CliqueTop swMATH ID: 29766 Software Authors: Giusti C Description: 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]) Homepage: https://github.com/nebneuron/clique-top Source Code: https://github.com/nebneuron/clique-top Dependencies: Matlab Related Software: Holes; Ripser; GitHub; javaPlex; PersistenceImages; Gudhi; SciPy; Brain Connectivity Toolbox; Eirene; NetworkX; Dionysus; GenLouvain; Ripser.py; Statsmodels; Python; AGL-Score; DioDe; TopologyNet; HERMES; DIPHA Cited in: 30 Documents Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year Clique topology reveals intrinsic geometric structure in neural correlations. Zbl 1355.92015Giusti, Chad; Pastalkova, Eva; Curto, Carina; Itskov, Vladimir 2015 all top 5 Cited by 95 Authors 4 Curto, Carina Pamela 2 Bassett, Danielle S. 2 Giusti, Chad 2 Hernández Serrano, Daniel 2 Kališnik Verovšek, Sara 2 Mémoli, Facundo 2 Nie, Chun-Xiao 2 Sánchez Gómez, Darío 1 Baas, Nils Andreas 1 Battiston, Federico 1 Belton, Robin Lynne 1 Benson, Austin R. 1 Bergomi, Mattia Giuseppe 1 Beshkov, Kosio 1 Betzel, Richard F. 1 Bianconi, Ginestra 1 Blevins, Ann Sizemore 1 Bubenik, Peter 1 Buchet, Mickaël 1 Cencetti, Giulia 1 Centeno, Eduarda Gervini Zampieri 1 Chen, Jiahui 1 Chowdhury, Samir 1 Crawford, Lorin 1 Ding, Li 1 Douw, Linda 1 Dunn, Benjamin 1 Eliassi-Rad, Tina 1 Escolar, Emerson G. 1 Fasy, Brittany Terese 1 Ferri, Massimo 1 Grange, Pascal 1 Gross, Elizabeth 1 Hernández-Serrano, Juan 1 Horn, Paul S. 1 Hu, Ping 1 Hull, Michael B. 1 Iacopini, Iacopo 1 Itskov, Vladimir 1 Jadbabaie, Ali 1 Jaquette, Jonathan 1 Jeffries, Jack 1 Kahn, Ari 1 Kim, Woojin 1 Latora, Vito 1 Lehn, Christian 1 Leng, Hui 1 Lim, Lek-Heng 1 Limic, Vlada 1 Lippner, Gábor 1 Lucas, Maxime 1 Mertz, Rostik 1 Micka, Samuel 1 Millman, David L. 1 Monod, Anthea 1 Moreni, Giulia 1 Morrison, Katherine 1 Mulder, Daan 1 Naitzat, Gregory 1 Omar, Mohamed 1 Paik, Joshua 1 Pastalkova, Eva 1 Patania, Alice 1 Patel, Dhruv V. 1 Patiño-Galindo, Juan Ángel 1 Petri, Giovanni 1 Ribando-Gros, Emily 1 Rivin, Igor 1 Rosen, Zvi 1 Rybakken, Erik 1 Salinas, Daniel 1 Santos, Fernando Antônio Nóbrega 1 Schaub, Michael T. 1 Schenfisch, Anna 1 Schupbach, Jordan 1 Schweinhart, Benjamin 1 Shiu, Anne 1 Sizemore, Ann E. 1 Small, Michael 1 Tiesinga, Paul H. E. 1 Tong, Yiying 1 Torres, Leo 1 Vettel, Jean M. 1 Vriend, Chris 1 Wang, Dong 1 Wang, Rui 1 Wei, Guowei 1 Whittle, Benjamin 1 Williams, Lucia 1 Young, Jean-Gabriel 1 Youngs, Nora 1 Zhao, Rundong 1 Zhao, Yi 1 Zhitnikov, Andrey 1 Zuffi, Lorenzo all top 5 Cited in 24 Serials 2 SIAM Review 2 Communications in Nonlinear Science and Numerical Simulation 2 SIAM Journal on Applied Algebra and Geometry 1 Biological Cybernetics 1 Inverse Problems 1 Journal of Statistical Physics 1 Physics Letters. A 1 Physics Reports 1 Chaos, Solitons and Fractals 1 Applied Mathematics and Computation 1 Advances in Applied Mathematics 1 Discrete & Computational Geometry 1 Neural Computation 1 Computational Geometry 1 Proceedings of the National Academy of Sciences of the United States of America 1 Bulletin of the American Mathematical Society. New Series 1 International Journal of Bifurcation and Chaos in Applied Sciences and Engineering 1 Journal of Computational Neuroscience 1 Complexity 1 Journal of Machine Learning Research (JMLR) 1 Communications in Applied and Industrial Mathematics 1 Journal of Applied and Computational Topology 1 Computational and Mathematical Biophysics 1 Foundations of Data Science all top 5 Cited in 18 Fields 15 Algebraic topology (55-XX) 12 Biology and other natural sciences (92-XX) 11 Combinatorics (05-XX) 7 Game theory, economics, finance, and other social and behavioral sciences (91-XX) 6 Statistics (62-XX) 5 Computer science (68-XX) 3 Information and communication theory, circuits (94-XX) 2 Commutative algebra (13-XX) 2 Algebraic geometry (14-XX) 2 Dynamical systems and ergodic theory (37-XX) 2 Probability theory and stochastic processes (60-XX) 2 Statistical mechanics, structure of matter (82-XX) 2 Operations research, mathematical programming (90-XX) 1 General and overarching topics; collections (00-XX) 1 Measure and integration (28-XX) 1 General topology (54-XX) 1 Manifolds and cell complexes (57-XX) 1 Systems theory; control (93-XX) Citations by Year