Assessment of community efforts to advance network-based prediction of protein–protein interactions
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-37079-7
Download full text from publisher
References listed on IDEAS
- Takaya Saito & Marc Rehmsmeier, 2015. "The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-21, March.
- Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
- Aaron Clauset & Cristopher Moore & M. E. J. Newman, 2008. "Hierarchical structure and the prediction of missing links in networks," Nature, Nature, vol. 453(7191), pages 98-101, May.
- Marinka Zitnik & Rok Sosič & Jure Leskovec, 2018. "Prioritizing network communities," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
- Lü, Linyuan & Zhou, Tao, 2011. "Link prediction in complex networks: A survey," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 390(6), pages 1150-1170.
- Pablo M. Gleiser & Leon Danon, 2003. "Community Structure In Jazz," Advances in Complex Systems (ACS), World Scientific Publishing Co. Pte. Ltd., vol. 6(04), pages 565-573.
- Leo Katz, 1953. "A new status index derived from sociometric analysis," Psychometrika, Springer;The Psychometric Society, vol. 18(1), pages 39-43, March.
- Li Li, 2015. "Support Vector Machines," Springer Optimization and Its Applications, in: Selected Applications of Convex Optimization, edition 127, chapter 0, pages 17-52, Springer.
- Tao Zhou & Linyuan Lü & Yi-Cheng Zhang, 2009. "Predicting missing links via local information," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 71(4), pages 623-630, October.
- Kumar, Ajay & Singh, Shashank Sheshar & Singh, Kuldeep & Biswas, Bhaskar, 2020. "Link prediction techniques, applications, and performance: A survey," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 553(C).
- John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
- Katja Luck & Dae-Kyum Kim & Luke Lambourne & Kerstin Spirohn & Bridget E. Begg & Wenting Bian & Ruth Brignall & Tiziana Cafarelli & Francisco J. Campos-Laborie & Benoit Charloteaux & Dongsic Choi & At, 2020. "A reference map of the human binary protein interactome," Nature, Nature, vol. 580(7803), pages 402-408, April.
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.- Kumar, Ajay & Singh, Shashank Sheshar & Singh, Kuldeep & Biswas, Bhaskar, 2020. "Link prediction techniques, applications, and performance: A survey," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 553(C).
- Lee, Yan-Li & Zhou, Tao, 2021. "Collaborative filtering approach to link prediction," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 578(C).
- Mishra, Shivansh & Singh, Shashank Sheshar & Kumar, Ajay & Biswas, Bhaskar, 2022. "ELP: Link prediction in social networks based on ego network perspective," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 605(C).
- Liao, Hao & Zeng, An & Zhang, Yi-Cheng, 2015. "Predicting missing links via correlation between nodes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 436(C), pages 216-223.
- Liu, Shuxin & Ji, Xinsheng & Liu, Caixia & Bai, Yi, 2017. "Extended resource allocation index for link prediction of complex network," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 479(C), pages 174-183.
- Chen, Xing & Wu, Tao & Xian, Xingping & Wang, Chao & Yuan, Ye & Ming, Guannan, 2020. "Enhancing robustness of link prediction for noisy complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 555(C).
- Zhou, Tao, 2023. "Discriminating abilities of threshold-free evaluation metrics in link prediction," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 615(C).
- Chunning Wang & Fengqin Tang & Xuejing Zhao, 2023. "LPGRI: A Global Relevance-Based Link Prediction Approach for Multiplex Networks," Mathematics, MDPI, vol. 11(14), pages 1-15, July.
- Mueller, Falko, 2023. "Link and edge weight prediction in air transport networks — An RNN approach," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 613(C).
- Wang, Zuxi & Wu, Yao & Li, Qingguang & Jin, Fengdong & Xiong, Wei, 2016. "Link prediction based on hyperbolic mapping with community structure for complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 450(C), pages 609-623.
- Peng Liu & Liang Gui & Huirong Wang & Muhammad Riaz, 2022. "A Two-Stage Deep-Learning Model for Link Prediction Based on Network Structure and Node Attributes," Sustainability, MDPI, vol. 14(23), pages 1-15, December.
- Wu, Tao & Chen, Leiting & Zhong, Linfeng & Xian, Xingping, 2017. "Predicting the evolution of complex networks via similarity dynamics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 465(C), pages 662-672.
- Zhang, Xue & Wang, Xiaojie & Zhao, Chengli & Yi, Dongyun & Xie, Zheng, 2014. "Degree-corrected stochastic block models and reliability in networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 393(C), pages 553-559.
- Ziqi Gao & Chenran Jiang & Jiawen Zhang & Xiaosen Jiang & Lanqing Li & Peilin Zhao & Huanming Yang & Yong Huang & Jia Li, 2023. "Hierarchical graph learning for protein–protein interaction," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Zhou, Tao & Lee, Yan-Li & Wang, Guannan, 2021. "Experimental analyses on 2-hop-based and 3-hop-based link prediction algorithms," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 564(C).
- Yu, Jiating & Wu, Ling-Yun, 2022. "Multiple Order Local Information model for link prediction in complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 600(C).
- Wang, Xiaojie & Zhang, Xue & Zhao, Chengli & Xie, Zheng & Zhang, Shengjun & Yi, Dongyun, 2015. "Predicting link directions using local directed path," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 419(C), pages 260-267.
- Charikhi, Mourad, 2024. "Association of the PageRank algorithm with similarity-based methods for link prediction in complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 637(C).
- Park, Ji Hwan & Chang, Woojin & Song, Jae Wook, 2020. "Link prediction in the Granger causality network of the global currency market," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 553(C).
- Lee, Yan-Li & Dong, Qiang & Zhou, Tao, 2021. "Link prediction via controlling the leading eigenvector," Applied Mathematics and Computation, Elsevier, vol. 411(C).
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:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37079-7. 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: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.