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README: CliqueTop

CliqueTop is a collection of matlab scripts for doing topological analysis of symmetric matrices.

The syntax for using the package is


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. These should function automatically without installation, except Perseus on a mac, for which you should open the Perseus folder and double-click the PerseusMac icon after downloading to complete setup:

  • For persistent homology computations, we make use of Perseus by Vidit Nanda. As of this writing, the current version can be found at 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

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])


Topological data analysis tools for cross correlation matrices







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