An Interpretable Double-Scale Attention Model for Enzyme Protein Class Prediction Based on Transformer Encoders and Multi-Scale Convolutions

Abstract

Background Classification and annotation of enzyme proteins are fundamental for enzyme research on biological metabolism. Enzyme Commission (EC) numbers provide a standard for hierarchical enzyme class prediction, on which several computational methods have been proposed. However, most of these methods are dependent on prior distribution information and none explicitly quantifies amino-acid-level relations and possible contribution of sub-sequences. Methods In this study, we propose a double-scale attention enzyme class prediction model named DAttProt with high reusability and interpretability. DAttProt encodes sequence by self-supervised Transformer encoders in pre-training and gathers local features by multi-scale convolutions in fine-tuning. Specially, a probabilistic double-scale attention weight matrix is designed to aggregate multi-scale features and positional prediction scores. Finally, a full connection linear classifier conducts a final inference through the aggregated features and prediction scores. Results On DEEPre and ECPred datasets, DAttProt performs as competitive with the compared methods on level 0 and outperforms them on deeper task levels, reaching 0.788 accuracy on level 2 of DEEPre and 0.967 macro-F ₁ on level 1 of ECPred. Moreover, through case study, we demonstrate that the double-scale attention matrix learns to discover and focus on the positions and scales of bio-functional sub-sequences in the protein. Conclusion Our DAttProt provides an effective and interpretable method for enzyme class prediction. It can predict enzyme protein classes accurately and furthermore discover enzymatic functional sub-sequences such as protein motifs from both positional and spatial scales.

Keywords: double-scale attention; enzyme class prediction; feature agreement; multi-scale convolutions; self-attention.