javaPlex: A Research Software Package for Persistent (Co)Homology

By Henry Adams, A. Tausz, Mikael Vejdemo-Johansson. International Congress on Mathematical Software, 2014

301 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Ripser: efficient computation of Vietoris–Rips persistence barcodes (2019, background): “The computation of persistent homology has attracted strong interest in recent years [7, 23], with at least 14 different implementations publicly available to date [2–4, 15, 17, 21, 24, 25, 28, 30, 31, 33–36].”
On the topology of random complexes built over stationary point processes. (2012, methodology): “4These barcodes were simulated using the easy-to-use and open access package javaPlex [39].”
Persistent homology analysis of protein structure, flexibility and folding (2014, methodology): “In this work, all the computations are carried out by using Javaplex [72] and the persistent diagram is visualized through barcodes [47].”
Clique topology reveals intrinsic geometric structure in neural correlations (2015, methodology): “Several software packages [19, 20, 21] have been developed based on the persistence algorithm, and recent work using discrete Morse theory has led to further improvements in speed and memory efficiency [22].”
Statistical topological data analysis using persistence landscapes (2012, methodology): “Examples The persistent homologies in this section were calculated using javaPlex (Tausz et al., 2011) and Perseus by Nanda (2013).”
Topological Consistency via Kernel Estimation (2014, background): “Note that there are several eﬃcient algorithms to compute persistent homology that can also be used here (see [23, 34, 43]).”