medsci-skills 5.16.0 → 5.18.0

package/README.md

@@ -2,15 +2,16 @@
 
 # MedSci Skills
 
-**54 skills that actually work.** Built by a physician-researcher, tested on real publications.
+**55 skills that actually work.** Built by a physician-researcher, tested on real publications.
 
 *MedSci Skills is an end-to-end research tool for physician and medical-engineering researchers — design → scaffold → validate → publish — for the clinical manuscript and the medical-AI model behind it. Its moat is the compliance layer — 44 reporting guidelines and risk-of-bias tools, reference/citation verification, and deterministic integrity gates before peer review — now extended by a model-engineering lane that scaffolds reproducible, leakage-safe training repos and audits model validation. Clinical AI model research engineering is in scope; a general AI-scientist platform is not. It competes on clinical submission reliability, not skill count.*
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
 [![Release](https://img.shields.io/github/v/release/Aperivue/medsci-skills?style=flat-square&color=blue)](https://github.com/Aperivue/medsci-skills/releases/latest)
 [![CI](https://img.shields.io/github/actions/workflow/status/Aperivue/medsci-skills/validate.yml?branch=main&style=flat-square&label=CI)](https://github.com/Aperivue/medsci-skills/actions/workflows/validate.yml)
-![Skills](https://img.shields.io/badge/Skills-54-brightgreen?style=flat-square)
+![Skills](https://img.shields.io/badge/Skills-55-brightgreen?style=flat-square)
 [![npm](https://img.shields.io/npm/v/medsci-skills?style=flat-square&label=npm&color=cb3837)](https://www.npmjs.com/package/medsci-skills)
+[![npm downloads](https://img.shields.io/npm/dw/medsci-skills?style=flat-square&label=npm%20downloads&color=cb3837)](https://www.npmjs.com/package/medsci-skills)
 [![Watch the 2-min intro](https://img.shields.io/badge/▶_Watch-2--min_intro-FF0000?style=flat-square&logo=youtube&logoColor=white)](https://youtu.be/MclQ_RIofpE)
 [![good first issues](https://img.shields.io/github/issues/Aperivue/medsci-skills/good%20first%20issue?style=flat-square&label=good%20first%20issues&color=7057ff)](https://github.com/Aperivue/medsci-skills/contribute)
 
@@ -41,8 +42,9 @@
 
 ## What is MedSci Skills?
 
-MedSci Skills is an open-source Claude Code skill collection for **clinical
-research — the manuscript and the medical-AI model alike**. It helps
+MedSci Skills is an open-source **Agent Skills** collection for **clinical
+research — the manuscript and the medical-AI model alike** — designed to be driven
+directly by AI coding agents (Claude Code, Codex, Cursor, and GitHub Copilot). It helps
 physician-researchers and biomedical/medical-engineering investigators move from
 literature search, study design, statistics, and figures to reporting-guideline
 compliance, citation/reference auditing, numerical-consistency checks, and
@@ -155,15 +157,16 @@ protocol scaffolding, screening/extraction structure, PRISMA-consistent counts a
 diagram, pooled-estimate figures, and a manuscript draft. *Safety:* screening and
 extraction decisions stay with the human review team.
 
-## Live Demos: Three Study Types, Three Full Pipelines
+## Live Demos: Four Study Types, Four Full Pipelines
 
-Three public datasets. Three study types. Each produces a complete manuscript, publication-ready figures, and a reporting compliance audit.
+Four public datasets. Four study types. Demos 1–3 each produce a complete manuscript, publication-ready figures, and a reporting-compliance audit; Demo 4 runs the medical-AI **model-engineering lane** end to end (scaffold → gates → training → evaluation → interpretability).
 
 | Demo | Dataset | Study Type | Compliance |
 |------|---------|------------|------------|
 | [Demo 1: Wisconsin BC](demo/01_wisconsin_bc/) | `sklearn` built-in | Diagnostic accuracy | STARD 2015 |
 | [Demo 2: BCG Vaccine](demo/02_metafor_bcg/) | `metafor::dat.bcg` (13 RCTs) | Meta-analysis | PRISMA 2020 |
 | [Demo 3: NHANES Obesity](demo/03_nhanes_obesity/) | CDC NHANES 2017-18 | Epidemiology (survey) | STROBE |
+| [Demo 4: PneumoniaMNIST CNN](demo/04_pneumoniamnist_cnn/) | `medmnist` (CC BY 4.0) | Medical-AI model engineering (CNN) | CLAIM / TRIPOD+AI |
 
 ### Demo 1: Diagnostic Accuracy — Wisconsin Breast Cancer
 
@@ -285,6 +288,10 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 ## What's New
 
+**v5.18** — reliability & workflow-integrity batch. A new deterministic **response-claim gate** for `/revise` and `/peer-review` (verifies a response letter's "we added / we now cite X" against the *revised manuscript body* — a claimed-but-absent edit is caught before it reaches a reviewer; **detectors 50 → 51**), a **reframe / headline-change survivor scan** (`--retired-term` / `--old-value`, finds stale framing or superseded values left in the body, supplement, and figure legends after a reframe), a pre-drafting **backbone full-text readiness gate** for `/write-paper` (the backbone article is *used*, not merely detected), a **skill-registry consistency validator** (`capabilities.yml` ⇄ `skill.yml`, CI-enforced), AI-tool **citation-framing** guidance for `/academic-aio`, and **Demo 4** (PneumoniaMNIST CNN, the model-engineering lane end to end). Additive and backward-compatible; **55 skills / 44 guidelines / 51 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.17.)
+
+**v5.17** — model-engineering produce-side depth, **completion**. Deployment safety + the final roadmap/candidate items: a new **`uncertainty-imaging`** skill + `check_uncertainty_reporting` gate (calibrated per-case uncertainty / OOD guard on a held-out set / abstention at a pre-specified target / calibration-under-shift — for a deployment-framed model), an **MLOps wiring reference** for `model-scaffold` (experiment tracking, config/data/environment versioning, CI-for-ML — pointing to W&B / MLflow / nnU-Net, reimplementing nothing), and an **`architecture-zoo` graph-neural-net family card** (GCN / GraphSAGE / GAT / GIN / BrainGNN for brain connectomes) that closes the last candidate gap. The six-item produce-side depth roadmap and its candidate list are now complete. Additive and backward-compatible; **55 skills / 44 guidelines / 50 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.16.)
+
 **v5.16** — model-engineering produce-side depth, clinical fine-tuning focus (Items 3–4 of the [produce-side depth roadmap](docs/roadmap_model_engineering_depth.md)). A new **`radiomics-ml`** skill + `check_radiomics_ml` gate for the most common solo-doable clinical-ML workflow — radiomics / tabular features → any classical learner (LASSO / SVM / random forest / XGBoost / …) → a clinical outcome, no GPU — with a learner-agnostic nested-CV / calibration / stability gate; plus a **`model-scaffold` fine-tuning mode** (`--task finetune` + `--from-pretrained`) that adapts a pretrained backbone on collected clinical data with a frozen→unfrozen schedule, discriminative learning rates, and a pretrained-weight provenance record (`PRETRAINED.md` + a `PRETRAINED_PROVENANCE_MISSING` verdict on the existing `check_training_hygiene`, plus a MedSAM-adaptation + train-only diffusion-augmentation guide). Additive and backward-compatible; **54 skills / 44 guidelines / 49 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.15.)
 
 **v5.15** — model-engineering produce-side depth. Two new skills that *produce* what the review lane previously only audited: **`preprocess-imaging`** (DICOM/NIfTI data prep + a `check_preprocessing_leakage` gate that extends the split-leakage moat upstream to the data stage) and **`explainability`** (Grad-CAM / saliency held to the reviewer bar — Adebayo sanity checks, quantitative localisation vs ground truth, attribution-not-validation framing, via `check_explainability_report`). Plus a by-stage skill index, multi-host README/About (Claude Code · Codex · Cursor · Copilot), copy-paste citation ergonomics, and a real-project precision fix. Additive and backward-compatible; **53 skills / 44 guidelines / 48 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.14.)
@@ -455,14 +462,14 @@ ma-scout -> search-lit -> fulltext-retrieval -> design-study ──> write-proto
 
 ### By research stage
 
-All 54 skills, grouped by where they fit in the clinical-manuscript and medical-AI lifecycle. Full descriptions are in the table below; one page per skill lives in the [per-skill reference](docs/skills/).
+All 55 skills, grouped by where they fit in the clinical-manuscript and medical-AI lifecycle. Full descriptions are in the table below; one page per skill lives in the [per-skill reference](docs/skills/).
 
 | Stage | Skills |
 |-------|--------|
 | 🔭 **Discover & scope** | `ma-scout` · `find-cohort-gap` · `search-lit` · `fulltext-retrieval` · `lit-sync` · `author-strategy` |
 | 📐 **Design & plan** | `design-study` · `calc-sample-size` · `define-variables` · `write-protocol` · `fill-protocol` · `design-ai-benchmarking` |
 | 🧹 **Data & analysis** | `deidentify` · `clean-data` · `generate-codebook` · `version-dataset` · `analyze-stats` · `batch-cohort` · `cross-national` · `replicate-study` |
-| 🤖 **Medical-AI model engineering** | `preprocess-imaging` · `architecture-zoo` · `model-scaffold` · `model-validation` · `model-evaluation` · `explainability` · `radiomics-ml` · `model-card` · `mllm-eval` |
+| 🤖 **Medical-AI model engineering** | `preprocess-imaging` · `architecture-zoo` · `model-scaffold` · `model-validation` · `model-evaluation` · `uncertainty-imaging` · `explainability` · `radiomics-ml` · `model-card` · `mllm-eval` |
 | ✍️ **Write & visualize** | `write-paper` · `make-figures` · `review-paper` · `present-paper` · `humanize` · `polish-language` · `academic-aio` |
 | ✅ **Comply & verify** | `check-reporting` · `self-review` · `verify-refs` · `manage-refs` |
 | 📤 **Submit & respond** | `find-journal` · `add-journal` · `sync-submission` · `revise` · `peer-review` · `fill-icmje-coi` |
@@ -491,6 +498,7 @@ All 54 skills, grouped by where they fit in the clinical-manuscript and medical-
 | **model-evaluation** | Compute and report task-correct held-out metrics for a trained medical-imaging model — segmentation (Dice + a boundary metric HD95/NSD, per structure), classification (AUROC + AUPRC + sensitivity/specificity with bootstrap CIs at the deployment prevalence), or detection (FROC/mAP with a stated IoU criterion) — plus calibration and subgroup slices. Emits a per-case table for analyze-stats and gates the metric choice against Metrics Reloaded / CLAIM 2024 (`check_metric_reporting`). Numbers come only from executed code. |
 | **explainability** | Produce or audit the interpretability/explainability analysis of a medical-imaging model — Grad-CAM / Grad-CAM++ / attention-rollout / saliency / integrated-gradients — so it clears the rigor bar: mandatory Adebayo sanity checks (model- and data-randomisation), a quantitative localisation metric against ground truth (IoU / pointing game / Dice) instead of eyeballed examples, a cohort-level result, and attribution framing rather than "proof the model is correct". Emits an explainability-report manifest + a deterministic gate (`check_explainability_report`): `SALIENCY_AS_VALIDATION`, `NO_SANITY_CHECK`, `NO_LOCALIZATION_METRIC` (Major); `INSUFFICIENT_SANITY`, `CHERRY_PICKED_EXAMPLES`, `MISSING_METHOD` (Minor). Integrates captum / pytorch-grad-cam; never reimplements them or touches real patient data. |
 | **radiomics-ml** | Produce or audit a radiomics / tabular clinical-ML study — features → random forest / XGBoost / regularised logistic → clinical outcome — the most common solo-doable clinical-ML workflow (no GPU, no engineer). Emits a pipeline manifest + a deterministic rigor gate (`check_radiomics_ml`): `NO_NESTED_CV`, `HIGH_DIM_LOW_EVENTS`, `SELECTION_OUTSIDE_CV` (Major); `NO_FEATURE_STABILITY`, `NO_CALIBRATION`, `NO_EXTERNAL_VALIDATION` (Minor). pyradiomics/IBSI settings, nested CV with in-fold selection, ICC stability, SHAP, calibration + decision curve, CLEAR/TRIPOD+AI/PROBAST-AI reporting. Integrates scikit-learn / xgboost / pyradiomics; never reimplements them. |
+| **uncertainty-imaging** | Design or audit the uncertainty / out-of-distribution / selective-prediction layer of a deployment-framed medical-imaging model — so a clinical-use claim carries calibrated per-case uncertainty (MC-dropout / deep ensemble / conformal / Bayesian), an OOD guard validated on a held-out OOD set, an abstention rule at a pre-specified operating point, and calibration checked under distribution shift. Emits an uncertainty manifest + a deterministic gate (`check_uncertainty_reporting`): `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). Integrates MAPIE / captum / OOD scorers; never reimplements them or touches real patient data. |
 | **mllm-eval** | Model-agnostic evaluation harness (closed API or open weights) for an LLM/MLLM on a clinical task — radiology report generation, VQA, clinical text extraction — covering the adjudicated reference standard, clinical-efficacy metrics (RadGraph-F1 / CheXbert-F1 beyond BLEU/ROUGE), faithfulness/hallucination, pretraining-contamination, prompt sensitivity, and a reader study; gates the plan with `check_mllm_eval_completeness` and routes the reviewer audit to the MLLM probe. |
 | **intake-project** | Classifies new research projects, summarizes current state, identifies missing inputs, and recommends next steps. |
 | **grant-builder** | Structures grant proposals: significance, innovation, approach, milestones, and consortium roles. |
@@ -644,7 +652,7 @@ matrices without CSV-coordinate comments are flagged as structural risks even wh
 are currently correct, since the next revision will re-introduce the same failure mode.
 
 ### Reference Safety (Phase 1)
-Projects declare their source-of-truth layout in `SSOT.yaml`, and a `qc/migration_complete` marker gates strict enforcement. `/verify-refs` is the sole writer of `qc/reference_audit.json`. The `MEDSCI_VERIFY_REFS_MODE` env var (`auto` default, `warn`, `enforce`, `off`) controls behavior — `auto` blocks only when both SSOT.yaml and the migration marker are present, otherwise warns. Legacy projects freeze as warn-only; new projects opt in via `scripts/migrate_project_to_ssot.py`. An optional PostToolUse hook (not shipped in this repo — document only) can invoke `/verify-refs` automatically on manuscript saves for users who install it locally at `~/.claude/hooks/verify-refs-guard.sh`; the regression suite (`tests/test_phase1c_hooks.sh`) runs end-to-end only when that local hook is present and is skipped otherwise.
+Projects declare their source-of-truth layout in `SSOT.yaml`, and a `qc/migration_complete` marker gates strict enforcement. `/verify-refs` is the sole writer of `qc/reference_audit.json`. The `MEDSCI_VERIFY_REFS_MODE` env var (`auto` default, `warn`, `enforce`, `off`) controls behavior — `auto` blocks only when both SSOT.yaml and the migration marker are present, otherwise warns. Legacy projects freeze as warn-only; new projects opt in via `scripts/migrate_project_to_ssot.py`. An optional PostToolUse hook (not shipped in this repo — document only) can invoke `/verify-refs` automatically on manuscript saves for users who install it locally at `~/.claude/hooks/verify-refs-guard.sh`; the regression suite (`tests/test_phase1c_hooks.sh`) runs end-to-end only when that local hook is present and is skipped otherwise. The hook gates saves under `*/submission/*/manuscript/*.{docx,md}` and `*/revision/R*/…circulation….docx` (enforce-eligible), and — added for issue #14 — also **warn-only** on pre-submission and mentor-circulation drafts that previously skipped the audit entirely: `*/outgoing/*.{docx,md}`, `*/8_Review_Comments/*/outgoing/*.{docx,md}`, and any `*/circulation/*.{docx,md}`. Warn-only patterns surface a missing audit without blocking rapid iteration and never enforce, regardless of SSOT/migration state.
 
 ### Meta-Analysis Failure Modes
 `/meta-analysis` ships empirical failure-mode references (data integrity, review orchestration, submission package drift, post-submission release ops) with four automation hooks: `scripts/prisma_5way_consistency.py` (DI-6 PRISMA number consistency), `scripts/extraction_consensus_log_init.py` (DI-1 dual-extraction scaffold), `scripts/tag_cleanup_gate.sh` (DI-8 placeholder tag gate), and `scripts/verify_package_integrity.py` (SPD SHA-256 manifest for submission bundles).
@@ -779,12 +787,18 @@ from one of these:
 
 | Want to add… | How | Issue |
 |---|---|---|
-| **A journal profile** (submission rules for a journal we don't cover) | `/add-journal`, or copy an existing `journal_profiles/*.md` | [#115](https://github.com/Aperivue/medsci-skills/issues/115) |
+| **A CSL citation style** for a journal that lacks one | drop one `.csl` into `manage-refs/citation_styles/` | [#117](https://github.com/Aperivue/medsci-skills/issues/117) |
+| **A de-identification locale pack** for one more country | add one patterns file under `deidentify/` | [#116](https://github.com/Aperivue/medsci-skills/issues/116) |
+| **A README translation** (e.g., zh-CN) | one translated `README` file | [#119](https://github.com/Aperivue/medsci-skills/issues/119) |
 | **A figure exemplar** (ROC, KM, forest, Bland–Altman, confusion matrix…) | one `make-figures/references/exemplar_plots/*.md` anatomy model | [#118](https://github.com/Aperivue/medsci-skills/issues/118) |
-| **A CSL citation style** for a journal that lacks one | drop a `.csl` into `manage-refs/citation_styles/` | [#117](https://github.com/Aperivue/medsci-skills/issues/117) |
-| **A de-identification locale pack** for one more country | add patterns to `deidentify/` | [#116](https://github.com/Aperivue/medsci-skills/issues/116) |
+| **A journal profile** (submission rules for a journal we don't cover) | `/add-journal`, or copy an existing `journal_profiles/*.md` | [#115](https://github.com/Aperivue/medsci-skills/issues/115) |
 | **A reporting checklist or peer-review exemplar** | one reference file in the matching skill | [#120](https://github.com/Aperivue/medsci-skills/issues/120) |
-| **A README translation** (e.g., zh-CN) | a translated `README` | [#119](https://github.com/Aperivue/medsci-skills/issues/119) |
+
+Each of these adds **exactly one new file** — none requires editing a count, a generated
+page, or the build config, and the catalog-consistency check auto-derives profile counts from
+disk so it won't flag you. **No assignment needed: just open a PR — the first one that passes
+CI wins, and a maintainer handles any bookkeeping in review.** See the
+[5-minute first-PR quickstart](CONTRIBUTING.md#quickstart-your-first-pr-5-minutes) to get going.
 
 Every contribution is gated the same way the maintainers are: it must be a self-contained
 file, pass the CI (`validate.yml` — PII scan, structure, catalog consistency), and carry no
@@ -798,6 +812,8 @@ or a [detector request](https://github.com/Aperivue/medsci-skills/issues/new?tem
 [`docs/maintainer_workflow.md`](docs/maintainer_workflow.md) (review + release process),
 and [`SECURITY.md`](SECURITY.md) (vulnerability reporting + the medical-scope boundary).
 A change that touches a medical/research claim needs Clinical-Lead review.
+Community members who have reported, verified, or shaped the project are credited in
+[`CONTRIBUTORS.md`](CONTRIBUTORS.md).
 
 ## In the Wild
 
@@ -833,9 +849,9 @@ software citation is how a tool like this earns academic recognition, and it tak
 }
 
 @article{nam2026agentic,
-  author  = {Nam, Yoojin and Kim, Namkug},
-  title   = {{Agentic Skills for Auditable and Reproducible Medical Research Writing:
-             An Integrity-gated Architecture for LLM-Assisted Clinical Manuscripts}},
+  author  = {Nam, Yoojin and Jeong, Jinhoon and Kim, Namkug},
+  title   = {{Deterministic Integrity Gates for LLM-Assisted Clinical Manuscript
+             Preparation: An Auditable Biomedical Informatics Architecture}},
   year    = {2026},
   journal = {arXiv preprint arXiv:2606.09500},
   url     = {https://arxiv.org/abs/2606.09500}

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@@ -4038,8 +4133,8 @@
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@@ -4048,13 +4143,13 @@
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package/metadata/distribution_manifest.json

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 {
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     "add-journal",
@@ -52,6 +52,7 @@
     "self-review",
     "setup-medsci",
     "sync-submission",
+    "uncertainty-imaging",
     "verify-refs",
     "version-dataset",
     "write-paper",

package/metadata/skills_catalog.json

@@ -1,6 +1,6 @@
 {
   "_comment": "AUTO-GENERATED by scripts/gen_skills_catalog_json.py from each skills/<slug>/SKILL.md + skill.yml. Machine-readable skill catalog (single source of truth) consumed by external surfaces such as the aperivue.com storefront to gate skill-list completeness. Do not hand-edit; CI gate: python3 scripts/gen_skills_catalog_json.py --check.",
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@@ -39,7 +39,8 @@
         "model-scaffold",
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         "preprocess-imaging",
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+        "radiomics-ml",
+        "uncertainty-imaging"
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@@ -562,6 +563,15 @@
       "maturity": "official",
       "description": "Audit SSOT-to-submission drift and create journal submission manifests from canonical manuscript artifacts."
     },
+    {
+      "slug": "uncertainty-imaging",
+      "category": "model_engineering",
+      "category_label": "Model Engineering & Validation",
+      "layer": "D",
+      "owner_domain": "model_validation",
+      "maturity": "official",
+      "description": "Design or audit the uncertainty-quantification, out-of-distribution (OOD) detection, and selective-prediction layer of a medical-imaging model framed for deployment — so a clinical-use claim carries c…"
+    },
     {
       "slug": "verify-refs",
       "category": "literature_references",