Training self-supervised peptide sequence models on artificially chopped proteins

Abstract: Representation learning for proteins has primarily focused on the global understanding of protein sequences regardless of their length. However, shorter proteins (known as peptides) take on distinct structures and functions compared to their longer counterparts. Unfortunately, there are not as many naturally occurring peptides available to be sequenced and therefore less peptide-specific data to train with. In this paper, we propose a new peptide data augmentation scheme, where we train peptide LLMs on artificially constructed peptides that are small contiguous subsets of longer, wild-type proteins; we refer to the training peptides as "chopped proteins". We evaluate the representation potential of models trained with chopped proteins versus natural peptides and find that training LLMs with chopped proteins results in more generalized embeddings for short protein sequences. These peptide-specific models also retain information about the original protein they were derived from better than LLMs trained on full-length proteins. We compare masked LLM training objectives to three novel peptide-specific training objectives: next-peptide prediction, contrastive peptide selection and evolution-weighted MLM. We demonstrate improved zero-shot learning performance for a deep mutational scan peptides benchmark.