{"schema_version":"1.0.0","engine_version":"structural-2026.07","tiers":[{"tier":1,"name":"GNN topology link prediction","graph_representation":":PREDICTED_TARGETS edge","produced_by":"api/discovery.py","model_version":"topology-heuristic-v0","confidence_source":"graph-topology co-occurrence heuristic","may_surface_in_clinical_module":false},{"tier":2,"name":"ESM zero-shot variant effect scoring","graph_representation":":Variant.esm_disruption_score property","produced_by":"api/structural.py","model_version":"esm-property-distance-proxy-v0","confidence_source":"amino acid physicochemical property L2 distance (Phase 1 proxy); ESM2 masked-LM log-likelihood (Phase 2 swap-in)","may_surface_in_clinical_module":false},{"tier":3,"name":"Boltz-2 co-folding + binding affinity","graph_representation":":PREDICTED_BINDING edge","produced_by":"api/structural.py","model_version":"boltz2-topology-affinity-proxy-v0","confidence_source":"topology-rescaled pIC50 + curated PDB/AlphaFold structure (Phase 1 proxy); real Boltz-2 co-folding (Phase 2 swap-in)","may_surface_in_clinical_module":false},{"tier":4,"name":"Wet-lab validated","graph_representation":":TARGETS edge (literature-sourced) or :Variant.effect (CPIC-classified)","produced_by":"External partner labs (Precigenetics-style) + curated literature ingestion","confidence_source":"wet-lab binding measurements / clinical classification","may_surface_in_clinical_module":true}],"hard_boundary_enforcement":{"code_level":"Tier 1-3 outputs write to distinct graph properties/edges. No API path returns them as :TARGETS or :effect. See api/structural.py _envelope() must_not_surface_through list.","api_level":"experimental_include_predictions=true required on every Tier 1-3 endpoint.","graph_query_level":"Clinical modules (IndoPGx / CardioRisk / AyurBridge / IndoG6PD / IndoAutoImmune / Orchestrator) query only :TARGETS and :effect. They do NOT read :PREDICTED_TARGETS, :PREDICTED_BINDING, or :esm_disruption_score."}}