medsci-skills 4.10.0 → 5.0.0

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.*
+*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 — 38 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-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)
@@ -42,14 +42,20 @@
 ## What is MedSci Skills?
 
 MedSci Skills is an open-source Claude Code skill collection for **clinical
-manuscript preparation**. It helps physician-researchers and biomedical
-investigators move from literature search, study design, statistics, and figures to
-reporting-guideline compliance, citation/reference auditing, numerical-consistency
-checks, and response-to-reviewer workflows — combining agentic writing with
-**deterministic integrity gates** for submission-grade biomedical research. It is
-**not** a diagnostic tool, an autonomous author, or a general AI-scientist platform;
-every output requires human-expert verification. New here? See the
-[3 workflows below](#start-here-3-workflows), the [FAQ](docs/faq.md), and the
+research — the manuscript and the medical-AI model alike**. 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
+response-to-reviewer workflows — combining agentic writing with **deterministic
+integrity gates** for submission-grade biomedical research. As of **v5.0** it adds a
+**model-engineering lane**: choose a paper-grounded architecture, scaffold a
+reproducible, leakage-safe PyTorch training repo, and validate, document, and
+evaluate a medical-imaging or LLM/MLLM model so the work reaches a paper — it
+**integrates** MONAI / nnU-Net, never reimplements them. Clinical AI model research
+engineering is in scope; it is **not** a diagnostic tool, an autonomous author, or a
+general AI-scientist platform, and every output requires human-expert verification.
+New here? See the [3 workflows below](#start-here-3-workflows), the
+[FAQ](docs/faq.md), and the
 [scope boundary](ROADMAP.md#not-planned--explicitly-out-of-scope).
 
 ---
@@ -82,17 +88,18 @@ Restart Claude Code, then start with **`/orchestrate`** — it classifies your r
 
 ### Install as a Claude Code plugin
 
-Prefer plugins? One line adds the marketplace; `/plugin` then lets you browse eight category plugins and enable the ones you want:
+Prefer plugins? One line adds the marketplace; `/plugin` then lets you browse nine category plugins and enable the ones you want:
 
 ```text
 /plugin marketplace add Aperivue/medsci-skills
-/plugin            # browse eight category plugins; enable the ones you want
+/plugin            # browse nine category plugins; enable the ones you want
 ```
 
 | Plugin | Covers |
 |--------|--------|
 | `medsci-literature` | Literature search, full-text retrieval, Zotero sync, reference-integrity audits |
 | `medsci-data` | Study design, variable operationalization, sample size, data cleaning, de-identification, codebooks, dataset versioning |
+| `medsci-modeling` | Architecture selection, reproducible model-scaffold repos, model-validation audits, Model Card/Datasheet, model & LLM/MLLM evaluation |
 | `medsci-analysis` | Statistics, figures, batch/cross-national/replication analysis, meta-analysis |
 | `medsci-writing` | IMRAD & protocol drafting, AI-pattern removal, AI-search optimization, reviewer responses |
 | `medsci-review` | Self-review, peer review, reporting-guideline compliance |
@@ -451,6 +458,12 @@ 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 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. Integrates with MONAI / nnU-Net / TorchIO / timm / torchvision — 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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