Predicting Failures of LLMs to Link Biomedical Ontology Terms to Identifiers Evidence Across Models and Ontologies
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arXiv
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| Autores principales: | , , |
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| Formato: | Preprint |
| Publicado: |
2025
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| _version_ | 1866909981940383744 |
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| author | Hier, Daniel B. Platt, Steven Keith Obafemi-Ajayi, Tayo |
| author_facet | Hier, Daniel B. Platt, Steven Keith Obafemi-Ajayi, Tayo |
| contents | Large language models often perform well on biomedical NLP tasks but may fail to link ontology terms to their correct identifiers. We investigate why these failures occur by analyzing predictions across two major ontologies, Human Phenotype Ontology and Gene Ontology, and two high-performing models, GPT-4o and LLaMa 3.1 405B. We evaluate nine candidate features related to term familiarity, identifier usage, morphology, and ontology structure. Univariate and multivariate analyses show that exposure to ontology identifiers is the strongest predictor of linking success. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_04458 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Predicting Failures of LLMs to Link Biomedical Ontology Terms to Identifiers Evidence Across Models and Ontologies Hier, Daniel B. Platt, Steven Keith Obafemi-Ajayi, Tayo Computation and Language I.2 Large language models often perform well on biomedical NLP tasks but may fail to link ontology terms to their correct identifiers. We investigate why these failures occur by analyzing predictions across two major ontologies, Human Phenotype Ontology and Gene Ontology, and two high-performing models, GPT-4o and LLaMa 3.1 405B. We evaluate nine candidate features related to term familiarity, identifier usage, morphology, and ontology structure. Univariate and multivariate analyses show that exposure to ontology identifiers is the strongest predictor of linking success. |
| title | Predicting Failures of LLMs to Link Biomedical Ontology Terms to Identifiers Evidence Across Models and Ontologies |
| topic | Computation and Language I.2 |
| url | https://arxiv.org/abs/2509.04458 |