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

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

doi:10.24963/ijcai.2021/490

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

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Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence. Main Track. Pages 3559-3565.

https://doi.org/10.24963/ijcai.2021/490

Keywords

Machine Learning Applications: Bio/Medicine
Natural Language Processing: NLP Applications and Tools

Abstract

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).

Qin Wang, Jun Wei, Boyuan Wang, Zhen Li, Sheng Wang, and Shuguang Cui. 2021. Adaptive Residue-wise Profile Fusion for Low Homologous Protein Secondary Structure Prediction Using External Knowledge. In Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, IJCAI-21. IJCAI, 3559–3565. https://doi.org/10.24963/ijcai.2021/490

@inproceedings{ijcai2021p490,
  title     = {Adaptive Residue-wise Profile Fusion for Low Homologous Protein Secondary Structure Prediction Using External Knowledge},
  author    = {Wang, Qin and Wei, Jun and Wang, Boyuan and Li, Zhen and Wang, Sheng and Cui, Shuguang},
  booktitle = {Proceedings of the Thirtieth International Joint Conference on
               Artificial Intelligence, {IJCAI-21}},
  publisher = {International Joint Conferences on Artificial Intelligence Organization},
  editor    = {Prof. Zhi-Hua Zhou},
  pages     = {3559--3565},
  year      = {2021},
  month     = {8},
  note      = {Main Track},
  doi       = {10.24963/ijcai.2021/490},
  url       = {https://doi.org/10.24963/ijcai.2021/490},
}

TY  - CPAPER
TI  - Adaptive Residue-wise Profile Fusion for Low Homologous Protein Secondary Structure Prediction Using External Knowledge
AU  - Wang, Qin
AU  - Wei, Jun
AU  - Wang, Boyuan
AU  - Li, Zhen
AU  - Wang, Sheng
AU  - Cui, Shuguang
T2  - Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, IJCAI-21
PB  - International Joint Conferences on Artificial Intelligence Organization
PY  - 2021
SP  - 3559
EP  - 3565
DO  - 10.24963/ijcai.2021/490
UR  - https://doi.org/10.24963/ijcai.2021/490
ER  -