Paper · arXiv 2307.05628
DNAGPT: A Generalized Pre-trained Tool for Versatile DNA Sequence Analysis Tasks
Daoan Zhang, Weitong Zhang, Bing He, Jianguo Zhang, Chenchen Qin, Jianhua Yao
DNAGPT is a generalized pre-trained model for DNA analysis that excels in various tasks through enhanced GPT architecture and diverse training objectives.
Abstract
Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.