Wasserstein Dictionaries of Persistence Diagrams
This work provides a computational tool for topological data analysis, offering efficient compression and visualization of persistence diagrams, which is incremental but practically useful for researchers in that domain.
The paper tackles the problem of efficiently encoding ensembles of persistence diagrams by introducing a framework that computes Wasserstein dictionaries as weighted barycenters of atom diagrams, achieving computations in minutes for large examples. It demonstrates utility in data reduction and dimensionality reduction applications with quantitative assessments.
This paper presents a computational framework for the concise encoding of an ensemble of persistence diagrams, in the form of weighted Wasserstein barycenters [100], [102] of a dictionary of atom diagrams. We introduce a multi-scale gradient descent approach for the efficient resolution of the corresponding minimization problem, which interleaves the optimization of the barycenter weights with the optimization of the atom diagrams. Our approach leverages the analytic expressions for the gradient of both sub-problems to ensure fast iterations and it additionally exploits shared-memory parallelism. Extensive experiments on public ensembles demonstrate the efficiency of our approach, with Wasserstein dictionary computations in the orders of minutes for the largest examples. We show the utility of our contributions in two applications. First, we apply Wassserstein dictionaries to data reduction and reliably compress persistence diagrams by concisely representing them with their weights in the dictionary. Second, we present a dimensionality reduction framework based on a Wasserstein dictionary defined with a small number of atoms (typically three) and encode the dictionary as a low dimensional simplex embedded in a visual space (typically in 2D). In both applications, quantitative experiments assess the relevance of our framework. Finally, we provide a C++ implementation that can be used to reproduce our results.