Utilizing graph machine learning within drug discovery and development
Open accessAbstract
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
LeCun, Y., Bengio, Y., & Hinton, G. (2015) · Nature · doi:10.1038/nature14539 · Cited by 84,126 · see citing works
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
Efficient Estimation of Word Representations in Vector Space
Mikolov, T., Chen, K., Corrado, G., & Dean, J. (2013) · arXiv · doi:10.48550/arxiv.1301.3781 · Cited by 26,568 · see citing works
Semi-supervised classification with graph convolutional networks
Kipf, T. N., & Welling, M. (2016) · arXiv · doi:10.48550/arxiv.1609.02907 · Cited by 24,853 · see citing works
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001) · Advanced Drug Delivery Reviews · doi:10.1016/s0169-409x(00)00129-0 · Cited by 18,139 · see citing works
Proceedings of IEEE Conference on Computer Vision and Pattern Recognition
(1993) · doi:10.1109/cvpr.1993 · Cited by 17,989 · see citing works
Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1131 · Cited by 17,749 · see citing works
Advances in Neural Information Processing Systems 19
(2007) · The MIT Press eBooks · doi:10.52202/085713 · Cited by 16,037 · see citing works
Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness
Nishita, M., Park, S.-Y., Nishio, T., Kamizaki, K., Wang, Z., Tamada, K., Takumi, T., Hashimoto, R., Otani, H., Pazour, G. J., et al. (2017) · Scientific Reports · doi:10.1038/s41598-016-0028-x · Cited by 15,947 · see citing works
Advances in Neural Information Processing Systems 29
Teymur, O., Zygalakis, K., & Calderhead, B. (2016) · Cited by 13,881 · see citing works
Proceedings of the 24th international conference on Machine learning
(2007) · doi:10.1145/1273496 · Cited by 11,869 · see citing works
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997) · Advanced Drug Delivery Reviews · doi:10.1016/s0169-409x(96)00423-1 · Cited by 11,484 · see citing works
A Comprehensive Survey on Graph Neural Networks
Wu, Z., Pan, S., Chen, F., Long, G., Zhang, C., & Yu, P. S. (2021) · IEEE Transactions on Neural Networks and Learning Systems · doi:10.1109/tnnls.2020.2978386 · Cited by 11,000 · see citing works
node2vec: Scalable Feature Learning for Networks
Grover, A., & Leskovec, J. (2016) · Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining · doi:10.1145/2939672.2939754 · Cited by 10,926 · see citing works
DeepWalk: online learning of social representations
Perozzi, B., Al-Rfou, R., & Skiena, S. (2014) · Proceedings of the 20th ACM SIGKDD international conference on Knowledge discovery and data mining · doi:10.1145/2623330.2623732 · Cited by 10,123 · see citing works
(2012) · Cited by 9,062 · see citing works
DrugBank 5.0: a major update to the DrugBank database for 2018
Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1037 · Cited by 8,404 · see citing works
Network motifs: simple building blocks of complex networks.
Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., & Alon, U. (2002) · Science · doi:10.1126/science.298.5594.824 · Cited by 7,368 · see citing works
Dynamic Graph CNN for Learning on Point Clouds
Wang, Y., Sun, Y., Liu, Z., Sarma, S. E., Bronstein, M. M., & Solomon, J. M. (2019) · ACM Transactions on Graphics · doi:10.1145/3326362 · Cited by 7,199 · see citing works
Self-citationGraph neural networks: A review of methods and applications
Zhou, J., Cui, G., Hu, S., Zhang, Z., Yang, C., Liu, Z., Wang, L., Li, C., & Sun, M. (2020) · AI Open · doi:10.1016/j.aiopen.2021.01.001 · Cited by 6,880 · see citing works
Proceedings of the 25th international conference on Machine learning - ICML '08
(2008) · doi:10.1145/1390156 · Cited by 6,865 · see citing works
International Conference on Learning Representations (ICLR 2013)
松尾, 豊. (2013) · 人工知能学会誌 = Journal of Japanese Society for Artificial Intelligence · Cited by 6,286 · see citing works
Proceedings of the 19th International Joint Conference on Artificial Intelligence
Pujol, J. M., Delgado, J., Ramon Sangüesa, A., & Flache, A. (2005) · International Joint Conference on Artificial Intelligence · Cited by 5,771 · see citing works
Modeling Relational Data with Graph Convolutional Networks
Schlichtkrull, M., Kipf, T. N., Bloem, P., van den Berg, R., Titov, I., & Welling, M. (2018) · Lecture Notes in Computer Science · doi:10.1007/978-3-319-93417-4_38 · Cited by 5,570 · see citing works
LINE: Large-scale Information Network Embedding
Tang, J., Qu, M., Wang, M., Zhang, M., Yan, J., & Mei, Q. (2015) · Proceedings of the 24th International Conference on World Wide Web · doi:10.1145/2736277.2741093 · Cited by 5,416 · see citing works
Self-citationNetwork medicine: a network-based approach to human disease
Barabási, A.-L., Gulbahce, N., & Loscalzo, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2918 · Cited by 5,034 · see citing works
Formal Semantics for Kolmogorov-Arnold Network Representations of Operational GamesPreprint
Xu, K., Hu, W., Leskovec, J., & Jegelka, S. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1810.00826 · Cited by 4,904 · see citing works
Laplacian Eigenmaps and Spectral Techniques for Embedding and Clustering
Belkin, M., & Niyogi, P. (2002) · The MIT Press eBooks · doi:10.7551/mitpress/1120.003.0080 · Cited by 4,534 · see citing works
KEGG: integrating viruses and cellular organisms
Kanehisa, M. I., Furumichi, M., Sato, Y., Ishiguro-Watanabe, M., & Tanabe, M. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa970 · Cited by 4,042 · see citing works
BioGRID: a general repository for interaction datasets
Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960 · see citing works
PubChem in 2021: new data content and improved web interfaces
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa971 · Cited by 3,953 · see citing works
Geometric Deep Learning: Going beyond Euclidean data
Bronstein, M. M., Bruna, J., LeCun, Y., Szlam, A., & Vandergheynst, P. (2017) · IEEE Signal Processing Magazine · doi:10.1109/msp.2017.2693418 · Cited by 3,661 · see citing works
Self-citationHow to improve R&D productivity: the pharmaceutical industry's grand challenge
Paul, S. M., Mytelka, D. S., Dunwiddie, C. T., Persinger, C. C., Munos, B. H., Lindborg, S. R., & Schacht, A. L. (2010) · Nature Reviews Drug Discovery · doi:10.1038/nrd3078 · Cited by 3,566 · see citing works
The Gene Ontology resource: enriching a GOld mine
The Gene Ontology Consortium, Carbon, S., Douglass, E., Good, B. M., Unni, D. R., Harris, N. L., Mungall, C. J., Basu, S., Chisholm, R. L., Dodson, R. J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1113 · Cited by 3,555 · see citing works
Deep learning for computer vision: A brief review
Voulodimos, A., Doulamis, N., Doulamis, A., & Protopapadakis, E. (2018) · Computational Intelligence and Neuroscience · doi:10.1155/2018/7068349 · Cited by 3,403 · see citing works
Innovation in the pharmaceutical industry: New estimates of R&D costs
DiMasi, J. A., Grabowski, H. G., & Hansen, R. W. (2016) · Journal of Health Economics · doi:10.1016/j.jhealeco.2016.01.012 · Cited by 3,359 · see citing works
Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2016239118 · Cited by 3,286 · see citing works
Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2019) · doi:10.1101/622803 · Cited by 3,280 · see citing works
Applications of machine learning in drug discovery and development
Vamathevan, J., Clark, D., Czodrowski, P., Dunham, I., Ferran, E., Lee, G., Li, B., Madabhushi, A., Shah, P., Spitzer, M., et al. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-019-0024-5 · Cited by 3,228 · see citing works
ZINC 15 – Ligand Discovery for Everyone
Sterling, T., & Irwin, J. J. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00559 · Cited by 3,224 · see citing works
A Comprehensive Survey on Graph Neural Networks
Wu, Z., Pan, S., Chen, F., Long, G., Zhang, C., & Yu, P. (2020) · UTS ePRESS (University of Technology Sydney) · Cited by 3,174 · see citing works
Recent Trends in Deep Learning Based Natural Language ProcessingPreprint
Young, T., Hazarika, D., Poria, S., & Cambria, E. (2017) · IEEE Computational Intelligence Magazine · doi:10.48550/arxiv.1708.02709 · Cited by 3,133 · see citing works
Recent Trends in Deep Learning Based Natural Language Processing [Review Article]
Young, T., Hazarika, D., Poria, S., & Cambria, E. (2018) · IEEE Computational Intelligence Magazine · doi:10.1109/mci.2018.2840738 · Cited by 2,921 · see citing works
Principles of early drug discovery
Hughes, J., Rees, S., Kalindjian, S., & Philpott, K. (2011) · British Journal of Pharmacology · doi:10.1111/j.1476-5381.2010.01127.x · Cited by 2,859 · see citing works
The Reactome Pathway Knowledgebase
Fabregat, A., Jupe, S., Matthews, L. R., Sidiropoulos, K., Gillespie, M. E., Garapati, P. V., Haw, R., Jassal, B., Korninger, F., May, B., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1132 · Cited by 2,798 · see citing works
Piñero, J., Bravo, À., Queralt-Rosinach, N., Gutiérrez-Sacristán, A., Deu-Pons, J., Centeno, E., García-García, J., Sanz, F., & Furlong, L. I. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw943 · Cited by 2,680 · see citing works
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
Raj, A., & van Oudenaarden, A. (2008) · Cell · doi:10.1016/j.cell.2008.09.050 · Cited by 2,593 · see citing works
Rapid generation of functional human IgG antibodies derived from Fab-on-phage display libraries
Jostock, T., Vanhove, M., Brepoels, E., van Gool, R., Daukandt, M., Wehnert, A., van Hegelsom, R., Dransfield, D., Sexton, D., Devlin, M., et al. (2004) · Journal of Immunological Methods · doi:10.1016/j.jim.2004.03.014 · Cited by 2,562 · see citing works
A Deep Learning Approach to Antibiotic Discovery
Stokes, J. M., Yang, K., Swanson, K., Jin, W., Cubillos-Ruiz, A., Donghia, N. M., MacNair, C. R., French, S., Carfrae, L. A., Bloom-Ackermann, Z., et al. (2020) · Cell · doi:10.1016/j.cell.2020.01.021 · Cited by 2,463 · see citing works
Graph Regularized Nonnegative Matrix Factorization for Data Representation
Cai, D., He, X., Han, J., & Huang, T. S. (2010) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2010.231 · Cited by 2,454 · see citing works
ChEMBL: towards direct deposition of bioassay data
Mendez, D., Gaulton, A., Bento, A. P., Chambers, J., De Veij, M., Félix, E., Magariños, M. P., Mosquera, J. F., Mutowo, P., Nowotka, M., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1075 · Cited by 2,372 · see citing works
Embedding Entities and Relations for Learning and Inference in Knowledge Bases
Yang, B., Yih, W.-T., He, X., Gao, J., & Deng, L. (2014) · arXiv · doi:10.48550/arxiv.1412.6575 · Cited by 2,252 · see citing works
SchNet – A deep learning architecture for molecules and materials
Schütt, K. T., Sauceda, H. E., Kindermans, P.-J., Tkatchenko, A., & Müller, K.-R. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5019779 · Cited by 2,217 · see citing works
Representation Learning on Graphs: Methods and ApplicationsPreprint
Hamilton, W. L., Ying, R., & Leskovec, J. (2017) · IEEE Data Engineering Bulletin · doi:10.48550/arxiv.1709.05584 · Cited by 2,203 · see citing works
Exploiting the PI3K/AKT Pathway for Cancer Drug Discovery
Hennessy, B. T., Smith, D. L., Ram, P. T., Lu, Y., & Mills, G. B. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1902 · Cited by 2,183 · see citing works
Complex Embeddings for Simple Link Prediction
Trouillon, T., Welbl, J., Riedel, S., Gaussier, É., & Bouchard, G. (2016) · arXiv · doi:10.48550/arxiv.1606.06357 · Cited by 2,100 · see citing works
A new model for learning in graph domains
Gori, M., Monfardini, G., & Scarselli, F. (2006) · Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005. · doi:10.1109/ijcnn.2005.1555942 · Cited by 2,075 · see citing works
Quantum chemistry structures and properties of 134 kilo molecules
Ramakrishnan, R., Dral, P. O., Rupp, M., & von Lilienfeld, O. A. (2014) · Scientific Data · doi:10.1038/sdata.2014.22 · Cited by 1,966 · see citing works
How were new medicines discovered?
Swinney, D. C., & Anthony, J. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3480 · Cited by 1,812 · see citing works
Junction Tree Variational Autoencoder for Molecular Graph GenerationPreprint
Jin, W.-G., Barzilay, R., & Jaakkola, T. (2018) · International Conference on Machine Learning · doi:10.48550/arxiv.1802.04364 · Cited by 1,783 · see citing works
Learning to Simulate Complex Physics with Graph NetworksPreprint
Sanchez-Gonzalez, A., Godwin, J., Pfaff, T., Ying, R., Leskovec, J., & Battaglia, P. (2020) · International Conference on Machine Learning · doi:10.48550/arxiv.2002.09405 · Cited by 1,739 · see citing works
Deep Learning on Graphs: A Survey
Zhang, Z., Cui, P., & Zhu, W. (2020) · IEEE Transactions on Knowledge and Data Engineering · doi:10.1109/tkde.2020.2981333 · Cited by 1,729 · see citing works
A Review of Relational Machine Learning for Knowledge Graphs
Nickel, M., Murphy, K. P., Tresp, V., & Gabrilovich, E. (2015) · Proceedings of the IEEE · doi:10.1109/jproc.2015.2483592 · Cited by 1,684 · see citing works
The support of human genetic evidence for approved drug indications
Nelson, M. R., Tipney, H., Painter, J. L., Shen, J., Nicoletti, P., Shen, Y., Floratos, A., Sham, P. C., Li, M. J., Wang, J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3314 · Cited by 1,666 · see citing works
Weisfeiler-Lehman Graph Kernels
Shervashidze, N., Schweitzer, P., van Leeuwen, E. J., Mehlhorn, K., & Borgwardt, K. M. (2010) · Max Planck Digital Library · Cited by 1,608 · see citing works
Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2
Zhou, Y., Hou, Y., Shen, J., Huang, Y., Martin, W., & Cheng, F. (2020) · Cell Discovery · doi:10.1038/s41421-020-0153-3 · Cited by 1,588 · see citing works
Deep learning enables rapid identification of potent DDR1 kinase inhibitors
Zhavoronkov, A., Ivanenkov, Y. A., Aliper, A., Veselov, M. S., Aladinskiy, V. A., Aladinskaya, A. V., Terentiev, V. A., Polykovskiy, D. A., Kuznetsov, M. D., Asadulaev, A., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0224-x · Cited by 1,573 · see citing works
Mass spectrometry–based proteomics turns quantitative
Ong, S.-E., & Mann, M. (2005) · Nature Chemical Biology · doi:10.1038/nchembio736 · Cited by 1,572 · see citing works
Estimated Research and Development Investment Needed to Bring a New Medicine to Market, 2009-2018
Wouters, O. J., McKee, M., & Luyten, J. (2020) · JAMA · doi:10.1001/jama.2020.1166 · Cited by 1,531 · see citing works
Modeling polypharmacy side effects with graph convolutional networks
Zitnik, M., Agrawal, M., & Leskovec, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty294 · Cited by 1,501 · see citing works
Targeting the TGFβ signalling pathway in disease
Akhurst, R. J., & Hata, A. (2012) · Nature Reviews Drug Discovery · doi:10.1038/nrd3810 · Cited by 1,466 · see citing works
Representation Learning on Graphs with Jumping Knowledge NetworksPreprint
Xu, K., Li, C., Tian, Y., Sonobe, T., Kawarabayashi, K., & Jegelka, S. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1806.03536 · Cited by 1,379 · see citing works
Hierarchical graph representation learning with differentiable pooling
Ying, Z., You, J., Morris, C., Ren, X., Hamilton, W. L., & Leskovec, J. (2018) · neural information processing systems · Cited by 1,353 · see citing works
Cell-signalling dynamics in time and space
Kholodenko, B. N. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1838 · Cited by 1,347 · see citing works
Selective enzyme purification by affinity chromatography.
Cuatrecasas, P., Wilchek, M., & Anfinsen, C. B. (1968) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.61.2.636 · Cited by 1,224 · see citing works
The Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 1,201 · see citing works
Mass Cytometry: Single Cells, Many Features
Spitzer, M. H., & Nolan, G. P. (2016) · Cell · doi:10.1016/j.cell.2016.04.019 · Cited by 1,199 · see citing works
Machine learning of accurate energy-conserving molecular force fields
Chmiela, S., Tkatchenko, A., Sauceda, H. E., Poltavsky, I., Schütt, K. T., & Müller, K. (2017) · Science Advances · doi:10.1126/sciadv.1603015 · Cited by 1,165 · see citing works
Target identification and mechanism of action in chemical biology and drug discovery
Schenone, M., Dančík, V., Wagner, B. K., & Clemons, P. A. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1199 · Cited by 1,107 · see citing works
Machine-learning-guided directed evolution for protein engineering
Yang, K., Wu, Z., & Arnold, F. H. (2019) · Nature Methods · doi:10.1038/s41592-019-0496-6 · Cited by 1,082 · see citing works
A large-scale evaluation of computational protein function prediction
Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2340 · Cited by 1,028 · see citing works
The Drug Repurposing Hub: a next-generation drug library and information resource
Corsello, S. M., Bittker, J. A., Liu, Z., Gould, J., McCarren, P. R., Hirschman, J., Johnston, S. E., Vrcic, A., Wong, B., Khan, M., et al. (2017) · Nature Medicine · doi:10.1038/nm.4306 · Cited by 1,028 · see citing works
IEEE Winter Conference on Applications of Computer Vision
(2014) · doi:10.1109/wacv31811.2014 · Cited by 1,001 · see citing works
Opportunities and challenges in phenotypic drug discovery: an industry perspective
Moffat, J. G., Vincent, F., Lee, J. A., Eder, J., & Prunotto, M. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2017.111 · Cited by 939 · see citing works
Data-driven prediction of drug effects and interactions
Tatonetti, N. P., Ye, P. P., Daneshjou, R., & Altman, R. B. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003377 · Cited by 936 · see citing works
Structure-based protein function prediction using graph convolutional networks
Gligorijević, V., Renfrew, P. D., Kościółek, T., Leman, J. K., Berenberg, D., Vatanen, T., Chandler, C., Taylor, B. C., Fisk, I., Vlamakis, H. C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23303-9 · Cited by 913 · see citing works
Advances in Neural Information Processing Systems 7
Tesauro, G., Touretzky, D. S., & Leen, T. K. (1995) · Cited by 869 · see citing works
Self-Attention Graph PoolingPreprint
Lee, J., Lee, I., & Kang, J. (2019) · arXiv (Cornell University) · doi:10.48550/arxiv.1904.08082 · Cited by 869 · see citing works
Protein–Ligand Scoring with Convolutional Neural Networks
Ragoza, M., Hochuli, J. E., Idrobo, E., Sunseri, J., & Koes, D. R. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00740 · Cited by 835 · see citing works
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Gaínza, P., Sverrisson, F., Monti, F., Rodolà, E., Boscaini, D., Bronstein, M. M., & Correia, B. E. (2019) · Nature Methods · doi:10.1038/s41592-019-0666-6 · Cited by 811 · see citing works
Self-citationMulticomponent therapeutics for networked systems
Keith, C. T., Borisy, A. A., & Stockwell, B. R. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1609 · Cited by 769 · see citing works
Can you teach old drugs new tricks?
Nosengo, N. (2016) · Nature · doi:10.1038/534314a · Cited by 732 · see citing works
Evaluating Protein Transfer Learning with TAPE
Rao, R., Bhattacharya, N., Thomas, N., Duan, Y., Chen, X., Canny, J., Abbeel, P., & Song, Y. S. (2019) · doi:10.1101/676825 · Cited by 719 · see citing works
Modeling interactome: scale-free or geometric?
Pržulj, N., Corneil, D. G., & Jurišica, I. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth436 · Cited by 709 · see citing works
Design, synthesis and selection of DNA-encoded small-molecule libraries
Clark, M., Acharya, R. A., Arico-Muendel, C. C., Belyanskaya, S. L., Benjamin, D. R., Carlson, N. R., Chiu, C. H., Creaser, S. P., Cuozzo, J. W., Davie, C. P., et al. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.211 · Cited by 682 · see citing works
Wang, T., Shao, W., Huang, Z., Tang, H., Zhang, J., Ding, Z., & Huang, K. (2021) · Nature Communications · doi:10.1038/s41467-021-23774-w · Cited by 671 · see citing works
Supervised neural networks for the classification of structures
Sperduti, A., & Starita, A. (1997) · IEEE Transactions on Neural Networks · doi:10.1109/72.572108 · Cited by 666 · see citing works
King, E. A., Davis, J. W., & Degner, J. F. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008489 · Cited by 649 · see citing works
Erlanson, D. A., McDowell, R. S., & O'Brien, T. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm040031v · Cited by 645 · see citing works
MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
McGinnis, C. S., Patterson, D. M., Winkler, J., Conrad, D. N., Hein, M. Y., Srivastava, V., Hu, J. L., Murrow, L. M., Weissman, J. S., Werb, Z., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0433-8 · Cited by 643 · see citing works
Systems biology in drug discovery
Butcher, E. C., Berg, E. L., & Kunkel, E. J. (2004) · Nature Biotechnology · doi:10.1038/nbt1017 · Cited by 605 · see citing works
Sun, F.-Y., Hoffmann, J., Verma, V., & Tang, J. (2019) · arXiv (Cornell University) · doi:10.48550/arxiv.1908.01000 · Cited by 604 · see citing works
Self-citationHeterogeneous Network Embedding via Deep Architectures
Chang, S., Han, W., Tang, J., Qi, G.-J., Aggarwal, C. C., & Huang, T. S. (2015) · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/2783258.2783296 · Cited by 602 · see citing works
Self-citationKnowledge Graph Embedding for Link Prediction
Rossi, A., Barbosa, D., Firmani, D., Matinata, A., & Merialdo, P. (2021) · ACM Transactions on Knowledge Discovery from Data · doi:10.1145/3424672 · Cited by 601 · see citing works
Handbook of Mathematical Models in Computer Vision
(2006) · doi:10.1007/0-387-28831-7 · Cited by 574 · see citing works
Diffusion-Convolutional Neural Networks
Atwood, J. R., & Towsley, D. (2016) · neural information processing systems · Cited by 566 · see citing works
Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells
Daniloski, Z., Jordan, T. X., Wessels, H., Hoagland, D. A., Kasela, S., Legut, M., Maniatis, S., Mimitou, E. P., Lu, L., Geller, E. T., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.030 · Cited by 549 · see citing works
Beyond natural antibodies: the power of in vitro display technologies
Bradbury, A. M., Sidhu, S. S., Dübel, S., & McCafferty, J. (2011) · Nature Biotechnology · doi:10.1038/nbt.1791 · Cited by 548 · see citing works
Deep Graph InfomaxPreprint
Veličković, P., Fedus, W., Hamilton, W. L., Lió, P., Bengio, Y., & Hjelm, R. D. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1809.10341 · Cited by 537 · see citing works
Rifaioğlu, A. S., Ataş, H., Martin, M. J., Çetin-Atalay, R., Atalay, V., & Doğan, T. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby061 · Cited by 535 · see citing works
High-throughput crystallography for lead discovery in drug design
Blundell, T. L., Jhoti, H., & Abell, C. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd706 · Cited by 529 · see citing works
Self-citationThe discovery of first-in-class drugs: origins and evolution
Eder, J., Sedrani, R., & Wiesmann, C. (2014) · Nature Reviews Drug Discovery · doi:10.1038/nrd4336 · Cited by 514 · see citing works
Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR
Boettcher, M., & McManus, M. T. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.028 · Cited by 510 · see citing works
Label Informed Attributed Network Embedding
Huang, X. X., Li, J., & Hu, X. (2017) · ACM International Conference on Web Search and Data Mining (WSDM) · doi:10.1145/3018661.3018667 · Cited by 498 · see citing works
Utilizing social media data for pharmacovigilance: A review
Sarker, A., Ginn, R., Nikfarjam, A., O’Connor, K., Smith, K. L., Jayaraman, S., Upadhaya, T., & Gonzalez‐Hernandez, G. (2015) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2015.02.004 · Cited by 497 · see citing works
PotentialNet for Molecular Property Prediction
Feinberg, E. N., Sur, D., Wu, Z., Husic, B. E., Mai, H., Li, Y., Sun, S., Yang, J., Ramsundar, B., & Pande, V. S. (2018) · ACS Central Science · doi:10.1021/acscentsci.8b00507 · Cited by 485 · see citing works
Single-cell analysis tools for drug discovery and development
Heath, J. R., Ribas, A., & Mischel, P. S. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2015.16 · Cited by 473 · see citing works
Human Disease Ontology 2018 update: classification, content and workflow expansion
Schriml, L. M., Mitraka, E., Munro, J. B., Tauber, B., Schor, M., Nickle, L., Felix, V., Jeng, L. J. B., Bearer, C. F., Lichenstein, R., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1032 · Cited by 471 · see citing works
From Big Data to Precision Medicine
Hulsen, T., Jamuar, S. S., Moody, A. R., Karnes, J. H., Varga, O., Hedensted, S., Spreafico, R., Hafler, D. A., & McKinney, E. F. (2019) · Frontiers in Medicine · doi:10.3389/fmed.2019.00034 · Cited by 466 · see citing works
Open Targets Platform: new developments and updates two years on
Carvalho‐Silva, D., Pierleoni, A., Pignatelli, M., Ong, C. K., Fumis, L., Karamanis, N., Carmona, M., Faulconbridge, A., Hercules, A., McAuley, E., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1133 · Cited by 449 · see citing works
Intrinsically Disordered Proteins and Their “Mysterious” (Meta)Physics
Uversky, V. (2019) · Frontiers of Physics · doi:10.3389/fphy.2019.00010 · Cited by 449 · see citing works
Phenotypic screens as a renewed approach for drug discovery
Zheng, W., Thorne, N., & McKew, J. C. (2013) · Drug Discovery Today · doi:10.1016/j.drudis.2013.07.001 · Cited by 421 · see citing works
Proceedings of the 2017 SIAM International Conference on Data Mining
(2017) · Society for Industrial and Applied Mathematics eBooks · doi:10.1137/1.9781611974973 · Cited by 413 · see citing works
Fake news detection on social media using geometric deep learning
Monti, F., Frasca, F., Eynard, D., Mannion, D., & Bronstein, M. M. (2019) · arXiv · doi:10.48550/arxiv.1902.06673 · Cited by 392 · see citing works
Self-citationTemporal Graph Networks for Deep Learning on Dynamic Graphs
Rossi, E., Chamberlain, B., Frasca, F., Eynard, D., Monti, F., & Bronstein, M. (2020) · arXiv · doi:10.48550/arxiv.2006.10637 · Cited by 382 · see citing works
Self-citationGraph Convolutional Neural Networks for Predicting Drug-Target Interactions
Torng, W., & Altman, R. B. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00628 · Cited by 371 · see citing works
Directional Message Passing for Molecular GraphsPreprint
Gasteiger, J., Groß, J., & Günnemann, S. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2003.03123 · Cited by 347 · see citing works
Hyperbolic Graph Convolutional Neural Networks
Chami, I., Ying, R., Ré, C., & Leskovec, J. (2019) · arXiv · doi:10.48550/arxiv.1910.12933 · Cited by 344 · see citing works
Acharya, C., Coop, A., Polli, J. E., & MacKerell, A. D. (2010) · Current Computer - Aided Drug Design · doi:10.2174/157340911793743547 · Cited by 343 · see citing works
Position-aware Graph Neural NetworksPreprint
You, J., Ying, R., & Leskovec, J. (2019) · arXiv (Cornell University) · doi:10.48550/arxiv.1906.04817 · Cited by 338 · see citing works
In silico methods for drug repurposing and pharmacology
Hodos, R. A., Kidd, B. A., Shameer, K., Readhead, B., & Dudley, J. T. (2016) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1337 · Cited by 333 · see citing works
Formulation and manufacturability of biologics
Shire, S. J. (2009) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2009.10.006 · Cited by 331 · see citing works
Instability and dynamic pattern in cellular networks
Othmer, H. G., & Scriven, L. E. (1971) · Journal of Theoretical Biology · doi:10.1016/0022-5193(71)90154-8 · Cited by 326 · see citing works
Spatial transcriptomics coming of age
Burgess, D. J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0129-z · Cited by 323 · see citing works
A three-hybrid system for detecting small ligand–protein receptor interactions
Licitra, E. J., & Liu, J. O. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.23.12817 · Cited by 299 · see citing works
Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers
Ryu, J. Y., Kim, H. U., & Lee, S. Y. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1821905116 · Cited by 294 · see citing works
Integrated Multi-Omics Analyses in Oncology: A Review of Machine Learning Methods and Tools
Nicora, G., Vitali, F., Dagliati, A., Geifman, N., & Bellazzi, R. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.01030 · Cited by 284 · see citing works
Graph neural networks in particle physics
Shlomi, J., Battaglia, P., & Vlimant, J.-R. (2020) · Machine Learning Science and Technology · doi:10.1088/2632-2153/abbf9a · Cited by 279 · see citing works
Learning the Graphical Structure of Electronic Health Records with Graph Convolutional Transformer
Choi, E., Xu, Z., Li, Y., Dusenberry, M. W., Flores, G., Xue, E., & Dai, A. M. (2020) · Proceedings of the AAAI Conference on Artificial Intelligence · doi:10.1609/aaai.v34i01.5400 · Cited by 277 · see citing works
SIGN: Scalable Inception Graph Neural NetworksPreprint
Frasca, F., Rossi, E., Eynard, D., Chamberlain, B., Bronstein, M. M., & Monti, F. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2004.11198 · Cited by 266 · see citing works
Self-citationDrugComb: an integrative cancer drug combination data portal
Zagidullin, B., Aldahdooh, J., Zheng, S., Wang, W., Wang, Y., Saad, J. J., Malyutina, A., Jafari, M., Tanoli, Z., Pessia, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz337 · Cited by 265 · see citing works
Self-citationRepurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning
Zeng, X., Song, X. H., Ma, T., Pan, X., Zhou, Y., Hou, Y., Zhang, Z., Li, K., Karypis, G., & Cheng, F. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00316 · Cited by 258 · see citing works
Wu, L., Yang, Y., Guo, X., Shu, X., Cai, Q., Shu, X., Li, B., Tao, R., Wu, C., Nikas, J. B., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17673-9 · Cited by 244 · see citing works
Target Identification Using Drug Affinity Responsive Target Stability (DARTS)
Lomenick, B., Jung, G., Wohlschlegel, J. A., & Huang, J. (2011) · Current Protocols in Chemical Biology · doi:10.1002/9780470559277.ch110180 · Cited by 241 · see citing works
A multiple kernel learning algorithm for drug-target interaction prediction
do Nascimento, A. C. A., Prudêncio, R. B. C., & Costa, I. G. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0890-3 · Cited by 235 · see citing works
Methods for High-throughput Drug Combination Screening and Synergy Scoring
He, L., Kulesskiy, E., Saarela, J., Turunen, L., Wennerberg, K., Aittokallio, T., & Tang, J. (2018) · Methods in Molecular Biology · doi:10.1007/978-1-4939-7493-1_17 · Cited by 232 · see citing works
Self-citationOlayan, R. S., Ashoor, H., & Bajić, V. B. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx731 · Cited by 231 · see citing works
Machine Learning on Graphs: A Model and Comprehensive TaxonomyPreprint
Chami, I., Abu-El-Haija, S., Perozzi, B., Ré, C., & Murphy, K. P. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2005.03675 · Cited by 228 · see citing works
Discovering protein drug targets using knowledge graph embeddings
Mohamed, S. K., Nováček, V., & Nounu, A. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz600 · Cited by 227 · see citing works
Machine learning applications in drug development
Réda, C., Kaufmann, E., & Delahaye‐Duriez, A. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.12.006 · Cited by 224 · see citing works
Fast and Flexible Protein Design Using Deep Graph Neural Networks
Strokach, A. V., Becerra, D., Corbi‐Verge, C., Perez‐Riba, A., & Kim, P. M. (2020) · Cell Systems · doi:10.1016/j.cels.2020.08.016 · Cited by 218 · see citing works
Directional Message Passing for Molecular GraphsPreprint
Klicpera, J., Groß, J., & Günnemann, S. (2020) · arXiv (Cornell University) · Cited by 217 · see citing works
Generating functional protein variants with variational autoencoders
Hawkins‐Hooker, A., Depardieu, F., Baur, S., Couairon, G., Chen, A., & Bikard, D. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008736 · Cited by 211 · see citing works
Structural biology in fragment-based drug design
Murray, C. W., & Blundell, T. L. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.04.003 · Cited by 208 · see citing works
Self-citationA genetics-led approach defines the drug target landscape of 30 immune-related traits
Fang, H., Wolf, H. D., Knezevic, B., Burnham, K. L., Osgood, J. A., Sanniti, A., Lara, A. L., Kasela, S., Cesco, S. D., Wegner, J. K., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0456-1 · Cited by 207 · see citing works
An omics perspective on drug target discovery platforms
Paananen, J., & Fortino, V. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz122 · Cited by 207 · see citing works
Improvement in ADMET Prediction with Multitask Deep Featurization
Feinberg, E. N., Joshi, E., Pande, V. S., & Cheng, A. C. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.9b02187 · Cited by 203 · see citing works
AliGraph: A Comprehensive Graph Neural Network Platform
Yang, H. (2019) · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/3292500.3340404 · Cited by 196 · see citing works
Towards Sparse Hierarchical Graph ClassifiersPreprint
Cangea, C., Veličković, P., Jovanović, N., Kipf, T., & Lió, P. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1811.01287 · Cited by 195 · see citing works
“Omics”-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives
Matthews, H., Hanison, J., & Nirmalan, N. J. (2016) · Proteomes · doi:10.3390/proteomes4030028 · Cited by 192 · see citing works
Graph Cuts in Vision and Graphics: Theories and Applications
Boykov, Y. Y., & Veksler, O. (2005) · Springer eBooks · doi:10.1007/0-387-28831-7_5 · Cited by 191 · see citing works
3D Ken Burns effect from a single image
Niklaus, S., Mai, L., Yang, J., & Liu, F. (2019) · ACM Transactions on Graphics · doi:10.1145/3355089.3356528 · Cited by 191 · see citing works
Cowley, G. S., Weir, B. A., Vázquez, F., Tamayo, P., Scott, J. A., Rusin, S. F., East-Seletsky, A., Ali, L. D., Gerath, W. F., Pantel, S. E., et al. (2014) · Scientific Data · doi:10.1038/sdata.2014.44 · Cited by 189 · see citing works
Smith, I. C. P., Greenside, P., Natoli, T. E., Lahr, D. L., Wadden, D., Tirosh, I., Narayan, R., Root, D. E., Golub, T. R., Subramanian, A., et al. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2003213 · Cited by 188 · see citing works
Drug repositioning based on bounded nuclear norm regularization
Yang, M., Luo, H., Li, Y., & Wang, J. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz331 · Cited by 185 · see citing works
Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies
Baharlou, H., Canete, N. P., Cunningham, A. L., Harman, A. N., & Patrick, E. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02657 · Cited by 176 · see citing works
Invariant and Equivariant Graph NetworksPreprint
Maron, H., Ben-Hamu, H., Shamir, N., & Lipman, Y. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1812.09902 · Cited by 176 · see citing works
Glem, R. C., Bender, A., Arnby, C. H., Carlsson, L., Boyer, S. K., & Smith, J. (2006) · PubMed · Cited by 173 · see citing works
Understanding biological functions through molecular networks
Han, J. J. (2008) · Cell Research · doi:10.1038/cr.2008.16 · Cited by 171 · see citing works
Drugs derived from phage display
Nixon, A. E., Sexton, D. J., & Ladner, R. C. (2013) · mAbs · doi:10.4161/mabs.27240 · Cited by 169 · see citing works
Dalkıran, A., Rifaioğlu, A. S., Martin, M. J., Çetin-Atalay, R., Atalay, V., & Doğan, T. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2368-y · Cited by 164 · see citing works
Distance Encoding: Design Provably More Powerful Neural Networks for Graph Representation LearningPreprint
Li, P., Wang, Y., Wang, H., & Leskovec, J. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2009.00142 · Cited by 142 · see citing works
Pillaiyar, T., Meenakshisundaram, S., Manickam, M., & Sankaranarayanan, M. (2020) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2020.112275 · Cited by 140 · see citing works
Social media and pharmacovigilance: A review of the opportunities and challenges
Sloane, R., Osanlou, O., Lewis, D. J., Bollegala, D., Maskell, S. R., & Pirmohamed, M. (2015) · British Journal of Clinical Pharmacology · doi:10.1111/bcp.12717 · Cited by 139 · see citing works
Comprehensive prediction of drug-protein interactions and side effects for the human proteome
Zhou, H., Gao, M., & Skolnick, J. (2015) · Scientific Reports · doi:10.1038/srep11090 · Cited by 138 · see citing works
ReDO_DB: the repurposing drugs in oncology database
Pantziarka, P., Verbaanderd, C., Sukhatme, V. V., Capistrano, R., Crispino, S., Gyawali, B., Rooman, I., Nuffel, A. M. T. V., Meheus, L., Sukhatme, V. P., et al. (2018) · ecancermedicalscience · doi:10.3332/ecancer.2018.886 · Cited by 137 · see citing works
Deiana, A., Forcelloni, S., Porrello, A., & Giansanti, A. (2019) · PLoS ONE · doi:10.1371/journal.pone.0217889 · Cited by 137 · see citing works
Pal, A., Eksombatchai, C., Zhou, Y., Zhao, B., Rosenberg, C., & Leskovec, J. (2020) · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/3394486.3403280 · Cited by 137 · see citing works
Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition
Lensink, M. F., Nadzirin, N., Velankar, S. S., & Wodak, S. J. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25870 · Cited by 136 · see citing works
Differentiable Graph Module (DGM) for Graph Convolutional Networks
Kazi, A., Cosmo, L., Ahmadi, S., Navab, N., & Bronstein, M. M. (2022) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2022.3170249 · Cited by 133 · see citing works
Self-citationEmbedding Uncertain Knowledge Graphs
Chen, X., Chen, M., Shi, W., Sun, Y., & Zaniolo, C. (2019) · Proceedings of the AAAI Conference on Artificial Intelligence · doi:10.1609/aaai.v33i01.33013363 · Cited by 132 · see citing works
A global network of biomedical relationships derived from text
Percha, B., & Altman, R. B. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty114 · Cited by 131 · see citing works
X-rays in the Cryo-Electron Microscopy Era: Structural Biology’s Dynamic Future
Shoemaker, S., & Ando, N. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b01031 · Cited by 117 · see citing works
Library-based display technologies: where do we stand?
Galán, A., Comor, L., Horvatić, A., Kuleš, J., Guillemin, N., Mrljak, V., & Bhide, M. R. (2016) · Molecular BioSystems · doi:10.1039/c6mb00219f · Cited by 114 · see citing works
Hierarchical Generation of Molecular Graphs using Structural MotifsPreprint
Jin, W., Barzilay, R., & Jaakkola, T. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2002.03230 · Cited by 112 · see citing works
Sosa, D. N., Derry, A., Guo, M. G., Wei, E., Brinton, C., & Altman, R. B. (2019) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789811215636_0041 · Cited by 110 · see citing works
Multiview learning for understanding functional multiomics
Nguyen, N. D., & Wang, D. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007677 · Cited by 107 · see citing works
Network medicine framework for identifying drug-repurposing opportunities for COVID-19
Morselli Gysi, D., do Valle, Í., Zitnik, M., Ameli, A., Gan, X., Varol, O., Ghiassian, S. D., Patten, J. J., Davey, R. A., Loscalzo, J., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2025581118 · Cited by 107 · see citing works
Ma, T., & Zhang, A. (2019) · BMC Genomics · doi:10.1186/s12864-019-6285-x · Cited by 105 · see citing works
Automatic Generation of Complementary Descriptors with Molecular Graph Networks
Merkwirth, C., & Lengauer, T. (2005) · Journal of Chemical Information and Modeling · doi:10.1021/ci049613b · Cited by 103 · see citing works
Is Resistance Training to Muscular Failure Necessary?
Nóbrega, S. R., & Libardi, C. A. (2016) · Frontiers in Physiology · doi:10.3389/fphys.2016.00010 · Cited by 100 · see citing works
Yeast two-hybrid methods and their applications in drug discovery
Hamdi, A., & Colas, P. (2011) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2011.10.008 · Cited by 98 · see citing works
DiPette, D. J., Skeete, J., Ridley, E., Campbell, N. R. C., López-Jaramillo, P. A., Kishore, S. P., Jaffe, M. G., Coca, A., Townsend, R. R., & Ordúñez, P. (2018) · Journal of Clinical Hypertension · doi:10.1111/jch.13426 · Cited by 95 · see citing works
Can Graph Neural Networks Count Substructures?Preprint
Chen, Z., Chen, L., Villar, S., & Bruna, J. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2002.04025 · Cited by 93 · see citing works
THE LOGICAL EXPRESSIVENESS OF GRAPH NEURAL NETWORKS
Barceló, P., Kostylev, E. V., Monet, M., Pérez, J. E. P., Reutter, J. L., & Silva, J.-P. (2020) · HAL · Cited by 92 · see citing works
Wang, Z., Zhou, M., & Arnold, C. W. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa437 · Cited by 91 · see citing works
Technology-Enabled Clinical Trials
Marquis‐Gravel, G., Roe, M. T., Turakhia, M. P., Boden, W. E., Temple, R., Sharma, A., Hirshberg, B., Slater, P., Craft, N. A., Stockbridge, N., et al. (2019) · Circulation · doi:10.1161/circulationaha.119.040798 · Cited by 85 · see citing works
Pavlíková, N., Daniel, P., Šrámek, J., Jelínek, M., Šrámková, V., Němcová‐Fürstová, V., Balušíková, K., Halada, P., & Kovár̆, J. (2019) · Scientific Reports · doi:10.1038/s41598-019-54579-z · Cited by 79 · see citing works
Crichton, G., Guo, Y., Pyysalo, S., & Korhonen, A. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2163-9 · Cited by 78 · see citing works
Flagged first, then by citations
Research works printed but not linked: 18
- [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.
- [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.
- [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.
- [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.
- [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.
- [90]Zaheer M, Kottur S, Ravanbakhsh S, et al. Deep sets. In: NIPS. Red Hook, NY, USA: Curran Associates, Inc., 2017.
- [91]Vaswani A, Shazeer N, Parmar N, et al. Attention is all you need. In: NIPS. Red Hook, NY, USA: Curran Associates, Inc., 2017.
- [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.
- [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.
- [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.
- [113]Jin W, Barzilay R, Jaakkola T. Modeling drug combinations based on molecular structures and biological targets arXiv preprint arXiv:2011.04651. 2020. · arXiv
- [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
- [164]Wang T, Shao W, Huang Z, et al. Moronet: multi-omics integration via graph convolutional networks for biomedical data classification. bioRxiv 2020.
- [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.
- [188]Jamasb AR, Lio P, Blundell T. Graphein - a python library for geometric deep learning and network analysis on protein structures. In: bioRxiv, 2020.
- [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.
- [233]Kenta Oono and Taiji Suzuki. Graph neural networks exponentially lose expressive power for node classification. International Conference on Learning Representations, 2019.
- [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.
Cited by
Sorted by citations
Computational approaches streamlining drug discovery
Sadybekov, A., & Katritch, V. (2023) · Nature · doi:10.1038/s41586-023-05905-z · Cited by 1,342 · see citing works
Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and GaugesPreprint
Bronstein, M. M., Bruna, J., Cohen, T., & Veličković, P. (2021) · arXiv (Cornell University) · doi:10.4230/oasics.dx.2026.1 · Cited by 928 · see citing works
Self-citationSerrano, D. R., Luciano, F. C., Anaya, B. J., Öngoren, B., Kara, A., Molina, G., Ramirez, B. I., Sánchez-Guirales, S. A., Simon, J. A., Tomietto, G., et al. (2024) · Pharmaceutics · doi:10.3390/pharmaceutics16101328 · Cited by 561 · see citing works
A Comprehensive Survey on Deep Graph Representation Learning
Ju, W., Fang, Z., Gu, Y., Liu, Z., Long, Q., Qiao, Z., Qin, Y., Shen, J., Sun, F., Xiao, Z., et al. (2024) · Neural Networks · doi:10.1016/j.neunet.2024.106207 · Cited by 359 · see citing works
Structure-based drug design with equivariant diffusion models
Schneuing, A., Harris, C. B., Du, Y., Didi, K., Jamasb, A. R., Igashov, I., Du, W., Gomes, C. P., Blundell, T. L., Lió, P., et al. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00737-x · Cited by 327 · see citing works
Self-citationAI in drug discovery and its clinical relevance
Qureshi, R., Irfan, M., Gondal, T. M., Khan, S., Wu, J., Hadi, M. U., Heymach, J., Le, X., Yan, H., & Alam, T. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e17575 · Cited by 319 · see citing works
Graph representation learning in biomedicine and healthcare
Li, M. M., Huang, K., & Zitnik, M. (2022) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00942-x · Cited by 294 · see citing works
Chakraborty, C., Bhattacharya, M., Pal, S., & Lee, S. (2023) · Current Research in Biotechnology · doi:10.1016/j.crbiot.2023.100164 · Cited by 295 · see citing works
A review of large language models and autonomous agents in chemistry
Ramos, M. C., Collison, C. J., & White, A. D. (2025) · Chemical Science · doi:10.1039/d4sc03921a · Cited by 274 · see citing works
The transformational role of GPU computing and deep learning in drug discovery
Pandey, M., Fernandez, M., Gentile, F., Isayev, O., Tropsha, A., Stern, A. C., & Cherkasov, A. (2022) · Nature Machine Intelligence · doi:10.1038/s42256-022-00463-x · Cited by 255 · see citing works
Generative AI for designing and validating easily synthesizable and structurally novel antibiotics
Swanson, K., Liu, G., Catacutan, D. B., Arnold, A., Zou, J., & Stokes, J. M. (2024) · Nature Machine Intelligence · doi:10.1038/s42256-024-00809-7 · Cited by 190 · see citing works
Self-citationFederated Learning on Non-IID Graphs via Structural Knowledge Sharing
Tan, Y., Liu, Y., Long, G., Jiang, J., Lu, Q., & Zhang, C. (2023) · Proceedings of the AAAI Conference on Artificial Intelligence · doi:10.1609/aaai.v37i8.26187 · Cited by 181 · see citing works
Translation between Molecules and Natural Language
Edwards, C., Lai, T., Ros, K., Honke, G., Cho, K., & Ji, H. (2022) · Conference on Empirical Methods in Natural Language Processing (EMNLP) · doi:10.18653/v1/2022.emnlp-main.26 · Cited by 225 · see citing works
Goshisht, M. K. (2024) · ACS Omega · doi:10.1021/acsomega.3c05913 · Cited by 169 · see citing works
Meli, R., Morris, G. M., & Biggin, P. C. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.885983 · Cited by 164 · see citing works
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective
Bonner, S., Barrett, I. P., Ye, C., Swiers, R., Engkvist, O., Bender, A., Hoyt, C. T., & Hamilton, W. L. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac404 · Cited by 150 · see citing works
Deep learning methods for drug response prediction in cancer: Predominant and emerging trends
Partin, A., Brettin, T. S., Zhu, Y., Narykov, O., Clyde, A., Overbeek, J., & Stevens, R. L. (2023) · Frontiers in Medicine · doi:10.3389/fmed.2023.1086097 · Cited by 149 · see citing works
Artificial Intelligence in Pharmaceutical Sciences
Lu, M., Yin, J., Zhu, Q., Lin, G., Mou, M., Liu, F., Pan, Z., You, N., Lian, X., Li, F., et al. (2023) · Engineering · doi:10.1016/j.eng.2023.01.014 · Cited by 139 · see citing works
Advances in Artificial Intelligence (AI)-assisted approaches in drug screening
Singh, S., Gupta, H., Sharma, P., & Sahi, S. (2023) · Artificial Intelligence Chemistry · doi:10.1016/j.aichem.2023.100039 · Cited by 144 · see citing works
The Role of AI in Drug Discovery
Abbas, M. K. G., Rassam, A., Karamshahi, F., Abunora, R., & Abouseada, M. (2024) · ChemBioChem · doi:10.1002/cbic.202300816 · Cited by 116 · see citing works
Graph Neural Networks with Learnable Structural and Positional RepresentationsPreprint
Dwivedi, V. P., Luu, A. T., Laurent, T., Bengio, Y., & Bresson, X. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2110.07875 · Cited by 108 · see citing works
Graph Pooling for Graph Neural Networks: Progress, Challenges, and Opportunities
Liu, C., Zhan, Y., Wu, J. X., Li, C., Du, B., Hu, W., Liu, T., & Tao, D. (2023) · International Joint Conference on Artificial Intelligence · doi:10.24963/ijcai.2023/752 · Cited by 96 · see citing works
CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides
Li, J., Yanagisawa, K., Sugita, M., Fujie, T., Ohue, M., & Akiyama, Y. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c01573 · Cited by 95 · see citing works
A Survey on Malware Detection with Graph Representation Learning
Bilot, T., Madhoun, N. E., Agha, K. A., & Zouaoui, A. (2024) · ACM Computing Surveys · doi:10.1145/3664649 · Cited by 99 · see citing works
Structure and dynamics in drug discovery
Wei, H., & McCammon, J. A. (2024) · npj Drug Discovery. · doi:10.1038/s44386-024-00001-2 · Cited by 94 · see citing works
Weisfeiler and Lehman Go Cellular: CW NetworksPreprint
Bodnar, C., Frasca, F., Otter, N., Wang, Y. G., Lió, P., Montúfar, G., & Bronstein, M. M. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2106.12575 · Cited by 81 · see citing works
Self-citationMobileViG: Graph-Based Sparse Attention for Mobile Vision Applications
Munir, M., Avery, W., & Mărculescu, R. (2023) · IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) · doi:10.1109/cvprw59228.2023.00215 · Cited by 76 · see citing works
Zhou, P., Xiao, X., Zhu, X., Chen, Y., Lü, W., Piao, M., Cao, Z., Lu, M., Fang, F., Li, Z., et al. (2023) · Energy storage materials · doi:10.1016/j.ensm.2023.102964 · Cited by 76 · see citing works
Compound–protein interaction prediction by deep learning: Databases, descriptors and models
Du, B.-X., Qin, Y., Jiang, Y., Xu, Y., Yiu, S., Yu, H., & Shi, J. (2022) · Drug Discovery Today · doi:10.1016/j.drudis.2022.02.023 · Cited by 73 · see citing works
Vatter, J., Mayer, R., & Jacobsen, H. (2023) · ACM Computing Surveys · doi:10.1145/3597428 · Cited by 78 · see citing works
Anomaly Detection in Dynamic Graphs: A Comprehensive Survey
Ekle, O. A., & Eberle, W. (2024) · ACM Transactions on Knowledge Discovery from Data · doi:10.1145/3669906 · Cited by 85 · see citing works
A review of mechanistic learning in mathematical oncology
Metzcar, J., Jutzeler, C. R., Macklin, P., Köhn‐Luque, A., & Brüningk, S. C. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1363144 · Cited by 74 · see citing works
Application of artificial intelligence in drug design: A review
Singh, S., Kaur, N., & Gehlot, A. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.108810 · Cited by 75 · see citing works
GNN-SubNet: disease subnetwork detection with explainable graph neural networks
Pfeifer, B., Saranti, A., & Holzinger, A. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac478 · Cited by 69 · see citing works
Applied machine learning in Alzheimer's disease research: omics, imaging, and clinical data
Li, Z., Jiang, X., Wang, Y., & Kim, Y. (2021) · Emerging Topics in Life Sciences · doi:10.1042/etls20210249 · Cited by 67 · see citing works
MACHINE LEARNING IN DRUG DISCOVERY: A CRITICAL REVIEW OF APPLICATIONS AND CHALLENGES
Udegbe, F. C., Ebulue, O. R., Ebulue, C. C., & Ekesiobi, C. S. (2024) · Computer Science & IT Research Journal · doi:10.51594/csitrj.v5i4.1048 · Cited by 63 · see citing works
Understanding the performance of knowledge graph embeddings in drug discovery
Bonner, S., Barrett, I. P., Ye, C., Swiers, R., Engkvist, O., Hoyt, C. T., & Hamilton, W. L. (2022) · Artificial Intelligence in the Life Sciences · doi:10.1016/j.ailsci.2022.100036 · Cited by 62 · see citing works
PDE-GCN: Novel Architectures for Graph Neural Networks Motivated by Partial Differential EquationsPreprint
Eliasof, M., Haber, E., & Treister, E. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2108.01938 · Cited by 56 · see citing works
HyGNN: Drug-Drug Interaction Prediction via Hypergraph Neural Network
Saifuddin, K. M., Bumgardner, B., Tanvir, F., & Akbaş, E. (2023) · IEEE International Conference on Data Engineering (ICDE) · doi:10.1109/icde55515.2023.00119 · Cited by 51 · see citing works
Explaining Link Prediction Systems based on Knowledge Graph Embeddings
Rossi, A., Firmani, D., Paolo Merialdo, A., & Teofili, T. (2022) · ACM SIGMOD International Conference on Management of Data (SIGMOD) · doi:10.1145/3514221.3517887 · Cited by 50 · see citing works
Learning Strong Graph Neural Networks with Weak Information
Liu, Y., Ding, K., Wang, J., Lee, V. C. S., Liu, H., & Pan, S. (2023) · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/3580305.3599410 · Cited by 52 · see citing works
Machine learning applications for therapeutic tasks with genomics data
Huang, K., Xiao, C., Glass, L. M., Critchlow, C. W., Gibson, G. C., & Sun, J. (2021) · Patterns · doi:10.1016/j.patter.2021.100328 · Cited by 46 · see citing works
Machine learning-based optimisation of microalgae biomass production by using wastewater
Singh, V., Verma, M., Chivate, M. S., & Mishra, V. (2023) · Journal of environmental chemical engineering · doi:10.1016/j.jece.2023.111387 · Cited by 44 · see citing works
Feng, X., Li, Y., & Xu, M. (2024) · Advanced Engineering Informatics · doi:10.1016/j.aei.2024.102362 · Cited by 44 · see citing works
The application of artificial intelligence to accelerate G protein‐coupled receptor drug discovery
Nguyen, A. T. N., Nguyen, D. T. N., Koh, H. Y., Toskov, J., MacLean, W., Xu, A., Zhang, D., Webb, G. I., May, L. T., & Halls, M. L. (2023) · British Journal of Pharmacology · doi:10.1111/bph.16140 · Cited by 42 · see citing works
Recent advances and challenges in experiment-oriented polymer informatics
Hatakeyama‐Sato, K. (2022) · Polymer Journal · doi:10.1038/s41428-022-00734-9 · Cited by 44 · see citing works
Unbalanced Optimal Transport, from theory to numerics
Séjourné, T., Gabriel Peyré, A., & Vialard, F. (2022) · Handbook of numerical analysis · doi:10.1016/bs.hna.2022.11.003 · Cited by 41 · see citing works
Graph neural networks for conditional de novo drug design
Abate, C., Decherchi, S., & Cavalli, A. (2023) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1651 · Cited by 38 · see citing works
Graph machine learning for design of high‐octane fuels
Rittig, J. G., Ritzert, M., Schweidtmann, A. M., Winkler, S., Weber, J. M., Morsch, P., Heufer, K. A., Grohe, M., Mitsos, A., & Dahmen, M. (2022) · AIChE Journal · doi:10.1002/aic.17971 · Cited by 37 · see citing works
Kengkanna, A., & Ohue, M. (2024) · Communications Chemistry · doi:10.1038/s42004-024-01155-w · Cited by 33 · see citing works
Node-Oriented Spectral Filtering for Graph Neural Networks
Zheng, S., Zhu, Z., Liu, Z., Li, Y., & Zhao, Y. (2023) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2023.3324937 · Cited by 33 · see citing works
Bridging machine learning and peptide design for cancer treatment: a comprehensive review
Rezaee, K., & Eslami, H. (2025) · Artificial Intelligence Review · doi:10.1007/s10462-025-11148-3 · Cited by 34 · see citing works
Graph Neural Networks as a Potential Tool in Improving Virtual Screening Programs
Alves, L. A., Ferreira, N. C. D. S., Maricato, V., Alberto, A. V. P., Dias, E. A., & Coelho, N. J. A. (2022) · Frontiers in Chemistry · doi:10.3389/fchem.2021.787194 · Cited by 30 · see citing works
Deep Learning Concepts and Applications for Synthetic Biology
Beardall, W., Stan, G.-B. V., & Dunlop, M. J. (2022) · GEN Biotechnology · doi:10.1089/genbio.2022.0017 · Cited by 28 · see citing works
Breast Cancer Classification From Digital Pathology Images via Connectivity-Aware Graph Transformer
Wang, K., Zheng, F., Cheng, L., Dai, H., Dou, Q., & Qin, J. (2024) · IEEE Transactions on Medical Imaging · doi:10.1109/tmi.2024.3381239 · Cited by 28 · see citing works
DNMG: Deep molecular generative model by fusion of 3D information for de novo drug design
Song, T., Ren, Y., Wang, S., Han, P., Wang, L., Li, X., & Rodríguez‐Patón, A. (2023) · Methods · doi:10.1016/j.ymeth.2023.02.001 · Cited by 27 · see citing works
Unlearning Graph Classifiers with Limited Data Resources
Pan, C., Chien, E., & Milenković, O. (2023) · International World Wide Web Conference (WWW) · doi:10.1145/3543507.3583547 · Cited by 26 · see citing works
Hu, X., Sun, Z., Nian, Y., Wang, Y., Dang, Y., Li, F., Feng, J., Yu, E., & Tao, C. (2024) · JMIR Aging · doi:10.2196/54748 · Cited by 26 · see citing works
Improving Inductive Link Prediction Using Hyper-relational Facts
Ali, M., Berrendorf, M., Galkin, M., Thost, V., Ma, T., Volker Tresp, C., & Lehmann, J. (2021) · Lecture notes in computer science · doi:10.1007/978-3-030-88361-4_5 · Cited by 26 · see citing works
Sun, J., Xu, M., Ru, J., James-Bott, A., Xiong, D., Wang, X., & Cribbs, A. P. (2023) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2023.115500 · Cited by 26 · see citing works
GraphPrior: Mutation-based Test Input Prioritization for Graph Neural Networks
Dang, X., Li, Y., Papadakis, M., Klein, J., Bissyandé, T. F., & Traon, Y. L. (2023) · ACM Transactions on Software Engineering and Methodology · doi:10.1145/3607191 · Cited by 26 · see citing works
Computer vision algorithms in healthcare: Recent advancements and future challenges
Kabir, M. M., Rahman, A., Hasan, M. N., & Mridha, M. F. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.109531 · Cited by 28 · see citing works
Biological Insights Knowledge Graph: an integrated knowledge graph to support drug developmentPreprint
Geleta, D., Nikolov, A., Edwards, G., Gogleva, A. A., Jackson, R., Jansson, E., Lamov, A., Nilsson, S., Pettersson, M., Poroshin, V., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.28.466262 · Cited by 25 · see citing works
Hsieh, K., Plascencia‐Villa, G., Lin, K., Perry, G. L., Jiang, X., & Kim, Y. (2022) · iScience · doi:10.1016/j.isci.2022.105678 · Cited by 24 · see citing works
Graph Machine Learning in the Era of Large Language Models (LLMs)
Wang, S., Huang, J., Chen, Z., Song, Y., Tang, W., Mao, H., Fan, W., Liu, H., Liu, X., Yin, D., et al. (2025) · ACM Transactions on Intelligent Systems and Technology · doi:10.1145/3732786 · Cited by 39 · see citing works
Du, H. Y., Yao, M. M.-S., Liu, S., Chen, L., Chan, W. P., & Feng, M. (2023) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2023.3249404 · Cited by 23 · see citing works
Nandi, S., Bhaduri, S., Das, D., Ghosh, P., Mandal, M., & Mitra, P. (2024) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.3c01161 · Cited by 23 · see citing works
Jamasb, A. R., Viñas, R., Ma, E. J., Harris, C., Huang, K., Hall, D., Lió, P., & Blundell, T. L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.15.204701 · Cited by 23 · see citing works
Self-citationFreshGNN: Reducing Memory Access via Stable Historical Embeddings for Graph Neural Network Training
Huang, K., Jiang, H., Wang, M., Xiao, G., Wipf, D., Song, X. H., Gan, Q., Huang, Z., Zhai, J., & Zhang, Z. (2024) · Proceedings of the VLDB Endowment · doi:10.14778/3648160.3648184 · Cited by 22 · see citing works
Implications of topological imbalance for representation learning on biomedical knowledge graphs
Bonner, S., Kirik, U., Engkvist, O., Tang, J., & Barrett, I. P. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac279 · Cited by 22 · see citing works
Self-citationmibPOPdb: An online database for microbial biodegradation of persistent organic pollutants
Ngara, T. R., Zeng, P., & Zhang, H. (2022) · iMeta · doi:10.1002/imt2.45 · Cited by 21 · see citing works
A comprehensive review of artificial intelligence for pharmacology research
Li, B., Tan, K., Lao, A. R., Wang, H., Zheng, H., & Zhang, L. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1450529 · Cited by 24 · see citing works
AI-Based Computational Methods in Early Drug Discovery and Post Market Drug Assessment: A Survey
Rajaei, F., Minoccheri, C., Wittrup, E. M., Wilson, R. C., Athey, B. D., Omenn, G. S., & Najarian, K. (2024) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2024.3492708 · Cited by 23 · see citing works
Enhancing foundation models for scientific discovery via multimodal knowledge graph representations
López, V., Hoang, L. T., Galindo, M. M., Fernández-Díaz, R., Sbodio, M. L., Ordóñez-Hurtado, R., Zayats, M., Mulligan, N., & Bettencourt‐Silva, J. H. (2024) · Journal of Web Semantics · doi:10.1016/j.websem.2024.100845 · Cited by 22 · see citing works
A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease
Timmons, J. A., Anighoro, A., Brogan, R. J., Stahl, J., Wahlestedt, C., Farquhar, D. G., Taylor‐King, J. P., Volmar, C., Kraus, W. E., & Phillips, S. M. (2021) · eLife · doi:10.7554/elife.68832 · Cited by 21 · see citing works
Self-citationIndustrializing AI-powered drug discovery: lessons learned from the Patrimony computing platform
Guedj, M., Swindle, J., Hamon, A., Hubert, S., Desvaux, E., Laplume, J., Xuereb, L., Lefèbvre, C., Haudry, Y., Gabarroca, C., et al. (2022) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2022.2095368 · Cited by 23 · see citing works
Deep Learning‐Based Multiomics Data Integration Methods for Biomedical Application
Wen, Y., Zheng, L., Leng, D., Dai, C., Jing, L., Zhang, Z., He, S., & Bo, X. (2023) · Advanced Intelligent Systems · doi:10.1002/aisy.202200247 · Cited by 20 · see citing works
Dual-View Learning Based on Images and Sequences for Molecular Property Prediction
Zhang, X., Xiang, H., Yang, X., Dong, J., Fu, X., Zeng, X., Chen, H., & Li, K. (2023) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2023.3347794 · Cited by 20 · see citing works
Investigating Brain Connectivity with Graph Neural Networks and GNNExplainer
Zhdanov, M., Steinmann, S., & Hoffmann, N. (2022) · Proceedings - International Conference on Pattern Recognition/Proceedings/International Conference on Pattern Recognition · doi:10.1109/icpr56361.2022.9956201 · Cited by 19 · see citing works
Sun, J., Kulandaisamy, A., Liu, J., Hu, K., Gromiha, M. M., & Zhang, Y. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.01.036 · Cited by 19 · see citing works
Ayuso-Muñoz, A., Santamaría, L. P., Carro, E. U., Serrano, E., & Rodríguez‐González, A. (2023) · Artificial Intelligence in Medicine · doi:10.1016/j.artmed.2023.102687 · Cited by 18 · see citing works
ChemicalX: A Deep Learning Library for Drug Pair Scoring
Rózemberczki, B., Hoyt, C. T., Gogleva, A. A., Grabowski, P., Karis, K., Lamov, A., Nikolov, A., Nilsson, S., Ughetto, M., Wang, Y., et al. (2022) · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/3534678.3539023 · Cited by 18 · see citing works
Computational Landscape in Drug Discovery: From AI/ML Models to Translational Application
Sharma, D., Anabala, M., Jain, V. V., Shyam, M., Prince, S. E., & Muniyan, R. (2025) · Scientifica · doi:10.1155/sci5/1688637 · Cited by 18 · see citing works
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing
Tayebi, J., & BabaAli, B. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01925 · Cited by 17 · see citing works
Ahmed, W., Ashraf, T., Saleem, M. T., Mahmoud, E. E., Ali, K., Zaman, S., & Belay, M. B. (2025) · Scientific Reports · doi:10.1038/s41598-025-01594-y · Cited by 16 · see citing works
DiNuzzo, M. (2022) · Frontiers in Drug Discovery · doi:10.3389/fddsv.2022.1019706 · Cited by 16 · see citing works
Privacy-Preserving Graph Machine Learning from Data to Computation: A Survey
Fu, D., Bao, W., Maciejewski, R., Tong, H., & He, J. (2023) · ACM SIGKDD Explorations Newsletter · doi:10.1145/3606274.3606280 · Cited by 19 · see citing works
RECOVER identifies synergistic drug combinations in vitro through sequential model optimization
Bertin, P., Rector-Brooks, J., Sharma, D. K., Gaudelet, T., Anighoro, A., Groß, T., Martínez‐Peña, F., Tang, E. L., Suraj, M. S., Regep, C., et al. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100599 · Cited by 16 · see citing works
Self-citationWang, L., Li, Z., Hu, J., Wong, L., Zhao, B.-W., & You, Z.-H. (2024) · Applied Soft Computing · doi:10.1016/j.asoc.2024.111523 · Cited by 16 · see citing works
IBCS: Learning Information Bottleneck-Constrained Denoised Causal Subgraph for Graph Classification
Yuan, R., Tang, Y., Xiao, Y., & Zhang, W. (2024) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2024.3508766 · Cited by 15 · see citing works
Deng, Z., Xu, J., Feng, Y., Dong, L., & Zhang, Y. (2024) · Computer Methods in Biomechanics & Biomedical Engineering · doi:10.1080/10255842.2024.2311315 · Cited by 15 · see citing works
Binding-Adaptive Diffusion Models for Structure-Based Drug Design
Huang, Z., Yang, L. Q., Zhang, Z., Zhou, X., Bao, Y., Zheng, X., Yang, Y., Wang, Y., & Yang, W. (2024) · Proceedings of the AAAI Conference on Artificial Intelligence · doi:10.1609/aaai.v38i11.29162 · Cited by 15 · see citing works
Glass Transition Temperature Prediction of Polymers via Graph Reinforcement Learning
Dong, C., Li, D., & Liu, J. (2024) · Langmuir · doi:10.1021/acs.langmuir.4c01906 · Cited by 15 · see citing works
Artificial Intelligence in Drug Discovery: Integrative Advances From Data to Therapeutic Innovation
Mehran, M. J., Mohammadzadeh, S., Bolideei, M., Barzigar, R., Haider, K. H., Jadgal, N., & Bahrami, Y. (2026) · Drug Development Research · doi:10.1002/ddr.70229 · Cited by 14 · see citing works
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey
Zhong, Z., Barkova, A., & Mottin, D. (2025) · ACM Computing Surveys · doi:10.1145/3744237 · Cited by 19 · see citing works
Papillon, M., Sanborn, S., Mathe, J., Cornelis, L., Bertics, A., Buracas, D., Lillemark, H. J., Shewmake, C., Dinç, F., Xavier Pennec, B., et al. (2025) · Machine Learning Science and Technology · doi:10.1088/2632-2153/adf375 · Cited by 22 · see citing works
Structure-aware generation of drug-like moleculesPreprint
Drotár, P., Jamasb, A. R., Day, B., Cangea, C., & Lió, P. (2021) · arXiv (Cornell University) · doi:10.17863/cam.79076 · Cited by 14 · see citing works
Self-citationBarozi, V., Chakraborty, S., Govender, S., Morgan, E., Ramahala, R., Graham, S. C., Bishop, N. T., & Bishop, Ö. T. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.10.031 · Cited by 13 · see citing works
JuryGCN: Quantifying Jackknife Uncertainty on Graph Convolutional Networks
Kang, J. L., Zhou, Q., & Tong, H. (2022) · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/3534678.3539286 · Cited by 13 · see citing works
REDIRECTION: Generating drug repurposing hypotheses using link prediction with DISNET data
Ayuso-Muñoz, A., Carro, E. U., Santamaría, L. P., Otero-Carrasco, B., Menasalvas, E., Gallardo, Y. P., & Rodríguez‐González, A. (2022) · Proceedings - IEEE Symposium on Computer-Based Medical Systems · doi:10.1109/cbms55023.2022.00009 · Cited by 13 · see citing works
- 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)
- ORCID
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-05-19
- Volume
- 22
- Issue
- 6
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- PMC
- PMC8574649
- 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
- hybrid
- doi.org
- Licence
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review