🍩 Database of Original & Non-Theoretical Uses of Topology

(found 10 matches in 0.001714s)

  1. Cubical Ripser: Software for Computing Persistent Homology of Image and Volume Data (2020)

    Shizuo Kaji, Takeki Sudo, Kazushi Ahara
    Abstract We introduce Cubical Ripser for computing persistent homology of image and volume data. To our best knowledge, Cubical Ripser is currently the fastest and the most memory-efficient program for computing persistent homology of image and volume data. We demonstrate our software with an example of image analysis in which persistent homology and convolutional neural networks are successfully combined. Our open source implementation is available at [14].

  2. Theory and Algorithms for Constructing Discrete Morse Complexes From Grayscale Digital Images (2011)

    V. Robins, P. J. Wood, A. P. Sheppard
    Abstract We present an algorithm for determining the Morse complex of a two or three-dimensional grayscale digital image. Each cell in the Morse complex corresponds to a topological change in the level sets (i.e., a critical point) of the grayscale image. Since more than one critical point may be associated with a single image voxel, we model digital images by cubical complexes. A new homotopic algorithm is used to construct a discrete Morse function on the cubical complex that agrees with the digital image and has exactly the number and type of critical cells necessary to characterize the topological changes in the level sets. We make use of discrete Morse theory and simple homotopy theory to prove correctness of this algorithm. The resulting Morse complex is considerably simpler than the cubical complex originally used to represent the image and may be used to compute persistent homology.

  3. The Weighted Euler Curve Transform for Shape and Image Analysis (2020)

    Qitong Jiang, Sebastian Kurtek, Tom Needham
    Abstract The Euler Curve Transform (ECT) of Turner et al. is a complete invariant of an embedded simplicial complex, which is amenable to statistical analysis. We generalize the ECT to provide a similarly convenient representation for weighted simplicial complexes, objects which arise naturally, for example, in certain medical imaging applications. We leverage work of Ghrist et al. on Euler integral calculus to prove that this invariant—dubbed the Weighted Euler Curve Transform (WECT)—is also complete. We explain how to transform a segmented region of interest in a grayscale image into a weighted simplicial complex and then into a WECT representation. This WECT representation is applied to study Glioblastoma Multiforme brain tumor shape and texture data. We show that the WECT representation is effective at clustering tumors based on qualitative shape and texture features and that this clustering correlates with patient survival time.

  4. Skeletonization and Partitioning of Digital Images Using Discrete Morse Theory (2015)

    Olaf Delgado-Friedrichs, Vanessa Robins, Adrian Sheppard
    Abstract We show how discrete Morse theory provides a rigorous and unifying foundation for defining skeletons and partitions of grayscale digital images. We model a grayscale image as a cubical complex with a real-valued function defined on its vertices (the voxel values). This function is extended to a discrete gradient vector field using the algorithm presented in Robins, Wood, Sheppard TPAMI 33:1646 (2011). In the current paper we define basins (the building blocks of a partition) and segments of the skeleton using the stable and unstable sets associated with critical cells. The natural connection between Morse theory and homology allows us to prove the topological validity of these constructions; for example, that the skeleton is homotopic to the initial object. We simplify the basins and skeletons via Morse-theoretic cancellation of critical cells in the discrete gradient vector field using a strategy informed by persistent homology. Simple working Python code for our algorithms for efficient vector field traversal is included. Example data are taken from micro-CT images of porous materials, an application area where accurate topological models of pore connectivity are vital for fluid-flow modelling.

  5. Revisiting Abnormalities in Brain Network Architecture Underlying Autism Using Topology-Inspired Statistical Inference (2018)

    Sourabh Palande, Vipin Jose, Brandon Zielinski, Jeffrey Anderson, P. Thomas Fletcher, Bei Wang
    Abstract A large body of evidence relates autism with abnormal structural and functional brain connectivity. Structural covariance magnetic resonance imaging (scMRI) is a technique that maps brain regions with covarying gray matter densities across subjects. It provides a way to probe the anatomical structure underlying intrinsic connectivity networks (ICNs) through analysis of gray matter signal covariance. In this article, we apply topological data analysis in conjunction with scMRI to explore network-specific differences in the gray matter structure in subjects with autism versus age-, gender-, and IQ-matched controls. Specifically, we investigate topological differences in gray matter structure captured by structural correlation graphs derived from three ICNs strongly implicated in autism, namely the salience network, default mode network, and executive control network. By combining topological data analysis with statistical inference, our results provide evidence of statistically significant network-specific structural abnormalities in autism.

  6. Topological Detection of Phenomenological Bifurcations With Unreliable Kernel Density Estimates (2024)

    Sunia Tanweer, Firas A. Khasawneh
    Abstract Phenomenological (P-type) bifurcations are qualitative changes in stochastic dynamical systems whereby the stationary probability density function (PDF) changes its topology. The current state of the art for detecting these bifurcations requires reliable kernel density estimates computed from an ensemble of system realizations. However, in several real world signals such as Big Data, only a single system realization is available—making it impossible to estimate a reliable kernel density. This study presents an approach for detecting P-type bifurcations using unreliable density estimates. The approach creates an ensemble of objects from Topological Data Analysis (TDA) called persistence diagrams from the system’s sole realization and statistically analyzes the resulting set. We compare several methods for replicating the original persistence diagram including Gibbs point process modelling, Pairwise Interaction Point Modelling, and subsampling. We show that for the purpose of predicting a bifurcation, the simple method of subsampling exceeds the other two methods of point process modelling in performance.

  7. Feature Detection and Hypothesis Testing for Extremely Noisy Nanoparticle Images Using Topological Data Analysis (2023)

    Andrew M. Thomas, Peter A. Crozier, Yuchen Xu, David S. Matteson
    Abstract We propose a flexible algorithm for feature detection and hypothesis testing in images with ultra-low signal-to-noise ratio using cubical persistent homology. Our main application is in the identification of atomic columns and other features in Transmission Electron Microscopy (TEM). Cubical persistent homology is used to identify local minima and their size in subregions in the frames of nanoparticle videos, which are hypothesized to correspond to relevant atomic features. We compare the performance of our algorithm to other employed methods for the detection of columns and their intensity. Additionally, Monte Carlo goodness-of-fit testing using real-valued summaries of persistence diagrams derived from smoothed images (generated from pixels residing in the vacuum region of an image) is developed and employed to identify whether or not the proposed atomic features generated by our algorithm are due to noise. Using these summaries derived from the generated persistence diagrams, one can produce univariate time series for the nanoparticle videos, thus, providing a means for assessing fluxional behavior. A guarantee on the false discovery rate for multiple Monte Carlo testing of identical hypotheses is also established.

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  8. Exploring Surface Texture Quantification in Piezo Vibration Striking Treatment (PVST) Using Topological Measures (2022)

    Melih C. Yesilli, Max M. Chumley, Jisheng Chen, Firas A. Khasawneh, Yang Guo
    Abstract Abstract. Surface texture influences wear and tribological properties of manufactured parts, and it plays a critical role in end-user products. Therefore, quantifying the order or structure of a manufactured surface provides important information on the quality and life expectancy of the product. Although texture can be intentionally introduced to enhance aesthetics or to satisfy a design function, sometimes it is an inevitable byproduct of surface treatment processes such as Piezo Vibration Striking Treatment (PVST). Measures of order for surfaces have been characterized using statistical, spectral, and geometric approaches. For nearly hexagonal lattices, topological tools have also been used to measure the surface order. This paper explores utilizing tools from Topological Data Analysis for measuring surface texture. We compute measures of order based on optical digital microscope images of surfaces treated using PVST. These measures are applied to the grid obtained from estimating the centers of tool impacts, and they quantify the grid’s deviations from the nominal one. Our results show that TDA provides a convenient framework for characterization of pattern type that bypasses some limitations of existing tools such as difficult manual processing of the data and the need for an expert user to analyze and interpret the surface images.

  9. A Topological Framework for Identifying Phenomenological Bifurcations in Stochastic Dynamical Systems (2024)

    Sunia Tanweer, Firas A. Khasawneh, Elizabeth Munch, Joshua R. Tempelman
    Abstract Changes in the parameters of dynamical systems can cause the state of the system to shift between different qualitative regimes. These shifts, known as bifurcations, are critical to study as they can indicate when the system is about to undergo harmful changes in its behavior. In stochastic dynamical systems, there is particular interest in P-type (phenomenological) bifurcations, which can include transitions from a monostable state to multi-stable states, the appearance of stochastic limit cycles and other features in the probability density function (PDF) of the system’s state. Current practices are limited to systems with small state spaces, cannot detect all possible behaviors of the PDFs and mandate human intervention for visually identifying the change in the PDF. In contrast, this study presents a new approach based on Topological Data Analysis that uses superlevel persistence to mathematically quantify P-type bifurcations in stochastic systems through a “homological bifurcation plot”—which shows the changing ranks of 0th and 1st homology groups, through Betti vectors. Using these plots, we demonstrate the successful detection of P-bifurcations on the stochastic Duffing, Raleigh-Vander Pol and Quintic Oscillators given their analytical PDFs, and elaborate on how to generate an estimated homological bifurcation plot given a kernel density estimate (KDE) of these systems by employing a tool for finding topological consistency between PDFs and KDEs.

  10. Pattern Characterization Using Topological Data Analysis: Application to Piezo Vibration Striking Treatment (2023)

    Max M. Chumley, Melih C. Yesilli, Jisheng Chen, Firas A. Khasawneh, Yang Guo
    Abstract Quantifying patterns in visual or tactile textures provides important information about the process or phenomena that generated these patterns. In manufacturing, these patterns can be intentionally introduced as a design feature, or they can be a byproduct of a specific process. Since surface texture has significant impact on the mechanical properties and the longevity of the workpiece, it is important to develop tools for quantifying surface patterns and, when applicable, comparing them to their nominal counterparts. While existing tools may be able to indicate the existence of a pattern, they typically do not provide more information about the pattern structure, or how much it deviates from a nominal pattern. Further, prior works do not provide automatic or algorithmic approaches for quantifying other pattern characteristics such as depths’ consistency, and variations in the pattern motifs at different level sets. This paper leverages persistent homology from Topological Data Analysis (TDA) to derive noise-robust scores for quantifying motifs’ depth and roundness in a pattern. Specifically, sublevel persistence is used to derive scores that quantify the consistency of indentation depths at any level set in Piezo Vibration Striking Treatment (PVST) surfaces. Moreover, we combine sublevel persistence with the distance transform to quantify the consistency of the indentation radii, and to compare them with the nominal ones. Although the tool in our PVST experiments had a semi-spherical profile, we present a generalization of our approach to tools/motifs of arbitrary shapes thus making our method applicable to other pattern-generating manufacturing processes.