A comprehensive survey of genome language models in bioinformatics

Large language models have revolutionized natural language processing by effectively modeling complex semantics and capturing long-range contextual relationships. Inspired by these advancements, genome language models (gLMs) have recently emerged, conceptualizing DNA and RNA sequences as biological texts and enabling the identification of intricate genomic grammar and distant regulatory interactions. This review examines the need for gLMs, emphasizing their capacity to overcome the limitations of traditional deep learning approaches in genomic sequence characterization. We comprehensively survey contemporary gLM architectures, including Transformer models, Hyena convolutions, and state space models, as well as various sequence tokenization strategies, assessing their applicability, and effectiveness across diverse genomic applications. Additionally, we discuss foundational pretraining strategies and provide an overview of genomic pretraining datasets spanning multiple species and functional domains. We critically analyze evaluation methodologies, including supervised, zero-shot, and few-shot learning paradigms, as well as fine-tuning approaches. An extensive taxonomy of downstream tasks is presented, alongside a summary of existing benchmarks and emerging trends. Finally, we contemplate key challenges such as data scarcity, interpretability, and the computational demands of genomic modeling, and propose a roadmap to guide future advances in genome language modeling.