medsci-skills 5.14.0 → 5.16.0

package/README.md

@@ -2,14 +2,14 @@
 
 # MedSci Skills
 
-**51 skills that actually work.** Built by a physician-researcher, tested on real publications.
+**54 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-51-brightgreen?style=flat-square)
+![Skills](https://img.shields.io/badge/Skills-54-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)
 [![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)
@@ -285,6 +285,10 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 ## What's New
 
+**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.)
+
 **v4.10** — reviewer-coverage expansion reverse-engineered from high-IF, CC-BY papers (learn-only under the `reverse_engineer/` license firewall), plus a clinician-friendly update path. Additive and backward-compatible; 45 skills / **44 guidelines** / 36 detectors / **15 domain-probe modules** (was 12):
 
 - **Three new reviewer domain-probe modules** (`/peer-review` + `/self-review`, vendored byte-identical): **Mendelian randomization** (MR1–MR8 — IV assumptions, pleiotropy-robust sensitivity suite, Steiger, sample overlap, NLMR, drug-target colocalization), **polygenic risk score** (PG1–PG8 — ancestry portability, base/target leakage, incremental value over the clinical model, screening-vs-discrimination, calibration), and **network meta-analysis** (NM1–NM8 — transitivity, incoherence, SUCRA over-interpretation, CINeMA/GRADE-NMA, component-NMA additivity). Plus observational **O17** (agnostic many-exposure-scan multiplicity: ExWAS/EWAS/MWAS).
@@ -400,6 +404,8 @@ MedSci Skills is **opinionated and narrow on purpose**: a single physician-resea
 
 📖 **Per-skill reference:** [`docs/skills/`](docs/skills/) — one page per skill (what it does, when it activates, its Quality Card — purpose, safety boundaries, known limitations, validation, evidence — and bundled resources), generated from each `SKILL.md` + `skill.yml`. See [`docs/skills/AUDIT.md`](docs/skills/AUDIT.md) for how the skills are validated.
 
+🧠 **ML / DL method coverage:** [`docs/method_coverage_map.md`](docs/method_coverage_map.md) — which machine-learning and deep-learning method families (CNN / transformer / segmentation / detection / foundation / diffusion / SSL for imaging; the full classical family — penalised regression, SVM, k-NN, trees, boosting [XGBoost / LightGBM / CatBoost], MLP, ensembles, clustering — for radiomics/tabular; LLM/MLLM) map to which skills for selection, production, validation, interpretation, and reporting.
+
 ```
                               ┌─────────────────────────────────┐
                               │  orchestrate: single entry point │
@@ -447,6 +453,21 @@ 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/).
+
+| 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` |
+| ✍️ **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` |
+| 🧭 **Orchestrate & manage** | `orchestrate` · `intake-project` · `manage-project` · `meta-analysis` · `grant-builder` · `publish-skill` · `render-pdf-doc` · `setup-medsci` |
+
 ### Available Now
 
 | Skill | What It Does |
@@ -463,10 +484,13 @@ ma-scout -> search-lit -> fulltext-retrieval -> design-study ──> write-proto
 | **design-study** | Study design review: identifies analysis unit, cohort logic, data leakage risks, comparator design, validation strategy, and reporting guideline fit. |
 | **design-ai-benchmarking** | Design and validity review for benchmarking AI system(s) against a human-expert panel: evaluation-question and arm definition, decoupled multi-dimensional rubrics with anchors, planted calibration probes (positive-control / known-bad / instability / mechanism-contradiction), reviewer-panel construction with per-reviewer randomization, inter-rater reliability targets with separate control-item reliability, LLM-as-judge vs human-as-judge adjudication, construct-independence guards, and a structured JSON rating-export schema. Locks the rubric before data collection. |
 | **model-validation** | Design or audit the clinical-validation study for an engineer-built medical-imaging model (segmentation / classification / detection): patient-level split disjointness and the data-leakage taxonomy, tuning-on-test, internal vs genuine external validation, comparator design, single-run vs multi-seed variance, task-correct metric selection (Metrics Reloaded), test-set sizing, and CLAIM 2024 / TRIPOD+AI / STARD-AI reporting fit. Ships a deterministic split-leakage gate that proves patient disjointness by set arithmetic on the emitted split table. Integrates with MONAI / nnU-Net — does not replace them. |
-| **model-scaffold** | Generate a reproducible, runnable PyTorch training repo for a medical-imaging task — segmentation (U-Net), classification, detection, image-to-image synthesis, or self-supervised pretraining — the missing middle link between choosing an architecture and validating a trained model. Emits a patient-level seed-locked split as an auditable artifact, a task-appropriate model, train/evaluate scripts that seed every RNG and infer under eval mode, a config, requirements, a reproducibility record, and a Methods stub with VERIFY placeholders (no fabricated numbers). Reproducibility holds by construction; ships a `check_training_hygiene` AST gate + a network-free build→validate challenge. Emits a minimal runnable default model for a forward-pass smoke test, and integrates with MONAI / nnU-Net / TorchIO / timm / torchvision for production-grade models. |
+| **preprocess-imaging** | Design or audit the data-preparation stage of a medical-imaging model — DICOM/NIfTI intake, resampling, intensity normalization, and the augmentation plan — so the pipeline is leakage-safe before `model-scaffold` builds the training repo. Emits a declarative preprocessing manifest and a deterministic data-stage leakage gate (`check_preprocessing_leakage`) that catches what the split table cannot see: a dataset-level normaliser fit on non-train data (`NORMALIZATION_LEAKAGE`), a data-fitted transform run before the split (`PREPROCESS_BEFORE_SPLIT`), and a patient's slices crossing splits (`PATIENT_CROSS_SPLIT`). Integrates MONAI / TorchIO transforms; never reimplements them or touches real patient data. |
+| **model-scaffold** | Generate a reproducible, runnable PyTorch training repo for a medical-imaging task — segmentation (U-Net), classification, detection, image-to-image synthesis, self-supervised pretraining, or fine-tuning a pretrained backbone (transfer learning) — the missing middle link between choosing an architecture and validating a trained model. Emits a patient-level seed-locked split as an auditable artifact, a task-appropriate model, train/evaluate scripts that seed every RNG and infer under eval mode, a config, requirements, a reproducibility record, and a Methods stub with VERIFY placeholders (no fabricated numbers). Fine-tuning mode (`--task finetune`) adds a frozen→unfrozen schedule, discriminative learning rates, and a pretrained-weight provenance record (`PRETRAINED.md`), with a MedSAM-adaptation + train-only diffusion-augmentation guide. Reproducibility holds by construction; ships a `check_training_hygiene` AST gate (RNG seeding, eval-mode inference, train-split-only loaders, pretrained-provenance) + a network-free build→validate challenge. Integrates with MONAI / nnU-Net / TorchIO / timm / torchvision for production-grade models. |
 | **architecture-zoo** | "Which architecture for which research question" decision tool: maps task (classification / segmentation / detection / transfer), modality, data scale, and class imbalance to a paper-grounded architecture shortlist. Curates the foundational curriculum (ResNet / DenseNet / EfficientNet / ViT / Swin; U-Net / 3-D U-Net / Attention & Residual U-Net / nnU-Net / Mask R-CNN; SAM/MedSAM / TotalSegmentator / BiomedCLIP / DINO / MAE / SimCLR) — each with core idea, when-to-use, medical-imaging use, reference implementation, validation setup, and the matching model-scaffold template. Advisory; teaches archetypes, not a live SOTA leaderboard. |
 | **model-card** | Generate the documentation an engineer-built medical-imaging model must carry — a Model Card (Mitchell et al. 2019), a Datasheet for its dataset (Gebru et al. 2021), and a METRIC-informed data-quality pass — filled from user-supplied facts (never fabricated), then verify every required section is present and non-empty with a deterministic completeness gate (`check_model_card_complete`). Model Card / Datasheet are documentation standards vendored as templates, not counted reporting checklists. |
 | **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. |
 | **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. |
@@ -787,15 +811,44 @@ It helps other researchers find the toolkit — and we list it (with your permis
 
 ## Citation
 
-If you use MedSci Skills in your research, please cite the software via
-[`CITATION.cff`](CITATION.cff) (Zenodo concept DOI
-[10.5281/zenodo.20155321](https://doi.org/10.5281/zenodo.20155321)).
+If MedSci Skills helped produce your manuscript, protocol, or analysis, please cite it —
+software citation is how a tool like this earns academic recognition, and it takes one line.
+
+**In your manuscript** (Methods or Acknowledgements — cite the version you actually used):
+
+> Reporting-guideline compliance, reference verification, and pre-submission integrity checks
+> were assisted by MedSci Skills (version X.Y.Z; https://github.com/Aperivue/medsci-skills;
+> archived at Zenodo, https://doi.org/10.5281/zenodo.20155321).
 
-The design and evaluation of the toolkit are described in a preprint:
+**BibTeX** (the software, and the preprint describing its design):
 
-> Nam Y, Kim N. *Agentic Skills for Auditable and Reproducible Medical Research
-> Writing: An Integrity-gated Architecture for LLM-Assisted Clinical Manuscripts.*
-> arXiv:2606.09500 (2026). https://arxiv.org/abs/2606.09500
+```bibtex
+@software{nam_medsci_skills,
+  author    = {Nam, Yoojin},
+  title     = {{MedSci Skills: Claude Code Skills for the Medical Research Lifecycle}},
+  year      = {2026},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.20155321},
+  url       = {https://github.com/Aperivue/medsci-skills}
+}
+
+@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}},
+  year    = {2026},
+  journal = {arXiv preprint arXiv:2606.09500},
+  url     = {https://arxiv.org/abs/2606.09500}
+}
+```
+
+The Zenodo **concept DOI** [10.5281/zenodo.20155321](https://doi.org/10.5281/zenodo.20155321)
+always resolves to the latest release; [`CITATION.cff`](CITATION.cff) carries the machine-readable
+metadata (GitHub's "Cite this repository" button reads it).
+
+**Used it in published or in-review work?** Tell us via the
+["Used in research" issue template](https://github.com/Aperivue/medsci-skills/issues/new?template=used-in-research.yml)
+— with your permission it is added to [`docs/citations.md`](docs/citations.md).
 
 ## Disclaimer
 
@@ -815,8 +868,16 @@ Bundled reporting guideline checklists retain their original Creative Commons li
 
 Optional dependency: `pdf_to_md.py` uses [pymupdf4llm](https://pymupdf.readthedocs.io) (AGPL-3.0). Not bundled -- installed separately by the user via `pip install pymupdf4llm`.
 
+## Star History
+
+<a href="https://star-history.com/#Aperivue/medsci-skills&Date">
+  <img src="https://api.star-history.com/svg?repos=Aperivue/medsci-skills&type=Date" alt="MedSci Skills star history" width="640">
+</a>
+
 ## About
 
 Built by [Aperivue](https://aperivue.com) -- tools for medical AI research and education.
 
+**Runs anywhere the [Agent Skills standard](https://agentskills.io) is supported** -- not Claude Code alone. Claude Code, OpenAI Codex, Cursor, and GitHub Copilot are all verified against each host's own docs: one install, four hosts, no per-host fork ([host compatibility](docs/host_compatibility.md)).
+
 If you find this useful, consider giving it a star. It helps other researchers discover these tools.

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+      "path": "skills/preprocess-imaging/scripts/check_preprocessing_leakage.py",
+      "size": 12992,
+      "sha256": "dcce1493a29122ed4259adc116ed7ad239b11ee1f45a10f6f7eb94698b3efa67"
+    },
+    {
+      "path": "skills/preprocess-imaging/scripts/check_preprocessing_leakage_challenge/expected/clean.txt",
+      "size": 370,
+      "sha256": "bc1efcfc1d8575d78a0448752e60a3b58d654a5bc1a7b11360e4d9ba690665ac"
+    },
+    {
+      "path": "skills/preprocess-imaging/scripts/check_preprocessing_leakage_challenge/expected/leak.txt",
+      "size": 1030,
+      "sha256": "fe046c81f20b34a6ff3fd6858f7832e786106ed56635b39f7e413b4853d4b7e8"
+    },
+    {
+      "path": "skills/preprocess-imaging/scripts/check_preprocessing_leakage_challenge/fixture/manifest_clean.json",
+      "size": 800,
+      "sha256": "e01ff6d09aae6f76d3b2b1cd05c333d66fd53499a2a2d1296380eefde720c515"
+    },
+    {
+      "path": "skills/preprocess-imaging/scripts/check_preprocessing_leakage_challenge/fixture/manifest_leak.json",
+      "size": 881,
+      "sha256": "a55389654128c577e16eefb3c6b8f85d8a47bdc06a817619f13036a1e1ebe4b4"
+    },
+    {
+      "path": "skills/preprocess-imaging/scripts/check_preprocessing_leakage_challenge/problem.md",
+      "size": 903,
+      "sha256": "042ddd4736133ccf63192ea65c4faa714b2854ec9bb704f29ca2f401cd4658ee"
+    },
+    {
+      "path": "skills/preprocess-imaging/scripts/check_preprocessing_leakage_challenge/verify.sh",
+      "size": 2188,
+      "sha256": "9201d264720627f7281f43bcf3b1093bf6940f67acd7c299c8b3ac64fb58b564"
+    },
+    {
+      "path": "skills/preprocess-imaging/skill.yml",
+      "size": 3518,
+      "sha256": "c6edc7ac6421438d4e0b64cd416202ac9f91092870ea1cb8531ba15fda7d5c72"
+    },
     {
       "path": "skills/present-paper/SKILL.md",
       "size": 33518,
@@ -3311,6 +3416,56 @@
       "size": 1372,
       "sha256": "81caa10775246f2db3f5e08948292f63076d44ffc039d8eec764f1d46aab275f"
     },
+    {
+      "path": "skills/radiomics-ml/SKILL.md",
+      "size": 8273,
+      "sha256": "cc65bfd50db2b6e9b6681e1c9649b306490cd5dd74192bfdf5316362b71f141b"
+    },
+    {
+      "path": "skills/radiomics-ml/references/radiomics_ml_guide.md",
+      "size": 6707,
+      "sha256": "29bf2b2b847c488ddb33e50cd21ea0e2cd4937a1a62ab2655f31227a0e42215a"
+    },
+    {
+      "path": "skills/radiomics-ml/scripts/check_radiomics_ml.py",
+      "size": 10179,
+      "sha256": "b1cfbd9991aa8871d5aabc528c9aa22eecf8e46cb5983872bca2359229223840"
+    },
+    {
+      "path": "skills/radiomics-ml/scripts/check_radiomics_ml_challenge/expected/strong.txt",
+      "size": 369,
+      "sha256": "c73c776e6558d9a78dacd3c63ae1cc3dee183d9e1a2f27d99b1e0db70f44997e"
+    },
+    {
+      "path": "skills/radiomics-ml/scripts/check_radiomics_ml_challenge/expected/weak.txt",
+      "size": 1408,
+      "sha256": "3bb90f31587e94f3f2b267874a9ac58cce5adf3436254bc206092e0acfb86cd7"
+    },
+    {
+      "path": "skills/radiomics-ml/scripts/check_radiomics_ml_challenge/fixture/pipeline_strong.json",
+      "size": 322,
+      "sha256": "83d128fe0b728ef52a1fd98ef5b5bd478c3e48455cdb07d8040f9d130df81cee"
+    },
+    {
+      "path": "skills/radiomics-ml/scripts/check_radiomics_ml_challenge/fixture/pipeline_weak.json",
+      "size": 313,
+      "sha256": "2fa1a3f98f952faf2e6e1faf1bdbf4675a44dc88679dcfaf18a4f32eb47ba9e7"
+    },
+    {
+      "path": "skills/radiomics-ml/scripts/check_radiomics_ml_challenge/problem.md",
+      "size": 894,
+      "sha256": "9a6abad4e12f9b4e9290eb305fb9ad04127fa1cde03961a38ac4ccb5431a2100"
+    },
+    {
+      "path": "skills/radiomics-ml/scripts/check_radiomics_ml_challenge/verify.sh",
+      "size": 1988,
+      "sha256": "b9e55aaf9b29f3e810b837fc373c7a212dc5f778a49bac11854bdb50ed84a184"
+    },
+    {
+      "path": "skills/radiomics-ml/skill.yml",
+      "size": 3790,
+      "sha256": "9b99b87add656873d3f7277ce12490ffea36d919e9538bc4f4fbe1ebbfedc18e"
+    },
     {
       "path": "skills/render-pdf-doc/SKILL.md",
       "size": 7490,
@@ -3758,8 +3913,8 @@
     },
     {
       "path": "skills/self-review/scripts/check_scope_coherence.py",
-      "size": 11920,
-      "sha256": "e600e54fcbe308060a8dadd871ec274b6ae19f89456ae0194490e152c0d09a91"
+      "size": 12989,
+      "sha256": "2444bce9c5bd2fc088c43eae97c1fc5791ae4da44f428a2caa0559b976dbe622"
     },
     {
       "path": "skills/self-review/scripts/check_supplement_hygiene.py",

package/metadata/distribution_manifest.json

@@ -1,6 +1,6 @@
 {
   "schema_version": 1,
-  "version": "5.14.0",
+  "version": "5.16.0",
   "owned_skills": [
     "academic-aio",
     "add-journal",
@@ -16,6 +16,7 @@
     "deidentify",
     "design-ai-benchmarking",
     "design-study",
+    "explainability",
     "fill-icmje-coi",
     "fill-protocol",
     "find-cohort-gap",
@@ -39,8 +40,10 @@
     "orchestrate",
     "peer-review",
     "polish-language",
+    "preprocess-imaging",
     "present-paper",
     "publish-skill",
+    "radiomics-ml",
     "render-pdf-doc",
     "replicate-study",
     "review-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.",
-  "skill_count": 51,
+  "skill_count": 54,
   "categories": [
     {
       "key": "literature_references",
@@ -32,11 +32,14 @@
       "label": "Model Engineering & Validation",
       "slugs": [
         "architecture-zoo",
+        "explainability",
         "mllm-eval",
         "model-card",
         "model-evaluation",
         "model-scaffold",
-        "model-validation"
+        "model-validation",
+        "preprocess-imaging",
+        "radiomics-ml"
       ]
     },
     {
@@ -235,6 +238,15 @@
       "maturity": "official",
       "description": "Study design and validity review for radiology and medical AI research."
     },
+    {
+      "slug": "explainability",
+      "category": "model_engineering",
+      "category_label": "Model Engineering & Validation",
+      "layer": "D",
+      "owner_domain": "model_validation",
+      "maturity": "official",
+      "description": "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 a re…"
+    },
     {
       "slug": "fill-icmje-coi",
       "category": "submission_journals",
@@ -404,7 +416,7 @@
       "layer": "B",
       "owner_domain": "model_development",
       "maturity": "official",
-      "description": "Generate a reproducible, runnable PyTorch training repo for a medical-imaging task — segmentation, classification, detection, image-to-image synthesis, or self-supervised pretraining — the missing mid…"
+      "description": "Generate a reproducible, runnable PyTorch training repo for a medical-imaging task — segmentation, classification, detection, image-to-image synthesis, self-supervised pretraining, or fine-tuning a pr…"
     },
     {
       "slug": "model-validation",
@@ -442,6 +454,15 @@
       "maturity": "official",
       "description": "Academic English consistency linting and non-native (ESL) language polish for medical manuscripts."
     },
+    {
+      "slug": "preprocess-imaging",
+      "category": "model_engineering",
+      "category_label": "Model Engineering & Validation",
+      "layer": "D",
+      "owner_domain": "model_validation",
+      "maturity": "official",
+      "description": "Design or audit the data-preparation stage of a medical-imaging model — DICOM/NIfTI intake, resampling and intensity normalisation, and the augmentation plan — so the pipeline is leakage-safe before m…"
+    },
     {
       "slug": "present-paper",
       "category": "presentation_tooling",
@@ -460,6 +481,15 @@
       "maturity": "official",
       "description": "Convert a personal agent skill into a distributable, open-source-ready skill."
     },
+    {
+      "slug": "radiomics-ml",
+      "category": "model_engineering",
+      "category_label": "Model Engineering & Validation",
+      "layer": "D",
+      "owner_domain": "model_validation",
+      "maturity": "official",
+      "description": "Produce or audit a radiomics / tabular clinical-ML study — imaging or clinical features → any classical learner (penalised logistic [LASSO / ridge / elastic-net], SVM, k-NN, naive Bayes, LDA/QDA, deci…"
+    },
     {
       "slug": "render-pdf-doc",
       "category": "presentation_tooling",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "medsci-skills",
-  "version": "5.14.0",
+  "version": "5.16.0",
   "description": "MedSci Skills — a medical/scientific research skill suite for AI coding agents (Claude Code, Codex, Cursor, Copilot). The npm package is a terminal-friendly installer shortcut; the canonical distribution remains the GitHub repository and the Claude Code plugin marketplace.",
   "license": "SEE LICENSE IN LICENSE",
   "homepage": "https://github.com/Aperivue/medsci-skills#readme",

package/skills/explainability/SKILL.md

@@ -0,0 +1,109 @@
+---
+name: explainability
+description: >
+  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 a reviewer expects: 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 rather than cherry-picked cases, and attribution framing rather than
+  "proof the model is correct". Emits an explainability-report manifest and a deterministic rigor gate.
+  Integrates captum / pytorch-grad-cam; it does not reimplement them, and never runs a model on real
+  patient data.
+triggers: explainability, interpretability, saliency, saliency map, grad-cam, gradcam, grad-cam++, attention map, attention rollout, integrated gradients, captum, pytorch-grad-cam, heatmap, class activation map, CAM, feature attribution, sanity check, Adebayo, model randomization, localization metric, pointing game, IoU with ground truth, XAI, explainable AI, model looks at, faithfulness
+tools: Read, Write, Edit, Bash, Grep, Glob
+model: inherit
+---
+
+# Explainability Skill
+
+## Purpose
+
+A saliency / Grad-CAM heat-map is the **most over-interpreted artifact** in medical-imaging AI: a
+colourful map over the lesion is routinely presented as proof the model "looks at the right thing."
+Adebayo et al. (*NeurIPS* 2018) showed many saliency methods produce visually convincing maps that are
+**independent of the model's learned weights and of the labels** — so they explain nothing. This skill
+produces an explainability analysis that clears the rigor bar, and audits an existing one, so the map
+is trustworthy before it reaches a manuscript (CLAIM 2024 / TRIPOD+AI interpretability items).
+
+It sits alongside evaluation in the lane: `/architecture-zoo` → `/preprocess-imaging` →
+`/model-scaffold` → `/model-validation` → `/model-evaluation` + **explainability** →
+`/write-paper` + `/check-reporting`. It **integrates** captum / pytorch-grad-cam (referenced in the
+plan); it does not reimplement them and never runs a model on real patient data.
+
+## When to use
+- You produced (or are about to produce) saliency / Grad-CAM / attention maps and want them reported
+  to the standard a reviewer expects.
+- You want to audit an explainability analysis for the four failure modes below.
+
+## When NOT to use
+- Discrimination / calibration metrics → `/model-evaluation` then `/analyze-stats`.
+- Split or preprocessing leakage → `/model-validation` / `/preprocess-imaging`.
+- LLM/MLLM faithfulness & hallucination → `/mllm-eval`.
+- Reimplementing captum / pytorch-grad-cam → out of scope (this skill wires and audits them).
+
+## The four failure modes (what the gate enforces)
+1. **Saliency as validation.** A map is *attribution*, not proof the model is correct or that the
+   relationship is causal. Frame it as "where signal is attributed", never as "the model is right".
+2. **No sanity check.** Run the Adebayo **model-randomisation** and **data-randomisation** tests. A map
+   that survives neither is uninterpretable; both axes are the minimum bar.
+3. **No quantitative localisation.** If you claim the map localises the finding, measure it — IoU /
+   pointing game / Dice against ground-truth masks — do not eyeball a few examples.
+4. **Cherry-picked examples.** Report a cohort-level result, not a handful of hand-picked cases.
+
+## Workflow
+
+### Phase 1 — Produce the maps (integrate, don't reimplement)
+Choose the method for the architecture (`references/explainability_guide.md`): Grad-CAM / Grad-CAM++
+for CNNs, attention-rollout for ViTs, integrated-gradients / SHAP for attribution. Wire captum or
+pytorch-grad-cam; do not write a new CAM implementation.
+
+### Phase 2 — Sanity-check and quantify
+- Run the **model-parameter randomisation** and **data (label) randomisation** tests (Adebayo 2018);
+  a faithful map degrades when the model/labels are randomised.
+- Compute a **quantitative localisation metric** against ground-truth masks (IoU / pointing game /
+  Dice) over the cohort — not a visual impression.
+
+### Phase 3 — Emit the explainability-report manifest
+```json
+{
+  "method": "grad-cam++",
+  "n_examples": 200,
+  "cohort_level": true,
+  "localization_metric": "iou",
+  "localization_value": 0.63,
+  "sanity_checks": ["model_randomization", "data_randomization"],
+  "interpretation": "localization"
+}
+```
+`interpretation`: `attribution` / `localization` / `faithfulness` (descriptive) — never
+`validation` / `causal` (overclaim).
+
+### Phase 4 — Gate the report (deterministic)
+```bash
+python3 scripts/check_explainability_report.py --manifest explainability_report.json --strict
+```
+Verdicts: `SALIENCY_AS_VALIDATION`, `NO_SANITY_CHECK`, `NO_LOCALIZATION_METRIC` (Major);
+`INSUFFICIENT_SANITY`, `CHERRY_PICKED_EXAMPLES`, `MISSING_METHOD` (Minor). The verdict is reproduced
+by rule on the manifest, never asserted from prose.
+
+## Integration
+- **`/model-evaluation`** — explainability accompanies the held-out metrics as a secondary analysis.
+- **`/self-review`** `ai_overclaiming` / `image_synthesis` probes audit saliency overclaiming in a
+  finished manuscript; this skill *produces* the rigorous analysis they look for.
+- **`/check-reporting`** — the manifest documents the CLAIM 2024 / TRIPOD+AI interpretability items.
+
+## Anti-Hallucination
+
+- **Never fabricate saliency maps, localisation metrics, or sanity-check results.** Every value in the
+  manifest comes from the researcher's executed XAI code — never invented. This skill designs and
+  audits the analysis; it does not run a model on real patient data.
+- **Never present a saliency map as proof of model correctness or causation.** A map is attribution;
+  claiming it validates the model is the overclaim this skill exists to prevent (`SALIENCY_AS_VALIDATION`).
+- **Never report an explainability-audit "pass" without running `check_explainability_report.py`.** The
+  rigor verdict is reproduced deterministically, never asserted from prose.
+- **Integrate, don't reimplement.** Reference captum / pytorch-grad-cam; do not write a new CAM /
+  attribution implementation or claim results for one.
+
+## Reproducible challenge
+`scripts/check_explainability_report_challenge/` ships a synthetic weak/strong report pair with a
+network-free `verify.sh` wired into the skill's validation commands.