IDEAS home Printed from https://ideas.repec.org/a/gam/jftint/v13y2021i1p13-d476018.html
   My bibliography  Save this article

Knowledge-Graph-Based Drug Repositioning against COVID-19 by Graph Convolutional Network with Attention Mechanism

Author

Listed:
  • Mingxuan Che

    (Department of Information Engineering, Dalian University, Dalian 116622, China)

  • Kui Yao

    (Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, Dalian University, Dalian 116622, China)

  • Chao Che

    (Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, Dalian University, Dalian 116622, China)

  • Zhangwei Cao

    (Department of Software Engineering, Dalian University, Dalian 116622, China)

  • Fanchen Kong

    (Department of Software Engineering, Dalian University, Dalian 116622, China)

Abstract

The current global crisis caused by COVID-19 almost halted normal life in most parts of the world. Due to the long development cycle for new drugs, drug repositioning becomes an effective method of screening drugs for COVID-19. To find suitable drugs for COVID-19, we add COVID-19-related information into our medical knowledge graph and utilize a knowledge-graph-based drug repositioning method to screen potential therapeutic drugs for COVID-19. Specific steps are as follows. Firstly, the information about COVID-19 is collected from the latest published literature, and gene targets of COVID-19 are added to the knowledge graph. Then, the information of COVID-19 of the knowledge graph is extracted and a drug–disease interaction prediction model based on Graph Convolutional Network with Attention (Att-GCN) is established. Att-GCN is used to extract features from the knowledge graph and the prediction matrix reconstructed through matrix operation. We evaluate the model by predicting drugs for both ordinary diseases and COVID-19. The model can achieve area under curve (AUC) of 0.954 and area under the precise recall area curve (AUPR) of 0.851 for ordinary diseases. On the drug repositioning experiment for COVID-19, five drugs predicted by the models have proved effective in clinical treatment. The experimental results confirm that the model can predict drug–disease interaction effectively for both normal diseases and COVID-19.

Suggested Citation

  • Mingxuan Che & Kui Yao & Chao Che & Zhangwei Cao & Fanchen Kong, 2021. "Knowledge-Graph-Based Drug Repositioning against COVID-19 by Graph Convolutional Network with Attention Mechanism," Future Internet, MDPI, vol. 13(1), pages 1-10, January.
  • Handle: RePEc:gam:jftint:v:13:y:2021:i:1:p:13-:d:476018
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/1999-5903/13/1/13/pdf
    Download Restriction: no

    File URL: https://www.mdpi.com/1999-5903/13/1/13/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    1. Yong Liu & Min Wu & Chunyan Miao & Peilin Zhao & Xiao-Li Li, 2016. "Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction," PLOS Computational Biology, Public Library of Science, vol. 12(2), pages 1-26, February.
    2. Yunan Luo & Xinbin Zhao & Jingtian Zhou & Jinglin Yang & Yanqing Zhang & Wenhua Kuang & Jian Peng & Ligong Chen & Jianyang Zeng, 2017. "A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Francesco Piccialli & Vincenzo Schiano Cola & Fabio Giampaolo & Salvatore Cuomo, 2021. "The Role of Artificial Intelligence in Fighting the COVID-19 Pandemic," Information Systems Frontiers, Springer, vol. 23(6), pages 1467-1497, December.
    2. Jie Yu & Yaliu Li & Chenle Pan & Junwei Wang, 2021. "A Classification Method for Academic Resources Based on a Graph Attention Network," Future Internet, MDPI, vol. 13(3), pages 1-16, March.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Qing Ye & Chang-Yu Hsieh & Ziyi Yang & Yu Kang & Jiming Chen & Dongsheng Cao & Shibo He & Tingjun Hou, 2021. "A unified drug–target interaction prediction framework based on knowledge graph and recommendation system," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Benoit Playe & Chloé-Agathe Azencott & Véronique Stoven, 2018. "Efficient multi-task chemogenomics for drug specificity prediction," PLOS ONE, Public Library of Science, vol. 13(10), pages 1-34, October.
    3. Hansaim Lim & Aleksandar Poleksic & Yuan Yao & Hanghang Tong & Di He & Luke Zhuang & Patrick Meng & Lei Xie, 2016. "Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing," PLOS Computational Biology, Public Library of Science, vol. 12(10), pages 1-26, October.
    4. Yuxuan Wang & Ying Xia & Junchi Yan & Ye Yuan & Hong-Bin Shen & Xiaoyong Pan, 2023. "ZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Wen Zhang & Xiang Yue & Guifeng Tang & Wenjian Wu & Feng Huang & Xining Zhang, 2018. "SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions," PLOS Computational Biology, Public Library of Science, vol. 14(12), pages 1-21, December.
    6. Jiahua Rao & Jiancong Xie & Qianmu Yuan & Deqin Liu & Zhen Wang & Yutong Lu & Shuangjia Zheng & Yuedong Yang, 2024. "A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Xiaomin Liang & Daifeng Li & Min Song & Andrew Madden & Ying Ding & Yi Bu, 2019. "Predicting biomedical relationships using the knowledge and graph embedding cascade model," PLOS ONE, Public Library of Science, vol. 14(6), pages 1-23, June.
    8. Anna Cichonska & Balaguru Ravikumar & Elina Parri & Sanna Timonen & Tapio Pahikkala & Antti Airola & Krister Wennerberg & Juho Rousu & Tero Aittokallio, 2017. "Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors," PLOS Computational Biology, Public Library of Science, vol. 13(8), pages 1-28, August.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jftint:v:13:y:2021:i:1:p:13-:d:476018. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.