Advancing bioinformatics with language models: components, applications, and perspectives.

Authors

Jiajia Liu, Mengyuan Yang, Yankai Yu, Haixia Xu, Tiangang Wang, Kang Li, Xiaobo Zhou

Published in

Briefings in bioinformatics. Volume 27. Issue 4. Jul 03, 2026.

Abstract

Large language models (LLMs) are deep learning-based artificial intelligence models that have achieved remarkable success in natural language processing. Typically composed of neural networks with billions of parameters, they are trained on massive unlabeled datasets using self-supervised or semi-supervised learning. Beyond language, LLMs hold immense potential for addressing complex bioinformatics challenges. This review provides a comprehensive overview of transformer-based model applications in genomics, transcriptomics, proteomics, drug discovery, and single-cell analysis. We discuss critical components, including tokenization strategies for diverse biological data, transformer architectures, attention mechanisms, and pretraining approaches. We also survey currently available foundation models and their downstream applications across bioinformatics domains. Finally, we highlight major challenges that remain insufficiently addressed in prior reviews and outline future perspectives and design principles for next-generation biological language models, offering practical guidance for both users and developers.

PMID:
42430786
Bibliographic data and abstract were imported from PubMed on 11 Jul 2026.

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