We present an algorithm for computing the barcode of the image of a morphisms in persistent homology induced by an inclusion of filtered finite-dimensional chain complexes. These algorithms make use of the clearing optimization and can be applied to inclusion-induced maps in persistent absolute homology and persistent relative cohomology for filtrations of pairs of simplicial complexes. They form the basis for our implementation for Vietoris-Rips complexes in the framework of the software Ripser.
Zigzag persistence is a powerful extension of the standard persistence which allows deletions of simplices besides insertions. However, computing zigzag persistence usually takes considerably more time than the standard persistence. We propose an algorithm called FastZigzag which narrows this efficiency gap. Our main result is that an input simplex-wise zigzag filtration can be converted to a cell-wise non-zigzag filtration of a $Δ$-complex with the same length, where the cells are copies of the input simplices. This conversion step in FastZigzag incurs very little cost. Furthermore, the barco…
Persistent homology is currently one of the more widely known tools from computational topology and topological data analysis. We present in this note a brief survey on the evolution of the subject. The goal is to highlight the main ideas, starting from the subject's computational inception more than 20 years ago, to the more modern categorical and representation-theoretic point of view.
The matching distance is a pseudometric on multi-parameter persistence modules, defined in terms of the weighted bottleneck distance on the restriction of the modules to affine lines. It is known that this distance is stable in a reasonable sense, and can be efficiently approximated, which makes it a promising tool for practical applications. In this work, we show that in the 2-parameter setting, the matching distance can be computed exactly in polynomial time. Our approach subdivides the space of affine lines into regions, via a line arrangement. In each region, the matching distance restrict…
We present an algorithm for the computation of Vietoris-Rips persistence barcodes and describe its implementation in the software Ripser. The method relies on implicit representations of the coboundary operator and the filtration order of the simplices, avoiding the explicit construction and storage of the filtration coboundary matrix. Moreover, it makes use of apparent pairs, a simple but powerful method for constructing a discrete gradient field from a total order on the simplices of a simplicial complex, which is also of independent interest. Our implementation shows substantial improvement…
University of North Carolina at Greensboro（北卡罗来纳大学格林斯伯勒分校）；William & Mary（威廉玛丽学院）；National Taiwan Normal University（国立台湾师范大学）
The field of mathematical morphology offers well-studied techniques for image processing. In this work, we view morphological operations through the lens of persistent homology, a tool at the heart of the field of topological data analysis. We demonstrate that morphological operations naturally form a multiparameter filtration and that persistent homology can then be used to extract information about both topology and geometry in the images as well as to automate methods for optimizing the study and rendering of structure in images. For illustration, we apply this framework to analyze noisy bi…
The main aim of this paper is to explore the ideas of persistent homology and extended persistent homology, and their stability theorems, using ideas from [Bubenik and Scott, 2014; Cohen-Steiner, Edelsbrunner, and Harer, 2007; and Cohen-Steiner, Edelsbrunner, and Harer, 2009], as well as other sources. The secondary aim is to explore the homology (and cohomology) of non-orientable surfaces, using the Klein bottle as an example. We also use the Klein bottle as an example for the computation of (extended) persistent homology, referring to it throughout the paper.
Multi-parameter persistent homology naturally arises in applications of persistent topology to data that come with extra information depending on additional parameters, like for example time series data. We introduce the concept of a Vietoris-Rips transformation, a method that reduces the computation of the one-parameter persistent homology of pathwise subcomplexes in multi-filtered flag complexes to the computation of the Vietoris-Rips persistent homology of certain semimetric spaces. The corresponding pathwise persistence barcodes track persistence features of the ambient multi-filtered comp…
The goal of this work is to extend the standard persistent homology pipeline for exploratory data analysis to the 2-D persistence setting, in a practical, computationally efficient way. To this end, we introduce RIVET, a software tool for the visualization of 2-D persistence modules, and present mathematical foundations for this tool. RIVET provides an interactive visualization of the barcodes of 1-D affine slices of a 2-D persistence module $M$. It also computes and visualizes the dimension of each vector space in $M$ and the bigraded Betti numbers of $M$. At the heart of our computational ap…
Many datasets can be viewed as a noisy sampling of an underlying space, and tools from topological data analysis can characterize this structure for the purpose of knowledge discovery. One such tool is persistent homology, which provides a multiscale description of the homological features within a dataset. A useful representation of this homological information is a persistence diagram (PD). Efforts have been made to map PDs into spaces with additional structure valuable to machine learning tasks. We convert a PD to a finite-dimensional vector representation which we call a persistence image …
We approach the problem of the computation of persistent homology for large datasets by a divide-and-conquer strategy. Dividing the total space into separate but overlapping components, we are able to limit the total memory residency for any part of the computation, while not degrading the overall complexity much. Locally computed persistence information is then merged from the components and their intersections using a spectral sequence generalizing the Mayer-Vietoris long exact sequence. We describe the Mayer-Vietoris spectral sequence and give details on how to compute with it. This allows …
We introduce a theoretical and computational framework to use discrete Morse theory as an efficient preprocessing in order to compute zigzag persistent homology. From a zigzag filtration of complexes $(K_i)$, we introduce a zigzag Morse filtration whose complexes $(A_i)$ are Morse reductions of the original complexes $(K_i)$, and we prove that they both have same persistent homology. This zigzag Morse filtration generalizes the filtered Morse complex of Mischaikow and Nanda, defined for standard persistence. The maps in the zigzag Morse filtration are forward and backward inclusions, as is sta…
It has long been envisioned that the strength of the barcode invariant of filtered cellular complexes could be increased using cohomology operations. Leveraging recent advances in the computation of Steenrod squares, we introduce a new family of computable invariants on mod 2 persistent cohomology termed $Sq^k$-barcodes. We present a complete algorithmic pipeline for their computation and illustrate their real-world applicability using the space of conformations of the cyclo-octane molecule.
The notion of generalized rank invariant in the context of multiparameter persistence has become an important ingredient for defining interesting homological structures such as generalized persistence diagrams. Naturally, computing these rank invariants efficiently is a prelude to computing any of these derived structures efficiently. We show that the generalized rank over a finite interval $I$ of a $\mathbb{Z}^2$-indexed persistence module $M$ is equal to the generalized rank of the zigzag module that is induced on a certain path in $I$ tracing mostly its boundary. Hence, we can compute the g…
Persistence diagrams, combining geometry and topology for an effective shape description used in pattern recognition, have already proven to be an effective tool for shape representation with respect to a certainfiltering function. Comparing the persistence diagram of a query with those of a database allows automatic classification or retrieval, but unfortunately, the standard method for comparing persistence diagrams, the bottleneck distance, has a high computational cost. A possible algebraic solution to this problem is to switch to comparisons between the complex polynomials whose roots are…
We present a generalization of the induced matching theorem and use it to prove a generalization of the algebraic stability theorem for $\mathbb{R}$-indexed pointwise finite-dimensional persistence modules. Via numerous examples, we show how the generalized algebraic stability theorem enables the computation of rigorous error bounds in the space of persistence diagrams that go beyond the typical formulation in terms of bottleneck (or log bottleneck) distance.
The concept of topological persistence, introduced recently in computational topology, finds applications in studying a map in relation to the topology of its domain. Since its introduction, it has been extended and generalized in various directions. However, no attempt has been made so far to extend the concept of topological persistence to a generalization of `maps' such as cocycles which are discrete analogs of closed differential forms, a well known concept in differential geometry. We define a notion of topological persistence for 1-cocycles in this paper and show how to compute its relev…
Persistent homology was shown by Carlsson and Zomorodian to be homology of graded chain complexes with coefficients in the graded ring $\kk[t]$. As such, the behavior of persistence modules -- graded modules over $\kk[t]$ is an important part in the analysis and computation of persistent homology. In this paper we present a number of facts about persistence modules; ranging from the well-known but under-utilized to the reconstruction of techniques to work in a purely algebraic approach to persistent homology. In particular, the results we present give concrete algorithms to compute the persist…
Arizona State University（亚利桑那州立大学）；IBM Research（IBM研究院）
Topological features such as persistence diagrams and their functional approximations like persistence images (PIs) have been showing substantial promise for machine learning and computer vision applications. This is greatly attributed to the robustness topological representations provide against different types of physical nuisance variables seen in real-world data, such as view-point, illumination, and more. However, key bottlenecks to their large scale adoption are computational expenditure and difficulty incorporating them in a differentiable architecture. We take an important step in this…
University of Manitoba（曼尼托巴大学）；University of Texas at Dallas（德克萨斯大学达拉斯分校）
Topological data analysis (TDA) delivers invaluable and complementary information on the intrinsic properties of data inaccessible to conventional methods. However, high computational costs remain the primary roadblock hindering the successful application of TDA in real-world studies, particularly with machine learning on large complex networks. Indeed, most modern networks such as citation, blockchain, and online social networks often have hundreds of thousands of vertices, making the application of existing TDA methods infeasible. We develop two new, remarkably simple but effective algorithm…
Persistence diagrams, which summarize the birth and death of homological features extracted from data, are employed as stable signatures for applications in image analysis and other areas. Besides simply considering the multiset of intervals included in a persistence diagram, some applications need to find representative cycles for the intervals. In this paper, we address the problem of computing these representative cycles, termed as persistent 1-cycles, for $\text{H}_1$-persistent homology with $\mathbb{Z}_2$ coefficients. The definition of persistent cycles is based on the interval module d…
The intrinsic connection between lattice theory and topology is fairly well established, For instance, the collection of open subsets of a topological subspace always forms a distributive lattice. Persistent homology has been one of the most prominent areas of research in computational topology in the past 20 years. In this paper we will introduce an alternative interpretation of persistence based on the study of the order structure of its correspondent lattice. Its algorithmic construction leads to two operations on homology groups which describe a diagram of spaces as a complete Heyting alge…
We redevelop persistent homology (topological persistence) from a categorical point of view. The main objects of study are diagrams, indexed by the poset of real numbers, in some target category. The set of such diagrams has an interleaving distance, which we show generalizes the previously-studied bottleneck distance. To illustrate the utility of this approach, we greatly generalize previous stability results for persistence, extended persistence, and kernel, image and cokernel persistence. We give a natural construction of a category of interleavings of these diagrams, and show that if the t…
We show that computing the interleaving distance between two multi-graded persistence modules is NP-hard. More precisely, we show that deciding whether two modules are $1$-interleaved is NP-complete, already for bigraded, interval decomposable modules. Our proof is based on previous work showing that a constrained matrix invertibility problem can be reduced to the interleaving distance computation of a special type of persistence modules. We show that this matrix invertibility problem is NP-complete. We also give a slight improvement of the above reduction, showing that also the approximation …
Persistence Pairing Graphs: Tracking Changes of Selected Homology Bases
Dioscuri Centre in Topological Data Analysis, Institute of Mathematics of the Polish Academy of Sciences（波兰科学院数学研究所拓扑数据分析迪奥斯库里中心）；International Environmental Doctoral School, University of Silesia in Katowice（卡托维兹西里西亚大学国际环境博士学院）
The University of Buckingham（白金汉大学）；Salahaddin University（萨拉赫丁大学）
An Important tool in the field topological data analysis is known as persistent Homology (PH) which is used to encode abstract representation of the homology of data at different resolutions in the form of persistence diagram (PD). In this work we build more than one PD representation of a single image based on a landmark selection method, known as local binary patterns, that encode different types of local textures from images. We employed different PD vectorizations using persistence landscapes, persistence images, persistence binning (Betti Curve) and statistics. We tested the effectiveness…
The Extended Persistent Homology Transform (XPHT) is a topological transform which takes as input a shape embedded in Euclidean space, and to each unit vector assigns the extended persistence module of the height function over that shape with respect to that direction. We can define a distance between two shapes by integrating over the sphere the distance between their respective extended persistence modules. By using extended persistence we get finite distances between shapes even when they have different Betti numbers. We use Morse theory to show that the extended persistence of a height fun…
The topological morphology descriptor of a neuron is a multiset of intervals associated to the shape of the neuron represented as a tree. In practice, topological morphology descriptors are vectorized using persistence images, which can help classify and characterize the morphology of broad groups of neurons. We study the stability of topological morphology descriptors under small changes to neuronal morphology. We show that the persistence diagram arising from the topological morphology descriptor of a neuron is stable for the 1-Wasserstein distance against a range of perturbations to the tre…
Biological and physical systems often exhibit distinct structures at different spatial/temporal scales. Persistent homology is an algebraic tool that provides a mathematical framework for analyzing the multi-scale structures frequently observed in nature. In this paper a theoretical framework for the algorithmic computation of an arbitrarily good approximation of the persistent homology is developed. We study the filtrations generated by sub-level sets of a function $f : X \to \mathbb{R}$, where $X$ is a CW-complex. In the special case $X = [0,1]^N$, $N \in \mathbb{N}$ we discuss implementatio…
This paper tackles the problem of coefficient field choice in persistent homology. When we compute a persistence diagram, we need to select a coefficient field before computation. We should understand the dependency of the diagram on the coefficient field to facilitate computation and interpretation of the diagram. We clarify that the dependency is strongly related to the torsion of $\mathbb{Z}$ relative homology in the filtration. We show the sufficient and necessary conditions of the independence of coefficient field choice. An efficient algorithm is proposed to verify the independence. In a…
Multi-parameter persistent homology is a recent branch of topological data analysis. In this area, data sets are investigated through the lens of homology with respect to two or more scale parameters. The high computational cost of many algorithms calls for a preprocessing step to reduce the input size. In general, a minimal presentation is the smallest possible representation of a persistence module. Lesnick and Wright proposed recently an algorithm (the LW-algorithm) for computing minimal presentations based on matrix reduction. In this work, we propose, implement and benchmark several impro…
We use persistent homology to build a quantitative understanding of large complex systems that are driven far-from-equilibrium; in particular, we analyze image time series of flow field patterns from numerical simulations of two important problems in fluid dynamics: Kolmogorov flow and Rayleigh-Bénard convection. For each image we compute a persistence diagram to yield a reduced description of the flow field; by applying different metrics to the space of persistence diagrams, we relate characteristic features in persistence diagrams to the geometry of the corresponding flow patterns. We also e…
We expand the toolbox of (co)homological methods in computational topology by applying the concept of persistence to sheaf cohomology. Since sheaves (of modules) combine topological information with algebraic information, they allow for variation along an algebraic dimension and along a topological dimension. Consequently, we introduce two different constructions of sheaf cohomology (co)persistence modules. One of them can be viewed as a natural generalization of the construction of simplicial or singular cohomology copersistence modules. We discuss how both constructions relate to each other …
