REFERENCES

1. Yan, J.; Risacher, S. L.; Shen, L.; Saykin, A. J. Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data. Brief. Bioinform. 2018, 19, 1370-81.

2. Baião, A. R.; Cai, Z.; Poulos, R. C.; et al. A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches. Brief. Bioinform. 2025, 26, bbaf355.

3. Li, J.; Liao, Q.; Zhou, H.; et al. Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum. Nat. Commun. 2025, 16, 10339.

4. Wright, S. N.; Colton, S.; Schaffer, L. V.; et al. State of the interactomes: an evaluation of molecular networks for generating biological insights. Mol. Syst. Biol. 2025, 21, 1-29.

5. Köhler, D.; Rügamer, D.; Boyle, L. J.; Maloney, K. O.; Schmid, M. Achieving interpretable machine learning by functional decomposition of black-box models into explainable predictor effects. npj. Artif. Intell. 2025, 1, 34.

6. Murdoch, W. J.; Singh, C.; Kumbier, K.; Abbasi-Asl, R.; Yu, B. Interpretable machine learning: definitions, methods, and applications. arXiv 2019, arXiv: 190104592.

7. Lagemann, K.; Lagemann, C.; Taschler, B.; Mukherjee, S. Deep learning of causal structures in high dimensions under data limitations. Nat. Mach. Intell. 2023, 5, 1306-16.

8. Rudin, C.; Chen, C.; Chen, Z.; Huang, H.; Semenova, L.; Zhong, C. Interpretable machine learning: fundamental principles and 10 grand challenges. Statist. Surv. 2022, 16.

9. Bick, C.; Gross, E.; Harrington, H. A.; Schaub, M. T. What are higher-order networks? SIAM. Rev. 2023, 65, 686-731.

10. Majhi, S.; Perc, M.; Ghosh, D. Dynamics on higher-order networks: a review. J. R. Soc. Interface. 2022, 19, 20220043.

11. Zhang, Y.; Lucas, M.; Battiston, F. Higher-order interactions shape collective dynamics differently in hypergraphs and simplicial complexes. Nat. Commun. 2023, 14, 1605.

12. Bian, J.; Zhou, T.; Bi, Y. Unveiling the role of higher-order interactions via stepwise reduction. Commun. Phys. 2025, 8, 228.

13. Terry, J. C. D.; Bonsall, M. B.; Morris, R. J. The impact of structured higher-order interactions on ecological network stability. Theor. Ecol. 2025, 18, 9.

14. Lucas, M.; Gallo, L.; Ghavasieh, A.; Battiston, F.; De Domenico, M. Reducibility of higher-order networks via information flow. arXiv 2024, arXiv: 240408547.

15. Kim, S.; Lee, S. Y.; Gao, Y.; Antelmi, A.; Polato, M.; Shin, K. A survey on hypergraph neural networks: an in-depth and step-by-step guide. In Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining; 2024. pp. 6534-44.

16. Boccaletti, S.; De Lellis, P.; Del Genio, C.; et al. The structure and dynamics of networks with higher order interactions. Phys. Rep. 2023, 1018, 1-64.

17. Lambiotte, R.; Rosvall, M.; Scholtes, I. From networks to optimal higher-order models of complex systems. Nat. Phys. 2019, 15, 313-20.

18. Coyte, K. Z.; Schluter, J.; Foster, K. R. The ecology of the microbiome: networks, competition, and stability. Science 2015, 350, 663-6.

19. Grilli, J.; Barabás, G.; Michalska-Smith, M. J.; Allesina, S. Higher-order interactions stabilize dynamics in competitive network models. Nature 2017, 548, 210-3.

20. Battiston, F.; Amico, E.; Barrat, A.; et al. The physics of higher-order interactions in complex systems. Nat. Phys. 2021, 17, 1093-8.

21. Liu, C.; Ma, Y.; Zhao, J.; et al. Computational network biology: data, models, and applications. Phys. Rep. 2020, 846, 1-66.

22. Wang, Y.; Li, A.; Wang, L. Networked dynamic systems with higher-order interactions: stability versus complexity. Natl. Sci. Rev. 2024, 11, nwae103.

23. Wang, Y.; Kleinberg, J. From graphs to hypergraphs: hypergraph projection and its remediation. arXiv 2024, arXiv: 240108519.

24. Tian, H.; Zafarani, R. Higher-order networks representation and learning: a survey. ACM. SIGKDD. Explor. Newsl. 2024, 26, 1-18.

25. Shang, Y. Non-linear consensus dynamics on temporal hypergraphs with random noisy higher-order interactions. J. Complex. Netw. 2023, 11, cnad009.

26. Shang, Y. A system model of three-body interactions in complex networks: consensus and conservation. Proc. R. Soc. A. 2022, 478, 20210564.

27. Shang, Y. Percolation in random hypergraphs with anchor nodes. Phys. Rev. E. 2025, 111, 054304.

28. Skardal, P.S.; Arenas, A. Higher order interactions in complex networks of phase oscillators promote abrupt synchronization switching. Commun. Phys. 2020, 3, 218.

29. Champion, K.; Lusch, B.; Kutz, J. N.; Brunton, S. L. Data-driven discovery of coordinates and governing equations. Proc. Natl. Acad. Sci. USA. 2019, 116, 22445-51.

30. Brunton, S. L.; Proctor, J. L.; Kutz, J. N. Discovering governing equations from data by sparse identification of nonlinear dynamical systems. Proc. Natl. Acad. Sci. USA. 2016, 113, 3932-7.

31. Battiston, F.; Bick, C.; Lucas, M.; Millán, A. P.; Skardal, P. S.; Zhang, Y. Collective dynamics on higher-order networks. Nat. Rev. Phys. 2026, 8, 146-59.

32. Delabays, R.; De Pasquale, G.; Dorfler, F.; Zhang, Y. Hypergraph reconstruction from dynamics. Nat. Commun. 2025, 16, 2691.

33. Antelmi, A.; Cordasco, G.; Polato, M.; Scarano, V.; Spagnuolo, C.; Yang, D. A survey on hypergraph representation learning. ACM. Comput. Surv. 2023, 56, 1-38.

34. Zhang, Y.; Khan, S. A.; Mahmud, A.; Yang, H.; Lavin, A.; et al. Exploring the role of large language models in the scientific method: from hypothesis to discovery. NPJ. Artif. Intell. 2025, 1, 14.

35. Zheng, T.; Deng, Z.; Tsang, H. T.; et al. From automation to autonomy: a survey on large language models in scientific discovery. In Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing; 2025. pp. 17744-61.

36. Alkan, A. K.; Sourav, S.; Jablonska, M, et al. A survey on hypothesis generation for scientific discovery in the era of large language models. arXiv 2025, arXiv: 250405496.

37. Gridach, M.; Nanavati, J.; Abidine, K. Z. E.; Mendes, L.; Mack, C. Agentic ai for scientific discovery: a survey of progress, challenges, and future directions. arXiv 2025, arXiv: 250308979.

Complex Engineering Systems
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