) (in module biological_analysis.biological_validation) load_data() (in module biological_analysis.rare_cell_utility) load_dataset() (in module data_generation.garage) load_gan_data() (in module analysis.mmd_analysis) (in module analysis.swd_analysis) load_garage_data() (in module analysis.marker_clustering_grid) (in module analysis.mmd_analysis) (in module analysis.swd_analysis) (in module biological_analysis.marker_gene_clustering) load_gen() (in module analysis.clustering_evaluation) load_gen_data() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering) load_generated() (in module data_generation.wasserstein_distance) (in module data_validation.data_validation) load_labels() (in module ablation_study.multi_seed_synthesis) (in module analysis.clustering_evaluation) (in module data_validation.data_validation) load_lsh_gan_data() (in module analysis.mmd_analysis) (in module analysis.swd_analysis)

load_muraro() (in module ablation_study.leakage_ablation) load_pollen() (in module ablation_study.leakage_ablation) load_real() (in module ablation_study.multi_seed_synthesis) (in module analysis.clustering_evaluation) (in module analysis.distribution_metrics) (in module analysis.sc_specific_benchmark) (in module data_generation.wasserstein_distance) (in module data_validation.data_validation) load_real_data() (in module analysis.marker_clustering_grid) (in module analysis.mmd_analysis) (in module analysis.swd_analysis) (in module biological_analysis.marker_gene_clustering) load_synthetic() (in module analysis.distribution_metrics) load_yan() (in module ablation_study.leakage_ablation) LSHDiscriminator (class in ablation_study.multi_seed_synthesis) (class in biological_analysis.rare_cell_utility) LSHGenerator (class in ablation_study.multi_seed_synthesis) (class in biological_analysis.rare_cell_utility)

M

main() (in module ablation_study.leakage_ablation) (in module ablation_study.multi_seed_synthesis) (in module analysis.build_summary_tables) (in module analysis.clustering_evaluation) (in module analysis.distribution_metrics) (in module analysis.marker_clustering_grid) (in module analysis.mmd_analysis) (in module analysis.sc_specific_benchmark) (in module analysis.swd_analysis) (in module biological_analysis.biological_validation) (in module biological_analysis.marker_gene_clustering) (in module biological_analysis.rare_cell_utility) (in module data_generation.garage) (in module data_generation.wasserstein_distance) (in module data_validation.data_validation) (in module data_validation.feature_selection) marker_expression_analysis() (in module biological_analysis.biological_validation) mmd_rbf() (in module analysis.distribution_metrics) (in module analysis.mmd_analysis)

module ablation_study.leakage_ablation ablation_study.multi_seed_synthesis analysis.build_summary_tables analysis.clustering_evaluation analysis.distribution_metrics analysis.marker_clustering_grid analysis.mmd_analysis analysis.sc_specific_benchmark analysis.swd_analysis biological_analysis.biological_validation biological_analysis.marker_gene_clustering biological_analysis.rare_cell_utility config data_generation.garage data_generation.wasserstein_distance data_validation.data_validation data_validation.feature_selection

P

pca_loading_selection() (in module data_validation.feature_selection) per_celltype_positive_rate_analysis() (in module biological_analysis.biological_validation)

plot_umap() (in module data_validation.data_validation) print_summary_interpretation() (in module biological_analysis.biological_validation)

R

rbf_kernel() (in module analysis.mmd_analysis) run_feature_selection() (in module data_validation.feature_selection)

run_garage() (in module data_generation.garage) run_gat_and_get_attention() (in module biological_analysis.biological_validation)

S

sample_Z() (in module ablation_study.leakage_ablation) (in module ablation_study.multi_seed_synthesis) (in module biological_analysis.rare_cell_utility) (in module data_generation.garage) select_markers_cbmc() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering) select_markers_muraro() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering)

select_markers_pollen() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering) select_markers_yan() (in module analysis.marker_clustering_grid) (in module biological_analysis.marker_gene_clustering) sliced_wasserstein() (in module analysis.distribution_metrics) (in module analysis.swd_analysis) split_rare() (in module biological_analysis.rare_cell_utility) sweep_resolution() (in module data_validation.data_validation)

T

train_and_generate_fgan() (in module ablation_study.multi_seed_synthesis) train_and_generate_gan() (in module ablation_study.multi_seed_synthesis) train_and_generate_gatgan() (in module ablation_study.multi_seed_synthesis) train_and_generate_lshgan() (in module ablation_study.multi_seed_synthesis) train_and_generate_wgan() (in module ablation_study.multi_seed_synthesis)

train_gan() (in module data_generation.garage) train_gan_with_leakage() (in module ablation_study.leakage_ablation) train_garage_gan() (in module biological_analysis.rare_cell_utility) train_lsh_gan() (in module biological_analysis.rare_cell_utility) train_vanilla_gan() (in module biological_analysis.rare_cell_utility)

V

VanillaDiscriminator (class in ablation_study.multi_seed_synthesis) (class in biological_analysis.rare_cell_utility)

VanillaGenerator (class in ablation_study.multi_seed_synthesis) (class in biological_analysis.rare_cell_utility)

W

wasserstein_distance() (in module data_generation.wasserstein_distance)

WGenerator (class in ablation_study.multi_seed_synthesis)