Motivation: Bridging the exponentially growing gap between the number of unlabeled and labeled proteins, a couple of works have adopted semi-supervised learning for protein sequence modeling. They pre-train a model with a substantial amount of unlabeled data and transfer the learned representations to various downstream tasks. Nonetheless, the current pre-training methods mostly rely on a language modeling task and often show limited performances. Therefore, a complementary protein-specific task for pre-training is necessary to better capture the information contained within unlabeled protein sequences. Results: In this paper, we introduce a novel pre-training scheme called PLUS, which stands for Protein sequence representations Learned Using Structural information. PLUS consists of masked language modeling and a complementary protein-specific pre-training task, namely same family prediction. PLUS can be used to pre-train various model architectures. In this work, we mainly use PLUS to pre-train a recurrent neural network (RNN) and refer to the resulting model as PLUS-RNN. It advances state-of-the-art pre-training methods on six out of seven tasks, i.e., (1) three protein(-pair)-level classification, (2) two protein-level regression, and (3) two amino-acid-level classification tasks. Furthermore, we present results from our ablation studies and interpretation analyses to better understand the strengths of PLUS-RNN. Availability: The codes and pre-trained models are available at https://github.com/mswzeus/PLUS/
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