LLM-Assisted Functional Gene Annotation

Boyce, C.; Pereira, C.; Kim, G. D.; Petti, A. A.

doi:10.1101/2025.08.06.668957

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bioRxiv · 10.1101/2025.08.06.668957

LLM-Assisted Functional Gene Annotation

Boyce, C.·Pereira, C.·Kim, G. D.·Petti, A. A.

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Abstract

Functional gene annotation is a highly manual and subjective process that requires analysis of large amounts of statistical and literature results. Here we present Artificial Intelligence Gene Enrichment (AIGE), a careful automation of the current state of the art process used by bioinformatic experts to deter-mine functions enriched in novel or experimentally derived gene lists. In 1206 test cases, AIGE is able to accurately recover 87% of biological functions, path-ways, and cell types, is robust to noise contamination, and accurately assesses its own self-confidence. AIGE reports provide accurate functional annotations and encourage further research in a broad set of contexts.

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Boyce, C., Pereira, C., Kim, G. D., Petti, A. A.. 2025-08-09. LLM-Assisted Functional Gene Annotation. https://doi.org/10.1101/2025.08.06.668957

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