MuRiT: Efficient Computation of Pathwise Persistence Barcodes in Multi-Filtered Flag Complexes via Vietoris-Rips Transformations

TL;DR

MuRiT is a scalable algorithm that efficiently computes pathwise persistence barcodes in multi-filtered flag complexes using Vietoris-Rips transformations, aiding in multi-parameter persistent homology analysis of complex data.

Contribution

The paper introduces the Vietoris-Rips transformation and MuRiT algorithm, enabling efficient computation of pathwise persistence barcodes in multi-filtered complexes, with practical implementation and real-world application.

Findings

MuRiT efficiently computes pathwise persistence barcodes.

The software implementation leverages Ripser for computation.

MuRiT is applied to SARS-CoV-2 evolution data.

Abstract

Multi-parameter persistent homology naturally arises in applications of persistent topology to data that come with extra information depending on additional parameters, like for example time series data. We introduce the concept of a Vietoris-Rips transformation, a method that reduces the computation of the one-parameter persistent homology of pathwise subcomplexes in multi-filtered flag complexes to the computation of the Vietoris-Rips persistent homology of certain semimetric spaces. The corresponding pathwise persistence barcodes track persistence features of the ambient multi-filtered complex and can in particular be used to recover the rank invariant in multi-parameter persistent homology. We present MuRiT, a scalable algorithm that computes the pathwise persistence barcodes of multi-filtered flag complexes by means of Vietoris-Rips transformations. Moreover, we provide an efficient software implementation of the MuRiT algorithm which resorts to Ripser for the actual computation of Vietoris-Rips persistence barcodes. To demonstrate the applicability of MuRiT to real-world datasets, we establish MuRiT as part of our CoVtRec pipeline for the surveillance of the convergent evolution of the coronavirus SARS-CoV-2 in the current COVID-19 pandemic.