javaPlex

javaPlex - an extensible platform for persistence. javaPlex is the newest member of the Stanford-based Plex family of persistent homology and cohomology software packages. Written in Java, it is optimized for easy interfacing with Matlab as well as anything running in the Java ecosystem - including Processing, Scala, Jython, and Mathematica. javaPlex was written to create a platform easier to extend and experiment with than its predecessor jPlex. In its last release, the platform support absolute and relative persistence (co)homology, as well as hom-complexes of simplicial complexes, cellular and simplicial complex constructions and fast Vietoris-Rips and witness complex constructions. We will demonstrate the architecture, usage, development and extension features of javaPlex, focusing on interoperability with Matlab as an interface to the library.


References in zbMATH (referenced in 39 articles , 1 standard article )

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  1. Watanabe, Satoru; Yamana, Hayato: Topological measurement of deep neural networks using persistent homology (2022)
  2. Zhao, Yan; Wang, Yanying; Ding, Yanhong; Han, Huiyun: Topological data analysis for the energy and stability of endohedral metallofullerenes (2022)
  3. Bauer, Ulrich: Ripser: efficient computation of Vietoris-Rips persistence barcodes (2021)
  4. Luo, Hengrui; Patania, Alice; Kim, Jisu; Vejdemo-Johansson, Mikael: Generalized penalty for circular coordinate representation (2021)
  5. Wang, Rui; Zhao, Rundong; Ribando-Gros, Emily; Chen, Jiahui; Tong, Yiying; Wei, Guo-Wei: HERMES: persistent spectral graph software (2021)
  6. Adams, Henry; Aminian, Manuchehr; Farnell, Elin; Kirby, Michael; Mirth, Joshua; Neville, Rachel; Peterson, Chris; Shonkwiler, Clayton: A fractal dimension for measures via persistent homology (2020)
  7. Cang, Zixuan; Munch, Elizabeth; Wei, Guo-Wei: Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis (2020)
  8. Charó, Gisela D.; Artana, Guillermo; Sciamarella, Denisse: Topology of dynamical reconstructions from Lagrangian data (2020)
  9. Chowdhury, Samir; Clause, Nathaniel; Mémoli, Facundo; Sánchez, Jose Ángel; Wellner, Zoe: New families of stable simplicial filtration functors (2020)
  10. Ehsan, Tayyaba; Anjum, Hafiz Junaid; Asghar, Saleem: Peristaltic flows: a quantitative measure for the size of a bolus (2020)
  11. Grange, Pascal: Topology of the mesoscale connectome of the mouse brain (2020)
  12. Hart, Allen; Hook, James; Dawes, Jonathan: Embedding and approximation theorems for echo state networks (2020)
  13. Ruehle, Fabian: Data science applications to string theory (2020)
  14. Som, Anirudh; Ramamurthy, Karthikeyan Natesan; Turaga, Pavan: Geometric metrics for topological representations (2020)
  15. Wang, Dong; Zhao, Yi; Leng, Hui; Small, Michael: A social communication model based on simplicial complexes (2020)
  16. Cirafici, Michele: BPS spectra, barcodes and walls (2019)
  17. Cole, Alex; Shiu, Gary: Topological data analysis for the string landscape (2019)
  18. Mémoli, Facundo; Singhal, Kritika: A primer on persistent homology of finite metric spaces (2019)
  19. Salnikov, Vsevolod; Cassese, Daniele; Lambiotte, Renaud: Simplicial complexes and complex systems (2019)
  20. Alan Hylton, Gregory Henselman-Petrusek, Janche Sang, Robert Short: Tuning the Performance of a Computational Persistent Homology Package (2018) arXiv

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