Adversarial Contrastive Pre-training for Protein Sequences

Matthew B. A. McDermott, Brendan Yap, Tzu-Ming Harry Hsu, Di Jin, Peter Szolovits

Abstract: Recent developments in Natural Language Processing (NLP) demonstrate that large-scale, self-supervised pre-training can be extremely beneficial for downstream tasks. These ideas have been adapted to other domains, including the analysis of the amino acid sequences of proteins. However, to date most attempts on protein sequences rely on direct masked language model style pre-training. In this work, we design a new, adversarial pre-training method for proteins, extending and specializing similar advances in NLP. We show compelling results in comparison to traditional MLM pre-training, though further development is needed to ensure the gains are worth the significant computational cost.