Uncertainty-Imaging Skill

Purpose

A medical-imaging model framed for deployment must say more than "class 1, 0.87". It needs a calibrated uncertainty on each case, an out-of-distribution (OOD) guard validated on data known to be out-of-distribution, and — if it abstains — a pre-specified operating point. The failures are predictable and reviewer-visible: a clinical-use claim built on point predictions, conformal intervals quoted without ever measuring their coverage, an "OOD detector" evaluated only on in-distribution data, a deep ensemble whose members share a seed, and uncertainty validated only in-distribution when deployment sees scanner/site/case-mix shift. This skill designs that layer and audits an existing one (Gal 2016; Lakshminarayanan 2017; Angelopoulos & Bates; Ovadia 2019; DECIDE-AI).

It is the deployment-safety companion in the model-engineering lane: /model-evaluation computes the held-out metrics and calibration, and uncertainty-imaging covers the uncertainty / OOD / abstention machinery a deployment claim rests on. It integrates MAPIE (conformal), captum, and pretrained OOD scorers; it does not reimplement them and never runs a model on real patient data.

When to use

• Your model is framed for clinical use / deployment and a reviewer will ask "what does it do when it is

unsure, or off-distribution?"

• You report conformal / MC-dropout / ensemble uncertainty and want the coverage, independence, and

shift checks right before submission.

• You want to audit an existing uncertainty/OOD section for the failure modes below.

When NOT to use

• Held-out discrimination / calibration metrics of the point predictor → /model-evaluation then

/analyze-stats.

• Training-repo scaffolding / the split → /model-scaffold (+ /model-validation).
• Interpretability / saliency of a trained network → /explainability.
• Classical-ML calibration of a tabular model → /radiomics-ml + /analyze-stats.
• Reimplementing MAPIE / an OOD library → out of scope (this skill wires and audits them).

The failure modes (what the gate enforces)

1. Point predictions under a deployment claim. A clinical-use claim with no uncertainty method at

all — add MC-dropout, a deep ensemble, conformal prediction, or a Bayesian estimate.

1. Conformal without coverage validation. Conformal's guarantee holds under exchangeability, which

can fail on clinical data — measure achieved coverage on a held-out calibration/test set.

1. OOD claim with no held-out OOD set. An OOD detector's operating point and AUROC are unmeasured

until you evaluate on data known to be out-of-distribution (different scanner / site / pathology).

1. Non-independent ensemble. A deep ensemble whose members share a seed/init (or has < 2 members)

underestimates epistemic uncertainty.

1. MC-dropout with dropout off at inference. Dropout must stay active during sampling; off, every

pass is identical and the estimate collapses to a point prediction.

1. Selective prediction without a target. Abstention chosen post hoc inflates accuracy-at-coverage;

pre-specify the coverage / risk operating point.

1. No calibration under shift. Uncertainty evaluated in-distribution only; deployment uncertainty

degrades under shift, so report it on shifted / external data.

Workflow

Phase 1 — Choose the uncertainty method (integrate, don't reimplement)

• Conformal prediction (MAPIE) — distribution-free prediction sets/intervals at a nominal coverage;

the strongest default when a calibration set is available. Validate empirical coverage.

• Deep ensembles (Lakshminarayanan 2017) — train K independent members (distinct seeds/inits); the

best-quality epistemic uncertainty, at K× cost.

• MC-dropout (Gal 2016) — keep dropout active at inference and sample T passes; cheap, weaker.
• Bayesian / Laplace — a last-layer Laplace approximation is a light option.

See references/uncertainty_guide.md.

Phase 2 — Add the OOD guard and the abstention rule

• OOD detection — an energy score, Mahalanobis distance on features, ODIN, or max-softmax; evaluate

on a held-out OOD set (different scanner/site/pathology) and report detection AUROC + the operating point.

• Selective prediction — abstain below a confidence/uncertainty threshold set to a pre-specified

target coverage or risk; report the risk–coverage curve.

Phase 3 — Stress it under shift

Report calibration / coverage on shifted or external data, not in-distribution only (Ovadia 2019).

Phase 4 — Emit the uncertainty manifest

json
{
  "task": "classification",
  "deployment_claim": true,
  "uncertainty_method": "conformal",
  "coverage_target": 0.90,
  "coverage_validated": true,
  "ood_method": "mahalanobis",
  "ood_heldout_set": "external-ood-cohort",
  "selective_prediction": true,
  "selective_target": 0.95,
  "calibration_under_shift": true
}

Phase 5 — Gate the spec (deterministic)

bash
python3 scripts/check_uncertainty_reporting.py --manifest uncertainty_manifest.json --strict

Verdicts: POINT_PREDICTION_NO_UNCERTAINTY, CONFORMAL_NO_COVERAGE_VALIDATION, OOD_NO_HELDOUT_SET (Major); ENSEMBLE_NOT_INDEPENDENT, MCDROPOUT_DISABLED_AT_INFERENCE, SELECTIVE_NO_TARGET, NO_CALIBRATION_UNDER_SHIFT (Minor). Audits the declared spec at design/report time; it complements /model-evaluation's executed calibration/subgroup metrics.

Integration

• /model-evaluation — the point predictor's held-out metrics + calibration this layer sits on top of.
• /analyze-stats — calibration curve / risk–coverage plotting for the report.
• /check-reporting — TRIPOD+AI / DECIDE-AI deployment-monitoring items.
• /model-validation — the DECIDE-AI monitoring seam (the deployment-time counterpart of the split

audit).

Anti-Hallucination

• Never fabricate coverage, OOD AUROC, or calibration numbers. Every value in the manifest and every

reported number comes from the researcher's executed code — never invented. This skill designs and audits the uncertainty spec; it does not run a model on real patient data.

• Never report conformal coverage as guaranteed without measuring it. Exchangeability can fail on

clinical data (CONFORMAL_NO_COVERAGE_VALIDATION).

• Never report an uncertainty/OOD audit "pass" without running check_uncertainty_reporting.py. The

verdict is reproduced deterministically, never asserted from prose.

• Integrate, don't reimplement. Reference MAPIE / captum / OOD scorers; do not write a new conformal

or OOD library or claim results for one.

Reproducible challenge

scripts/check_uncertainty_reporting_challenge/ ships a synthetic weak/strong uncertainty-manifest pair with a network-free verify.sh wired into the skill's validation commands.