HERMES: Persistent spectral graph software

Persistent homology (PH) is one of the most popular tools in topological data analysis (TDA), while graph theory has had a significant impact on data science. Our earlier work introduced the persistent spectral graph (PSG) theory as a unified multiscale paradigm to encompass TDA and geometric analysis. In PSG theory, families of persistent Laplacians (PLs) corresponding to various topological dimensions are constructed via a filtration to sample a given dataset at multiple scales. The harmonic spectra from the null spaces of PLs offer the same topological invariants, namely persistent Betti numbers, at various dimensions as those provided by PH, while the non-harmonic spectra of PLs give rise to additional geometric analysis of the shape of the data. In this work, we develop an open-source software package, called highly efficient robust multidimensional evolutionary spectra (HERMES), to enable broad applications of PSGs in science, engineering, and technology. To ensure the reliability and robustness of HERMES, we have validated the software with simple geometric shapes and complex datasets from three-dimensional (3D) protein structures. We found that the smallest non-zero eigenvalues are very sensitive to data abnormality.