arXiv subjects

Elizabeth Munch

Publications and source records attributed to Elizabeth Munch.

49 records · Page 3Linked to original sources

arXiv2018

Isolating phyllotactic patterns embedded in the secondary growth of sweet cherry (Prunus avium L.) using magnetic resonance imaging

Epicormic branches arise from dormant buds patterned during the growth of previous years. Dormant epicormic buds remain on the surface of trees, pushed outward from the pith during secondary growth, but maintaining vascular connections. Epicormic buds can be reactivated, either through natural processes or intentionally, to rejuvenate orchards and control tree architecture. Because epicormic structures are embedded within secondary growth, tomographic approaches are a useful method to study them and understand their development. We apply techniques from image processing to determine the locations of epicormic vascular traces embedded within secondary growth of sweet cherry (Prunus avium L.), revealing the juvenile phyllotactic pattern in the trunk of an adult tree. Techniques include breadth-first search to find the pith of the tree, edge detection to approximate the radius, and a conversion to polar coordinates to threshold and segment phyllotactic features. Intensity values from Magnetic Resonance Imaging (MRI) of the trunk are projected onto the surface of a perfect cylinder to find the locations of traces in the "boundary image". Mathematical phyllotaxy provides a means to capture the patterns in the boundary image by modeling phyllotactic parameters. Our cherry tree specimen has the conspicuous parastichy pair $(2,3)$, phyllotactic fraction 2/5, and divergence angle of approximately 143 degrees. The methods described not only provide a framework to study phyllotaxy, but for image processing of volumetric image data in plants. Our results have practical implications for orchard rejuvenation and directed approaches to influence tree architecture. The study of epicormic structures, which are hidden within secondary growth, using tomographic methods also opens the possibility of studying the genetic and environmental basis of such structures.

q-bio.QM↗

arXiv2018

Computing Wasserstein Distance for Persistence Diagrams on a Quantum Computer

Persistence diagrams are a useful tool from topological data analysis which can be used to provide a concise description of a filtered topological space. What makes them even more useful in practice is that they come with a notion of a metric, the Wasserstein distance (closely related to but not the same as the homonymous metric from probability theory). Further, this metric provides a notion of stability; that is, small noise in the input causes at worst small differences in the output. In this paper, we show that the Wasserstein distance for persistence diagrams can be computed through quantum annealing. We provide a formulation of the problem as a Quadratic Unconstrained Binary Optimization problem, or QUBO, and prove correctness. Finally, we test our algorithm, exploring parameter choices and problem size capabilities, using a D-Wave 2000Q quantum annealing computer.

cs.CG↗

arXiv2018

Theory of interleavings on categories with a flow

The interleaving distance was originally defined in the field of Topological Data Analysis (TDA) by Chazal et al. as a metric on the class of persistence modules parametrized over the real line. Bubenik et al. subsequently extended the definition to categories of functors on a poset, the objects in these categories being regarded as `generalized persistence modules'. These metrics typically depend on the choice of a lax semigroup of endomorphisms of the poset. The purpose of the present paper is to develop a more general framework for the notion of interleaving distance using the theory of `actegories'. Specifically, we extend the notion of interleaving distance to arbitrary categories equipped with a flow, i.e. a lax monoidal action by the monoid $[0,\infty)$. In this way, the class of objects in such a category acquires the structure of a Lawvere metric space. Functors that are colax $[0,\infty)$-equivariant yield maps that are $1$-Lipschitz. This leads to concise proofs of various known stability results from TDA, by considering appropriate colax $[0,\infty)$-equivariant functors. Along the way, we show that several common metrics, including the Hausdorff distance and the $L^{\infty}$-norm, can be realized as interleaving distances in this general perspective.

math.CT↗

arXiv2018

Topological Data Analysis for True Step Detection in Piecewise Constant Signals

This paper introduces a simple yet powerful approach based on topological data analysis (TDA) for detecting the true steps in a piecewise constant (PWC) signal. The signal is a two-state square wave with randomly varying in-between-pulse spacing, and subject to spurious steps at the rising or falling edges which we refer to as digital ringing. We use persistent homology to derive mathematical guarantees for the resulting change detection which enables accurate identification and counting of the true pulses. The approach is described and tested using both synthetic and experimental data obtained using an engine lathe instrumented with a laser tachometer. The described algorithm enables the accurate calculation of the spindle speed with the appropriate error bounds. The results of the described approach are compared to the frequency domain approach via Fourier transform. It is found that both our approach and the Fourier analysis yield comparable results for numerical and experimental pulses with regular spacing and digital ringing. However, the described approach significantly outperforms Fourier analysis when the spacing between the peaks is varied. We also generalize the approach to higher dimensional PWC signals, although utilizing this extension remains an interesting question for future research.

eess.SP↗

arXiv2018

Chatter Classification in Turning Using Machine Learning and Topological Data Analysis

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.

stat.ML↗

arXiv2018

The $\ell^\infty$-Cophenetic Metric for Phylogenetic Trees as an Interleaving Distance

There are many metrics available to compare phylogenetic trees since this is a fundamental task in computational biology. In this paper, we focus on one such metric, the $\ell^\infty$-cophenetic metric introduced by Cardona et al. This metric works by representing a phylogenetic tree with $n$ labeled leaves as a point in $\mathbb{R}^{n(n+1)/2}$ known as the cophenetic vector, then comparing the two resulting Euclidean points using the $\ell^\infty$ distance. Meanwhile, the interleaving distance is a formal categorical construction generalized from the definition of Chazal et al., originally introduced to compare persistence modules arising from the field of topological data analysis. We show that the $\ell^\infty$-cophenetic metric is an example of an interleaving distance. To do this, we define phylogenetic trees as a category of merge trees with some additional structure; namely labelings on the leaves plus a requirement that morphisms respect these labels. Then we can use the definition of a flow on this category to give an interleaving distance. Finally, we show that, because of the additional structure given by the categories defined, the map sending a labeled merge tree to the cophenetic vector is, in fact, an isometric embedding, thus proving that the $\ell^\infty$-cophenetic metric is, in fact, an interleaving distance.

cs.CG↗

arXiv2018

Evolutionary homology on coupled dynamical systems

Time dependence is a universal phenomenon in nature, and a variety of mathematical models in terms of dynamical systems have been developed to understand the time-dependent behavior of real-world problems. Originally constructed to analyze the topological persistence over spatial scales, persistent homology has rarely been devised for time evolution. We propose the use of a new filtration function for persistent homology which takes as input the adjacent oscillator trajectories of a dynamical system. We also regulate the dynamical system by a weighted graph Laplacian matrix derived from the network of interest, which embeds the topological connectivity of the network into the dynamical system. The resulting topological signatures, which we call evolutionary homology (EH) barcodes, reveal the topology-function relationship of the network and thus give rise to the quantitative analysis of nodal properties. The proposed EH is applied to protein residue networks for protein thermal fluctuation analysis, rendering the most accurate B-factor prediction of a set of 364 proteins. This work extends the utility of dynamical systems to the quantitative modeling and analysis of realistic physical systems.

math.AT↗

arXiv2016

Convergence between Categorical Representations of Reeb Space and Mapper

The Reeb space, which generalizes the notion of a Reeb graph, is one of the few tools in topological data analysis and visualization suitable for the study of multivariate scientific datasets. First introduced by Edelsbrunner et al., it compresses the components of the level sets of a multivariate mapping and obtains a summary representation of their relationships. A related construction called mapper, and a special case of the mapper construction called the Joint Contour Net have been shown to be effective in visual analytics. Mapper and JCN are intuitively regarded as discrete approximations of the Reeb space, however without formal proofs or approximation guarantees. An open question has been proposed by Dey et al. as to whether the mapper construction converges to the Reeb space in the limit. In this paper, we are interested in developing the theoretical understanding of the relationship between the Reeb space and its discrete approximations to support its use in practical data analysis. Using tools from category theory, we formally prove the convergence between the Reeb space and mapper in terms of an interleaving distance between their categorical representations. Given a sequence of refined discretizations, we prove that these approximations converge to the Reeb space in the interleaving distance; this also helps to quantify the approximation quality of the discretization at a fixed resolution.

cs.CG↗

arXiv2015

Categorified Reeb Graphs

The Reeb graph is a construction which originated in Morse theory to study a real valued function defined on a topological space. More recently, it has been used in various applications to study noisy data which creates a desire to define a measure of similarity between these structures. Here, we exploit the fact that the category of Reeb graphs is equivalent to the category of a particular class of cosheaf. Using this equivalency, we can define an `interleaving' distance between Reeb graphs which is stable under the perturbation of a function. Along the way, we obtain a natural construction for smoothing a Reeb graph to reduce its topological complexity. The smoothed Reeb graph can be constructed in polynomial time.

cs.CG↗

arXiv2014

Strong Equivalence of the Interleaving and Functional Distortion Metrics for Reeb Graphs

The Reeb graph is a construction that studies a topological space through the lens of a real valued function. It has widely been used in applications, however its use on real data means that it is desirable and increasingly necessary to have methods for comparison of Reeb graphs. Recently, several methods to define metrics on the space of Reeb graphs have been presented. In this paper, we focus on two: the functional distortion distance and the interleaving distance. The former is based on the Gromov--Hausdorff distance, while the latter utilizes the equivalence between Reeb graphs and a particular class of cosheaves. However, both are defined by constructing a near-isomorphism between the two graphs of study. In this paper, we show that the two metrics are strongly equivalent on the space of Reeb graphs. In particular, this gives an immediate proof of bottleneck stability for persistence diagrams in terms of the Reeb graph interleaving distance.

math.AT↗

arXiv2014

Probabilistic Fréchet Means for Time Varying Persistence Diagrams

In order to use persistence diagrams as a true statistical tool, it would be very useful to have a good notion of mean and variance for a set of diagrams. In 2011, Mileyko and his collaborators made the first study of the properties of the Fréchet mean in $(\mathcal{D}_p,W_p)$, the space of persistence diagrams equipped with the p-th Wasserstein metric. In particular, they showed that the Fréchet mean of a finite set of diagrams always exists, but is not necessarily unique. The means of a continuously-varying set of diagrams do not themselves (necessarily) vary continuously, which presents obvious problems when trying to extend the Fréchet mean definition to the realm of vineyards. We fix this problem by altering the original definition of Fréchet mean so that it now becomes a probability measure on the set of persistence diagrams; in a nutshell, the mean of a set of diagrams will be a weighted sum of atomic measures, where each atom is itself a persistence diagram determined using a perturbation of the input diagrams. This definition gives for each $N$ a map $(\mathcal{D}_p)^N \to \mathbb{P}(\mathcal{D}_p)$. We show that this map is Hölder continuous on finite diagrams and thus can be used to build a useful statistic on time-varying persistence diagrams, better known as vineyards.

math.PR↗

arXiv2014

Topological and Statistical Behavior Classifiers for Tracking Applications

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.

eess.SY↗

arXiv2011

Failure Filtrations for Fenced Sensor Networks

In this paper we consider the question of sensor network coverage for a 2-dimensional domain. We seek to compute the probability that a set of sensors fails to cover given only non-metric, local (who is talking to whom) information and a probability distribution of failure of each node. This builds on the work of de Silva and Ghrist who analyzed this problem in the deterministic situation. We first show that a it is part of a slightly larger class of problems which is #P-complete, and thus fast algorithms likely do not exist unless P$=$NP. We then give a deterministic algorithm which is feasible in the case of a small set of sensors, and give a dynamic algorithm for an arbitrary set of sensors failing over time which utilizes a new criterion for coverage based on the one proposed by de Silva and Ghrist. These algorithms build on the theory of topological persistence.

cs.CG↗