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| name: stem-ai | |
| description: "Deterministic Evidence-Surface Scanner for Bio/Medical AI Repositories. Audits and reviews open-source bio/medical AI repositories for repository evidence-surface triage using a rubric-based 3-stage evaluation protocol with governance overlay. Produces scored review-priority reports with evidence chains. Supports 4 execution modes: LOCAL_ANALYSIS (AI CLI + local clone), FULL (web search + fetch), SEARCH_ONLY, and MANUAL. Use when asked to evaluate, audit, review, or assess evidence signals for any bio-AI, medical AI, or clinical-adjacent repository." | |
| version: "1.7.2" | |
| author: "Flamehaven" | |
| license: "Apache-2.0" | |
| platforms: ["claude-code", "codex", "gemini-cli", "cursor", "copilot", "antigravity", "universal"] | |
| # STEM BIO-AI -- Deterministic Evidence-Surface Scanner for Bio/Medical AI Repositories | |
| **Version:** 1.7.2 | |
| **Codename:** Hippocratic_Code_Engine_Unified | |
| **Runtime:** LLM-Native + AI CLI (Universal) | |
| > "Code works. But does the author care about the patient? | |
| > Governance without evidence is theater. | |
| > Evidence without accountability is still not trust. | |
| > Measurement beats interpretation." | |
| ## When to Use This Skill | |
| - Evaluating repository evidence signals for a bio-AI or medical AI repository | |
| - Auditing open-source clinical-adjacent tools before procurement or pilot | |
| - Assessing governance maturity of repositories handling patient data | |
| - Generating structured audit reports with evidence chains and scores | |
| - Comparing repository review-priority tiers across an ecosystem | |
| - Producing institutional-grade documentation (Claim Matrix, Evidence Ledger) | |
| ## What This Skill Produces | |
| 1. **STEM BIO-AI Audit Report** -- scored repository evidence-surface triage (T0-T4 review-priority tier) | |
| 2. **Executive Summary** -- 1-page institutional decision support | |
| 3. **Claim Matrix** -- line-level evidence anchors for every finding | |
| 4. **Evidence Ledger** -- snapshot provenance and artifact tracking | |
| 5. **Code Integrity Report** -- C1-C4 findings (LOCAL_ANALYSIS only) | |
| ## Audit Layering | |
| STEM BIO-AI sits on top of technical audit. It should not replace it. | |
| - **Technical audit** determines what the repository actually does. | |
| - **STEM BIO-AI** determines whether the observable artifact surface is sufficient for institutional review triage. | |
| Use this skill after or alongside technical inspection, not instead of it. | |
| ## Quick Start | |
| To audit a repository, provide: | |
| - GitHub URL or README text | |
| - (Optional) CHANGELOG, social media activity, CI/CD status | |
| - (Optional) Governance overlay materials | |
| The skill will: | |
| 1. Detect execution mode (LOCAL_ANALYSIS / FULL / MANUAL) | |
| 2. Run 3-stage evaluation (README Evidence Signal, Repo-Local Consistency, Code/Bio Responsibility) | |
| 3. Score with fixed rubric (cross-LLM target: +/-10 points) | |
| 4. Evaluate governance overlay if artifacts present | |
| 5. Generate multi-file output package | |
| ## Skill Architecture | |
| ``` | |
| stem-ai/ | |
| SKILL.md <-- You are here (entry point) | |
| memory/ <-- MICA v0.2.0 memory layer (load first) | |
| mica.yaml <-- composition contract | |
| stem-ai.mica.v1.7.2.json <-- active archive (selected by mica.yaml) | |
| stem-ai-playbook.v1.7.2.md <-- active session protocol (selected by mica.yaml) | |
| stem-ai-lessons.v1.7.2.md <-- active lessons history (selected by mica.yaml) | |
| spec/ <-- Core rubric, scoring, execution rules | |
| discrimination/ <-- YES/NO example pairs for scoring consistency | |
| templates/ <-- Output templates (report, claim matrix, etc.) | |
| scripts/ <-- Automation scripts (scans, provenance) | |
| references/ <-- Lookup tables (tiers, triggers, taxonomy) | |
| examples/ <-- Real audit examples | |
| ``` | |
| ## Instructions | |
| When activated, load files in this order: | |
| 0. **Load MICA memory layer first (before any audit work):** | |
| - Load `memory/mica.yaml` -- verify package structure and mode | |
| - Load the archive file referenced by `memory/mica.yaml` -- activate 18 IMMUTABLE rules as design_invariants | |
| - Load the playbook file referenced by `memory/mica.yaml` -- session protocol and rubric drift guard | |
| - Run PCT self-tests (PCT-001 through PCT-007). Halt on PCT-001/002/003 failure. | |
| - Report: `[MICA READY] stem-ai-bio v1.7.2 | invariants: 18 active` | |
| 1. **Always load next:** `spec/STEM-AI_v1.1.2_CORE.md` | |
| This is the canonical rubric and execution instruction. | |
| 2. **Load on demand during Stage 1:** | |
| - `discrimination/H1-H6_examples.md` | |
| - `references/clinical_adjacent_triggers.md` | |
| 3. **Load on demand during Stage 3:** | |
| - `discrimination/T2_examples.md` | |
| - `discrimination/B3_COI_guide.md` | |
| - `discrimination/CA_severity_examples.md` | |
| 4. **Load if governance overlay detected:** | |
| - `discrimination/G1-G5_examples.md` | |
| 5. **Load for output generation:** | |
| - `templates/audit_report.md` | |
| - `templates/claim_matrix.md` | |
| - `templates/executive_summary.md` | |
| - `templates/evidence_ledger.md` | |
| 6. **Run in LOCAL_ANALYSIS mode:** | |
| - `scripts/local_analysis_scan.sh` | |
| - `scripts/ca_detection_scan.sh` | |
| - `scripts/snapshot_provenance.sh` | |
| ## Execution Modes | |
| | Mode | Environment | Evidence Quality | C1-C4 | | |
| |------|------------|-----------------|-------| | |
| | LOCAL_ANALYSIS | AI CLI + local clone | CODE_PATH (measurement) | Active | | |
| | FULL | Online LLM + web tools | TEXT_PATH + web fetch | N/A | | |
| | SEARCH_ONLY | Online LLM + search only | TEXT_PATH + search | N/A | | |
| | MANUAL | Online LLM, no tools | TEXT_PATH only | N/A | | |
| ## Tier Definitions | |
| | Tier | Score | Meaning | | |
| |------|-------|---------| | |
| | T0 Rejected | 0-39 | Trust not established -- clinical use prohibited | | |
| | T1 Quarantine | 40-54 | High risk -- independent verification required | | |
| | T2 Caution | 55-69 | Research reference only -- clinical automation forbidden | | |
| | T3 Review | 70-84 | Supervised clinical pilot eligible -- oversight mandatory | | |
| | T4 Candidate | 85-100 | Strongest structural audit-readiness signal -- clinical deployment still requires independent validation | | |