2024/09/15 by Yanjun Lyu, Lyu, Yanjun, Zihao Wu +24 · 4 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · #Artificial Intelligence (cs.AI) #Biomedical Text Mining and Ontologies #Computation and Language (cs.CL) #FOS: Computer and information sciences #Genetics, Bioinformatics, and Biomedical Research #Machine Learning in Healthcare
paper · pdf · doi:10.48550/arxiv.2409.09825
openalex publication_date 2024/09/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.