Persistent spectral graph

Rui Wang, Duc Duy Nguyen, Guo Wei Wei

Research output: Contribution to journalArticlepeer-review

19 Scopus citations

Abstract

Persistent homology is constrained to purely topological persistence, while multiscale graphs account only for geometric information. This work introduces persistent spectral theory to create a unified low-dimensional multiscale paradigm for revealing topological persistence and extracting geometric shapes from high-dimensional datasets. For a point-cloud dataset, a filtration procedure is used to generate a sequence of chain complexes and associated families of simplicial complexes and chains, from which we construct persistent combinatorial Laplacian matrices. We show that a full set of topological persistence can be completely recovered from the harmonic persistent spectra, that is, the spectra that have zero eigenvalues, of the persistent combinatorial Laplacian matrices. However, non-harmonic spectra of the Laplacian matrices induced by the filtration offer another powerful tool for data analysis, modeling, and prediction. In this work, fullerene stability is predicted by using both harmonic spectra and non-harmonic persistent spectra, while the latter spectra are successfully devised to analyze the structure of fullerenes and model protein flexibility, which cannot be straightforwardly extracted from the current persistent homology. The proposed method is found to provide excellent predictions of the protein B-factors for which current popular biophysical models break down.

Original languageEnglish
Article numbere3376
JournalInternational Journal for Numerical Methods in Biomedical Engineering
Volume36
Issue number9
DOIs
StatePublished - Sep 1 2020

Bibliographical note

Funding Information:
This work was supported in part by NSF Grants DMS1721024, DMS1761320, IIS1900473, NIH grants GM126189 and GM129004, Bristol‐Myers Squibb, and Pfizer. RW thanks Dr. Jiahui Chen and Dr. Zixuan Cang for useful discussions.

Funding Information:
This work was supported in part by NSF Grants DMS1721024, DMS1761320, IIS1900473, NIH grants GM126189 and GM129004, Bristol-Myers Squibb, and Pfizer. RW thanks Dr. Jiahui Chen and Dr. Zixuan Cang for useful discussions.

Publisher Copyright:
© 2020 John Wiley & Sons, Ltd.

Keywords

  • persistent spectral analysis
  • persistent spectral graph
  • persistent spectral theory
  • spectral data analysis

ASJC Scopus subject areas

  • Software
  • Biomedical Engineering
  • Modeling and Simulation
  • Molecular Biology
  • Computational Theory and Mathematics
  • Applied Mathematics

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