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test(benchmark): expand biological benchmark suite to 100 validated cases - #13

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engkinandatama merged 3 commits into
CORE-Lab-Research:mainfrom
engkinandatama:test/benchmark-100-cases
Sep 28, 2026
Merged

engkinandatama merged 3 commits into
CORE-Lab-Research:mainfrom
engkinandatama:test/benchmark-100-cases

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Description

This PR expands the biological benchmark test suite in tests/test_benchmark.py to 100 curated test cases, completing the Phase 1 milestone.

Benchmark Coverage (100 Cases)

  • 1–15 & 51–65: Well-known human cancer, metabolism, and signaling genes (approved symbols).
  • 16–25 & 66–75: Clinical aliases, historical names, and surface markers (HER2, p53, MLL, OCT4, p27Kip1, Bcl-xL, PD-1, PD-L1, CTLA-4, TNF-alpha, CD20, etc.).
  • 26–33 & 76–85: NCBI Entrez Gene ID queries across key oncogenes and tumor suppressors.
  • 34–41 & 86–92: UniProtKB accession lookups.
  • 42–50 & 93–100: Model organism (Mus musculus, taxon 10090) cross-species queries covering official symbols, Entrez Gene IDs, and MGI accession IDs.

Validation Results

  • Benchmark Suite: 100 passed in 384.15s (100% accuracy, exceeding the target KPI of $\ge 95%$).
  • Full Unit Test Suite: 30 passed, 5 skipped (due to external Ensembl rate-limits) in 52.68s.

@engkinandatama
engkinandatama merged commit f4e5b31 into CORE-Lab-Research:main Sep 28, 2026
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