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Article

Biomedical Text Link Prediction for Drug Discovery: A Case Study with COVID-19

1
Laboratory for Pathology Dynamics, Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
2
Computer Science, Georgia Institute of Technology, Atlanta, GA 30332, USA
3
Computer Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
4
Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
5
Institute for Machine Learning, Georgia Institute of Technology, Atlanta, GA 30332, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Jakub Szlęk, Adam Pacławski and David Barlow
Pharmaceutics 2021, 13(6), 794; https://doi.org/10.3390/pharmaceutics13060794
Received: 8 April 2021 / Revised: 5 May 2021 / Accepted: 19 May 2021 / Published: 26 May 2021
(This article belongs to the Special Issue Computational Intelligence (CI) Tools in Drug Discovery and Design)
Link prediction in artificial intelligence is used to identify missing links or derive future relationships that can occur in complex networks. A link prediction model was developed using the complex heterogeneous biomedical knowledge graph, SemNet, to predict missing links in biomedical literature for drug discovery. A web application visualized knowledge graph embeddings and link prediction results using TransE, CompleX, and RotatE based methods. The link prediction model achieved up to 0.44 [email protected] on the entity prediction tasks. The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as COVID-19, served as a case study to demonstrate the efficacy of link prediction modeling for drug discovery. The link prediction algorithm guided identification and ranking of repurposed drug candidates for SARS-CoV-2 primarily by text mining biomedical literature from previous coronaviruses, including SARS and middle east respiratory syndrome (MERS). Repurposed drugs included potential primary SARS-CoV-2 treatment, adjunctive therapies, or therapeutics to treat side effects. The link prediction accuracy for nodes ranked highly for SARS coronavirus was 0.875 as calculated by human in the loop validation on existing COVID-19 specific data sets. Drug classes predicted as highly ranked include anti-inflammatory, nucleoside analogs, protease inhibitors, antimalarials, envelope proteins, and glycoproteins. Examples of highly ranked predicted links to SARS-CoV-2: human leukocyte interferon, recombinant interferon-gamma, cyclosporine, antiviral therapy, zidovudine, chloroquine, vaccination, methotrexate, artemisinin, alkaloids, glycyrrhizic acid, quinine, flavonoids, amprenavir, suramin, complement system proteins, fluoroquinolones, bone marrow transplantation, albuterol, ciprofloxacin, quinolone antibacterial agents, and hydroxymethylglutaryl-CoA reductase inhibitors. Approximately 40% of identified drugs were not previously connected to SARS, such as edetic acid or biotin. In summary, link prediction can effectively suggest repurposed drugs for emergent diseases. View Full-Text
Keywords: COVID-19; SARS-CoV-2; repurposed drugs; coronavirus; natural language processing; text mining; machine learning; literature review COVID-19; SARS-CoV-2; repurposed drugs; coronavirus; natural language processing; text mining; machine learning; literature review
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MDPI and ACS Style

McCoy, K.; Gudapati, S.; He, L.; Horlander, E.; Kartchner, D.; Kulkarni, S.; Mehra, N.; Prakash, J.; Thenot, H.; Vanga, S.V.; Wagner, A.; White, B.; Mitchell, C.S. Biomedical Text Link Prediction for Drug Discovery: A Case Study with COVID-19. Pharmaceutics 2021, 13, 794. https://doi.org/10.3390/pharmaceutics13060794

AMA Style

McCoy K, Gudapati S, He L, Horlander E, Kartchner D, Kulkarni S, Mehra N, Prakash J, Thenot H, Vanga SV, Wagner A, White B, Mitchell CS. Biomedical Text Link Prediction for Drug Discovery: A Case Study with COVID-19. Pharmaceutics. 2021; 13(6):794. https://doi.org/10.3390/pharmaceutics13060794

Chicago/Turabian Style

McCoy, Kevin, Sateesh Gudapati, Lawrence He, Elaina Horlander, David Kartchner, Soham Kulkarni, Nidhi Mehra, Jayant Prakash, Helena Thenot, Sri V. Vanga, Abigail Wagner, Brandon White, and Cassie S. Mitchell. 2021. "Biomedical Text Link Prediction for Drug Discovery: A Case Study with COVID-19" Pharmaceutics 13, no. 6: 794. https://doi.org/10.3390/pharmaceutics13060794

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