Author

Hongyi Yu

Yale UniversityORCID 0009-0004-9884-4400Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:large language model· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Research Focus:spatial domain detection· 1 Assay:spatial transcriptomics· 1 Approach:statistical model· 1

Frequent Co-Authors

Alexandra PopaiD· 1 shared Huanhuan WeiiD· 1 shared Inessa CoheniD· 1 shared J Liang· 1 shared Lixing LiniD· 1 shared Luning Yang· 1 shared Maor SauleriD· 1 shared Naftali KaminskiiD· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperBioinformatics

Alexandra PopaORCID

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintJun 26, 2026

SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics

Huanhuan Wei, Xiao Luo, Hongyi Yu…·Xiting Yan

SPEAK identifies spatial domains in spatial transcriptomics data using a large language model and expert-aligned prompts, showing improved accuracy and interpretability.

DOI 10.64898/2026.06.22.733750

spatial transcriptomicslarge language model

𝕏 PostBluesky

NeurosciencebioRxivPreprintApr 27, 2026

All Models are Wrong, Some are Annotated: Automating Metadata in Biomedical Repositories

Inessa Cohen, Hongyi Yu, Robert A. McDougal

This paper evaluates using large language models to infer ion channel and receptor subtype metadata from neuroscience model code, finding LLMs outperform feature-engineered models.

DOI 10.64898/2026.04.23.720371

large language modelstatistical model

𝕏 PostBluesky