Protein Family Classification with Multi-Layer Graph Convolutional Networks

Da Zhang; Mansur R. Kabuka

doi:10.1109/BIBM.2018.8621520

Protein Family Classification with Multi-Layer Graph Convolutional Networks

Da Zhang, Mansur R. Kabuka

Electrical and Computer Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Next-generation sequencing techniques provide us with an opportunity for generating sequenced proteins and identifying the biological families and functions of the proteins. However, compared with identified proteins, uncharacterized proteins consist of a notable percentage of the predicted proteins in bioinformatics research field. However, previous clustering based algorithms heavily relying on large data samples are not accurate enough to assign protein families given a small amount of family annotated proteins. Therefore, considering limited protein data with annotated protein families, a more accurate and faster protein family prediction method is required. In this paper, we apply the Multi-layer Graph Convolutional Networks (GCN) architecture on a Protein-Protein Interaction (PPI) network with limited characterized proteins to explore the performance of protein family classification by taking into account both of the network topology and physicochemical protein amino acid features.

Original language	English (US)
Title of host publication	Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Editors	Harald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	2390-2393
Number of pages	4
ISBN (Electronic)	9781538654880
DOIs	https://doi.org/10.1109/BIBM.2018.8621520
State	Published - Jan 21 2019
Event	2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain Duration: Dec 3 2018 → Dec 6 2018

Publication series

Name	Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference	2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Country	Spain
City	Madrid
Period	12/3/18 → 12/6/18

Fingerprint

Keywords

Graph Convolutional Networks
Protein Family Classification
Protein-Protein Interaction Network

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics

Cite this

Zhang, D., & Kabuka, M. R. (2019). Protein Family Classification with Multi-Layer Graph Convolutional Networks. In H. Schmidt, D. Griol, H. Wang, J. Baumbach, H. Zheng, Z. Callejas, X. Hu, J. Dickerson, & L. Zhang (Eds.), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 (pp. 2390-2393). [8621520] (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2018.8621520

Protein Family Classification with Multi-Layer Graph Convolutional Networks. / Zhang, Da; Kabuka, Mansur R.

Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. ed. / Harald Schmidt; David Griol; Haiying Wang; Jan Baumbach; Huiru Zheng; Zoraida Callejas; Xiaohua Hu; Julie Dickerson; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. p. 2390-2393 8621520 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Zhang, D & Kabuka, MR 2019, Protein Family Classification with Multi-Layer Graph Convolutional Networks. in H Schmidt, D Griol, H Wang, J Baumbach, H Zheng, Z Callejas, X Hu, J Dickerson & L Zhang (eds), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018., 8621520, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Institute of Electrical and Electronics Engineers Inc., pp. 2390-2393, 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, 12/3/18. https://doi.org/10.1109/BIBM.2018.8621520

Zhang D, Kabuka MR. Protein Family Classification with Multi-Layer Graph Convolutional Networks. In Schmidt H, Griol D, Wang H, Baumbach J, Zheng H, Callejas Z, Hu X, Dickerson J, Zhang L, editors, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Institute of Electrical and Electronics Engineers Inc. 2019. p. 2390-2393. 8621520. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). https://doi.org/10.1109/BIBM.2018.8621520

Zhang, Da ; Kabuka, Mansur R. / Protein Family Classification with Multi-Layer Graph Convolutional Networks. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. editor / Harald Schmidt ; David Griol ; Haiying Wang ; Jan Baumbach ; Huiru Zheng ; Zoraida Callejas ; Xiaohua Hu ; Julie Dickerson ; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 2390-2393 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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Access to Document

10.1109/BIBM.2018.8621520