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arXiv · 2107.05412

giotto-ph: A Python Library for High-Performance Computation of Persistent Homology of Vietoris-Rips Filtrations

Julián Burella Pérez·Sydney Hauke·Umberto Lupo·Matteo Caorsi·Alberto Dassatti
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Abstract

We introduce giotto-ph, a high-performance, open-source software package for the computation of Vietoris-Rips barcodes. giotto-ph is based on Morozov and Nigmetov's lockfree (multicore) implementation of Ulrich Bauer's Ripser package. It also contains a re-working of the GUDHI library's implementation of Boissonnat and Pritam's Edge Collapser, which can be used as a pre-processing step to dramatically reduce overall run-times in certain scenarios. Our contribution is twofold: on the one hand, we integrate existing state-of-the-art ideas coherently in a single library and provide Python bindings to the C++ code. On the other hand, we increase parallelization opportunities and improve overall performance by adopting more efficient data structures. Our persistent homology backend establishes a new state of the art, surpassing even GPU-accelerated implementations such as Ripser++ when using as few as 5-10 CPU cores. Furthermore, our implementation of Edge Collapser has fewer software dependencies and improved run-times relative to GUDHI's original implementation.

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Julián Burella Pérez, Sydney Hauke, Umberto Lupo, Matteo Caorsi, Alberto Dassatti. 2021-07-12. giotto-ph: A Python Library for High-Performance Computation of Persistent Homology of Vietoris-Rips Filtrations. https://arxiv.org/abs/2107.05412

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