LLM-powered Functional Gene Set Summarization with genesetGPT

Abstract

Transcriptomics datasets generated using next-generation sequencing techniques such as single cell RNA-sequencing (scRNA-seq) and spatially-resolved transcriptomics (SRT) allow researchers to study patterns in gene expression across celltypes, temporal processes, and spatial organization at ever-higher resolutions and depths. scRNA-seq analyses produce gene expression profiles and celltype-specific gene sets that require annotation to provide biological meaning, a process that has traditionally relied on the manual interpretations of clinical scientists. Similarly, SRT experiments typically require subjective, time-consuming annotation of spatial domains. Recent advances in large language model (LLM) methods offer opportunities to assist in the interpretation of such datasets. Many current LLM-based approaches aim to annotate transcriptomics-derived gene sets by integrating information from publicly available and online biological resources. While these approaches can be effective, they often struggle when presented with weakly-related or fully uncorrelated genes, sometimes inferring and justifying biological relationships that are not supported by existing literature. Additionally, the quality of LLM-generated interpretations is dependent on the provision of appropriate biological context and careful prompt design, both of which can present significant barriers to effective use. To address these limitations we propose genesetGPT, an efficient, LLM-based framework that emphasizes both curated biological context and iterative prompt construction, thus enabling realistic summarization of heterogeneous gene sets at scale. genesetGPT is implemented as an open-source Python package available for download at https://github.com/jr-leary7/genesetGPT.