mllm-eval

Files (13)

• SKILL.md
• eval_manifest_schema.md · references/
• evaluation_axes.md · references/
• check_mllm_eval_completeness.py · scripts/
• manifest_bad.json · scripts/mllm_eval_completeness_challenge/fixture/
• manifest_good.json · scripts/mllm_eval_completeness_challenge/fixture/
• plan_bad.md · scripts/mllm_eval_completeness_challenge/fixture/
• plan_good.md · scripts/mllm_eval_completeness_challenge/fixture/
• problem.md · scripts/mllm_eval_completeness_challenge/
• verify.sh · scripts/mllm_eval_completeness_challenge/
• skill.yml
• eval_manifest.json · templates/
• test_mllm_eval_completeness.sh · tests/

SKILL.md (first lines)

# MLLM-Eval Skill

## Purpose

This skill makes an **LLM / MLLM clinical evaluation defensible**: a real adjudicated reference standard,
faithfulness measured not assumed, clinical-efficacy metrics beyond n-gram overlap, a pretraining-
contamination check, prompt-sensitivity disclosed, and a reader study where text is generated. It is
**model-agnostic** — every check applies to a closed API and to open weights — and **read-only** (an
advisory design/audit skill): it audits the evaluation design and **specifies and routes** the
clinical-efficacy metrics (RadGraph-F1 / CheXbert-F1 via their published extractors) rather than running
the model or computing the metrics itself.

It is the LLM/MLLM **evaluation-design counterpart** in the lane — an auditor that hands the specified
metrics to their extractors and `/analyze-stats`, parallel to how `/model-assessment` audits an imaging
model's design and computes its metrics. The reviewer-side
audit of a finished manuscript uses the `mllm_evaluation.md` (ME0–ME8) probe via `/self-review` and
`/peer-review`; this skill is the author-side harness design. It routes the reader study to
`/design-ai-benchmarking`, the sizing to `/calc-sample-size`, and TRIPOD-LLM / MI-CLEAR-LLM compliance to
`/check-reporting`.

## When to use
- You are designing or auditing an evaluation of an LLM/MLLM on a clinical task and want it to cover the
  axes a reviewer will check (reference standard, faithfulness, contamination, prompt sensitivity, reader
  study).

## When NOT to use
- AI-vs-human-expert benchmark with a rated rubric → `/design-ai-benchmarking`.
- Imaging prediction/segmentation model → `/model-assessment`.
- Image-to-image generative model → the `image_synthesis` probe.
- Training / serving the LLM → out of scope.
- Item-level TRIPOD-LLM / MI-CLEAR-LLM audit of a finished manuscript → `/check-reporting`.

## Workflow

### Phase 1 — Pin the task, model, comparator, decoding (ME0)
State the task (report generation / VQA / extraction-classification), the exact model + version/date
(closed API or open-weights id), the decoding settings (temperature, seed, max tokens), and what the
outputs are scored against.

### Phase 2 — Reference standard + metrics (ME1, ME2)
Require an **adjudicated expert reference** (not a single unverified report or a model-derived label).
For report generation, report a **clinical-efficacy metric** — **RadGraph-F1** (Jain et al., NeurIPS
2021) or **CheXbert-F1** (Smit et al., 2020), or the composite **RadCliQ** (Yu et al., *Patterns* 2023)
— **alongside** any BLEU/ROUGE, with CIs. For VQA/classification, state the answer-matching rule and
report **per-class sensitivity/specificity** (or precision/recall/F1) and **PPV at the real
prevalence**, with CIs; accuracy only alongside them — at 2% prevalence, answering "negative" every
time scores 98% accuracy.

### Phase 3 — Faithfulness + contamination (ME3, ME4)
Add an **atomic-fact faithfulness** measure + a **false-premise / abstention** probe (MedVH, Med-HALT) —
report a hallucination rate, not just accuracy. For any public benchmark (VQA-RAD, SLAKE, MIMIC-CXR-
derived, MedQA), add a **contamination** statement: training cutoff vs benchmark release, a held-out /
post-cutoff set, or a contamination probe.

### Phase 4 — Prompt sensitivity + reader study (ME5, ME7)
Disclose the **exact prompt(s)**, temperature/seed, **≥ 3 runs** with variance, and a prompt-robustness
check. For a deployment/utility claim, design a **blinded reader study** with an error taxonomy (route
the rubric/IRR to `/design-ai-benchmarking`, ICC/κ to `/analyze-stats`, sizing to `/calc-sample-size`).

### Phase 5 — Gate the plan (deterministic)
Declare the axes in `eval_manifest.json` (copy `${CLAUDE_SKILL_DIR}/templates/eval_manifest.json`;
fields and allowed values in `references/eval_manifest_schema.md`), then:
```bash
python3 ${CLAUDE_SKILL_DIR}/scripts/check_mllm_eval_completeness.py \
  --manifest eval_manifest.json --strict
```
Use `"none"` for an axis not done and `"other:<description>"` for a method not listed; any other
value exits 2. `--plan plan.md --task report_generation|vqa|classification` still runs the older
keyword check on prose (see Known limits).
`NGRAM_ONLY` / `FAITHFULNESS_MISSING` / `REFERENCE_STANDARD_MISSING` / `CONTAMINATION_UNADDRESSED` /
`READER_STUDY_MISSING` must be resolved. A classification manifest always reports
`CLASSIFICATION_METRICS_NOT_ASSESSED` (Minor): the manifest has no metric field for it, so check
per-class sensitivity/specificity and PPV at the real prevalence by eye.

### Phase 6 — Hand off
Methods/Results → `/write-paper`; compliance (TRIPOD-LLM / MI-CLEAR-LLM) → `/check-reporting`; reviewer
audit → `/self-review` (loads ME0–ME8).

## Anti-Hallucination

- **Never fabricate model outputs, reference labels, or metric scores.** Compute only what the supplied
  outputs allow; if a reference standard or outputs are missing, say so and stop.
- **Never report n-gram overlap (BLEU/ROUGE) as clinical correctness** — pair it with a clinical-efficacy
  metric, and flag the n-gram score for what it is.
- **Never claim "no contamination" without a stated check** when a public benchmark is used.
- If a metric (RadGraph-F1 / CheXbert-F1) or its extractor is uncertain, flag `[VERIFY]` and ask rather
  than inventing a number.

## Deterministic gate
`scripts/check_mllm_eval_completeness.py` — task-aware presence gate on the evaluation plan (stdlib,
network-free). Reproducible challenge:
`bash ${CLAUDE_SKILL_DIR}/scripts/mllm_eval_completeness_challenge/verify.sh`.

**Known limits.** Manifest mode checks what is declared, not that the work was done; keep the
manifest in step with the Methods. It also does not check that a declared metric suits the task:
report-generation metrics (BLEU, RadGraph F1) declared for a VQA task are accepted without
comment. Prose mode (`--plan`) checks that a term is present; it does not read negation or sense.
"No human evaluation was performed" or "hallucination was not assessed" still counts as covering
that axis, and a word used in another sense still clears it: "green" anywhere clears the clinical-metric check, "unsupported"
clears faithfulness, "data leakage" from a patient split clears contamination, and "ground truth"
clears the reference standard whatever it refers to. Read each cleared axis in the plan yourself
before treating an exit 0 as clean.

## Boundaries

```
mllm-eval (this skill: harness design + completeness gate, model-agnostic)
  ├─ design-ai-benchmarking (reader-study rubric / IRR)
  ├─ calc-sample-size (reader + case sizing)
  ├─ write-paper + check-reporting (TRIPOD-LLM / MI-CLEAR-LLM)
  └─ self-review / peer-review (ME0–ME8 reviewer probe)
```

## Reference Files

- `${CLAUDE_SKILL_DIR}/references/evaluation_axes.md` — the *why* behind the ME2–ME7 axes:
  clinical-efficacy metrics beyond n-gram overlap (e.g. RadGraph-F1 / CheXbert-F1 vs BLEU/ROUGE),
  faithfulness & hallucination, pretraining/benchmark contamination, prompt-sensitivity &
  determinism, answer-matching, and the reader study — each mapped to its gate verdict. Load on

From Aperivue/medsci-skills, MIT.

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