A survey on large language models in biology and chemistry
Abstract
Artificial intelligence (AI) is reshaping biomedical research by providing scalable computational frameworks suited to the complexity of biological systems. Central to this revolution are bio/chemical language models, including large language models, which are reconceptualizing molecular structures as a form of 'language' amenable to advanced computational techniques. Here we critically examine the role of these models in biology and chemistry, tracing their evolution from molecular representation to molecular generation and optimization. This review covers key molecular representation strategies for both biological macromolecules and small organic compounds-ranging from protein and nucleotide sequences to single-cell data, string-based chemical formats, graph-based encodings and three-dimensional point clouds-highlighting their respective advantages and inherent limitations in AI applications. The discussion further explores core model architectures, such as bidirectional encoder representations from transformers-like encoders, generative pretrained transformer-like decoders and encoder-decoder transformers, alongside their sophisticated pretraining strategies such as self-supervised learning, multitask learning and retrieval-augmented generation. Key biomedical applications, spanning protein structure and function prediction, de novo protein design, genomic analysis, molecular property prediction, de novo molecular design, reaction prediction and retrosynthesis, are…
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