A Generic Software Framework for Distributed Topological Analysis Pipelines

This system paper presents a software framework for the support of topological analysis pipelines in a distributed-memory model. While several recent papers introduced topology-based approaches for distributed-memory environments, these were reporting experiments obtained with tailored, mono-algorithm implementations. In contrast, we describe in this paper a general-purpose, generic framework for topological analysis pipelines, i.e. a sequence of topological algorithms interacting together, possibly on distinct numbers of processes. Specifically, we instantiated our framework with the MPI model, within the Topology ToolKit (TTK). While developing this framework, we faced several algorithmic and software engineering challenges, which we document in this paper. We provide a taxonomy for the distributed-memory topological algorithms supported by TTK, depending on their communication needs and provide examples of hybrid MPI+thread parallelizations. Detailed performance analyses show that parallel efficiencies range from $20\%$ to $80\%$ (depending on the algorithms), and that the MPI-specific preconditioning introduced by our framework induces a negligible computation time overhead. We illustrate the new distributed-memory capabilities of TTK with an example of advanced analysis pipeline, combining multiple algorithms, run on the largest publicly available dataset we have found (120 billion vertices) on a standard cluster with 64 nodes (for a total of 1,536 cores). Finally, we provide a roadmap for the completion of TTK's MPI extension, along with generic recommendations for each algorithm communication category.

Wasserstein Auto-Encoders of Merge Trees (and Persistence Diagrams)

This paper presents a computational framework for the Wasserstein auto-encoding of merge trees (MT-WAE), a novel extension of the classical auto-encoder neural network architecture to the Wasserstein metric space of merge trees. In contrast to traditional auto-encoders which operate on vectorized data, our formulation explicitly manipulates merge trees on their associated metric space at each layer of the network, resulting in superior accuracy and interpretability. Our novel neural network approach can be interpreted as a non-linear generalization of previous linear attempts [65] at merge tree encoding. It also trivially extends to persistence diagrams. Extensive experiments on public ensembles demonstrate the efficiency of our algorithms, with MT-WAE computations in the orders of minutes on average. We show the utility of our contributions in two applications adapted from previous work on merge tree encoding [65]. First, we apply MT-WAE to data reduction and reliably compress merge trees by concisely representing them with their coordinates in the final layer of our auto-encoder. Second, we document an application to dimensionality reduction, by exploiting the latent space of our auto-encoder, for the visual analysis of ensemble data. We illustrate the versatility of our framework by introducing two penalty terms, to help preserve in the latent space both the Wasserstein distances between merge trees, as well as their clusters. In both applications, quantitative experiments assess the relevance of our framework. Finally, we provide a C++ implementation that can be used for reproducibility.

Wasserstein Dictionaries of Persistence Diagrams

This paper presents a computational framework for the concise encoding of an ensemble of persistence diagrams, in the form of weighted Wasserstein barycenters [99], [101] 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.

Topological Analysis of Ensembles of Hydrodynamic Turbulent Flows -- An Experimental Study

This application paper presents a comprehensive experimental evaluation of the suitability of Topological Data Analysis (TDA) for the quantitative comparison of turbulent flows. Specifically, our study documents the usage of the persistence diagram of the maxima of flow enstrophy (an established vorticity indicator), for the topological representation of 180 ensemble members, generated by a coarse sampling of the parameter space of five numerical solvers. We document five main hypotheses reported by domain experts, describing their expectations regarding the variability of the flows generated by the distinct solver configurations. We contribute three evaluation protocols to assess the validation of the above hypotheses by two comparison measures: (i) a standard distance used in scientific imaging (the L2 norm) and (ii) an established topological distance between persistence diagrams (the L2-Wasserstein metric). Extensive experiments on the input ensemble demonstrate the superiority of the topological distance (ii) to report as close to each other flows which are expected to be similar by domain experts, due to the configuration of their vortices. Overall, the insights reported by our study bring an experimental evidence of the suitability of TDA for representing and comparing turbulent flows, thereby providing to the fluid dynamics community confidence for its usage in future work. Also, our flow data and evaluation protocols provide to the TDA community an application-approved benchmark for the evaluation and design of further topological distances.

Principal Geodesic Analysis of Merge Trees (and Persistence Diagrams)

This paper presents a computational framework for the Principal Geodesic Analysis of merge trees (MT-PGA), a novel adaptation of the celebrated Principal Component Analysis (PCA) framework [87] to the Wasserstein metric space of merge trees [92]. We formulate MT-PGA computation as a constrained optimization problem, aiming at adjusting a basis of orthogonal geodesic axes, while minimizing a fitting energy. We introduce an efficient, iterative algorithm which exploits shared-memory parallelism, as well as an analytic expression of the fitting energy gradient, to ensure fast iterations. Our approach also trivially extends to extremum persistence diagrams. Extensive experiments on public ensembles demonstrate the efficiency of our approach - with MT-PGA computations in the orders of minutes for the largest examples. We show the utility of our contributions by extending to merge trees two typical PCA applications. First, we apply MT-PGA to data reduction and reliably compress merge trees by concisely representing them by their first coordinates in the MT-PGA basis. Second, we present a dimensionality reduction framework exploiting the first two directions of the MT-PGA basis to generate two-dimensional layouts of the ensemble. We augment these layouts with persistence correlation views, enabling global and local visual inspections of the feature variability in the ensemble. In both applications, quantitative experiments assess the relevance of our framework. Finally, we provide a lightweight C++ implementation that can be used to reproduce our results.

Discrete Morse Sandwich: Fast Computation of Persistence Diagrams for Scalar Data -- An Algorithm and A Benchmark

This paper introduces an efficient algorithm for persistence diagram computation, given an input piecewise linear scalar field f defined on a d-dimensional simplicial complex K, with $d \leq 3$. Our method extends the seminal "PairCells" algorithm by introducing three main accelerations. First, we express this algorithm within the setting of discrete Morse theory, which considerably reduces the number of input simplices to consider. Second, we introduce a stratification approach to the problem, that we call "sandwiching". Specifically, minima-saddle persistence pairs ($D_0(f)$) and saddle-maximum persistence pairs ($D_{d-1}(f)$) are efficiently computed by respectively processing with a Union-Find the unstable sets of 1-saddles and the stable sets of (d-1)-saddles. This fast processing of the dimensions 0 and (d-1) further reduces, and drastically, the number of critical simplices to consider for the computation of $D_1(f)$, the intermediate layer of the sandwich. Third, we document several performance improvements via shared-memory parallelism. We provide an open-source implementation of our algorithm for reproducibility purposes. We also contribute a reproducible benchmark package, which exploits three-dimensional data from a public repository and compares our algorithm to a variety of publicly available implementations. Extensive experiments indicate that our algorithm improves by two orders of magnitude the time performance of the seminal "PairCells" algorithm it extends. Moreover, it also improves memory footprint and time performance over a selection of 14 competing approaches, with a substantial gain over the fastest available approaches, while producing a strictly identical output. We illustrate the utility of our contributions with an application to the fast and robust extraction of persistent 1-dimensional generators on surfaces, volume data and high-dimensional point clouds.

Wasserstein Distances, Geodesics and Barycenters of Merge Trees

This paper presents a unified computational framework for the estimation of distances, geodesics and barycenters of merge trees. We extend recent work on the edit distance [106] and introduce a new metric, called the Wasserstein distance between merge trees, which is purposely designed to enable efficient computations of geodesics and barycenters. Specifically, our new distance is strictly equivalent to the L2-Wasserstein distance between extremum persistence diagrams, but it is restricted to a smaller solution space, namely, the space of rooted partial isomorphisms between branch decomposition trees. This enables a simple extension of existing optimization frameworks [112] for geodesics and barycenters from persistence diagrams to merge trees. We introduce a task-based algorithm which can be generically applied to distance, geodesic, barycenter or cluster computation. The task-based nature of our approach enables further accelerations with shared-memory parallelism. Extensive experiments on public ensembles and SciVis contest benchmarks demonstrate the efficiency of our approach -- with barycenter computations in the orders of minutes for the largest examples -- as well as its qualitative ability to generate representative barycenter merge trees, visually summarizing the features of interest found in the ensemble. We show the utility of our contributions with dedicated visualization applications: feature tracking, temporal reduction and ensemble clustering. We provide a lightweight C++ implementation that can be used to reproduce our results.

TopoMap: A 0-dimensional Homology Preserving Projection of High-Dimensional Data

Multidimensional Projection is a fundamental tool for high-dimensional data analytics and visualization. With very few exceptions, projection techniques are designed to map data from a high-dimensional space to a visual space so as to preserve some dissimilarity (similarity) measure, such as the Euclidean distance for example. In fact, although adopting distinct mathematical formulations designed to favor different aspects of the data, most multidimensional projection methods strive to preserve dissimilarity measures that encapsulate geometric properties such as distances or the proximity relation between data objects. However, geometric relations are not the only interesting property to be preserved in a projection. For instance, the analysis of particular structures such as clusters and outliers could be more reliably performed if the mapping process gives some guarantee as to topological invariants such as connected components and loops. This paper introduces TopoMap, a novel projection technique which provides topological guarantees during the mapping process. In particular, the proposed method performs the mapping from a high-dimensional space to a visual space, while preserving the 0-dimensional persistence diagram of the Rips filtration of the high-dimensional data, ensuring that the filtrations generate the same connected components when applied to the original as well as projected data. The presented case studies show that the topological guarantee provided by TopoMap not only brings confidence to the visual analytic process but also can be used to assist in the assessment of other projection methods.

Statistical Parameter Selection for Clustering Persistence Diagrams

In urgent decision making applications, ensemble simulations are an important way to determine different outcome scenarios based on currently available data. In this paper, we will analyze the output of ensemble simulations by considering so-called persistence diagrams, which are reduced representations of the original data, motivated by the extraction of topological features. Based on a recently published progressive algorithm for the clustering of persistence diagrams, we determine the optimal number of clusters, and therefore the number of significantly different outcome scenarios, by the minimization of established statistical score functions. Furthermore, we present a proof-of-concept prototype implementation of the statistical selection of the number of clusters and provide the results of an experimental study, where this implementation has been applied to real-world ensemble data sets.

Ranking Viscous Finger Simulations to an Acquired Ground Truth with Topology-aware Matchings

This application paper presents a novel framework based on topological data analysis for the automatic evaluation and ranking of viscous finger simulation runs in an ensemble with respect to a reference acquisition. Individual fingers in a given time-step are associated with critical point pairs in the distance field to the injection point, forming persistence diagrams. Different metrics, based on optimal transport, for comparing time-varying persistence diagrams in this specific applicative case are introduced. We evaluate the relevance of the rankings obtained with these metrics, both qualitatively thanks to a lightweight web visual interface, and quantitatively by studying the deviation from a reference ranking suggested by experts. Extensive experiments show the quantitative superiority of our approach compared to traditional alternatives. Our web interface allows experts to conveniently explore the produced rankings. We show a complete viscous fingering case study demonstrating the utility of our approach in the context of porous media fluid flow, where our framework can be used to automatically discard physically-irrelevant simulation runs from the ensemble and rank the most plausible ones. We document an in-situ implementation to lighten I/O and performance constraints arising in the context of parametric studies.