GP-GPT: Large Language Model for Gene-Phenotype Mapping

TL;DR

GP-GPT is a specialized large language model designed for gene-phenotype mapping, demonstrating superior performance in genomics relation analysis and information retrieval compared to general LLMs.

Contribution

The paper introduces GP-GPT, the first LLM tailored for genetic-phenotype knowledge, trained on extensive genomics data, and outperforming existing models in domain-specific tasks.

Findings

GP-GPT outperforms Llama2, Llama3, and GPT-4 in genomics tasks.

It accurately retrieves medical genetics information.

Subtle bio-factor entity representations suggest new research opportunities.

Abstract

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.