- Open Access
Edge correlations and link prediction in growing hypergraphs
Phys. Rev. E 112, 024305 – Published 25 August, 2025
DOI: https://doi.org/10.1103/4lkd-mtzq
Abstract
We propose a generative, mechanistic model of temporally evolving hypergraphs in which hyperedges form via noisy copying of previous hyperedges. Our proposed model reproduces several stylized facts from many empirical hypergraphs, is learnable from data, and defines a likelihood over a complete hypergraph rather than ego-based or other subhypergraphs. Analyzing our model, we derive asymptotic descriptions of the node degree, edge size, and edge intersection size distributions in terms of the model parameters. We also show several features of empirical hypergraphs which are and are not successfully captured by our model. We provide a scalable stochastic expectation maximization algorithm with which we can fit our model to hypergraph data sets with millions of nodes and edges. Finally, we assess our model on a hypergraph link prediction task, finding that an instantiation of our model with just 11 parameters can achieve competitive predictive performance with large neural networks.
Physics Subject Headings (PhySH)
Article Text
References (52)
- C. Bick, E. Gross, H. A. Harrington, and M. T. Schaub, What are higher-order networks? SIAM Rev. 65, 686 (2023).
- F. Battiston, E. Amico, A. Barrat, G. Bianconi, G. F. de Arruda, B. Franceschiello, I. Iacopini, S. Kéfi, V. Latora, Y. Moreno et al., The physics of higher-order interactions in complex systems, Nat. Phys. 17, 1093 (2021).
- F. Battiston, G. Cencetti, I. Iacopini, V. Latora, M. Lucas, A. Patania, J.-G. Young, and G. Petri, Networks beyond pairwise interactions: Structure and dynamics, Phys. Rep. 874, 1 (2020).
- U. Chitra and B. Raphael, Random walks on hypergraphs with edge-dependent vertex weights, in Proceedings of the 36th International Conference on Machine Learning, Vol. 97 of Proceedings of Machine Learning Research, edited by Kamalika Chaudhuri and Ruslan Salakhutdinov (PMLR, 2019).
- F. Baccini, F. Geraci, and G. Bianconi, Weighted simplicial complexes and their representation power of higher-order network data and topology, Phys. Rev. E 106, 034319 (2022).
- L. Torres, A. S. Blevins, D. Bassett, and T. Eliassi-Rad, The why, how, and when of representations for complex systems, SIAM Rev. 63, 435 (2021).
- N. W. Landry, J.-G. Young, and N. Eikmeier, The simpliciality of higher-order networks, EPJ Data Sci. 13, 17 (2024).
- A. Badalyan, N. Ruggeri, and C. De Bacco, Structure and inference in hypergraphs with node attributes, Nature Commun. 15, 7073 (2024).
- P. S. Chodrow and, A. Mellor, Annotated hypergraphs: Models and applications, Appl. Netw. Sci. 5, 9 (2020).
- G. Gallo, G. Longo, S. Pallottino, and S. Nguyen, Directed hypergraphs and applications, Discrete Appl. Math. 42, 177 (1993).
- G. Lee and K. Shin, THyMe+: Temporal hypergraph motifs and fast algorithms for exact counting, in Proceedings of the IEEE International Conference on Data Mining (ICDM) (IEEE, Auckland, New Zealand, 2021), pp. 310–319.
- A. Myers, C. Joslyn, B. Kay, E. Purvine, G. Roek, and M. Shapiro, Topological analysis of temporal hypergraphs, in Algorithms and Models for the Web Graph, Vol. 13894, edited by M. Dewar, P. Prałat, P. Szufel, F. Théberge and M. Wrzosek (Springer Nature, Cham, Switzerland, 2023), pp. 127–146.
- G. Cencetti, F. Battiston, B. Lepri, and M. Karsai, Temporal properties of higher-order interactions in social networks, Sci. Rep. 11, 7028 (2021).
- L. Neuhäuser, R. Lambiotte, and M. T. Schaub, Consensus dynamics on temporal hypergraphs, Phys. Rev. E 104, 064305 (2021).
- R. Sahasrabuddhe, L. Neuhäuser, and R. Lambiotte, Modelling non-linear consensus dynamics on hypergraphs, J. Phys. Complex. 2, 025006 (2021).
- R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, Network motifs: Simple building blocks of complex networks, Science 298, 824 (2002).
- G. Lee, J. Ko, and K. Shin, Hypergraph motifs: Concepts, algorithms, and discoveries, Proc. VLDB Endow. 13, 2256 (2020).
- Q. F. Lotito, F. Musciotto, A. Montresor, and F. Battiston, Higher-order motif analysis in hypergraphs, Commun. Phys. 5, 79 (2022).
- G. Lee, M. Choe, and K. Shin, How do hyperedges overlap in real-world hypergraphs?—patterns, measures, and generators, in Proceedings of the Web Conference (ACM, Ljubljana, Slovenia, 2021), pp. 3396–3407.
- P. S. Chodrow, Configuration models of random hypergraphs, J. Complex Netw. 8, cnaa018 (2020).
- G. Lee, F. Bu, T. Eliassi-Rad, and K. Shin, A survey on hypergraph mining: Patterns, tools, and generators, ACM Comput. Surveys 57, 203 (2025).
- A. R. Benson, R. Kumar, and, A. Tomkins, Sequences of sets, in Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (ACM, London, UK, 2018), pp. 1148–1157.
- J. M. Kleinberg, R. Kumar, P. Raghavan, S. Rajagopalan, and A. S. Tomkins, The web as a graph: Measurements, models, and methods, in Computing and Combinatorics, Vol. 1627, edited by G. Goos, J. Hartmanis, J. Van Leeuwen, Takano Asano, Hideki Imai, D. T. Lee, Shin-ichi Nakano and Takeshi Tokuyama (Springer, Berlin, Heidelberg, 1999), pp. 1–17.
- M. E. J. Newman, Networks: An Introduction (Oxford University Press, Oxford, UK, 2018).
- R. V. Solé, R. Pastor-Satorras, E. Smith, and T. B. Kepler, A model of large-scale proteome evolution, Adv. Complex Syst. 05, 43 (2002).
- A. Vázquez, A. Flammini, A. Maritan, and A. Vespignani, Modeling of protein interaction networks, Complexus 1, 38 (2003).
- D. Roh and K. I. Goh, Growing hypergraphs with preferential linking, J. Korean Phys. Soc. 83, 713 (2023).
- C. Avin, Z. Lotker, Y. Nahum, and D. Peleg, Random preferential attachment hypergraph, in Proceedings of the IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ACM, Vancouver, British Columbia, Canada, 2019), pp. 398–405.
- F. Giroire, N. Nisse, T. Trolliet, and M. Sulkowska, Preferential attachment hypergraph with high modularity, Netw. Sci. 10, 400 (2022).
- D. Liben-Nowell and J. Kleinberg, The link-prediction problem for social networks, J. Am. Soc. Inf. Sci. Technol. 58, 1019 (2007).
- A. R. Benson, R. Abebe, M. T. Schaub, A. Jadbabaie, and J. Kleinberg, Simplicial closure and higher-order link prediction, Proc. Natl. Acad. Sci. USA 115, E11221 (2018).
- C. Chen and Y.-Y. Liu, A survey on hyperlink prediction, IEEE Trans. Neural Netw. Learn. Syst. 35, 15034 (2024).
- S. Lizotte, J.-G. Young, and A. Allard, Hypergraph reconstruction from uncertain pairwise observations, Sci. Rep. 13, 21364 (2023).
- J.-G. Young, G. Petri, and T. P. Peixoto, Hypergraph reconstruction from network data, Commun. Phys. 4, 135 (2021).
- N. Yadati, V. Nitin, M. Nimishakavi, P. Yadav, A. Louis, and P. Talukdar, NHP: Neural hypergraph link prediction, in Proceedings of the 29th ACM International Conference on Information & Knowledge Management (ACM, Virtual Event, Ireland, 2020), pp. 1705–1714.
- N. Ruggeri, M. Contisciani, F. Battiston, and C. De Bacco, Community detection in large hypergraphs, Sci. Adv. 9, eadg9159 (2023).
- F. Giroire, N. Nisse, K. Ohulchanskyi, M. Sulkowska, and T. Trolliet, Preferential attachment hypergraph with vertex deactivation, in Proceedings of the 31st International Symposium on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS) (IEEE, NY, USA, 2023), pp. 1–8.
- Z.-K. Zhang and C. Liu, A hypergraph model of social tagging networks, J. Stat. Mech. (2010) P10005.
- M. Tavakoli, A. Shmakov, F. Ceccarelli, and P. Baldi, Rxn hypergraph: A hypergraph attention model for chemical reaction representation, arXiv:2201.01196v1.
- Q. Suo, J.-L. Guo, S. Sun, and H. Liu, Exploring the evolutionary mechanism of complex supply chain systems using evolving hypergraphs, Physica A 489, 141 (2018).
- C. Meng and H. Motevalli, Link prediction in social networks using hyper-motif representation on hypergraph, Multimedia Syst. 30, 123 (2024).
- Z. Chen, X. Wang, C. Wang, and J. Li, Explainable link prediction in knowledge hypergraphs, in Proceedings of the 31st ACM International Conference on Information & Knowledge Management (ACM, New York, 2022), pp. 262–271.
- O. Cappé and E. Moulines, On-line expectation–maximization algorithm for latent data models, J. Roy. Stat. Soc. Ser. B: Stat. Methodol. 71, 593 (2009).
- Y. Yang, X. Li, Y. Guan, H. Wang, C. Kong, and J. Jiang, LHP: Logical hypergraph link prediction, Expert Syst. Appl. 222, 119842 (2023).
- M. Mitzenmacher, A brief history of generative models for power law and lognormal distributions, Internet Math. 1, 226 (2004).
- A.-L. Barabási and R. Albert, Emergence of scaling in random networks, Science 286, 509 (1999).
- S. R. Gallagher and D. S. Goldberg, Clustering coefficients in protein interaction hypernetworks, in Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM, Washington, DC, 2013), pp. 552–560.
- A. P. Dempster, N. M. Laird, and D. B. Rubin, Maximum likelihood from incomplete data via the EM algorithm, J. R. Stat. Soc. B 39, 1 (1977).
- N. W. Landry, M. Lucas, I. Iacopini, G. Petri, A. Schwarze, A. Patania, and L. Torres, XGI: A python package for higher-order interaction networks, J. Open Source Softw. 8, 5162 (2023).
- N. Menand and C. Seshadhri, Link prediction using low-dimensional node embeddings: The measurement problem, Proc. Natl. Acad. Sci. USA 121, e2312527121 (2024).
- C. Anderson, The end of theory: The data deluge makes the scientific method obsolete, Wired Mag. 16, 16 (2008).
- https://github.com/hexie1995/HyperGraph/tree/prod.