Latest Model Track
v24_source_feature_integration
set41 F1 @ 0.38
99.3%
set41 Recall @ 0.38
100.0%
set41 Specificity @ 0.38
98.6%
Evidence Cycles
115
Final Sign-off
approved for research triage use
Research triage only; clinical use prohibited

Final Governance State

Research-triage sign-off from Pass99 with candidate threshold 0.71; clinical use remains prohibited.

Research-triage sign-offapproved for research triage use
Manifest replaypassed
Clinical useprohibited
Model IDv24_source_feature_integration
Endpoint Readinessready for research triage endpoint
Candidate Threshold0.71
Set41 Rows144
Set41 Recall100.0%
Governed scorerscore_v24_research_genes_v1.py
Scoring command.venv-training/bin/python scripts/python/score_v24_research_genes_v1.py --threshold 0.71 GENE_SYMBOL

Clinical Translation Readiness

patient-level validation missing. The model is trained and research-triage ready, but clinical disease detection remains blocked.

Research triageready for governed research triage
Disease detectionnot ready for clinical disease detection
Clinical useprohibited
Clinical Readinessblocked pending clinical validation
Blocking Gates7
Disease Claimblocked
Retrospective Cohortready pending real adjudicated cohort
Prospective Studynot started
Risk Controlsnot started

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.

Validation packageready pending real adjudicated cohort
Clinical readinessblocked pending patient level validation
Clinical useprohibited
Prepared Gates4
Remaining Gates6
Frozen Threshold0.71
Real Cohortpending
Template Evidencenot clinical evidence
Disease Claimblocked

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.

Runner statusdry run sample not clinical evidence
Clinical useprohibited
Real cohortpending
Rows Scored4
Score Joincomplete
TP / FP1 / 1
TN / FN1 / 1
Threshold0.71
Disease Claimblocked

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.

Intake statusdry run sample not clinical evidence
Clinical useprohibited
Execution gatereal cohort pending
Candidate score input4
Cohort Validationschema passed sample not clinical evidence
Locked Validationdry run sample not clinical evidence
Score Joincomplete
Threshold0.71
Disease Claimblocked

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.

Acceptance statusblocked sample not clinical evidence
Prospective readinessblocked
Clinical useprohibited
Metric floorslocked
Blocking Gates5
Rows Evaluated4
Sensitivity50.0%
Specificity50.0%
Disease Claimblocked

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.

Manifest statusblocked template source manifest
Template placeholdersblocked
Clinical useprohibited
Blocking Gates1
Provenance Sites2
Deidentificationhipaa safe harbor
Schemalocked
Disease Claimblocked
Cohort admissibilityblocked

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.

Completion statusblocked missing owner evidence
Owner evidencemissing owner evidence
Clinical useprohibited
Blocking Items9
Pass105 readinessblocked
Upstream Gates4
Disease Claimblocked
First Fieldcohort id
Pass107handoff

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.

Preflight statusblocked template inputs pending real cohort
Pass108preflight
Clinical useprohibited
Blocking Gates4
Pass103 intakeblocked
Pass102 validationblocked
Manifestblocked template source manifest
Cohortschema passed sample not clinical evidence
Disease Claimblocked

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.

Handoff statusblocked preflight not ready for locked scoring
Pass109score handoff
Clinical useprohibited
Threshold0.71
Candidate Rows4
Score Columns5
Locked Rows0
Pass102 validationblocked
Disease Claimblocked

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.

Launch statusblocked preflight not ready for retrospective execution
Pass110launch sequence
Clinical useprohibited
Candidate Rows0
Locked Scores0
Rows Scored0
Retrospective Gateblocked
Prospectiveblocked
Disease Claimblocked

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.

Prospective statusblocked retrospective launch not ready for prospective validation
Prospective gateblocked
Clinical useprohibited
Event Rows0
Sites0
Template Evidenceblocked
Minimumsblocked
QMS Reviewblocked
Disease Claimblocked

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.

Dossier statusblocked missing real cohort evidence
Pass110 launchblocked
Clinical useprohibited
Blocking Gates10
Rows0 / 300
Controls0 / 100
Sites0 / 3
Template Evidenceblocked
Disease Claimblocked

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.

Bundle statusblocked pass112 dossier not ready
Retrospective gateblocked
Clinical useprohibited
Pass112 Statusblocked missing real cohort evidence
Pass110 Statusnot run
Locked Scores0
Rows Scored0
Prospective Handoffblocked
Disease Claimblocked

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.

Intake statusblocked owner upload manifest not ready
Pass112 completionblocked
Clinical useprohibited
Required Uploads11
Missing Uploads10
Template Manifestdetected
Pass112 Gates10
Pass113 Launchblocked
Disease Claimblocked

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.

Bridge statusblocked pass114 owner manifest not ready
Generated dossierblocked missing real cohort evidence
Clinical useprohibited
Pass114 Statusblocked owner upload manifest not ready
Missing Uploads10
Field Mappings15
Blocked Mappings13
Pass112 Replacementblocked
Disease Claimblocked

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.

Admissibility statusblocked sample not clinical evidence
Template fingerprintblocked
Clinical useprohibited
Blocking Gates3
PHI-like Values0
Rows Screened4
Sites2
Positive / Negative2 / 2
Disease Claimblocked

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.

Cohort Rows144
Best Model @ 0.38v24_sf
v24_sf F1 @ 0.3899.3%
v24_sf Recall @ 0.38100.0%
v24_sf Specificity @ 0.3898.6%
Residual FN Genesnone

Model Evolution Snapshot (v8-v22)

Condensed view of major challenger families using the same set11 holdout protocol and threshold anchor.

TrackSelected ModelHoldoutF1 @ 0.38Recall @ 0.38Specificity @ 0.38FN genes
v8_corrected_tabularrandom_forestset11 (16)93.3%87.5%100.0%TLK1
v9_mlp_neuralmlp_classifierset11 (16)93.3%87.5%100.0%TLK1
v10_softvote_blendedsoft_voting_hybridset11 (16)93.3%87.5%100.0%TLK1
v11_calibrated_blendedcalibrated_softvote_sigmoidset11 (16)93.3%87.5%100.0%TLK1
v13_hard_control_awarehard_control_weighted_rfset11 (16)100.0%100.0%100.0%none
v14_specificity_gatespecificity_gated_ensembleset11 (16)93.3%87.5%100.0%TLK1
v15_neural_rescue_gateneural_recall_rescue_gateset11 (16)93.3%87.5%100.0%TLK1
v16_evidence_gated_rescueevidence_gated_rescueset11 (16)85.7%75.0%100.0%ARID2, TLK1
v17_stacked_representationstacked_specificity_mlpset11 (16)88.9%100.0%75.0%none
v18_hard_negativehard_negative_stacked_mlpset11 (16)100.0%100.0%100.0%none
v19_set31_recall_rescueset31_recall_rescue_stacked_mlpset11 (16)100.0%100.0%100.0%none
v20_set32_specificity_repairset32_specificity_repair_stacked_mlpset11 (16)100.0%100.0%100.0%none
v21_set33_failure_repairset33_failure_repair_stacked_mlpset11 (16)100.0%100.0%100.0%none
v22_set34_residual_repairset34_residual_repair_stacked_mlpset11 (16)100.0%100.0%100.0%none
v23_set35_comparator_repairset35_comparator_repair_stacked_mlpset11 (16)93.3%87.5%100.0%TLK1
v24_source_feature_integrationsource_feature_integration_stacked_mlpset11 (16)93.3%87.5%100.0%TLK1

Evidence Posture

Current governance framing from the latest combined artifact.

Latest Model Trackv24_source_feature_integration
Plateau Window2
Promotion ReadinessResearch triage ready
External Cohortset41
Best Model @ 0.38v24_sf
Residual FN Genesnone

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.