LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology

LLMBDC is a training-free framework that leverages large language models to organize Gene Ontology terms into interpretable biological domains via zero-shot semantic reasoning with confidence scoring. Evaluated on Alzheimer’s disease and Fragile X syndrome datasets, LLMBDC substantially outperformed six existing GO clustering approaches on standard clustering metrics while maintaining biological specificity. The paper was accepted at the 25th International Workshop on Data Mining in Bioinformatics (BIOKDD’26), held in conjunction with KDD 2026.

Recommended citation: Ran X., Xu J., Jin P., Qin Z., Wen Z., & Lu J. (2026). "LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology." arXiv:2608.00099.
Download Paper