Adaptive Residue-wise Profile Fusion for Low Homologous Protein Secondary Structure Prediction Using External Knowledge

Adaptive Residue-wise Profile Fusion for Low Homologous Protein Secondary Structure Prediction Using External Knowledge

Qin Wang, Jun Wei, Boyuan Wang, Zhen Li, Sheng Wang, Shuguang Cui

Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence
Main Track. Pages 3559-3565. https://doi.org/10.24963/ijcai.2021/490

Protein secondary structure prediction (PSSP) is essential for protein function analysis. However, for low homologous proteins, the PSSP suffers from insufficient input features. In this paper, we explicitly import external self-supervised knowledge for low homologous PSSP under the guidance of residue-wise (amino acid wise) profile fusion. In practice, we firstly demonstrate the superiority of profile over Position-Specific Scoring Matrix (PSSM) for low homologous PSSP. Based on this observation, we introduce the novel self-supervised BERT features as the pseudo profile, which implicitly involves the residue distribution in all native discovered sequences as the complementary features. Furthermore, a novel residue-wise attention is specially designed to adaptively fuse different features (i.e., original low-quality profile, BERT based pseudo profile), which not only takes full advantage of each feature but also avoids noise disturbance. Besides, the feature consistency loss is proposed to accelerate the model learning from multiple semantic levels. Extensive experiments confirm that our method outperforms state-of-the-arts (i.e., 4.7% for extremely low homologous cases on BC40 dataset).
Keywords:
Machine Learning Applications: Bio/Medicine
Natural Language Processing: NLP Applications and Tools