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STEM BIO-AI Lessons & Failure Mode History
Memory Layer — protocol_evolution
Version: 1.1.2 | Updated: 2026-03-27
This document records protocol failure modes discovered through real-world use and their authoritative resolutions. Each entry represents a confirmed failure in a prior version. All resolutions are now encoded in IMMUTABLE or VARIABLE rules.
How to Use This Document
- Consult when a rubric edge case appears to have multiple valid interpretations.
- Each lesson maps to one or more PATCH numbers in CHANGELOG.md.
- Lessons are immutable records — they are never removed, only extended.
- When a new failure mode is found, append to this file and increment STEM BIO-AI version.
Lesson Registry
L-001: Narrative Scoring Drift
Patches: PATCH-001 through PATCH-006 Failure mode: Early versions allowed LLMs to narrate trust assessments without fixed point values. Different LLMs producing scores 20+ points apart on identical repositories. Resolution: Replaced narrative scoring with rubric-based point checklists. Fixed baselines, fixed point values, fixed tier boundaries. Cross-LLM target: ±10 points. Lesson: Narrative reasoning is not reproducible. Every scored item must have a fixed, citable point value.
L-002: NASCENT_REPO Baseline Contamination
Patch: PATCH-007 (v1.0.2) Failure mode: Repositories with age < 90 days scored against Stage 2 baseline of 60 (designed for established projects). Nascent repos with no social activity received -10 or more false deductions, pushing legitimate early-stage work into T0. Resolution: NASCENT_REPO flag. When true: Stage 2 baseline = 50. T4 PENDING path enabled. Lesson: Rubric baselines must account for project lifecycle stage. One baseline for all projects produces systematic false negatives against early-stage work.
L-003: T0 Hard Floor Missing
Patch: PATCH-008 (v1.0.3) Failure mode: Repositories with CA-DIRECT classification and zero code presence could still score above T0 based on strong Stage 1 README rhetoric. A well-written README was sufficient to escape T0 despite no actual code. Resolution: T0_HARD_FLOOR rule: CA-DIRECT + zero code presence = T0 regardless of stage scores. No override. No exception. Lesson: Hard floors must exist for combinations that represent absolute disqualifying risk. Stage scores can be gamed through documentation quality alone.
L-004: DERIVED Computation Order Error
Patch: PATCH-023 (v1.0.5) Failure mode: DERIVED-3 (trajectory signal) was computed after Stage 3, meaning the trajectory modifier (+/-5 pts) was not available during Stage 3 scoring. Auditors added it inconsistently — sometimes before clamp, sometimes after. Resolution: DERIVED-3 must be computed in Step 5a, before Stage 3 execution (Step 5b). Now enforced as IMMUTABLE rule in execution instruction Section 8.2. Lesson: Computation order is part of the spec. Ordering ambiguities produce silent errors that only appear when trajectory modifiers change tier boundaries.
L-005: Governance Overlay Inflating Base Tier
Patches: PATCH-015, PATCH-016, PATCH-020 (v1.0.5) Failure mode: Stage 3G governance overlay scores were being used to revise the formal base tier upward. A T0 repository with a governance framework was being reported as T1. Resolution: Governance overlay separation rule (IMMUTABLE): Stage 3G is advisory only. Base tier is never modified by overlay score. G3 = 0 caps overlay verdict at WEAK (Cosmetic Uplift Guard). Both tiers reported separately in output. Lesson: Governance documentation is not the same as governance in practice. Operational overlays must not allow paper governance to inflate clinical trust classification.
L-006: T4 PENDING Denominator Error
Patch: PATCH-032 (v1.0.6) Failure mode: When T4 PENDING path activated (governance overlay present), Stage 3 rubric was normalized to /85 instead of /80. This reduced all Stage 3 scores by ~6%, pushing some borderline T3 repositories below the T4 threshold incorrectly. Resolution: T4 PENDING denominator corrected to 80 (IMMUTABLE rule). All prior audits that activated T4 PENDING path should be re-run. Lesson: Normalization denominators are part of the scoring formula. Even small denominator errors compound across the weighted formula into tier-boundary violations.
L-007: LOCAL_ANALYSIS Mode Not Detected
Patch: PATCH-027 (v1.0.6) Failure mode: Without an explicit execution mode declaration, auditors running in AI CLI environments (with local repo access) defaulted to FULL or MANUAL mode, missing C1-C4 code integrity checks entirely. Resolution: Execution mode declared as mandatory Pre-Execution Check EM-0 (Step 1 of Section 8.2). Mode determines CODE_PATH availability. Lesson: Capability detection must be explicit, not inferred. Silent mode ambiguity causes systematic omission of higher-quality evidence paths.
L-008: Stage 3G Activating on Intent Statements
Patch: PATCH-036 (v1.0.6) Failure mode: Stage 3G was activating when README or CHANGELOG mentioned governance "plans" or "intent" without actual artifacts. This allowed repositories to claim governance overlay credit on aspirational statements. Resolution: Stage 3G activation requires actual governance artifacts (documents, schemas, policy files). Intent statements without artifacts = Stage 3G NOT_APPLICABLE. Lesson: Governance theater is the primary attack surface. Require material evidence, not rhetorical evidence.
L-009: Single-File Spec Context Window Overflow
Patch: v1.1.0 architecture revision Failure mode: v1.0.6 spec was a single file of 2000+ lines. Context window pressure caused LLMs to drop discrimination examples or governance overlay details in long audit sessions. This produced silent scoring errors that were undetectable in output. Resolution: Multi-file skill package architecture (v1.1.0). Core spec + discrimination examples + templates as separate files loaded on demand. Lesson: A spec that cannot be fully loaded in context is a spec that will be silently violated. File decomposition is an accuracy requirement, not just an organization preference.
L-010: Cosmetic Governance Uplift via G1-G2 Without Runtime Evidence
Patch: PATCH-020 (v1.0.5), strengthened in v1.0.6 Failure mode: Repositories could score G1 (bounded insertion) and G2 (capability preservation) on documentation alone, reaching BOUNDED verdict without any runtime fail-closed evidence. Clinical operators were making procurement decisions based on BOUNDED verdicts that had no operational substance. Resolution: Cosmetic Uplift Guard: G3 (Fail-Closed Runtime Evidence) = 0 caps overlay verdict at WEAK, regardless of G1/G2/G4/G5 scores. Stage3G_Score capped at 10. Lesson: Operational safety claims require operational safety evidence. Documentation governance and runtime governance are not interchangeable.
Lesson Addition Protocol
When a new failure mode is discovered:
- Document it as
L-NNNwith patches, failure mode, resolution, and lesson. - Verify the resolution is encoded in CORE spec (IMMUTABLE or VARIABLE rule).
- Increment STEM BIO-AI version (patch version for rubric refinement, minor for formula change).
- Update
operation_meta.update_countandlast_updatedin archive JSON. - Add provenance entry for the triggering repository if a real audit exposed the failure.
Drift Profile First Cycle -- 2026-03-28
MICA v0.2.0 Drift Profile applied to STEM-BIO-AI for the first time.
Drift events caught and resolved
| DRF | Stale surface | Stale value | Current value | Resolution |
|---|---|---|---|---|
| DRF-004 | CORE spec L1766 | Audit Report header v1.1.1 | v1.1.2 | Patched |
| DRF-004 | CORE spec L1781 | Disclaimer executing v1.1.1 | v1.1.2 | Patched |
| DRF-004 | CORE spec L2096 | Input Template header v1.1.1 | v1.1.2 | Patched |
| DRF-004 | CORE spec L2160 | Confirmation line v1.1.1 | v1.1.2 | Patched |
| DRF-004 | README BibTeX | version = {1.1.1} | {1.1.2} | Patched |
| DRF-004 | playbook L84 | on_version_increment | on_version_bump | Patched |
Pattern registered (high-risk zone)
CORE spec template sections do NOT auto-update on file copy. On every version bump, grep for ALL occurrences of the prior version string in:
- Output Format header (Section 8.1)
- Disclaimer line (Section 8.1)
- Input Template header (Section 8.3)
- Audit Report generation confirmation (Section 8.3 footer) This is now a mandatory DRF-004 pre-release check.