SoftGene: Protein Language Model-Enhanced Soft Prompting for Interpretable Gene Set Annotation

arXiv:2610.03029v1 Announce Type: new Abstract: Gene set analysis is a cornerstone of functional genomics, yet it remains labor-intensive and heavily dependent on manual curation and expert biological interpretation. While Large Language Models (LLMs) have emerged as powerful tools for genomic reasoning and annotation, most existing approaches rely on symbolic gene names and fail to capture domain-specific biological structure, particularly protein sequence information that governs molecular activity, interactions, and downstream gene function. In this work, we propose SoftGene, a novel framew

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