OAEI Bio-ML 2026

Baselines

Organiser-run baseline systems for all three competitions, published before the evaluation window. These are organiser baselines — participant submissions are not added to these tables. Participant results live on the CodaBench leaderboards and appear on the results page once the window opens (12 July 2026).

Track 1 · Subtrack 1 — global equivalence alignment

Repaired coherence-aware P/R/F1

Macro-averaged over the three pairs (NCIT–DOID, SNOMED–FMA, SNOMED–NCIT); sorted by the headline column. See evaluation metrics.

System F1 (repaired)F1 (standard)P (repaired)R (repaired)
LogMapLt 0.625 0.625 0.628 0.635
AML 0.535 0.579 0.451 0.766
LogMap 0.523 0.533 0.392 0.803
BERTMap 0.516 0.472 0.821 0.401
BERTMapLt 0.508 0.474 0.785 0.403
Naive-Lexical 0.161 0.150 0.424 0.126

Track 1 · Subtrack 2 — local equivalence ranking

MRR and Hits@k

Macro-averaged over the three pairs (NCIT–DOID, SNOMED–FMA, SNOMED–NCIT); sorted by the headline column. See evaluation metrics.

System MRRHits@1Hits@5Hits@10
Naive-Lexical 0.731 0.656 0.814 0.863
SapBERT 0.716 0.638 0.809 0.850
BERTMapLt 0.583 0.524 0.636 0.692
BERTMap-ss 0.496 0.463 0.510 0.539
BERTMap 0.445 0.421 0.447 0.470

Track 2 — mixed equivalence + subsumption typed ranking

Preferred Typed-MRR and Hierarchy-aware Typed-nDCG@10

Macro-averaged over the three pairs (NCIT–DOID, SNOMED–FMA, SNOMED–NCIT); sorted by the headline column. See evaluation metrics.

System Typed-MRRTyped-nDCG@10Typed-Hits@1
Naive-Lexical 0.401 0.363 0.340
SapBERT 0.383 0.346 0.334
BERTMapLt 0.308 0.267 0.272
BERTMap-ss 0.274 0.235 0.241
BERTMap 0.241 0.209 0.221

About these baselines

Organiser baselines (macro over the three pairs). Global = semi-supervised test-slice (option a): repaired coherence-aware F1 headline. Participant results appear on the CodaBench leaderboards. The global-alignment headline is the repaired coherence-aware F1 (the standard F1 is shown alongside); local ranking is headlined by MRR; typed ranking by preferred Typed-MRR. Full data: leaderboard.json. Participant results appear on the results page, fed by the CodaBench leaderboards.

Editions

Baselines and results by edition

OAEI Bio-ML 2026 is the current edition. As the track matures, each edition's final baselines and participant results will be archived here, and changes between editions are recorded in the changelog.

EditionStatusBaselinesMachine-readable snapshot
2026 current — evaluation & leaderboard open 12 July 2026 this page leaderboard.json