A roadmap for the computation of persistent homology
Nina Otter,Nina Otter,Mason A. Porter,Mason A. Porter,Ulrike Tillmann,Ulrike Tillmann,Peter Grindrod,Heather A. Harrington +7 more
TLDR
A friendly introduction to PH is given, the pipeline for the computation of PH is navigated with an eye towards applications, and a range of synthetic and real-world data sets are used to evaluate currently available open-source implementations for the computations of PH.Abstract:
Persistent homology (PH) is a method used in topological data analysis (TDA) to study qualitative features of data that persist across multiple scales. It is robust to perturbations of input data, independent of dimensions and coordinates, and provides a compact representation of the qualitative features of the input. The computation of PH is an open area with numerous important and fascinating challenges. The field of PH computation is evolving rapidly, and new algorithms and software implementations are being updated and released at a rapid pace. The purposes of our article are to (1) introduce theory and computational methods for PH to a broad range of computational scientists and (2) provide benchmarks of state-of-the-art implementations for the computation of PH. We give a friendly introduction to PH, navigate the pipeline for the computation of PH with an eye towards applications, and use a range of synthetic and real-world data sets to evaluate currently available open-source implementations for the computation of PH. Based on our benchmarking, we indicate which algorithms and implementations are best suited to different types of data sets. In an accompanying tutorial, we provide guidelines for the computation of PH. We make publicly available all scripts that we wrote for the tutorial, and we make available the processed version of the data sets used in the benchmarking.read more
Citations
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References
More filters
Journal ArticleDOI
Collective dynamics of small-world networks
TL;DR: Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.
Book
Finding Groups in Data: An Introduction to Cluster Analysis
TL;DR: An electrical signal transmission system, applicable to the transmission of signals from trackside hot box detector equipment for railroad locomotives and rolling stock, wherein a basic pulse train is transmitted whereof the pulses are of a selected first amplitude and represent a train axle count.
BookDOI
Finding Groups in Data
TL;DR: In this article, an electrical signal transmission system for railway locomotives and rolling stock is proposed, where a basic pulse train is transmitted whereof the pulses are of a selected first amplitude and represent a train axle count, and a spike pulse of greater selected amplitude is transmitted, occurring immediately after the axle count pulse to which it relates, whenever an overheated axle box is detected.
Journal ArticleDOI
Novel Type of Phase Transition in a System of Self-Driven Particles
TL;DR: Numerical evidence is presented that this model results in a kinetic phase transition from no transport to finite net transport through spontaneous symmetry breaking of the rotational symmetry.