medsci-skills 4.10.0 → 4.11.0

package/README.md

@@ -2,14 +2,14 @@
 
 # MedSci Skills
 
-**45 skills that actually work.** Built by a physician-researcher, tested on real publications.
+**51 skills that actually work.** Built by a physician-researcher, tested on real publications.
 
 *MedSci Skills is a submission-grade clinical manuscript workflow, not a generic biomedical skill catalog. Its moat is the compliance layer — 38 reporting guidelines and risk-of-bias tools, reference/citation verification, and deterministic integrity gates, before peer review sees the manuscript. 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-45-brightgreen?style=flat-square)
+![Skills](https://img.shields.io/badge/Skills-51-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)
@@ -451,6 +451,12 @@ ma-scout -> search-lit -> fulltext-retrieval -> design-study ──> write-proto
 | **make-figures** | Publication-ready figures and visual abstracts: ROC curves, forest plots, PRISMA/CONSORT/STARD flow diagrams, Kaplan-Meier curves, Bland-Altman plots, confusion matrices, and journal-specific visual/graphical abstracts (python-pptx template-based). Communication-first design principles (Nat Hum Behav 2026 — key message, audience, cognitive load, figure-vs-table decision) and five flow-diagram production lessons (official-template fidelity, VML fallback PDF export, docx XML escape, sequential placeholder mapping, version freeze); critic rubric Section G adds 5 communication-first checks. `--study-type` auto-generates the full required figure set; structured `_figure_manifest.md` output for downstream pipeline consumption; D2 enforced as default for flow diagrams. |
 | **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 segmentation task — 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 configurable U-Net, 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. Integrates with MONAI / nnU-Net / TorchIO — does not reimplement them. |
+| **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. |
+| **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. |
 | **present-paper** | Academic presentation preparation: paper analysis, supporting research, speaker scripts, slide note injection, and Q&A prep. |

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+      "sha256": "34be75bbbabf10073a1fd11587e019491b7319e2030b166a1ab3e82e4899f3c2"
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+      "sha256": "a4a15320685b58c4868737e40b4df0a07a942b39b5d94611e87d63d22e88aee0"
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+    {
+      "path": "skills/model-validation/scripts/check_split_leakage_challenge/fixture/splits_leak.csv",
+      "size": 145,
+      "sha256": "1bc2cc7b11a7a4a9ddc0168a83eab33ea1b03e3ca98bda5301679a18e19faf53"
+    },
+    {
+      "path": "skills/model-validation/scripts/check_split_leakage_challenge/problem.md",
+      "size": 2347,
+      "sha256": "f140095ec5d190120bf73dc62710b2ccac31c7f7d54307a0854c8438df61940e"
+    },
+    {
+      "path": "skills/model-validation/scripts/check_split_leakage_challenge/verify.sh",
+      "size": 1925,
+      "sha256": "9ae88c109caa1408a3a3b08ea0583fc97ce98b93c909f75d043f08a231e91e61"
+    },
+    {
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+      "size": 3079,
+      "sha256": "4891c0698445f98552ab2a2315bc8288a6cc4744f8711e20f939c8af8739e434"
+    },
     {
       "path": "skills/orchestrate/SKILL.md",
       "size": 35203,
@@ -2438,8 +2748,8 @@
     },
     {
       "path": "skills/peer-review/SKILL.md",
-      "size": 55415,
-      "sha256": "4b75d67b35444eada1a08700b9a0d27e6b8453fbca197893799db77811904b52"
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+      "sha256": "057c39cd131c49eeb1949560a0d510f176a012431a0c8d36dd803061f98e0629"
     },
     {
       "path": "skills/peer-review/references/aczel_2021_reviewer2_patterns.md",
@@ -2481,6 +2791,16 @@
       "size": 11244,
       "sha256": "197cfaa4bdcfe223a0ebfb69c229ccb3852160ab76870ade914eb8997ab684c5"
     },
+    {
+      "path": "skills/peer-review/references/domain-probes/mllm_evaluation.md",
+      "size": 7785,
+      "sha256": "1b63f7d987bc2ba8b9e67008b1713d4e874437f22c46002a12dcda1da0b73d2a"
+    },
+    {
+      "path": "skills/peer-review/references/domain-probes/model_development.md",
+      "size": 10438,
+      "sha256": "263db14ecedfc51caffb8b4966bade4566706b3ae4ce67d0b15840bdbbcdba07"
+    },
     {
       "path": "skills/peer-review/references/domain-probes/narrative_review.md",
       "size": 12598,
@@ -2933,8 +3253,8 @@
     },
     {
       "path": "skills/self-review/SKILL.md",
-      "size": 94121,
-      "sha256": "7222f5bc17832d84a23f1ea63fb090eb9a114c70bec3cf16ff2c7a16b24d0f40"
+      "size": 94657,
+      "sha256": "14c982c492d6305c238737366f0996415133fe02ff9aaad7e2c2207d78d260a2"
     },
     {
       "path": "skills/self-review/references/domain-probes/ai_overclaiming.md",
@@ -2971,6 +3291,16 @@
       "size": 11244,
       "sha256": "197cfaa4bdcfe223a0ebfb69c229ccb3852160ab76870ade914eb8997ab684c5"
     },
+    {
+      "path": "skills/self-review/references/domain-probes/mllm_evaluation.md",
+      "size": 7785,
+      "sha256": "1b63f7d987bc2ba8b9e67008b1713d4e874437f22c46002a12dcda1da0b73d2a"
+    },
+    {
+      "path": "skills/self-review/references/domain-probes/model_development.md",
+      "size": 10438,
+      "sha256": "263db14ecedfc51caffb8b4966bade4566706b3ae4ce67d0b15840bdbbcdba07"
+    },
     {
       "path": "skills/self-review/references/domain-probes/narrative_review.md",
       "size": 12598,
@@ -3418,8 +3748,8 @@
     },
     {
       "path": "skills/write-paper/references/journal_profiles/Clinical_and_Molecular_Hepatology.md",
-      "size": 7981,
-      "sha256": "666c53f8c68b3a3436beafdb76a3671825802c5d6fe0a92c052db9075848c7da"
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     },
     {
       "path": "skills/write-paper/references/journal_profiles/Diabetes_Metabolism_Journal.md",

package/metadata/distribution_manifest.json

@@ -1,10 +1,11 @@
 {
   "schema_version": 1,
-  "version": "4.10.0",
+  "version": "4.11.0",
   "owned_skills": [
     "academic-aio",
     "add-journal",
     "analyze-stats",
+    "architecture-zoo",
     "author-strategy",
     "batch-cohort",
     "calc-sample-size",
@@ -30,6 +31,11 @@
     "manage-project",
     "manage-refs",
     "meta-analysis",
+    "mllm-eval",
+    "model-card",
+    "model-evaluation",
+    "model-scaffold",
+    "model-validation",
     "orchestrate",
     "peer-review",
     "polish-language",

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": 45,
+  "skill_count": 51,
   "categories": [
     {
       "key": "literature_references",
@@ -17,6 +17,7 @@
       "key": "data_study_design",
       "label": "Data & Study Design",
       "slugs": [
+        "architecture-zoo",
         "calc-sample-size",
         "clean-data",
         "define-variables",
@@ -24,6 +25,11 @@
         "design-ai-benchmarking",
         "design-study",
         "generate-codebook",
+        "mllm-eval",
+        "model-card",
+        "model-evaluation",
+        "model-scaffold",
+        "model-validation",
         "version-dataset"
       ]
     },
@@ -124,6 +130,15 @@
       "maturity": "official",
       "description": "Statistical analysis for medical research papers."
     },
+    {
+      "slug": "architecture-zoo",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "D",
+      "owner_domain": "architecture_reference",
+      "maturity": "official",
+      "description": "Choose a model architecture for a medical-imaging research question before scaffolding."
+    },
     {
       "slug": "author-strategy",
       "category": "project_workflow",
@@ -349,6 +364,51 @@
       "maturity": "official",
       "description": "Systematic review and meta-analysis pipeline for medical research."
     },
+    {
+      "slug": "mllm-eval",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "D",
+      "owner_domain": "model_evaluation",
+      "maturity": "official",
+      "description": "Design or audit a model-agnostic evaluation harness for an LLM or multimodal LLM on a clinical task (radiology report generation, visual question answering, clinical text extraction/classification) —…"
+    },
+    {
+      "slug": "model-card",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "C",
+      "owner_domain": "model_reporting",
+      "maturity": "official",
+      "description": "Generate the documentation an engineer-built medical-imaging model must carry — a Model Card (Mitchell et al."
+    },
+    {
+      "slug": "model-evaluation",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "B",
+      "owner_domain": "model_evaluation",
+      "maturity": "official",
+      "description": "Compute and report task-correct held-out metrics for a trained medical-imaging model — segmentation (Dice plus a boundary metric such as HD95 or NSD, per structure), classification (AUROC plus AUPRC a…"
+    },
+    {
+      "slug": "model-scaffold",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "B",
+      "owner_domain": "model_development",
+      "maturity": "official",
+      "description": "Generate a reproducible, runnable PyTorch training repo for a medical-imaging segmentation task — the missing middle link between choosing an architecture and validating a trained model."
+    },
+    {
+      "slug": "model-validation",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "D",
+      "owner_domain": "model_validation",
+      "maturity": "official",
+      "description": "Design or audit the clinical-validation study for an engineer-built medical-imaging model (segmentation, classification, or detection) before the validation report or manuscript is written."
+    },
     {
       "slug": "orchestrate",
       "category": "project_workflow",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "medsci-skills",
-  "version": "4.10.0",
+  "version": "4.11.0",
   "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",