Enhanced Viral Genome Classification Using Large Language Models

Abstract

The classification of genomic sequences is a crucial area of research in the field of virology. This is due to the increasing number of outbreaks we have faced in recent times. We have a vast repository of genomic sequences from various species, including humans, animals, plants, bacteria, and viruses, which tend to mutate and form new variants or strains. In the realm of machine learning, several models are employed for genome sequence classification. Among these are traditional algorithms such as Random Forest (RF), K-nearest neighbors (KNNs), Decision Tree (DT), and Naive Bayes (NB), each offering unique advantages in handling genetic data. Additionally, deep learning models like Convolutional Neural Networks (CNNs), Long Short-Term Memory (LSTM) networks, and Bi-Directional LSTM networks are utilized for their robust capabilities in capturing complex patterns and dependencies within genomic sequences. In this study, we explored the application of Natural Language Processing (NLP) techniques to classify the genomic sequences. The focus of our research involves utilizing advanced large language models (LLMs) such as DNABERT, DNAGPT, and GENA LM, which are fine-tuned explicitly on the language of DNA. In this research, after a detailed analysis, we found that DNAGPT achieved an accuracy of 96%, which exceeds the performance of state-of-the-art machine learning and deep learning models.