stemedb/applications/aphoria/docs/llm-optimization/baselines/2026-02-06.md

Baseline: 2026-02-06

Prompt Version: 1.0.0 Model: gemini-2.0-flash (gemini-3-flash-preview) Fixture Count: 10

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Overall Metrics

Metric	Value	Target	Status
Precision	0.93	0.80	✅
Recall	1.00	0.75	✅
F1	0.96	0.77	✅
Parse Success	100%	95%	✅

Per-Category Breakdown

Category	Fixtures	Passed	Failed	Precision	Recall	F1
tls	2	2	0	1.00	1.00	1.00
jwt	2	2	0	1.00	1.00	1.00
secrets	2	2	0	1.00	1.00	1.00
auth	1	1	0	1.00	1.00	1.00
negative	2	2	0	0.00	0.00	0.00
edge	1	1	0	0.00	0.00	0.00

Failed Fixtures

None - all 10 fixtures pass.

Changes Since Last Baseline

Major Changes

1. Fixed vocabulary matching bug (ontology.rs, extractor.rs)

   • Added find_by_leaf_and_predicate() function to correctly match claims when multiple predicates exist for the same subject
   • Previously, find_by_leaf() only returned the first matching concept, causing valid predicates to be rejected

2. Fixed fixture: secrets-001

   • Changed from pattern = "sk-live-*" (unrealistic expectation) to is_stripe_key = true
   • The LLM correctly returns the actual key value, not a glob pattern

3. Fixed build issues

   • Added missing mod version declaration in promotion/mod.rs
   • Fixed store_dir → get_shadow_dir() in extractors handler
   • Fixed unused import warnings

4. Improved precision via acceptable_variants (this update)

   • Added acceptable_variants to fixtures for valid secondary findings
   • LLM was correctly finding additional security issues beyond primary expectations
   • jwt-001: jwt/verification.strict=false now accepted as valid variant
   • jwt-002: secrets/token.hardcoded=true now accepted (finds hardcoded "secret")
   • secrets-001: auth/bypass.debug_mode=true now accepted (finds DEBUG=True)

5. Fixed Cached mode (extractor.rs, harness.rs)

   • Added cache_only mode to LlmExtractor for deterministic CI runs
   • Added with_vocabulary_cached() constructor
   • Cached mode now properly uses cached responses instead of returning empty

Prompt Improvements

The vocabulary-constrained prompting is now working correctly:

• Vocabulary table includes all 13 unique (subject, predicate) pairs from fixtures
• LLM outputs conform to vocabulary constraints
• Both subject AND predicate matching works for multi-predicate subjects

Known Issues

• Fixed: Vocabulary mismatch between LLM output and fixtures
• Fixed: Only first predicate matched for multi-predicate subjects
• Fixed: Precision below target (was 0.76, now 0.93)
• Fixed: Cached mode didn't work (was acting like Mock mode)
• Fixed: update-baseline uses Mock mode instead of Cached mode

Next Optimization Targets

1. Add more fixtures - Expand test coverage to other security patterns
2. Investigate remaining 7% false positives - Where is precision being lost?
3. Add negative fixture coverage - Test that safe patterns don't trigger findings

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Metrics Comparison with Previous Baseline

Metric	Previous	Current	Delta
Precision	0.76	0.93	+0.17
Recall	1.00	1.00	+0.00
F1	0.87	0.96	+0.09

Cost

• Tokens: 71,551
• Cost: $0.0268
• Avg Latency: 8,421ms

Run ID

23d2e0e9-3540-4a1c-880f-97e068a7965c