templates/method_appendix.md

STEM BIO-AI Method Appendix

Spec Version: STEM BIO-AI v1.1.2 Execution Mode: [LOCAL_ANALYSIS / FULL / SEARCH_ONLY / MANUAL]

Rubric Summary

See spec/STEM-AI_v1.1.2_CORE.md for the full canonical rubric.

Audit-Layer Relationship

• Technical audit establishes what the repository actually does.
• STEM BIO-AI classifies whether the artifact surface built around that repository is sufficient for institutional trust establishment.

Technical audit is therefore the fact-extraction layer. STEM BIO-AI is the trust-classification layer.

Stage 1: README Intent (Weight: 0.40)

• H1-H6: Hype deductions (-5 to -10 pts each)
• R1-R5: Rigor additions (+10 to +15 pts each)
• R2/R3 active penalties for CA-DIRECT (-10) and CA-INDIRECT (-5)
• Baseline: 60 pts

Stage 2: Cross-Platform (Weight: 0.20)

• F1-F4: Fame-seeking deductions
• A1-A4: Authentic discourse additions
• Baseline: 50 (nascent) or 60 (established)

Stage 3: Code Debt (Weight: 0.40)

• T1-T4: Technical responsibility (0-15 pts each)
• B1-B3: Biological integrity (0-15 pts each)
• Trajectory modifier: +/-5 pts
• T4 PENDING normalization: denominator = 80

Stage 3G: Governance Overlay (Advisory)

• G1-G5: 0-5 pts each (max 25)
• Does not change base tier

C1-C4: Code Integrity (LOCAL_ANALYSIS only)

• C1 FAIL triggers RP3 (-10 pts)
• C2-C4 are advisory

Confidence Assignment Rule

• High: directly observed in code/config/workflow
• Moderate: indirectly supported through combined signals
• Low: surface-level observation, interpretation margin present

Audit Stop Conditions

• T0_HARD_FLOOR triggered: skip all score computation
• Private repository: refuse audit (TV-1)
• Personal attack purpose: refuse (TV-2)

Escalation Criteria

• Score within 3 points of tier boundary: flag for human review
• CODE_PATH contradicts TEXT_PATH: record explicitly, flag finding
• CA-DIRECT with Stage 3 <= 40: CA-DIRECT redistribution warning