Current Combined Findings
Unified research briefing focused on cumulative evidence, latest validated model posture, and actionable next steps. Historical passes remain archived, but this page only surfaces the latest and combined view.
Final Governance State
Research-triage sign-off from Pass99 with candidate threshold 0.71; clinical use remains prohibited.
.venv-training/bin/python scripts/python/score_v24_research_genes_v1.py --threshold 0.71 GENE_SYMBOLClinical Translation Readiness
patient-level validation missing. The model is trained and research-triage ready, but clinical disease detection remains blocked.
Patient-Level Validation Protocol
Pass101 adds the locked patient-level endpoint, schema, cohort CSV template, and validation runner needed before retrospective clinical validation can begin.
Retrospective Validation Runner
Pass102 adds the dry-run analysis path for patient-level scoring: frozen threshold metrics, residuals, subgroup suppression, dry-run JSON, and score-template CSV. The dry-run sample is not clinical evidence.
External Validation Intake
Pass103 freezes the external validation handoff: cohort/package hashes, locked v24 model reference, score-template linkage, and candidate score input for partner cohort execution.
Retrospective Acceptance Gates
Pass104 adds locked metric floors, calibration, subgroup reportability, residual-review, and prospective-validation gates on top of the Pass102/103 dry-run path.
Source Manifest Readiness
Pass106 supplies the source-manifest schema, template, validator, and blocked template check required before an external cohort can satisfy Pass105. It includes data-use, deidentification, provenance, adjudication, and training-overlap attestation fields.
Source Manifest Completion
Pass107 turns Pass106 into a cohort-owner completion packet: each missing owner evidence item is mapped to the Pass106 and Pass105 gate it clears before any real patient cohort can enter admissibility review.
Cohort Intake Preflight
Pass108 gives cohort owners one executable preflight for completed source manifests and deidentified cohort CSVs. The current default run is blocked template inputs, so it is not clinical evidence.
Frozen v24 Scoring Handoff
Pass109 packages the locked score CSV contract for Pass102. The current handoff is blocked preflight because Pass108 still points at template/sample inputs rather than a real cohort.
Retrospective Validation Launch
Pass110 gives the project one executable launch sequence for the locked retrospective validation path. The current launch is blocked preflight because default inputs are still templates.
Pass111 Prospective Validation Readiness
Pass111 adds the protocol, schema, and event-log template for the prospective multisite validation stage. It follows Pass110 and keeps clinical use prohibited until real prospective evidence and governance review pass.
Pass112 Retrospective Cohort Evidence
Pass112 converts the missing real-cohort evidence blocker into a governance, provenance, adjudication, score-artifact, and owner sign-off dossier. The default state is blocked missing real cohort evidence.
Pass113 Retrospective Execution Bundle
Pass113 chains the ready Pass112 dossier into the real Pass110 launcher. The current state is blocked Pass112 dossier, so retrospective execution and clinical use remain prohibited.
Pass114 Real Cohort Intake Packet
Pass114 turns the external-evidence blocker into an owner upload manifest, schema, and checklist. The current state is blocked owner upload manifest, so it prepares Pass112 completion but does not run retrospective validation or permit clinical use.
Pass115 Pass112 Dossier Bridge
Pass115 converts a ready Pass114 owner manifest into a Pass112-compatible generated dossier for owner review. It keeps Pass113 execution and clinical use blocked until real files are staged and approved.
Cohort Admissibility Audit
Pass105 adds the pre-evidence firewall for patient cohorts: template fingerprint checks, source-manifest governance, PHI-like value screening, duplicate candidate controls, and site/label diversity gates.
Executive Summary
Combined interpretation from recent model and evidence cycles.
Latest v24 source-feature integration challenger consumes set37 labels as training data, keeps the Set11 comparator window at F1 93.3%, recall 87.5%, specificity 100.0%, and repairs the set37 v23 boundary failure on training fit (delta F1 +48.1 pp, delta recall +56.2 pp, delta specificity +25.0 pp).
V24 preserves the current checks at set36 F1 90.9% (recall 83.3%, specificity 100.0%) and set29 F1 73.5%, but remains research-only because set37 is now training evidence and set38 fresh replication is required.
Disjoint external holdout set41 (n=144) shows v24_sf at F1 99.3%, recall 100.0%, specificity 98.6%.
Pass98 live-scores set41 as the first post-governance surveillance gate for v24, using a 144-row fresh cohort of adjudicated positives and hard boundary controls.
On set41 at the 0.38 anchor, v24_sf reaches F1 99.3%, recall 100.0%, specificity 98.6%; at candidate threshold 0.71, v24_sf reaches F1 99.3%, recall 100.0%, specificity 98.6%.
Pass98 set41 surveillance decision: set41 surveillance passed.
Pass95 calibration/stability analysis across set38+set39 identifies candidate threshold 0.71 with F1 99.0%, recall 100.0%, specificity 97.9%, and 0 false negatives; set40 is now frozen as a 192-row candidate gate.
Pass97 packages v24 governance and reproducibility artifacts, and Pass98 clears the required set41 surveillance gate; production use remains blocked pending final governance sign-off at candidate threshold 0.71 (F1 99.5%, recall 100.0%, specificity 99.0%).
Operational recommendation: v24 can be used for governed research triage through the approved scorer and readiness contract; clinical use remains prohibited.
Pass99 completes final governance sign-off for v24 research triage: approved for research triage use, endpoint readiness ready for research triage endpoint, with clinical diagnosis and treatment use still prohibited.
Pass100 clinical translation readiness: v24 is trained and ready for governed research triage, but patient-level validation missing means it is not ready for clinical disease detection.
Pass101 patient-level validation readiness: the patient-level validation runner, locked endpoint, schema, and cohort CSV template are ready pending a real adjudicated cohort; clinical use remains prohibited.
Pass102 retrospective validation runner dry-run: score join and locked threshold metric computation are executable on the sample template (TP 1, FP 1, TN 1, FN 1), but the dry-run sample is not clinical evidence.
Pass103 external validation intake: the frozen intake package and candidate score input are now executable for a DUA/IRB-appropriate cohort, but the current dry-run remains sample/template evidence only.
Pass104 retrospective acceptance gate: locked metric floors, calibration, subgroup, residual-review, and prospective-validation gates are now executable; the current dry-run is blocked as sample evidence only.
Pass105 cohort admissibility audit: template fingerprints, source-manifest governance, PHI-like cell values, duplicate candidate rows, site/label diversity, and Pass101 carry-forward gates are now executable before any patient cohort can become retrospective evidence.
Pass106 source manifest readiness: the external cohort source-manifest schema, template, validator, and template check are now available so cohort owners can satisfy Pass105's source-manifest gate without weakening the clinical-use boundary.
Pass107 source-manifest completion packet: the Pass106 template blocker is now translated into a cohort-owner checklist with required evidence roles and gate mappings; current status remains blocked by missing owner evidence.
Pass108 cohort-intake preflight: the source-manifest and patient-cohort gates are now orchestrated as one runnable preflight before Pass103/Pass102 execution; the default run remains blocked template inputs pending a real deidentified cohort.
Pass109 frozen v24 scoring handoff: the governed v24 scorer now has a locked Pass102 score CSV contract and assembly path; default status remains blocked preflight until real cohort files clear Pass108.
Pass110 retrospective validation launch: the full Pass108/103/109/102/104 execution chain now has a one-command launcher; default status remains blocked preflight until real cohort files and governed v24 scores are supplied.
Pass111 prospective validation readiness: the multisite prospective protocol, event schema, and event template now exist; default status remains blocked retrospective launch, and clinical use remains prohibited.
Pass112 retrospective cohort evidence dossier: the real cohort-owner evidence contract now exists for governance, provenance, adjudication, score artifacts, and sign-off; default status remains blocked missing real cohort evidence, and clinical use remains prohibited.
Pass113 retrospective execution bundle: the governed launch point now requires Pass112 real-cohort evidence before running Pass110; default status remains blocked Pass112 dossier, and clinical use remains prohibited.
Pass114 real cohort intake packet: the owner upload manifest, schema, and checklist now make the remaining real-cohort evidence handoff explicit; default status remains blocked owner upload manifest, and clinical use remains prohibited.
Pass115 Pass112 dossier bridge: the validated owner upload manifest can now be mapped into a Pass112-compatible generated dossier for owner review; default status remains blocked Pass114 owner manifest, and clinical use remains prohibited.
Latest External Holdout (set41)
Disjoint cohort used to pressure-test current challenger families outside set11 comparator lockstep.
Model Evolution Snapshot (v8-v22)
Condensed view of major challenger families using the same set11 holdout protocol and threshold anchor.
| Track | Selected Model | Holdout | F1 @ 0.38 | Recall @ 0.38 | Specificity @ 0.38 | FN genes |
|---|---|---|---|---|---|---|
| v8_corrected_tabular | random_forest | set11 (16) | 93.3% | 87.5% | 100.0% | TLK1 |
| v9_mlp_neural | mlp_classifier | set11 (16) | 93.3% | 87.5% | 100.0% | TLK1 |
| v10_softvote_blended | soft_voting_hybrid | set11 (16) | 93.3% | 87.5% | 100.0% | TLK1 |
| v11_calibrated_blended | calibrated_softvote_sigmoid | set11 (16) | 93.3% | 87.5% | 100.0% | TLK1 |
| v13_hard_control_aware | hard_control_weighted_rf | set11 (16) | 100.0% | 100.0% | 100.0% | none |
| v14_specificity_gate | specificity_gated_ensemble | set11 (16) | 93.3% | 87.5% | 100.0% | TLK1 |
| v15_neural_rescue_gate | neural_recall_rescue_gate | set11 (16) | 93.3% | 87.5% | 100.0% | TLK1 |
| v16_evidence_gated_rescue | evidence_gated_rescue | set11 (16) | 85.7% | 75.0% | 100.0% | ARID2, TLK1 |
| v17_stacked_representation | stacked_specificity_mlp | set11 (16) | 88.9% | 100.0% | 75.0% | none |
| v18_hard_negative | hard_negative_stacked_mlp | set11 (16) | 100.0% | 100.0% | 100.0% | none |
| v19_set31_recall_rescue | set31_recall_rescue_stacked_mlp | set11 (16) | 100.0% | 100.0% | 100.0% | none |
| v20_set32_specificity_repair | set32_specificity_repair_stacked_mlp | set11 (16) | 100.0% | 100.0% | 100.0% | none |
| v21_set33_failure_repair | set33_failure_repair_stacked_mlp | set11 (16) | 100.0% | 100.0% | 100.0% | none |
| v22_set34_residual_repair | set34_residual_repair_stacked_mlp | set11 (16) | 100.0% | 100.0% | 100.0% | none |
| v23_set35_comparator_repair | set35_comparator_repair_stacked_mlp | set11 (16) | 93.3% | 87.5% | 100.0% | TLK1 |
| v24_source_feature_integration | source_feature_integration_stacked_mlp | set11 (16) | 93.3% | 87.5% | 100.0% | TLK1 |
Evidence Posture
Current governance framing from the latest combined artifact.
Latest archived technical dossier remains available for audit: pass-115-pass112-dossier-bridge.html
Consolidated Evidence Links
Single-entry artifacts for executive and research review.