CliqueTop

CliqueTop is a collection of matlab scripts for doing topological analysis of symmetric matrices. The syntax for using the package is: ompute_clique_topology(A) for any symmetric matrix A. Options and details can be found in the documentation for the compute_clique_topology function. CliqueTop currently relies on the following software packages, which are included in this repository for convenience and should function automatically without installation: For persistent homology computations, we make use of Perseus by Vidit Nanda. As of this writing, the current version can be found at http://www.sas.upenn.edu/ vnanda/perseus/index.html. We recommend using the snapshot provided in this repository, as the input/output format for Perseus may change in the future. Cliquer, for the clique splitting version of the clique enumeration algorithm, a C package by Sampo Niskanen and Patric R. J. Östergård, available at http://users.aalto.fi/ pat/cliquer.html. The code was written by Chad Giusti, and the underlying ideas are the result of joint work with Vladimir Itskov and Carina Curto. The work was supported by NSF DMS-1122519. More details can be found in Giusti, Pastalkova, Curto and Itskov, ”Clique topology reveals instrinsic geometric structure in neural correlations.” (arXiv:1502.06172 [q-bio.NC] and arXiv:1502.06173 [q-bio.NC])


References in zbMATH (referenced in 31 articles , 1 standard article )

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  1. Beshkov, Kosio; Tiesinga, Paul: Geodesic-based distance reveals nonlinear topological features in neural activity from mouse visual cortex (2022)
  2. Nie, Chun-Xiao: Topological energy of the distance matrix (2022)
  3. Centeno, Eduarda Gervini Zampieri; Moreni, Giulia; Vriend, Chris; Douw, Linda; Santos, Fernando Antônio Nóbrega: A Python hands-on tutorial on network and topological neuroscience (2021)
  4. Curto, Carina; Paik, Joshua; Rivin, Igor: Betti curves of rank one symmetric matrices (2021)
  5. Dai, X.; Kovalenko, K.; Molodyk, M.; Wang, Z.; Li, X.; Musatov, D.; Raigorodskii, A. M.; Alfaro-Bittner, K.; Cooper, G. D.; Bianconi, G.; Boccaletti, S.: (D)-dimensional oscillators in simplicial structures: odd and even dimensions display different synchronization scenarios (2021)
  6. Kališnik, Sara; Lehn, Christian; Limic, Vlada: Geometric and probabilistic limit theorems in topological data analysis (2021)
  7. Kim, Woojin; Mémoli, Facundo: Spatiotemporal persistent homology for dynamic metric spaces (2021)
  8. Torres, Leo; Blevins, Ann S.; Bassett, Danielle; Eliassi-Rad, Tina: The why, how, and when of representations for complex systems (2021)
  9. Wang, Rui; Zhao, Rundong; Ribando-Gros, Emily; Chen, Jiahui; Tong, Yiying; Wei, Guo-Wei: HERMES: persistent spectral graph software (2021)
  10. Battiston, Federico; Cencetti, Giulia; Iacopini, Iacopo; Latora, Vito; Lucas, Maxime; Patania, Alice; Young, Jean-Gabriel; Petri, Giovanni: Networks beyond pairwise interactions: structure and dynamics (2020)
  11. Belton, Robin Lynne; Fasy, Brittany Terese; Mertz, Rostik; Micka, Samuel; Millman, David L.; Salinas, Daniel; Schenfisch, Anna; Schupbach, Jordan; Williams, Lucia: Reconstructing embedded graphs from persistence diagrams (2020)
  12. Bergomi, Mattia G.; Ferri, Massimo; Zuffi, Lorenzo: Topological graph persistence (2020)
  13. Bubenik, Peter; Hull, Michael; Patel, Dhruv; Whittle, Benjamin: Persistent homology detects curvature (2020)
  14. Grange, Pascal: Topology of the mesoscale connectome of the mouse brain (2020)
  15. Hernández Serrano, Daniel; Hernández-Serrano, Juan; Sánchez Gómez, Darío: Simplicial degree in complex networks. Applications of topological data analysis to network science (2020)
  16. Hernández Serrano, Daniel; Sánchez Gómez, Darío: Centrality measures in simplicial complexes: applications of topological data analysis to network science (2020)
  17. Jaquette, Jonathan; Schweinhart, Benjamin: Fractal dimension estimation with persistent homology: a comparative study (2020)
  18. Naitzat, Gregory; Zhitnikov, Andrey; Lim, Lek-Heng: Topology of deep neural networks (2020)
  19. Nie, Chun-Xiao: Nonlinear correlation analysis of time series based on complex network similarity (2020)
  20. Schaub, Michael T.; Benson, Austin R.; Horn, Paul; Lippner, Gabor; Jadbabaie, Ali: Random walks on simplicial complexes and the normalized Hodge 1-Laplacian (2020)

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