GEO-BERT: A Retrieval augmented LLM Framework for Intelligent Dataset Retrieval from the Gene Expression Omnibus
Journal:
bioRxiv
Published Date:
Oct 21, 2026
Abstract
The Gene Expression Omnibus (GEO) is a commonly used data repository of high throughput gene expression and other functional genomics data. This platform is globally used by researchers for submitting experimental datasets, accessing these datasets for hypothesis validation, reusing them in data-driven research, generating ideas for new research directions. Despite global usage, searching and identifying relevant and usable datasets in GEO remains challenging with an underlying keyword based search system needing manual intervention for the retrieval of desired datasets. GEO's inconsistent metadata and varying data annotation practices across submissions, variable data quality are contributing to its challenge for building structured query tools. With the recent advancement of Large Language Models (LLMs), it is timely to revisit the GEO datasets and its query system. Here, we present an AI chat-bot, GEO-BERT, leveraging an underlying retrieval augmented generator framework on the GEO metadata with a novel hierarchical hybrid field aware retrieval system to mine the datasets. GEO-BERT is locally installable, available for programmers and project developers (https://github.com/mrumi/GEOBERTtest) and readily usable by regular users on subset of test data. We demonstrated that GEO-BERT enhances the semantic search performance not currently available by any of the leading existing AI-powered chatbots, while improving the performance of GEO's traditional search performance for project development. Given the global usage of GEO and the latest advancement of the large language models, GEO-BERT fills the gap for context-aware extraction of GEO datasets.
