Deep Learning in Anatomy Ontology Matching: The VIEWAnatomy-DL System at OAEI 2026

This paper presents VIEWAnatomy-DL, an interactive ontology alignment system evaluated in the Anatomy track of OAEI 2026. The system combines lexical similarities, K-Means, Sentence-BERT em-beddings loaded via the Deep Java Library (DJL), a hybrid candidate generator, an SBERT-aware clustering threshold, a global bidirectional 1:1 filter and a final similarity floor. It reaches precision 0.9509, recall 0.7672 and F-measure 0.8492 (1,223 correspondences). Among the 14 official systems plus VIEWAnatomy-DL (15 entries), it ranks 7th in precision and 11th in F-measure. The comparison shows that generic SBERT embeddings are an effective low-cost step into deep learning, while domain-specific knowledge (SapBERT, UMLS) and LLM oracles remain the key differentiators of top systems. A roadmap targeting F-measure in the 0.955-0.960 range for OAEI 2027 is proposed.

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Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-10-26
DOI
https://doi.org/10.5281/zenodo.23675839
Primary Topic
Biomedical Text Mining and Ontologies
Type
preprint
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preprint

Deep Learning in Anatomy Ontology Matching: The VIEWAnatomy-DL System at OAEI 2026

Roberto Monteiro Dias
Zenodo (CERN European Organization for Nuclear Research)
Biomedical Text Mining and Ontologies
preprint

Deep Learning in Anatomy Ontology Matching: The VIEWAnatomy-DL System at OAEI 2026

Roberto Monteiro Dias
preprint en

Abstract

This paper presents VIEWAnatomy-DL, an interactive ontology alignment system evaluated in the Anatomy track of OAEI 2026. The system combines lexical similarities, K-Means, Sentence-BERT em-beddings loaded via the Deep Java Library (DJL), a hybrid candidate generator, an SBERT-aware clustering threshold, a global bidirectional 1:1 filter and a final similarity floor. It reaches precision 0.9509, recall 0.7672 and F-measure 0.8492 (1,223 correspondences). Among the 14 official systems plus VIEWAnatomy-DL (15 entries), it ranks 7th in precision and 11th in F-measure. The comparison shows that generic SBERT embeddings are an effective low-cost step into deep learning, while domain-specific knowledge (SapBERT, UMLS) and LLM oracles remain the key differentiators of top systems. A roadmap targeting F-measure in the 0.955-0.960 range for OAEI 2027 is proposed.

Zenodo (CERN European Organization for Nuclear Research)
Universidade Federal do Estado do Rio de Janeiro (BR)
Biomedical Text Mining and Ontologies
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Deep Learning in Anatomy Ontology Matching: The VIEWAnatomy-DL System at OAEI 2026 — Roberto Monteiro Dias · Zenodo (CERN European Organization for Nuclear Research) (2026) | TGRS Research Map | TGRS