Topological structures such as the merge tree provide an abstract and succinct representation of scalar fields. They facilitate effective visualization and interactive exploration of feature-rich data. A merge tree captures the topology of sub-level and super-level sets in a scalar field. Estimating the similarity between merge trees is an important problem with applications to feature-directed visualization of time-varying data. We present an approach based on tree edit distance to compare merge trees. The comparison measure satisfies metric properties, it can be computed efficiently, and the cost model for the edit operations is both intuitive and captures well-known properties of merge trees. Experimental results on time-varying scalar fields, 3D cryo electron microscopy data, shape data, and various synthetic datasets show the utility of the edit distance towards a feature-driven analysis of scalar fields.
Edit distances between merge trees of scalar fields have many applications in scientific visualization, such as ensemble analysis, feature tracking or symmetry detection. In this paper, we propose branch mappings, a novel approach to the construction of edit mappings for merge trees. Classic edit mappings match nodes or edges of two trees onto each other, and therefore have to either rely on branch decompositions of both trees or have to use auxiliary node properties to determine a matching. In contrast, branch mappings employ branch properties instead of node similarity information, and are i…
A merge tree is a topological descriptor of a real-valued function. Merge trees are used in visualization and topological data analysis, either directly or as a means to another end: computing a 0-dimensional persistence diagram, identifying connected components, performing topological simplification, etc. Scientific computing relies more and more on GPUs to achieve fast, scalable computation. For efficiency, data analysis should take place at the same location as the main computation, which motivates interest in parallel algorithms and portable software for merge trees that can run not only o…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by defining a tree structure on them (e.g. medial axis and contour trees). Hence, it is natural to study the problem of comparing similarity between trees. We study gapped edit distance between two ordered labeled trees, first proposed by Touzet \cite{Touzet2003}. Given two binary trees $T_{1}$ and $T_{2}$ with $m$ and $n$ nodes. We compute the general gap edit dis…
Distances on merge trees facilitate visual comparison of collections of scalar fields. Two desirable properties for these distances to exhibit are 1) the ability to discern between scalar fields which other, less complex topological summaries cannot and 2) to still be robust to perturbations in the dataset. The combination of these two properties, known respectively as stability and discriminativity, has led to theoretical distances which are either thought to be or shown to be computationally complex and thus their implementations have been scarce. In order to design similarity measures on me…
Australian National University（澳大利亚国立大学）；University of Utah（犹他大学）；Ohio State University（俄亥俄州立大学）；Union College（联合学院）；Michigan State University（密歇根州立大学）；Inria Saclay（法国国家信息与自动化研究所萨克莱中心）
Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First, they give compressed and topology-preserving representations of data instances. Second, their comparisons provide a basis for studying the relations among data instances, such as their distributions, clusters, outliers, and periodicities. A number of comparative measures have been developed for merge trees. However, these measures are often computationally expe…
University of Utah（犹他大学）；Michigan State University（密歇根州立大学）
Merge trees are a type of topological descriptors that record the connectivity among the sublevel sets of scalar fields. They are among the most widely used topological tools in visualization. In this paper, we are interested in sketching a set of merge trees. That is, given a large set T of merge trees, we would like to find a much smaller basis set S such that each tree in T can be approximately reconstructed from a linear combination of merge trees in S. A set of high-dimensional vectors can be sketched via matrix sketching techniques such as principal component analysis and column subset s…
Physical phenomena in science and engineering are frequently modeled using scalar fields. In scalar field topology, graph-based topological descriptors such as merge trees, contour trees, and Reeb graphs are commonly used to characterize topological changes in the (sub)level sets of scalar fields. One of the biggest challenges and opportunities to advance topology-based visualization is to understand and incorporate uncertainty into such topological descriptors to effectively reason about their underlying data. In this paper, we study a structural average of a set of labeled merge trees and us…
The purpose of this paper is to extend the definition of Frechet distance which measures the distance between two curves to a distance (Frechet-Like distance) which measures the similarity between two rooted trees. The definition of Frechet-Like distance is as follows: Tow men start from the roots of two trees. When they reach to a node with the degree of more than $2$, they construct $k-1$ men which $k$ is the outgoing degree of the node and each man monitor a man in another tree (there is a rope between them). The distance is the minimum length of the ropes between the men and the men whom a…
University at Albany, State University of New York (SUNY)（纽约州立大学奥尔巴尼分校）
Adapting a definition given by Bjerkevik and Lesnick for multiparameter persistence modules, we introduce an $\ell^p$-type extension of the interleaving distance on merge trees. We show that our distance is a metric, and that it upper-bounds the $p$-Wasserstein distance between the associated barcodes. For each $p\in[1,\infty]$, we prove that this distance is stable with respect to cellular sublevel filtrations and that it is the universal (i.e., largest) distance satisfying this stability property. In the $p=\infty$ case, this gives a novel proof of universality for the interleaving distance …
This thesis consists of two topics related to computational geometry and one topic related to topological data analysis (TDA), which combines fields of computational geometry and algebraic topology for analyzing data. The first part studies the classical problem of finding k nearest neighbors to m query points in a larger set of n reference points in any metric space. The second part is about the construction of a Minimum Spanning Tree (MST) on any finite metric space. The third part extends the key concept of persistence within Topological Data Analysis in a new direction.
In this paper we introduce the horizon visibility graph, a simple extension to the popular horizontal visibility graph representation of a time series, and show that it possesses a rigorous mathematical foundation in computational algebraic topology. This fills a longstanding gap in the literature on the horizontal visibility approach to nonlinear time series analysis which, despite a suite of successful applications across multiple domains, lacks a formal setting in which to prove general properties and develop natural extensions. The main finding is that horizon visibility graphs are dual to…
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 decompositio…
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 appr…
