Reflections on the use of LLMs for cell annotation.

Abstract

This letter comments on the recently published AICellType platform for large language model (LLM)-based cell type annotation in single-cell and spatial transcriptomics. While appreciating the authors' systematic benchmarking and practical contribution, concerns are raised regarding the continued dependence on proprietary commercial LLMs such as Claude 3.5 Sonnet for biomedical annotation. Greater emphasis is suggested on open-source biomedical LLMs, multimodal vision-language models, local deployment, reproducibility, privacy preservation, and regulatory compliance to ensure more transparent, reliable, and sustainable medical annotation systems for translational bioinformatics.