Cab biological regime map

data/processed/cab_biological_gene_regime_matrix.csv

@@ -8,11 +8,11 @@ CALM1,0,0,15,0,0,0
 CALM2,0,0,13,0,0,0
 CALM3,0,0,8,0,0,0
 CASQ2,0,0,65,0,0,0
-HCN4,0,0,18,0,0,0
+HCN4,2,1,5,1,9,0
 KCNE1,2,1,0,2,9,0
-KCNH2,10,56,0,5,407,0
+KCNH2,10,55,10,3,400,0
 KCNJ2,0,0,29,0,0,0
-KCNQ1,19,35,0,2,230,0
-RYR2,0,0,183,0,0,0
+KCNQ1,14,30,26,2,214,0
+RYR2,0,0,176,0,7,0
 SCN5A,0,0,394,0,0,0
 TRDN,0,0,51,0,0,0

data/processed/cab_biological_regime_sensitivity.csv

@@ -0,0 +1,12 @@
+scenario,description,n_assertions,disease_model_collision_n,disease_model_collision_percent,unanchored_assertion_state_n,unanchored_assertion_state_percent,collision_plus_unanchored_n,collision_plus_unanchored_percent,canonical_monogenic_n,canonical_monogenic_percent,collision_plus_unanchored_dominant,canonical_remains_minority,top_regime,top_regime_n,top_regime_percent
+baseline,Current CAB regime rules.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,87,5.025996533795494,True,True,disease_model_collision,963,55.63258232235702
+ancestry_strict_ratio_20,Requires stronger popmax/global enrichment.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,87,5.025996533795494,True,True,disease_model_collision,963,55.63258232235702
+ancestry_lenient_ratio_5,Allows weaker ancestry concentration.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,87,5.025996533795494,True,True,disease_model_collision,963,55.63258232235702
+ancestry_min_popmax_1e_5,Requires higher absolute popmax AF.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,87,5.025996533795494,True,True,disease_model_collision,963,55.63258232235702
+boundary_narrow_0p5log10,Narrow penetrance-boundary window.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,92,5.314846909300982,True,True,disease_model_collision,963,55.63258232235702
+boundary_wide_1p5log10,Wide penetrance-boundary window.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,58,3.3506643558636626,True,True,disease_model_collision,963,55.63258232235702
+canonical_lenient_validity_0p25,Allows limited gene-disease validity into canonical candidate set.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,88,5.083766608896592,True,True,disease_model_collision,963,55.63258232235702
+canonical_strict_validity_0p85,Requires strong/definitive-like gene-disease validity.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,85,4.910456383593298,True,True,disease_model_collision,963,55.63258232235702
+canonical_lenient_anchor_0p45,Allows representation-repairable alleles into canonical candidate set.,1731,963,55.63258232235702,286,16.522241478913923,1249,72.15482380127094,444,25.64991334488735,True,False,disease_model_collision,963,55.63258232235702
+collision_no_gene_fallback,Removes collision-prone gene fallback and uses only condition entropy/count.,1731,775,44.771808203350666,793,45.81166955517042,1568,90.58347775852108,107,6.1813980358174465,True,True,unanchored_assertion_state,793,45.81166955517042
+canonical_can_coexist_with_collision,Tests whether canonical calls reappear if collision is not exclusionary.,1731,963,55.63258232235702,643,37.14615829000578,1606,92.7787406123628,87,5.025996533795494,True,True,disease_model_collision,963,55.63258232235702

data/processed/cab_biological_regime_sensitivity_long.csv

@@ -0,0 +1,66 @@
+scenario,description,primary_regime,n_assertions,percent
+baseline,Current CAB regime rules.,disease_model_collision,963,55.63258232235702
+baseline,Current CAB regime rules.,unanchored_assertion_state,643,37.14615829000578
+baseline,Current CAB regime rules.,canonical_monogenic,87,5.025996533795494
+baseline,Current CAB regime rules.,ancestry_concentrated,29,1.6753321779318313
+baseline,Current CAB regime rules.,penetrance_boundary,8,0.4621606008087811
+baseline,Current CAB regime rules.,unknown_or_insufficient,1,0.057770075101097634
+ancestry_strict_ratio_20,Requires stronger popmax/global enrichment.,disease_model_collision,963,55.63258232235702
+ancestry_strict_ratio_20,Requires stronger popmax/global enrichment.,unanchored_assertion_state,643,37.14615829000578
+ancestry_strict_ratio_20,Requires stronger popmax/global enrichment.,canonical_monogenic,87,5.025996533795494
+ancestry_strict_ratio_20,Requires stronger popmax/global enrichment.,penetrance_boundary,24,1.3864818024263432
+ancestry_strict_ratio_20,Requires stronger popmax/global enrichment.,ancestry_concentrated,13,0.7510109763142692
+ancestry_strict_ratio_20,Requires stronger popmax/global enrichment.,unknown_or_insufficient,1,0.057770075101097634
+ancestry_lenient_ratio_5,Allows weaker ancestry concentration.,disease_model_collision,963,55.63258232235702
+ancestry_lenient_ratio_5,Allows weaker ancestry concentration.,unanchored_assertion_state,643,37.14615829000578
+ancestry_lenient_ratio_5,Allows weaker ancestry concentration.,canonical_monogenic,87,5.025996533795494
+ancestry_lenient_ratio_5,Allows weaker ancestry concentration.,ancestry_concentrated,31,1.7908723281340266
+ancestry_lenient_ratio_5,Allows weaker ancestry concentration.,penetrance_boundary,6,0.3466204506065858
+ancestry_lenient_ratio_5,Allows weaker ancestry concentration.,unknown_or_insufficient,1,0.057770075101097634
+ancestry_min_popmax_1e_5,Requires higher absolute popmax AF.,disease_model_collision,963,55.63258232235702
+ancestry_min_popmax_1e_5,Requires higher absolute popmax AF.,unanchored_assertion_state,643,37.14615829000578
+ancestry_min_popmax_1e_5,Requires higher absolute popmax AF.,canonical_monogenic,87,5.025996533795494
+ancestry_min_popmax_1e_5,Requires higher absolute popmax AF.,ancestry_concentrated,29,1.6753321779318313
+ancestry_min_popmax_1e_5,Requires higher absolute popmax AF.,penetrance_boundary,8,0.4621606008087811
+ancestry_min_popmax_1e_5,Requires higher absolute popmax AF.,unknown_or_insufficient,1,0.057770075101097634
+boundary_narrow_0p5log10,Narrow penetrance-boundary window.,disease_model_collision,963,55.63258232235702
+boundary_narrow_0p5log10,Narrow penetrance-boundary window.,unanchored_assertion_state,643,37.14615829000578
+boundary_narrow_0p5log10,Narrow penetrance-boundary window.,canonical_monogenic,92,5.314846909300982
+boundary_narrow_0p5log10,Narrow penetrance-boundary window.,ancestry_concentrated,29,1.6753321779318313
+boundary_narrow_0p5log10,Narrow penetrance-boundary window.,penetrance_boundary,3,0.1733102253032929
+boundary_narrow_0p5log10,Narrow penetrance-boundary window.,unknown_or_insufficient,1,0.057770075101097634
+boundary_wide_1p5log10,Wide penetrance-boundary window.,disease_model_collision,963,55.63258232235702
+boundary_wide_1p5log10,Wide penetrance-boundary window.,unanchored_assertion_state,643,37.14615829000578
+boundary_wide_1p5log10,Wide penetrance-boundary window.,canonical_monogenic,58,3.3506643558636626
+boundary_wide_1p5log10,Wide penetrance-boundary window.,penetrance_boundary,38,2.19526285384171
+boundary_wide_1p5log10,Wide penetrance-boundary window.,ancestry_concentrated,29,1.6753321779318313
+canonical_lenient_validity_0p25,Allows limited gene-disease validity into canonical candidate set.,disease_model_collision,963,55.63258232235702
+canonical_lenient_validity_0p25,Allows limited gene-disease validity into canonical candidate set.,unanchored_assertion_state,643,37.14615829000578
+canonical_lenient_validity_0p25,Allows limited gene-disease validity into canonical candidate set.,canonical_monogenic,88,5.083766608896592
+canonical_lenient_validity_0p25,Allows limited gene-disease validity into canonical candidate set.,ancestry_concentrated,29,1.6753321779318313
+canonical_lenient_validity_0p25,Allows limited gene-disease validity into canonical candidate set.,penetrance_boundary,8,0.4621606008087811
+canonical_strict_validity_0p85,Requires strong/definitive-like gene-disease validity.,disease_model_collision,963,55.63258232235702
+canonical_strict_validity_0p85,Requires strong/definitive-like gene-disease validity.,unanchored_assertion_state,643,37.14615829000578
+canonical_strict_validity_0p85,Requires strong/definitive-like gene-disease validity.,canonical_monogenic,85,4.910456383593298
+canonical_strict_validity_0p85,Requires strong/definitive-like gene-disease validity.,ancestry_concentrated,29,1.6753321779318313
+canonical_strict_validity_0p85,Requires strong/definitive-like gene-disease validity.,penetrance_boundary,8,0.4621606008087811
+canonical_strict_validity_0p85,Requires strong/definitive-like gene-disease validity.,unknown_or_insufficient,3,0.1733102253032929
+canonical_lenient_anchor_0p45,Allows representation-repairable alleles into canonical candidate set.,disease_model_collision,963,55.63258232235702
+canonical_lenient_anchor_0p45,Allows representation-repairable alleles into canonical candidate set.,canonical_monogenic,444,25.64991334488735
+canonical_lenient_anchor_0p45,Allows representation-repairable alleles into canonical candidate set.,unanchored_assertion_state,286,16.522241478913923
+canonical_lenient_anchor_0p45,Allows representation-repairable alleles into canonical candidate set.,ancestry_concentrated,29,1.6753321779318313
+canonical_lenient_anchor_0p45,Allows representation-repairable alleles into canonical candidate set.,penetrance_boundary,8,0.4621606008087811
+canonical_lenient_anchor_0p45,Allows representation-repairable alleles into canonical candidate set.,unknown_or_insufficient,1,0.057770075101097634
+collision_no_gene_fallback,Removes collision-prone gene fallback and uses only condition entropy/count.,unanchored_assertion_state,793,45.81166955517042
+collision_no_gene_fallback,Removes collision-prone gene fallback and uses only condition entropy/count.,disease_model_collision,775,44.771808203350666
+collision_no_gene_fallback,Removes collision-prone gene fallback and uses only condition entropy/count.,canonical_monogenic,107,6.1813980358174465
+collision_no_gene_fallback,Removes collision-prone gene fallback and uses only condition entropy/count.,ancestry_concentrated,41,2.368573079145003
+collision_no_gene_fallback,Removes collision-prone gene fallback and uses only condition entropy/count.,penetrance_boundary,13,0.7510109763142692
+collision_no_gene_fallback,Removes collision-prone gene fallback and uses only condition entropy/count.,unknown_or_insufficient,1,0.057770075101097634
+collision_no_gene_fallback,Removes collision-prone gene fallback and uses only condition entropy/count.,sads_sensitive,1,0.057770075101097634
+canonical_can_coexist_with_collision,Tests whether canonical calls reappear if collision is not exclusionary.,disease_model_collision,963,55.63258232235702
+canonical_can_coexist_with_collision,Tests whether canonical calls reappear if collision is not exclusionary.,unanchored_assertion_state,643,37.14615829000578
+canonical_can_coexist_with_collision,Tests whether canonical calls reappear if collision is not exclusionary.,canonical_monogenic,87,5.025996533795494
+canonical_can_coexist_with_collision,Tests whether canonical calls reappear if collision is not exclusionary.,ancestry_concentrated,29,1.6753321779318313
+canonical_can_coexist_with_collision,Tests whether canonical calls reappear if collision is not exclusionary.,penetrance_boundary,8,0.4621606008087811
+canonical_can_coexist_with_collision,Tests whether canonical calls reappear if collision is not exclusionary.,unknown_or_insufficient,1,0.057770075101097634

data/processed/cab_biological_regime_summary.csv

@@ -1,7 +1,7 @@
 primary_regime,n_assertions,percent,n_genes,median_global_af,median_popmax_af,median_popmax_global_ratio,median_condition_entropy,median_gene_disease_validity_score,fraction_ancestry_concentrated,fraction_penetrance_boundary,fraction_sads_label,dominant_phenotype_environment
-disease_model_collision,947,54.70826112073946,11,0.0,0.0,1.3146359698624628,1.0,1.0,0.05174234424498416,0.05279831045406547,0.7697993664202746,provocation_dependent
-unanchored_assertion_state,650,37.55054881571346,5,0.0,0.0,,0.0,1.0,0.0,0.0,0.0,ECG_visible
-canonical_monogenic,92,5.314846909300982,3,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,ECG_visible
-ancestry_concentrated,32,1.8486424032351243,4,1.2317234846745057e-06,2.5196533532935653e-05,21.349203364989183,0.0,1.0,1.0,1.0,0.0,ECG_visible
-penetrance_boundary,9,0.5199306759098787,3,3.5673706872718e-06,7.97089897247866e-06,1.4927950545584636,0.0,1.0,0.0,1.0,0.0,ECG_visible
+disease_model_collision,963,55.63258232235702,13,0.0,0.0,1.3146276697246606,1.0,1.0,0.05399792315680166,0.056074766355140186,0.32191069574247144,provocation_dependent
+unanchored_assertion_state,643,37.14615829000578,7,0.0,0.0,,0.0,1.0,0.0,0.0,0.0,ECG_visible
+canonical_monogenic,87,5.025996533795494,4,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,ECG_visible
+ancestry_concentrated,29,1.6753321779318313,5,1.3682454851319603e-06,2.5192724341210258e-05,18.40963463110593,0.0,1.0,1.0,1.0,0.0,ECG_visible
+penetrance_boundary,8,0.4621606008087811,4,2.814422760472438e-06,1.0240788138803646e-05,2.25231074024802,0.0,1.0,0.0,1.0,0.0,ECG_visible
 unknown_or_insufficient,1,0.057770075101097634,1,6.870028675499691e-07,9.019003039404024e-07,1.3128038232984225,0.0,0.25,0.0,0.0,0.0,provocation_dependent

data/processed/cab_biological_regime_validation.csv

@@ -1,7 +1,7 @@
 regime,n_in_regime,median_popmax_global_ratio_in,median_popmax_global_ratio_out,median_condition_entropy_in,median_condition_entropy_out,median_validity_score_in,median_validity_score_out,sads_label_fraction_in,sads_label_fraction_out
-canonical_monogenic,132,1.2696389895520963,1.3146359698624628,0.0,1.0,1.0,1.0,0.0,0.45590994371482174
-ancestry_concentrated,81,24.206523452964174,1.299805806439304,1.0,1.0,1.0,1.0,0.43209876543209874,0.4206060606060606
-penetrance_boundary,92,18.127673842298876,1.292500195982875,1.0,1.0,1.0,1.0,0.33695652173913043,0.425869432580842
-disease_model_collision,947,1.3146359698624628,1.2845172854730285,1.0,0.0,1.0,1.0,0.7697993664202746,0.0
-sads_sensitive,729,1.3146382309816362,1.3134481466749075,2.0,0.0,1.0,1.0,1.0,0.0
-unanchored_assertion_state,1397,,1.314531396274846,1.0,1.0,1.0,1.0,0.4108804581245526,0.46407185628742514
+canonical_monogenic,123,1.2800648600031863,1.3146276697246606,0.0,0.0,1.0,1.0,0.0,0.1927860696517413
+ancestry_concentrated,81,24.206523452964174,1.299805806439304,0.0,0.0,1.0,1.0,0.09876543209876543,0.18303030303030304
+penetrance_boundary,92,18.127673842298876,1.292500195982875,0.0,0.0,1.0,1.0,0.10869565217391304,0.18303843807199513
+disease_model_collision,963,1.3146276697246606,1.2889697109428708,1.0,0.0,1.0,1.0,0.32191069574247144,0.0
+sads_sensitive,310,1.3143795770110511,1.3145913397741669,2.0,0.0,1.0,1.0,1.0,0.0
+unanchored_assertion_state,1397,,1.314531396274846,0.0,1.0,1.0,1.0,0.19327129563350035,0.11976047904191617