Elizabeth Munch

Elizabeth Munch, Elena Xinyi Wang, Carola Wenk

The kinetic data structure (KDS) framework is a powerful tool for maintaining various geometric configurations of continuously moving objects. In this work, we introduce the kinetic hourglass, a novel KDS implementation designed to compute the bottleneck distance for geometric matching problems. We detail the events and updates required for handling general graphs, accompanied by a complexity analysis. Furthermore, we demonstrate the utility of the kinetic hourglass by applying it to compute the bottleneck distance between two persistent homology transforms (PHTs) derived from shapes in $\mathbb{R}^2$, which are topological summaries obtained by computing persistent homology from every direction in $\mathbb{S}^1$.

David E. Muñoz, Elizabeth Munch, Firas A. Khasawneh

Directed graphs arise in many applications where computing persistent homology helps to encode the shape and structure of the input information. However, there are only a few ways to turn the directed graph information into an undirected simplicial complex filtration required by the standard persistent homology framework. In this paper, we present a new filtration constructed from a directed graph, called the walk-length filtration. This filtration mirrors the behavior of small walks visiting certain collections of vertices in the directed graph. We show that, while the persistence is not stable under the usual $L_\infty$-style network distance, a generalized $L_1$-style distance is, indeed, stable. We further provide an algorithm for its computation, and investigate the behavior of this filtration in examples, including cycle networks and synthetic hippocampal networks with a focus on comparison to the often used Dowker filtration.

Audun D. Myers, Max M. Chumley, Firas A. Khasawneh et al.

This work is dedicated to the topological analysis of complex transitional networks for dynamic state detection. Transitional networks are formed from time series data and they leverage graph theory tools to reveal information about the underlying dynamic system. However, traditional tools can fail to summarize the complex topology present in such graphs. In this work, we leverage persistent homology from topological data analysis to study the structure of these networks. We contrast dynamic state detection from time series using a coarse-grained state-space network (CGSSN) and topological data analysis (TDA) to two state of the art approaches: ordinal partition networks (OPNs) combined with TDA and the standard application of persistent homology to the time-delay embedding of the signal. We show that the CGSSN captures rich information about the dynamic state of the underlying dynamical system as evidenced by a significant improvement in dynamic state detection and noise robustness in comparison to OPNs. We also show that because the computational time of CGSSN is not linearly dependent on the signal's length, it is more computationally efficient than applying TDA to the time-delay embedding of the time series.

Audun Myers, Firas A. Khasawneh, Elizabeth Munch

One of the most important problems arising in time series analysis is that of bifurcation, or change point detection. That is, given a collection of time series over a varying parameter, when has the structure of the underlying dynamical system changed? For this task, we turn to the field of topological data analysis (TDA), which encodes information about the shape and structure of data. The idea of utilizing tools from TDA for signal processing tasks, known as topological signal processing (TSP), has gained much attention in recent years, largely through a standard pipeline that computes the persistent homology of the point cloud generated by the Takens' embedding. However, this procedure is limited by computation time since the simplicial complex generated in this case is large, but also has a great deal of redundant data. For this reason, we turn to a more recent method for encoding the structure of the attractor, which constructs an ordinal partition network (OPN) representing information about when the dynamical system has passed between certain regions of state space. The result is a weighted graph whose structure encodes information about the underlying attractor. Our previous work began to find ways to package the information of the OPN in a manner that is amenable to TDA; however, that work only used the network structure and did nothing to encode the additional weighting information. In this paper, we take the next step: building a pipeline to analyze the weighted OPN with TDA and showing that this framework provides more resilience to noise or perturbations in the system and improves the accuracy of the dynamic state detection.

Erin Wolf Chambers, Ishika Ghosh, Elizabeth Munch et al.

Mapper graphs are widely used tools in topological data analysis and visualization. They can be understood as discrete approximations of Reeb graphs, providing insight into the shape and connectivity of complex data. Given a high-dimensional point cloud together with a real-valued function defined on it, a mapper graph summarizes the induced topological structure: each node represents a local neighborhood, and edges connect nodes whose corresponding neighborhoods overlap. Our focus is the interleaving distance for mapper graphs, arising as a discretized analogue of the interleaving distance for Reeb graphs-a quantity known to be NP-hard to compute. This distance measures how similar two mapper graphs are by quantifying how much they must be ``stretched'' to be made comparable. Recent work introduced a loss function that gives an upper bound on this distance. The loss evaluates how far a given collection of maps, called an assignment, is from being a true interleaving. Importantly, it is computationally tractable, offering a practical way to bound the distance, however the quality of the bound is dependent on the choice of assignment. In this paper, we develop the first framework for bounding the interleaving distance on mapper graphs. We present the bound in two ways: first, by formulating an integer linear program (ILP) that determines whether an $n$-interleaving exists for a given $n$; and second, by constructing an ILP that identifies an assignment with minimal loss for that $n$. We also evaluate the method on small examples where the interleaving distance is known, and on benchmark and simulated datasets, demonstrating the utility of the approach for classification tasks based on mapper graphs.

Sarah McGuire Scullen, Ernst Röell, Elizabeth Munch et al.

For deep learning problems on graph-structured data, pooling layers are important for down sampling, reducing computational cost, and to minimize overfitting. We define a pooling layer, nervePool, for data structured as simplicial complexes, which are generalizations of graphs that include higher-dimensional simplices beyond vertices and edges; this structure allows for greater flexibility in modeling higher-order relationships. The proposed simplicial coarsening scheme is built upon partitions of vertices, which allow us to generate hierarchical representations of simplicial complexes, collapsing information in a learned fashion. NervePool builds on the learned vertex cluster assignments and extends to coarsening of higher dimensional simplices in a deterministic fashion. While in practice the pooling operations are computed via a series of matrix operations, the topological motivation is a set-theoretic construction based on unions of stars of simplices and the nerve complex.

Kayla Makela, Tim Ophelders, Michelle Quigley et al.

Tree ring widths are an important source of climatic and historical data, but measuring these widths typically requires extensive manual work. Computer vision techniques provide promising directions towards the automation of tree ring detection, but most automated methods still require a substantial amount of user interaction to obtain high accuracy. We perform analysis on 3D X-ray CT images of a cross-section of a tree trunk, known as a tree disk. We present novel automated methods for locating the pith (center) of a tree disk, and ring boundaries. Our methods use a combination of standard image processing techniques and tools from topological data analysis. We evaluate the efficacy of our method for two different CT scans by comparing its results to manually located rings and centers and show that it is better than current automatic methods in terms of correctly counting each ring and its location. Our methods have several parameters, which we optimize experimentally by minimizing edit distances to the manually obtained locations.

Mustafa Hajij, Elizabeth Munch, Paul Rosen

The PageRank of a graph is a scalar function defined on the node set of the graph which encodes nodes centrality information of the graph. In this article, we use the PageRank function along with persistent homology to obtain a scalable graph descriptor and utilize it to compare the similarities between graphs. For a given graph $G(V,E)$, our descriptor can be computed in $O(|E|α(|V|))$, where $α$ is the inverse Ackermann function which makes it scalable and computable on massive graphs. We show the effectiveness of our method by utilizing it on multiple shape mesh datasets.

Melih C. Yesilli, Sarah Tymochko, Firas A. Khasawneh et al.

Chatter detection has become a prominent subject of interest due to its effect on cutting tool life, surface finish and spindle of machine tool. Most of the existing methods in chatter detection literature are based on signal processing and signal decomposition. In this study, we use topological features of data simulating cutting tool vibrations, combined with four supervised machine learning algorithms to diagnose chatter in the milling process. Persistence diagrams, a method of representing topological features, are not easily used in the context of machine learning, so they must be transformed into a form that is more amenable. Specifically, we will focus on two different methods for featurizing persistence diagrams, Carlsson coordinates and template functions. In this paper, we provide classification results for simulated data from various cutting configurations, including upmilling and downmilling, in addition to the same data with some added noise. Our results show that Carlsson Coordinates and Template Functions yield accuracies as high as 96% and 95%, respectively. We also provide evidence that these topological methods are noise robust descriptors for chatter detection.

Sarah Tymochko, Elizabeth Munch, Firas A. Khasawneh

As the field of Topological Data Analysis continues to show success in theory and in applications, there has been increasing interest in using tools from this field with methods for machine learning. Using persistent homology, specifically persistence diagrams, as inputs to machine learning techniques requires some mathematical creativity. The space of persistence diagrams does not have the desirable properties for machine learning, thus methods such as kernel methods and vectorization methods have been developed. One such featurization of persistence diagrams by Perea, Munch and Khasawneh uses continuous, compactly supported functions, referred to as "template functions," which results in a stable vector representation of the persistence diagram. In this paper, we provide a method of adaptively partitioning persistence diagrams to improve these featurizations based on localized information in the diagrams. Additionally, we provide a framework to adaptively select parameters required for the template functions in order to best utilize the partitioning method. We present results for application to example data sets comparing classification results between template function featurizations with and without partitioning, in addition to other methods from the literature.

Lin Yan, Yusu Wang, Elizabeth Munch et al.

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 use it to encode uncertainty in data. Specifically, we compute a 1-center tree that minimizes its maximum distance to any other tree in the set under a well-defined metric called the interleaving distance. We provide heuristic strategies that compute structural averages of merge trees whose labels do not fully agree. We further provide an interactive visualization system that resembles a numerical calculator that takes as input a set of merge trees and outputs a tree as their structural average. We also highlight structural similarities between the input and the average and incorporate uncertainty information for visual exploration. We develop a novel measure of uncertainty, referred to as consistency, via a metric-space view of the input trees. Finally, we demonstrate an application of our framework through merge trees that arise from ensembles of scalar fields. Our work is the first to employ interleaving distances and consistency to study a global, mathematically rigorous, structural average of merge trees in the context of uncertainty visualization.

Jose A. Perea, Elizabeth Munch, Firas A. Khasawneh

The persistence diagram is an increasingly useful tool from Topological Data Analysis, but its use alongside typical machine learning techniques requires mathematical finesse. The most success to date has come from methods that map persistence diagrams into vector spaces, in a way which maximizes the structure preserved. This process is commonly referred to as featurization. In this paper, we describe a mathematical framework for featurization called \emph{template functions}, and we show that it addresses the problem of approximating continuous functions on compact subsets of the space of persistence diagrams. Specifically, we begin by characterizing relative compactness with respect to the bottleneck distance, and then provide explicit theoretical methods for constructing compact-open dense subsets of continuous functions on persistence diagrams. These dense subsets -- obtained via template functions -- are leveraged for supervised learning tasks with persistence diagrams. Specifically, we test the method for classification and regression algorithms on several examples including shape data and dynamical systems.

Sarah Tymochko, Elizabeth Munch, Jason Dunion et al.

The diurnal cycle of tropical cyclones (TCs) is a daily cycle in clouds that appears in satellite images and may have implications for TC structure and intensity. The diurnal pattern can be seen in infrared (IR) satellite imagery as cyclical pulses in the cloud field that propagate radially outward from the center of nearly all Atlantic-basin TCs. These diurnal pulses, a distinguishing characteristic of the TC diurnal cycle, begin forming in the storm's inner core near sunset each day and appear as a region of cooling cloud-top temperatures. The area of cooling takes on a ring-like appearance as cloud-top warming occurs on its inside edge and the cooling moves away from the storm overnight, reaching several hundred kilometers from the circulation center by the following afternoon. The state-of-the-art TC diurnal cycle measurement has a limited ability to analyze the behavior beyond qualitative observations. We present a method for quantifying the TC diurnal cycle using one-dimensional persistent homology, a tool from Topological Data Analysis, by tracking maximum persistence and quantifying the cycle using the discrete Fourier transform. Using Geostationary Operational Environmental Satellite IR imagery data from Hurricane Felix (2007), our method is able to detect an approximate daily cycle.

Firas A. Khasawneh, Elizabeth Munch, Jose A. Perea

Chatter identification and detection in machining processes has been an active area of research in the past two decades. Part of the challenge in studying chatter is that machining equations that describe its occurrence are often nonlinear delay differential equations. The majority of the available tools for chatter identification rely on defining a metric that captures the characteristics of chatter, and a threshold that signals its occurrence. The difficulty in choosing these parameters can be somewhat alleviated by utilizing machine learning techniques. However, even with a successful classification algorithm, the transferability of typical machine learning methods from one data set to another remains very limited. In this paper we combine supervised machine learning with Topological Data Analysis (TDA) to obtain a descriptor of the process which can detect chatter. The features we use are derived from the persistence diagram of an attractor reconstructed from the time series via Takens embedding. We test the approach using deterministic and stochastic turning models, where the stochasticity is introduced via the cutting coefficient term. Our results show a 97% successful classification rate on the deterministic model labeled by the stability diagram obtained using the spectral element method. The features gleaned from the deterministic model are then utilized for characterization of chatter in a stochastic turning model where there are very limited analysis methods.

Paul Bendich, Sang Chin, Jesse Clarke et al.

We introduce the first unified theory for target tracking using Multiple Hypothesis Tracking, Topological Data Analysis, and machine learning. Our string of innovations are 1) robust topological features are used to encode behavioral information, 2) statistical models are fitted to distributions over these topological features, and 3) the target type classification methods of Wigren and Bar Shalom et al. are employed to exploit the resulting likelihoods for topological features inside of the tracking procedure. To demonstrate the efficacy of our approach, we test our procedure on synthetic vehicular data generated by the Simulation of Urban Mobility package.