title	STEM BIO-AI
emoji	🧬
colorFrom	blue
colorTo	green
sdk	gradio
sdk_version	5.29.0
python_version	3.11
app_file	app.py
pinned	false

STEM BIO-AI

Deterministic evidence-surface scanner for bio/medical AI repositories.
No LLM. No API key. No model runtime. No secrets sent anywhere.

---

Why STEM BIO-AI

Bio and medical AI repositories vary enormously in evidence quality — from rigorous academic tools to marketing-grade demos that carry clinical language with no data provenance, no reproducibility path, and no clinical-use disclaimer. Manual review is slow and inconsistent.

STEM BIO-AI scans the observable repository surface — README, docs, code structure, CI configuration, dependency manifests, changelogs — and maps detected signals to a structured evidence tier (T0–T4). The scan runs in seconds on a local clone, produces machine-readable JSON and PDF reports, and makes every scoring decision traceable to a specific file, line, and pattern.

A T4 score means strong observable evidence signals. It does not mean the repository is safe for clinical deployment — that requires independent expert validation.

---

Quick Start

git clone https://github.com/flamehaven01/STEM-BIO-AI.git
cd STEM-BIO-AI
pip install stem-ai

# editable local install with PDF output support
pip install -e .[pdf]

# fastest path: scan a local repository
stem /path/to/bio-ai-repo

# 5-page full evidence packet with proof trace
stem scan /path/to/bio-ai-repo --level 3 --format all --explain

# workflow-oriented CLI
stem scan /path/to/bio-ai-repo --level 2
stem scan /path/to/bio-ai-repo --policy strict_clinical_adjacency
stem gate /path/to/bio-ai-repo --min-tier T2
stem policy list
stem policy explain strict_clinical_adjacency
stem policy derive --clinical-strictness 4 --code-integrity-priority 3 --reproducibility-priority 2 --structured-limitations-requirement 3
stem policy simulate /path/to/bio-ai-repo --clinical-strictness 4 --code-integrity-priority 3 --reproducibility-priority 2 --structured-limitations-requirement 3
stem policy simulate /path/to/bio-ai-repo --profile-file policy/drafts/scoring_profile.reproducibility_first.v1.json
stem advisory validate /path/to/bio-ai-repo
stem advisory packet /path/to/bio-ai-repo --output advisory_out
stem advisory check-response /path/to/bio-ai-repo --response provider_advisory.json

# backward-compatible shortcuts still work
stem /path/to/bio-ai-repo --level 3 --format all --explain
stem audit /path/to/bio-ai-repo --tier-gate T3 --quiet

Clone the target repository first; the CLI operates on local paths only.

Calibration profiles are implemented in mirror_only mode in 1.7.4. --policy changes what profile is surfaced in artifacts, while policy derive and policy simulate provide governed preview lanes without mutating the authoritative deterministic score path. policy simulate --profile-file <path> allows local schema-valid profile experiments without registering a new named policy. In the current rule scope, strict_clinical_adjacency is the only release-grade named recommendation; stronger reproducibility postures still fall back to preview_only simulation deltas rather than a named profile.

Researchers and domain specialists are expected to influence calibration through derive, simulate, and documented preview/profile proposals. The intent interview uses a governed 1–5 posture scale, while official score-affecting policy changes still require profile promotion rather than direct ad hoc tuning.

Full CLI reference: docs/CLI_REFERENCE.md

Proof surfaces

• Demo: Hugging Face Space
• API contract: docs/API_CONTRACT.md
• Secret handling: docs/ADVISORY_SECRET_HANDLING.md
• Advisory runtime boundary: docs/ADVISORY_RUNTIME.md
• Example audits: docs/EXAMPLE_AUDITS.md
• Scoring rationale: docs/SCORING_RATIONALE.md
• Calibration profile architecture: docs/CALIBRATION_PROFILE_DESIGN.md
• AIRI data governance: docs/AIRI_DATA_GOVERNANCE.md
• Third-party data attribution: docs/THIRD_PARTY_DATA.md
• Deterministic diagnostics: docs/DETERMINISTIC_DIAGNOSTICS.md
• Regulatory traceability mapping: docs/REGULATORY_MAPPING.md
• Regulatory basis registry: docs/regulatory_basis_registry.v1.json
• CLI reference: docs/CLI_REFERENCE.md

---

Triage Tiers

• T0 Rejected (0–39): insufficient evidence — do not rely on without independent expert validation
• T1 Quarantine (40–54): exploratory review only — expert validation required before any use
• T2 Caution (55–69): research reference and supervised non-clinical technical review only
• T3 Supervised (70–84): supervised institutional review candidate
• T4 Candidate (85–100): strong evidence posture — clinical deployment still requires independent validation

Clinical-adjacent repositories without an explicit disclaimer are hard-capped at T2 (score ≤ 69). Repositories with unbounded CA-DIRECT claims are hard-capped at T0 (score ≤ 39).

Tier boundary derivation and calibration gap disclosures: docs/SCORING_RATIONALE.md.

---

Scoring Model

Final = (Stage 1 × 0.40) + (Stage 2R × 0.20) + (Stage 3 × 0.40) − C1 Penalty

Stage	Weight	What Is Measured
Stage 1 README Evidence	40%	Bio-domain vocabulary; H1–H6 hype-claim penalties; R1–R5 responsibility signals (limitations, regulatory framing, clinical disclaimer, demographic-bias, reproducibility)
Stage 2R Repo-Local Consistency	20%	Vocabulary overlap across README, docs, package metadata, CI, and tests; limitation repetition; contradiction, staleness, and unsupported-workflow deductions
Stage 3 Code/Bio Responsibility	40%	CI presence; domain test coverage; changelog hygiene (T3); data provenance and IRB/dataset citation (B1); bias/limitation measurement evidence (B2); conflict-of-interest disclosure (B3)
Stage 4 Replication Evidence	Separate lane	Containers; reproducibility targets; dependency locks/pins; dataset and model artifact references; seed, CLI, and citation signals; license/use-scope restrictions
C1–C4 Code Integrity	Penalty / advisory	Hardcoded credentials (C1, −10 pts); dependency pinning (C2); deprecated patient-adjacent paths (C3); fail-open exception handlers (C4)

Stage 4 is reported as replication_score / replication_tier and does not affect score.final_score. Full scoring rationale and calibration gap disclosures are in docs/SCORING_RATIONALE.md.

---

Architecture

flowchart LR
    A[Target repository] --> B[LOCAL_ANALYSIS scanner]
    B --> C[Stage 1\nREADME evidence]
    B --> D[Stage 2R\nRepo-local consistency]
    B --> E[Stage 3\nCode/bio responsibility]
    B --> F[Stage 4\nReplication lane]
    B --> K[C1–C4\nCode integrity]
    B --> CC[CC1–CC3\nAST contract detectors]
    C --> G[Weighted evidence score]
    D --> G
    E --> G
    K --> G
    CC --> R[code_contract + AIRI coverage]
    F --> H[replication_score / tier]
    G --> I[JSON result]
    H --> I
    R --> I
    I --> L[Evidence ledger]
    I --> M[Explain trace]
    G --> N[Markdown report]
    G --> O[PDF packet]
    G --> P[Interactive HTML dashboard]

Loading

Core modules: stem_ai/scanner.py, stem_ai/render.py, stem_ai/cli.py, stem_ai/detectors.py, stem_ai/detector_surface.py, stem_ai/detector_ast.py, stem_ai/detector_bio.py, stem_ai/detector_contract.py, stem_ai/detector_stage4.py, stem_ai/evidence.py, stem_ai/airi_risk_mapping.py, stem_ai/app.py

---

Output Artifacts

Each run writes to --out DIR (default: stem_output/).

Level	Pages	Audience	Artifacts
--level 1	1	Executive / triage	Score, tier, stage cards, code integrity summary
--level 2	3	Standard audit review	Level 1 + Stage 1/2R/3 breakdown, gap analysis
--level 3	5	Full evidence packet	Level 2 + code integrity deep dive, classification analysis, remediation roadmap

<repo>_experiment_results.json   # machine-readable score + full evidence object
<repo>_report.html               # interactive 5-section HTML dashboard (v1.7.0+)
<repo>_report.md                 # human-readable audit report
<repo>_brief_1p.pdf              # Level 1 executive dashboard
<repo>_detailed_3p.pdf           # Level 2 stage analysis
<repo>_detailed_5p.pdf           # Level 3 deep review packet
<repo>_explain.txt               # --explain: file/line/snippet proof trace

---

HTML Report Dashboard

--format html generates a self-contained interactive dashboard (v1.7.0+). Single .html file — no network, no external dependencies.

Example interactive HTML audit

• Open in browser: https://htmlpreview.github.io/?https://raw.githubusercontent.com/flamehaven01/STEM-BIO-AI/main/docs/examples/maziyarpanahi_openmed_report.html
• Raw HTML artifact: docs/examples/maziyarpanahi_openmed_report.html

5 sections: Executive Summary · Score Matrix · Code Integrity (expandable cards) · AIRI Risk Coverage (toggle) · Evidence Detail (filter chips)

Interactive features: sticky scroll-spy nav · ? tooltip icons on every metric · click-to-expand evidence cards · covered/gaps toggle for AIRI risks · FAIL/WARN/PASS/INFO filter on the evidence ledger.

The AIRI section now distinguishes between the full local AIRI registry, the curated runtime bundle used by deterministic scans, and the detector mapping registry that connects STEM BIO-AI findings to AIRI risk IDs. Upstream AIRI provenance is surfaced in runtime artifacts, not only in README/docs.

---

Report Preview

Sample PDF: Download the 5-page Level 3 report

View all 5 preview pages

Page 1	Page 2

Page 3	Page 4

Page 5

---

Detection Methods

Every scored item maps to a concrete, inspectable detection method. No inference, no LLM judgment.

Full detection table

Component	Detection Method
Stage 1 baseline	Non-zero README present (+60 base)
Stage 1 domain signal	Bio-domain keyword regex in README and package metadata
Stage 1 hype penalties (H1–H6)	Regex: clinical certainty, regulatory approval, autonomous replacement, breakthrough marketing, universal generalization, perfect accuracy claims
Stage 1 responsibility signals (R1–R5)	Regex: limitations section, regulatory framework, clinical disclaimer (CA-severity-weighted), demographic-bias disclosure, reproducibility provisions
Stage 2R consistency	Vocabulary set intersection across README/docs/package/tests; limitation repetition; clinical-boundary contradiction, version-staleness, and workflow-support deductions
Stage 3 T1 CI	.github/workflows/ contains at least one file
Stage 3 T2 domain tests	tests/ directory text contains bio-domain vocabulary (regex)
Stage 3 T3 changelog	CHANGELOG file presence + bug-fix/patch/security entry detection (3-tier: 0/+5/+15)
Stage 3 B1 data provenance	Dependency manifest presence + IRB/dataset-citation language detection (3-tier: 0/+10/+15)
Stage 3 B2 bias measurement	Bias/limitations vocabulary + quantitative measurement evidence (subgroup analysis, AUROC, demographic parity) (3-tier: 0/+8/+15)
Stage 3 B3 COI/funding	Funding, grant, sponsor, conflict-of-interest language in README/docs/FUNDING.md
Stage 4 containers	Dockerfile or compose file present
Stage 4 reproducibility target	Makefile with reproduce/eval/benchmark/test targets
Stage 4 dependency lock	Environment/lock/requirements file; exact pins or hash evidence
Stage 4 artifact references	Dataset/model/checkpoint URLs or checksum files
Stage 4 citation/interface	CITATION.cff; argparse CLI entry points (AST)
Stage 4 license restriction	Non-commercial, research-only, academic-only, no-clinical-use restrictions in LICENSE/README
CA severity	Clinical/diagnostic phrase regex in README, docs, and package metadata
C1 credentials	AWS AKIA*, OpenAI sk-*, GitHub ghp_*, api_key=... patterns; obvious placeholders excluded from penalty
C2 dependency pinning	== or hash pin vs. loose >=, ~=, <, > ranges
C3 deprecated paths	Patient-metadata patterns in deprecated/, legacy/, archive/ directories
C4 fail-open	except Exception: pass or except: pass in Python source (AST)
CC1 clinical zero default	AST scan of function defaults: keyword-only and positional params named confidence_threshold, score_threshold, min_confidence, etc. defaulted to 0.0
CC2 API contract	README-declared names cross-checked against __all__ exports; phantom APIs flagged
CC3 shallow validator	validate_* / check_* functions using only len() (no regex structure check) flagged as insufficient for clinical/PII validation

---

AI Advisory Contract

The advisory system exports a sanitized, provider-neutral handoff packet and validates provider responses — without making any provider API call.

stem advisory validate /path/to/repo                # offline contract check
stem advisory packet /path/to/repo                  # export sanitized input packet
stem advisory check-response /path/to/repo --response FILE

Non-negotiable rules (enforced by the validator):

• Provider output cannot override score.final_score or score.formal_tier
• Every advisory item must cite exact finding_id strings from allowed_finding_ids
• Raw repository source text is not included in provider packets
• Responses containing clinical safety, efficacy, regulatory, or medical-advice claims are rejected
• allowed_finding_ids is capped at 40 entries per packet

Packet hardening added in v1.5.7:

• provider_request now carries a secret-free request schema plus deterministic argument-validation status
• contract_schemas exports the advisory input/output contract shapes for downstream validators
• packet_contract confirms allowlist parity, snippet omission, and non-negative omission counts before handoff

Secret boundary hardening added in v1.5.9:

• provider-specific environment variables are recognized before the generic advisory key fallback
• provider handoff metadata exports endpoint-policy validation and the expected env-var name, never the key value
• embedded-credential URLs are rejected; cloud providers require https; plain http is limited to localhost
• .env files are ignored by default; .env.example documents supported variable names only
• --advisory call is now the explicit provider-call boundary, with centralized redaction, logging-policy export, child-env allowlist reporting, and artifact pre-write sanitization

Full contract: docs/API_CONTRACT.md Secret policy: docs/ADVISORY_SECRET_HANDLING.md Runtime boundary: docs/ADVISORY_RUNTIME.md

---

MICA Memory Layer

The repository keeps a versioned MICA memory layer under memory/ for agent-session initialization, drift control, and release provenance. Historical snapshots are retained as archive; the active layer is selected by memory/mica.yaml.

Operational reference: docs/MICA_MEMORY.md

---

Web Demo

Live demo: huggingface.co/spaces/Flamehaven/stem-bio-ai

The Space runs the same deterministic local scanner on public GitHub repositories. No provider API call is made.

Run locally:

pip install -e .[demo]
python app.py

---

Repository Structure

STEM-BIO-AI/
  stem_ai/              # Core Python package
  docs/                 # API contract, advisory runtime/secret policy, scoring rationale, MICA policy, report previews
  memory/               # Versioned MICA archive/playbook/lessons; active layer selected by mica.yaml
  audits/               # Reference benchmark artifacts
  scripts/              # Benchmark and validation scripts
  tests/                # Regression test suite
  app.py                # HuggingFace Spaces / Gradio entry point
  pyproject.toml        # Package metadata and extras
  SKILL.md              # Universal agent skill definition
  CHANGELOG.md          # Version history

---

Agent Skill Install

# Claude Code
git clone --depth 1 https://github.com/flamehaven01/STEM-BIO-AI.git ~/.claude/skills/stem-bio-ai

# Generic agent frameworks
git clone --depth 1 https://github.com/flamehaven01/STEM-BIO-AI.git ~/.agents/skills/stem-bio-ai

---

Contributing

See CONTRIBUTING.md. High-value areas: rubric discrimination examples, clinical-adjacency trigger refinements, additional bio-domain benchmark repositories, report rendering improvements.

---

Citation

Preferred citation metadata lives in CITATION.cff.

Current concept DOI-backed archive for the 1.7.4 line:

• https://doi.org/10.5281/zenodo.20154479

@software{stem-bio-ai,
  author  = {Yun, Kwansub},
  title   = {STEM BIO-AI: Deterministic Evidence-Surface Scanner for Bio/Medical AI Repositories},
  version = {1.7.4},
  year    = {2026},
  doi     = {10.5281/zenodo.20154479},
  url     = {https://doi.org/10.5281/zenodo.20154479}
}

---

License

Apache 2.0. See LICENSE.

Maintained by flamehaven01