Prot2Token: A multi-task framework for protein language processing using autoregressive language modeling

This paper proposes a versatile tokenization method and introduces Prot2Token, a model that combines autoregressive language modeling with protein language models (PLMs) to tackle various protein prediction tasks using protein sequences. Leveraging our tokenization method, Prot2Token adapts existing PLMs for multiple tasks such as protein-level prediction, residue-level prediction, and protein-protein interaction prediction through next-token prediction of tokenized target label sequences. By incorporating prompt tokens into the decoder, Prot2Token enables multi-task training in a single end-to-end session. Our results demonstrate that Prot2Token not only matches the performance of specialized models across various tasks but also paves the way for integrating protein tasks with large language models (LLMs), representing an important step towards creating general-purpose PLMs for advanced protein language processing (PLP). Additionally, we use Prot2Token to develop S-ESM, a structure-aware version of the ESM model, which achieves competitive performance with state-of-the-art methods in 3D structure-related tasks using only protein sequences.