Cab biological regime map

data/processed/cab_clinical_inference_summary.csv

@@ -0,0 +1,9 @@
+clinical_disease_group,inference_mode,primary_phenotype_tool,n_assertions,n_genes,collision_fraction,unanchored_fraction,canonical_fraction,ancestry_concentrated_fraction,penetrance_boundary_fraction,median_condition_entropy,median_popmax_af,median_phenotype_anchoring_score,median_genotype_substitution_score
+LQTS,phenotype-first with genotype support,ECG/QTc; Schwartz score components; exercise recovery QTc,883,11,0.18459796149490373,0.8301245753114382,0.12797281993204984,0.04190260475651189,0.053227633069082674,-0.0,0.0,0.9,0.25
+SADS,genotype-first/postmortem,Postmortem absence of explanatory phenotype; family cascade; molecular autopsy,310,7,1.0,0.8709677419354839,0.0,0.025806451612903226,0.03225806451612903,2.0,0.0,0.2,1.0
+CPVT,provocation-dependent,exercise or adrenergic stress testing; bidirectional/polymorphic ventricular tachycardia,258,4,1.0,0.6705426356589147,0.0,0.07364341085271318,0.03488372093023256,1.0,0.0,0.65,0.4
+Brugada,context/provocation-dependent,Type 1 ECG pattern; fever/drug provocation; Shanghai-style clinical scoring,181,6,0.9281767955801105,0.8397790055248618,0.022099447513812154,0.049723756906077346,0.06629834254143646,1.0,0.0,0.65,0.4
+arrhythmia,intermittent rhythm phenotype,ECG/Holter/patch monitoring; episode burden; clinical context,50,6,0.52,0.7,0.08,0.12,0.14,-0.0,0.0,0.55,0.0
+SQTS,phenotype-first with genotype support,ECG QT shortening; clinical/family context,23,2,0.9565217391304348,0.7391304347826086,0.043478260869565216,0.08695652173913043,0.21739130434782608,-0.0,0.0,0.9,0.25
+cardiomyopathy_overlap,structural-electrical hybrid,Cardiac MRI/echo; ECG; ventricular arrhythmia burden; family/genetic criteria,17,5,0.6470588235294118,0.5294117647058824,0.058823529411764705,0.0,0.11764705882352941,1.0,0.0,0.75,0.0
+conduction,intermittent/electrical phenotype,ECG conduction intervals; rhythm monitoring; family history,9,4,0.5555555555555556,0.8888888888888888,0.0,0.0,0.0,-0.0,0.0,0.55,0.4

data/processed/cab_inference_architecture_map.csv

@@ -0,0 +1,13 @@
+architecture_layer,data_source,unit_of_analysis,n_units,dominant_signal,key_metric,key_value,interpretation
+variant_assertion_landscape,ClinVar + gnomAD-derived CAB outputs,public P/LP assertion,1731,disease-model collision plus unanchored assertion states,collision + unanchored percent,92.7787406123628,"Public P/LP assertions mostly do not occupy clean canonical monogenic states after allele, population, and disease-model projection."
+canonical_mendelian_minor_state,ClinVar + gnomAD-derived CAB outputs,public P/LP assertion,87,canonical monogenic minority,canonical percent,5.025996533795494,The classical clean Mendelian arrhythmia assertion state is present but small relative to collision and anchoring-fragile states.
+clinical_inference_environment,CAB clinical inference overlay,LQTS,883,phenotype-first with genotype support,collision fraction,18.45979614949037,LQTS assertions occupy a phenotype-first with genotype support diagnostic environment rather than a generic variant-label space.
+clinical_inference_environment,CAB clinical inference overlay,SADS,310,genotype-first/postmortem,collision fraction,100.0,SADS assertions occupy a genotype-first/postmortem diagnostic environment rather than a generic variant-label space.
+clinical_inference_environment,CAB clinical inference overlay,CPVT,258,provocation-dependent,collision fraction,100.0,CPVT assertions occupy a provocation-dependent diagnostic environment rather than a generic variant-label space.
+clinical_inference_environment,CAB clinical inference overlay,Brugada,181,context/provocation-dependent,collision fraction,92.81767955801104,Brugada assertions occupy a context/provocation-dependent diagnostic environment rather than a generic variant-label space.
+clinical_inference_environment,CAB clinical inference overlay,arrhythmia,50,intermittent rhythm phenotype,collision fraction,52.0,arrhythmia assertions occupy a intermittent rhythm phenotype diagnostic environment rather than a generic variant-label space.
+clinical_inference_environment,CAB clinical inference overlay,SQTS,23,phenotype-first with genotype support,collision fraction,95.65217391304348,SQTS assertions occupy a phenotype-first with genotype support diagnostic environment rather than a generic variant-label space.
+clinical_inference_environment,CAB clinical inference overlay,cardiomyopathy_overlap,17,structural-electrical hybrid,collision fraction,64.70588235294117,cardiomyopathy_overlap assertions occupy a structural-electrical hybrid diagnostic environment rather than a generic variant-label space.
+clinical_inference_environment,CAB clinical inference overlay,conduction,9,intermittent/electrical phenotype,collision fraction,55.55555555555556,conduction assertions occupy a intermittent/electrical phenotype diagnostic environment rather than a generic variant-label space.
+phenotype_first_electrical_risk_anchor,MUSIC SCD heart-failure cohort subject-info.csv,patient ECG/Holter phenotype,992,measured electrical-risk burden without variant data,electrical-risk proxy percent,53.93145161290322,Arrhythmia-related risk can be represented through measured ECG/Holter phenotypes independently of genotype assertions.
+phenotype_first_high_risk_anchor,MUSIC SCD heart-failure cohort subject-info.csv,patient ECG/Holter phenotype,992,high electrical-risk burden without variant data,high electrical-risk proxy percent,34.778225806451616,"A substantial phenotype-first subset occupies a high-risk electrical state, forming the opposite pole from genotype-first SADS inference."

data/processed/cab_music_electrical_risk_by_cause_code.csv

@@ -0,0 +1,6 @@
+cause_of_death,n,electrical_risk_mean,electrical_risk_median,electrical_risk_flag_fraction,electrical_risk_high_fraction,qtc_median,qrs_median,lvef_median,vpb_24h_median,nsvt_fraction,vt_fraction,syncope_fraction
+0,726,3.309228650137741,2.5,0.49449035812672176,0.30303030303030304,438.0,113.0,35.0,195.0,0.24104683195592286,0.31267217630853994,0.14325068870523416
+6,100,4.935,5.0,0.71,0.51,457.0,133.0,30.0,800.0,0.44,0.54,0.18
+3,94,4.675531914893617,4.5,0.6595744680851063,0.5,445.5,126.0,30.0,1022.5,0.425531914893617,0.46808510638297873,0.14893617021276595
+1,61,3.778688524590164,3.5,0.6229508196721312,0.3770491803278688,441.0,118.0,33.5,349.0,0.26229508196721313,0.3770491803278688,0.14754098360655737
+7,11,3.0,2.0,0.45454545454545453,0.36363636363636365,426.0,100.0,35.0,547.0,0.18181818181818182,0.18181818181818182,0.2727272727272727