Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization

Thanh Son Do; Daniel B. Hier; Tayo Obafemi-Ajayi

doi:10.1109/CIBCB66090.2025.11177118

Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization

Electrical and Computer Engineering

Missouri State University

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Original language	English
Title of host publication	2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9798331502669
DOIs	https://doi.org/10.1109/CIBCB66090.2025.11177118
State	Published - 2025
Event	2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025 - Tainan, Taiwan, Province of China Duration: Aug 20 2025 → Aug 22 2025

Publication series

Name	2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025

Conference

Conference	2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025
Country/Territory	Taiwan, Province of China
City	Tainan
Period	8/20/25 → 8/22/25

ASJC Scopus Subject Areas

Artificial Intelligence
Information Systems
Information Systems and Management
Computational Mathematics
Health Informatics

Keywords

BioBERT
cosine similarity
Gene Ontology
Human Phenotype Ontology
large language models
normalization
ontology identifiers
Ontology mapping

Access to Document

10.1109/CIBCB66090.2025.11177118

Cite this

Do, T. S., Hier, D. B., & Obafemi-Ajayi, T. (2025). Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization. In 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025 (2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CIBCB66090.2025.11177118

Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization. / Do, Thanh Son; Hier, Daniel B.; Obafemi-Ajayi, Tayo.
2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025. Institute of Electrical and Electronics Engineers Inc., 2025. (2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Do, TS, Hier, DB & Obafemi-Ajayi, T 2025, Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization. in 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025. 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025, Institute of Electrical and Electronics Engineers Inc., 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025, Tainan, Taiwan, Province of China, 8/20/25. https://doi.org/10.1109/CIBCB66090.2025.11177118

Do TS, Hier DB , Obafemi-Ajayi T. Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization. In 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025. Institute of Electrical and Electronics Engineers Inc. 2025. (2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025). doi: 10.1109/CIBCB66090.2025.11177118

Do, Thanh Son ; Hier, Daniel B. ; Obafemi-Ajayi, Tayo. / Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization. 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025. Institute of Electrical and Electronics Engineers Inc., 2025. (2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025).

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title = "Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization",

keywords = "BioBERT, cosine similarity, Gene Ontology, Human Phenotype Ontology, large language models, normalization, ontology identifiers, Ontology mapping",

author = "Do, \{Thanh Son\} and Hier, \{Daniel B.\} and Tayo Obafemi-Ajayi",

note = "Publisher Copyright: {\textcopyright} 2025 IEEE.; 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025 ; Conference date: 20-08-2025 Through 22-08-2025",

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language = "English",

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KW - Gene Ontology

KW - Human Phenotype Ontology

KW - large language models

KW - normalization

KW - ontology identifiers

KW - Ontology mapping

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DO - 10.1109/CIBCB66090.2025.11177118

M3 - Conference contribution

AN - SCOPUS:105018912861

T3 - 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025

BT - 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2025

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ER -

Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization

Publication series

Conference

ASJC Scopus Subject Areas

Keywords

Access to Document

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