Cited by 313Computational Drug Discovery MethodsBioinformatics and Genomic NetworksAdvanced Graph Neural Networks

Utilizing graph machine learning within drug discovery and development

Open access
Gaudelet, Thomas, Day, Ben, Jamasb, Arian R, Soman, Jyothish, Regep, Cristian, Liu, Gertrude, Hayter, Jeremy B R, Vickers, Richard +6 more·2021·Briefings in Bioinformatics

Abstract

Graph machine learning (GML) is receiving growing interest within the pharmaceutical and biotechnology industries for its ability to model biomolecular structures, the functional relationships between them, and integrate multi-omic datasets — amongst other data types. Herein, we present a multidisciplinary academic-industrial review of the topic within the context of drug discovery and development. After introducing key terms and modelling approaches, we move chronologically through the drug development pipeline to identify and summarize work incorporating: target identification, design of small molecules and biologics, and drug repurposing. Whilst the field is still emerging, key milestones including repurposed drugs entering in vivo studies, suggest GML will become a modelling framework of choice within biomedical machine learning.

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  • Graph representation learning has been successful in characterizing drugs at the systems level without patient data to predict interactions with other drugs, protein targets, side effects, and diseases.

    “Graph representation learning has been successful in characterizing drugs at the systems level without patient data to make predictions about interactions with other drugs, protein targets, side effects, diseases [6, 38, 39, 40, 48, 165].”

    From Graph representation learning in biomedicine and healthcare (2022) · cites this paper as [38]

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Research works printed but not linked: 18

  1. [33]Veličković P, Cucurull G, Casanova A, et al. Graph attention networks. In: 6th International Conference on Learning Representations, ICLR 2018 – Conference Track Proceedings, 2018. https://openreview.net/forum?id=rJXMpikCZ.
  2. [34]Gilmer J, Schoenholz SS, Riley PF, et al. Neural message passing for quantum chemistry. In: Proceedings of Machine Learning Research, 2017; 1263– 72. http://proceedings.mlr.press/v70/gilmer17a.html.
  3. [68]Shervashidze N, Vishwanathan S., Petri T, Mehlhorn K, and Borgwardt K. Efficient graphlet kernels for large graph comparison. Proceedings of the Twelth International Conference on Artificial Intelligence and Statistics, in PMLR, 2009; 5: 488– 95.
  4. [72]Antoine Bordes, Nicolas Usunier, Alberto Garcia-Duran, Jason Weston, and Oksana Yakhnenko. Translating embeddings for modeling multi-relational data. Advances in NeurIPS Proceedings, Curran Associates, Inc., 2013; 2787– 2795.
  5. [85]Will Hamilton, Zhitao Ying, and Jure Leskovec. Inductive representation learning on large graphs. Advances in Neural Information Processing Systems. Long Beach, CA, USA: NeurIPS, Curran Associates, Inc., 2017; 1024– 1034.
  6. [90]Zaheer M, Kottur S, Ravanbakhsh S, et al. Deep sets. In: NIPS. Red Hook, NY, USA: Curran Associates, Inc., 2017.
  7. [91]Vaswani A, Shazeer N, Parmar N, et al. Attention is all you need. In: NIPS. Red Hook, NY, USA: Curran Associates, Inc., 2017.
  8. [93]Matthias Fey and Jan E. Lenssen. Fast graph representation learning with PyTorch Geometric. ICLR Workshop on Representation Learning on Graphs and Manifolds. International Conference on Learning Representations (ICLR), 2019. https://rlgm.github.io/papers/2.pdf.
  9. [97]Gao H and Ji S. Graph U-Nets. Proceedings of the 36th International Conference on Machine Learning, in Proceedings of Machine Learning Research, 2019; 97: 2083– 92. Available from http://proceedings.mlr.press/v97/gao19a.html.
  10. [102]Filippo Maria Bianchi, Daniele Grattarola, and Cesare Alippi. Spectral clustering with graph neural networks for graph pooling. In: Proceedings of the 37th International Conference on Machine Learning, PMLR. 2729– 2738. ACM, 2020 119:874.
  11. [113]Jin W, Barzilay R, Jaakkola T. Modeling drug combinations based on molecular structures and biological targets arXiv preprint arXiv:2011.04651. 2020. · arXiv
  12. [119]Corsello SM, Bittker JA, Liu Z, et al. The drug repurposing hub: a next-generation drug library and information resource. Nat Med April 2017; 23(4): 405– 8. 28388612 PMC5568558
  13. [164]Wang T, Shao W, Huang Z, et al. Moronet: multi-omics integration via graph convolutional networks for biomedical data classification. bioRxiv 2020.
  14. [186]Kumar A, Kiran. Characterization of protein-protein and protein-peptide interactions: implication for biologics design (February 2, 2020). Proceedings of International Conference on Drug Discovery (ICDD) 2020. Available at SSRN: https://ssrn.com/abstract=3530208.
  15. [188]Jamasb AR, Lio P, Blundell T. Graphein - a python library for geometric deep learning and network analysis on protein structures. In: bioRxiv, 2020.
  16. [191]John Ingraham, Vikas Garg, Regina Barzilay, and Tommi Jaakkola. Generative models for graph-based protein design. Advances in Neural Information Processing Systems, 2019; 32: 15820– 15831.
  17. [233]Kenta Oono and Taiji Suzuki. Graph neural networks exponentially lose expressive power for node classification. International Conference on Learning Representations, 2019.
  18. [235]Nima Dehmamy, Albert-László Barabási, and Rose Yu. Understanding the representation power of graph neural networks in learning graph topology. Advances in NeurIPS Proceedings, Curran Associates, Inc., 2019; 15413– 15423.

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Authors
Gaudelet, T., Day, B., Jamasb, A. R., Soman, J., Regep, C., Liu, G., Hayter, J. B. R., Vickers, R., Roberts, C., Tang, J., Roblin, D., Blundell, T. L., Bronstein, M. M., & Taylor-King, J. P.
Affiliations
  • Relation Therapeutics, London, UK
  • University of Cambridge (GB)
  • HEC Montréal (CA)
  • The Francis Crick Institute (GB)
  • Imperial College London (GB)
Venue
Briefings in Bioinformatics
Published
2021-05-19
Volume
22
Issue
6
ISSN
  • 1467-5463 (ISSN-L)
  • 1477-4054
OpenAlex
W3160021293
Cited by
313
References
246
Citations by year
2026: 57 · 2025: 72 · 2024: 78 · 2023: 48 · 2022: 39 · 2021: 18 · 2020: 1
FWCI
24.03
Type
journal article
Language
en
Open access
Locations
  • Briefings in Bioinformatics (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Topics
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Physical Sciences › Computer Science › Artificial Intelligence › Advanced Graph Neural Networks
Keywords
graph learning, drug discovery, drug development pipeline, target identification, small molecule design, drug repurposing, multi-omics integration
MeSH terms
Machine Learning, Drug Development, Algorithms, Computer Graphics, Models, Molecular, Molecular Structure, Neural Networks, Computer, Drug Discovery, Drug Repositioning

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