Index

A

allow_abundance_abundance (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute) allowed_diagnoses (isograph.validation.FreezeSelectionConfig attribute) (isograph.workflow.config.RealDataFreezeConfig attribute) alpha (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute) alpha_abundance (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute) alpha_abundance_grid (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute)

alpha_grid (isograph.evaluation.selection.StabilityResult attribute) (isograph.workflow.config.StabilitySelectionConfig attribute) alpha_switch (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute) alpha_switch_grid (isograph.workflow.config.VaeModelConfig attribute) ancestry_tsv (isograph.workflow.config.RealDataFreezeConfig attribute) annotations_root (isograph.workflow.config.RealDataFreezeConfig attribute) artifact_dir (isograph.workflow.config.ExplainCommandConfig attribute) artifacts_root (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) assay_name (isograph.validation.MatrixSpec attribute) AssayBundle (class in isograph.validation) assays_present() (isograph.validation.LoadedDataset method) available_assays (isograph.validation.LoadedDataset attribute)

B

backend (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) BaselineModelConfig (class in isograph.workflow.config) batch_size (isograph.workflow.config.VaeModelConfig attribute) benchmark() (in module isograph.evaluation.runner)

benchmark_root (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) BenchmarkCommandConfig (class in isograph.workflow.config) beta (isograph.workflow.config.VaeModelConfig attribute) build_feature_spec() (in module isograph.io.artifacts) build_matrix_spec() (in module isograph.io.artifacts)

C

cache_root (isograph.workflow.config.RealDataFreezeConfig attribute) candidate (isograph.workflow.config.CompareCommandConfig attribute) checkpoint_dir (isograph.workflow.config.VaeModelConfig attribute) collapse_threshold (isograph.workflow.config.VaeModelConfig attribute) column (isograph.workflow.config.RealDataFilterTerm attribute) command (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.CompareCommandConfig attribute) (isograph.workflow.config.ExplainCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute)

compare_reports() (in module isograph.evaluation.runner) CompareCommandConfig (class in isograph.workflow.config) corr_threshold (isograph.workflow.config.GraphModelConfig attribute) counts_root (isograph.workflow.config.RealDataFreezeConfig attribute)

D

dataset_name (isograph.validation.DatasetManifest attribute) dataset_path (isograph.workflow.config.FitCommandConfig attribute) dataset_root (isograph.workflow.config.BenchmarkCommandConfig attribute) dataset_suite (isograph.workflow.config.BenchmarkCommandConfig attribute) DatasetBundle (class in isograph.io.artifacts) DatasetManifest (class in isograph.validation)

deep_split (isograph.workflow.config.WgcnaModelConfig attribute) describe_dataset() (in module isograph.io.artifacts) description (isograph.validation.DatasetManifest attribute) device (isograph.workflow.config.VaeModelConfig attribute) df (isograph.workflow.config.RealDataFilterTerm attribute) diagnoses_must_not_be_empty() (isograph.validation.FreezeSelectionConfig class method)

E

early_stop_tol (isograph.workflow.config.VaeModelConfig attribute) edge_stability (isograph.evaluation.selection.StabilityResult attribute) edge_types (isograph.workflow.config.GraphModelConfig attribute)

encoding (isograph.validation.MatrixSpec attribute) ExplainCommandConfig (class in isograph.workflow.config) export_dataset_summary() (in module isograph.evaluation.runner)

F

fdr_method (isograph.workflow.config.ExplainCommandConfig attribute) feature_meta_path (isograph.workflow.config.ExplainCommandConfig attribute) feature_table_path (isograph.workflow.config.ExplainCommandConfig attribute) feature_tables (isograph.io.artifacts.DatasetBundle attribute) (isograph.validation.DatasetManifest attribute) FeatureTableSpec (class in isograph.validation) filename (isograph.validation.FeatureTableSpec attribute) (isograph.validation.MatrixSpec attribute) filter_design_terms (isograph.workflow.config.RealDataFreezeConfig attribute) filter_large_n (isograph.workflow.config.RealDataFreezeConfig attribute)

filter_min_count (isograph.workflow.config.RealDataFreezeConfig attribute) filter_min_prop (isograph.workflow.config.RealDataFreezeConfig attribute) filter_min_total_count (isograph.workflow.config.RealDataFreezeConfig attribute) FitCommandConfig (class in isograph.workflow.config) fixture_filter (isograph.workflow.config.BenchmarkCommandConfig attribute) fixture_graph_overrides (isograph.workflow.config.BenchmarkCommandConfig attribute) fixture_latent_overrides (isograph.workflow.config.BenchmarkCommandConfig attribute) fixture_model_overrides (isograph.workflow.config.BenchmarkCommandConfig attribute) fixture_vae_overrides (isograph.workflow.config.BenchmarkCommandConfig attribute) fixture_wgcna_overrides (isograph.workflow.config.BenchmarkCommandConfig attribute) FreezeSelectionConfig (class in isograph.validation)

G

gamma (isograph.workflow.config.GraphModelConfig attribute) gene_panel_size (isograph.validation.FreezeSelectionConfig attribute) (isograph.workflow.config.RealDataFreezeConfig attribute)

gene_table (isograph.validation.AssayBundle attribute) graph (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) GraphModelConfig (class in isograph.workflow.config)

H

hidden_dim (isograph.workflow.config.VaeModelConfig attribute)

I

isograph.evaluation.runner module isograph.evaluation.selection module isograph.io.artifacts module

isograph.validation module isograph.workflow.config module

K

kind (isograph.validation.FeatureTableSpec attribute) (isograph.workflow.config.RealDataFilterTerm attribute)

L

latent (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) latent_dim (isograph.workflow.config.VaeModelConfig attribute) latent_dim_grid (isograph.workflow.config.VaeModelConfig attribute) LatentModelConfig (class in isograph.workflow.config)

leiden_resolution (isograph.workflow.config.VaeModelConfig attribute) load_dataset_bundle() (in module isograph.io.artifacts) load_dense_matrix() (in module isograph.io.artifacts) LoadedDataset (class in isograph.validation) lr (isograph.workflow.config.VaeModelConfig attribute)

M

manifest (isograph.io.artifacts.DatasetBundle attribute) manifest_path (isograph.validation.LoadedDataset attribute) matrices (isograph.io.artifacts.DatasetBundle attribute) (isograph.validation.DatasetManifest attribute) matrix (isograph.validation.AssayBundle attribute) MatrixSpec (class in isograph.validation) max_iter (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) max_modules (isograph.workflow.config.BaselineModelConfig attribute) merge_cut_height (isograph.workflow.config.WgcnaModelConfig attribute) min_complete_pairs (isograph.workflow.config.ExplainCommandConfig attribute) min_module_size (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute) (isograph.workflow.config.WgcnaModelConfig attribute)

model (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) model_config (isograph.validation.AssayBundle attribute) (isograph.validation.DatasetManifest attribute) (isograph.validation.FeatureTableSpec attribute) (isograph.validation.FreezeSelectionConfig attribute) (isograph.validation.LoadedDataset attribute) (isograph.validation.MatrixSpec attribute) module isograph.evaluation.runner isograph.evaluation.selection isograph.io.artifacts isograph.validation isograph.workflow.config module_ids (isograph.workflow.config.ExplainCommandConfig attribute) module_score_table_path (isograph.workflow.config.ExplainCommandConfig attribute)

N

n_components (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) n_components_cv_folds (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) n_components_grid (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) n_epochs (isograph.workflow.config.VaeModelConfig attribute) n_features (isograph.validation.AssayBundle attribute) (isograph.validation.MatrixSpec attribute) n_genes (isograph.validation.LoadedDataset attribute) n_hidden_layers (isograph.workflow.config.VaeModelConfig attribute)

n_iterations (isograph.workflow.config.StabilitySelectionConfig attribute) n_rows (isograph.validation.FeatureTableSpec attribute) n_samples (isograph.validation.AssayBundle attribute) (isograph.validation.LoadedDataset attribute) (isograph.validation.MatrixSpec attribute) name (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute) (isograph.workflow.config.WgcnaModelConfig attribute) network_type (isograph.workflow.config.WgcnaModelConfig attribute) normalized_laplacian (isograph.workflow.config.GraphModelConfig attribute)

O

output_dir (isograph.workflow.config.ExplainCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute)

output_name (isograph.workflow.config.RealDataFreezeConfig attribute) output_path (isograph.workflow.config.CompareCommandConfig attribute)

P

patience (isograph.workflow.config.VaeModelConfig attribute) phenotype_tsv (isograph.workflow.config.RealDataFreezeConfig attribute) power (isograph.workflow.config.WgcnaModelConfig attribute) power_range (isograph.workflow.config.WgcnaModelConfig attribute)

prepare_core_suite() (in module isograph.evaluation.runner) prepare_multiplex_suite() (in module isograph.evaluation.runner) prepare_scale_suite() (in module isograph.evaluation.runner) provenance (isograph.validation.DatasetManifest attribute)

R

random_state (isograph.workflow.config.VaeModelConfig attribute) (isograph.workflow.config.WgcnaModelConfig attribute) real_data (isograph.workflow.config.BenchmarkCommandConfig attribute) RealDataFilterTerm (class in isograph.workflow.config) RealDataFreezeConfig (class in isograph.workflow.config) recommended_alpha (isograph.evaluation.selection.StabilityResult attribute) recovery_thresholds (isograph.workflow.config.BenchmarkCommandConfig attribute)

reference (isograph.workflow.config.CompareCommandConfig attribute) report_root (isograph.workflow.config.BenchmarkCommandConfig attribute) residualize_covariates (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute) (isograph.workflow.config.WgcnaModelConfig attribute) run_stability_selection (isograph.workflow.config.BenchmarkCommandConfig attribute)

S

sample_table (isograph.io.artifacts.DatasetBundle attribute) (isograph.validation.AssayBundle attribute) (isograph.validation.DatasetManifest attribute) save_dataset_bundle() (in module isograph.io.artifacts) save_dense_matrix() (in module isograph.io.artifacts) seed (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) (isograph.workflow.config.StabilitySelectionConfig attribute) sft_r2_threshold (isograph.workflow.config.WgcnaModelConfig attribute) split_percentile (isograph.workflow.config.ExplainCommandConfig attribute)

stability (isograph.workflow.config.BenchmarkCommandConfig attribute) stability_selection() (in module isograph.evaluation.selection) stability_threshold (isograph.workflow.config.StabilitySelectionConfig attribute) StabilityResult (class in isograph.evaluation.selection) StabilitySelectionConfig (class in isograph.workflow.config) stable_edge_counts (isograph.evaluation.selection.StabilityResult attribute) stage_name (isograph.workflow.config.BenchmarkCommandConfig attribute) standardize (isograph.workflow.config.RealDataFilterTerm attribute) subsample_fraction (isograph.workflow.config.StabilitySelectionConfig attribute) suite_name (isograph.validation.DatasetManifest attribute) summary_table() (isograph.evaluation.selection.StabilityResult method)

T

timeout_seconds (isograph.workflow.config.WgcnaModelConfig attribute) tol (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) tracking_uri (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) trait_columns (isograph.workflow.config.BaselineModelConfig attribute) (isograph.workflow.config.GraphModelConfig attribute) (isograph.workflow.config.LatentModelConfig attribute) (isograph.workflow.config.VaeModelConfig attribute) (isograph.workflow.config.WgcnaModelConfig attribute)

transcript_usage_feature_type (isograph.workflow.config.ExplainCommandConfig attribute) truth_tables (isograph.io.artifacts.DatasetBundle attribute) (isograph.validation.DatasetManifest attribute)

V

vae (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) VaeModelConfig (class in isograph.workflow.config)

val_fraction (isograph.workflow.config.VaeModelConfig attribute) validate_bundle_inputs() (in module isograph.io.artifacts) validate_tables() (isograph.validation.DatasetManifest method)

W

warmup_epochs (isograph.workflow.config.VaeModelConfig attribute) weight_decay (isograph.workflow.config.VaeModelConfig attribute)

wgcna (isograph.workflow.config.BenchmarkCommandConfig attribute) (isograph.workflow.config.FitCommandConfig attribute) WgcnaModelConfig (class in isograph.workflow.config)