Persistent Homology (PH) is a useful tool to study the underlying structure of a data set. Persistence Diagrams (PDs), which are 2D multisets of points, are a concise summary of the information found by studying the PH of a data set. However, PDs are difficult to incorporate into a typical machine learning workflow. To that end, two main methods for representing PDs have been developed: kernel methods and vectorization methods. In this paper we propose a new finite-dimensional vector, called the interconnectivity vector, representation of a PD adapted from Bag-of-Words (BoW). This new representation is constructed to demonstrate the connections between the homological features of a data set. This initial definition of the interconnectivity vector proves to be unstable, but we introduce a stabilized version of the vector and prove its stability with respect to small perturbations in the inputs. We evaluate both versions of the presented vectorization on several data sets and show their high discriminative power.
Persistent homology and zigzag persistent homology are techniques which track the homology over a sequence of spaces, outputting a set of intervals corresponding to birth and death times of homological features in the sequence. This paper presents a method for choosing a homology class to correspond to each of the intervals at each time point. For each homology class a specific representative cycle is stored, with the choice of homology class and representative cycle being both geometrically relevant and compatible with the birth-death interval decomposition. After describing the method in det…
We study distributions of persistent homology barcodes associated to taking subsamples of a fixed size from metric measure spaces. We show that such distributions provide robust invariants of metric measure spaces, and illustrate their use in hypothesis testing and providing confidence intervals for topological data analysis.
Graz University of Technology（格拉茨工业大学）；University of Modena and Reggio Emilia（摩德纳-雷焦艾米利亚大学）；University of Utah（犹他大学）
Topological data analysis and its main method, persistent homology, provide a toolkit for computing topological information of high-dimensional and noisy data sets. Kernels for one-parameter persistent homology have been established to connect persistent homology with machine learning techniques. We contribute a kernel construction for multi-parameter persistence by integrating a one-parameter kernel weighted along straight lines. We prove that our kernel is stable and efficiently computable, which establishes a theoretical connection between topological data analysis and machine learning for …
Persistent Homology (PH) allows tracking homology features like loops, holes and their higher-dimensional analogs, along with a single-parameter family of nested spaces. Currently, computing descriptors for complex data characterized by multiple functions is becoming an important task in several applications, including physics, chemistry, medicine, geography, etc. Multiparameter Persistent Homology (MPH) generalizes persistent homology opening to the exploration and analysis of shapes endowed with multiple filtering functions. Still, computational constraints prevent MPH to be feasible over re…
The classical Künneth formula in algebraic topology describes the homology of a product space in terms of that of its factors. In this paper, we prove Künneth-type theorems for the persistent homology of the categorical and tensor product of filtered spaces. That is, we describe the persistent homology of these product filtrations in terms of that of the filtered components. In addition to comparing the two products, we present two applications in the setting of Vietoris-Rips complexes: one towards more efficient algorithms for product metric spaces with the maximum metric, and the other recov…
We show that recent results on randomized dimension reduction schemes that exploit structural properties of data can be applied in the context of persistent homology. In the spirit of compressed sensing, the dimension reduction is determined by the Gaussian width of a structure associated to the data set, rather than its size, and such a reduction can be computed efficiently. We further relate the Gaussian width to the doubling dimension of a finite metric space, which appears in the study of the complexity of other methods for approximating persistent homology. We can therefore literally repl…
Persistent homology is a topological feature used in a variety of applications such as generating features for data analysis and penalizing optimization problems. We develop an approach to accelerate persistent homology computations performed on many similar filtered topological spaces which is based on updating associated matrix factorizations. Our approach improves the update scheme of Cohen-Steiner, Edelsbrunner, and Morozov for permutations by additionally handling addition and deletion of cells in a filtered topological space and by processing changes in a single batch. We show that the c…
Let $P$ be a finite poset. We will show that for any reasonable $P$-persistent object $X$ in the category of finite topological spaces, there is a $P-$ weighted graph, whose clique complex has the same $P$-persistent homology as $X$.
We introduce several geometric notions, including the width of a homology class, to the theory of persistent homology. These ideas provide geometric interpretations of persistence diagrams. Indeed, we give quantitative and geometric descriptions of the "life span" or "persistence" of a homology class. As a case study, we analyze the power filtration on unweighted graphs, and provide explicit bounds for the life spans of homology classes in persistence diagrams in all dimensions.
Santa Clara University（圣克拉拉大学）；University of South Florida（南佛罗里达大学）；Facebook Inc（脸书公司）
This article aims to study the topological invariant properties encoded in node graph representational embeddings by utilizing tools available in persistent homology. Specifically, given a node embedding representation algorithm, we consider the case when these embeddings are real-valued. By viewing these embeddings as scalar functions on a domain of interest, we can utilize the tools available in persistent homology to study the topological information encoded in these representations. Our construction effectively defines a unique persistence-based graph descriptor, on both the graph and node…
This article introduces an algorithm to compute the persistent homology of a filtered complex with various coefficient fields in a single matrix reduction. The algorithm is output-sensitive in the total number of distinct persistent homological features in the diagrams for the different coefficient fields. This computation allows us to infer the prime divisors of the torsion coefficients of the integral homology groups of the topological space at any scale, hence furnishing a more informative description of topology than persistence in a single coefficient field. We provide theoretical complex…
By general case we mean methods able to process simplicial sets and chain complexes not of finite type. A filtration of the object to be studied is the heart of both subjects persistent homology and spectral sequences. In this paper we present the complete relation between them, both from theoretical and computational points of view. One of the main contributions of this paper is the observation that a slight modification of our previous programs computing spectral sequences is enough to compute also persistent homology. By inheritance from our spectral sequence programs, we obtain for free pe…
We describe an approach to bounded-memory computation of persistent homology and betti barcodes, in which a computational state is maintained with updates introducing new edges to the underlying neighbourhood graph and percolating the resulting changes into the simplex stream feeding the persistence algorithm. We further discuss the memory consumption and resulting speed and complexity behaviours of the resulting algorithm.
We consider sequences of absolute and relative homology and cohomology groups that arise naturally for a filtered cell complex. We establish algebraic relationships between their persistence modules, and show that they contain equivalent information. We explain how one can use the existing algorithm for persistent homology to process any of the four modules, and relate it to a recently introduced persistent cohomology algorithm. We present experimental evidence for the practical efficiency of the latter algorithm.
The literature in persistent homology often refers to a "structure theorem for finitely generated graded modules over a graded principal ideal domain". We clarify the nature of this structure theorem in this context.
TDA (topological data analysis) is a relatively new area of research related to importing classical ideas from topology into the realm of data analysis. Under the umbrella term TDA, there falls, in particular, the notion of persistent homology, which can be described in a nutshell, as the study of scale dependent homological invariants of datasets. In these notes, we provide a terse self contained description of the main ideas behind the construction of persistent homology as an invariant feature of datasets, and its stability to perturbations.
Persistent homology is a multiscale method for analyzing the shape of sets and functions from point cloud data arising from an unknown distribution supported on those sets. When the size of the sample is large, direct computation of the persistent homology is prohibitive due to the combinatorial nature of the existing algorithms. We propose to compute the persistent homology of several subsamples of the data and then combine the resulting estimates. We study the risk of two estimators and we prove that the subsampling approach carries stable topological information while achieving a great redu…
This paper proposes a stable volume and a stable volume variant, referred to as a stable sub-volume, for more reliable data analysis using persistent homology. In prior research, an optimal cycle and similar ideas have been proposed to identify the homological structure corresponding to each birth-death pair in a persistence diagram. While this is helpful for data analysis using persistent homology, the results are sensitive to noise. In this paper, stable volumes and stable sub-volumes are proposed to solve this problem. For a special case, we prove that a stable volume is the robust part of …
Technion - Israel Institute of Technology（以色列理工学院）
In this article we propose a novel approach for comparing the persistent homology representations of two spaces (filtrations). Commonly used methods are based on numerical summaries such as persistence diagrams and persistence landscapes, along with suitable metrics (e.g. Wasserstein). These summaries are useful for computational purposes, but they are merely a marginal of the actual topological information that persistent homology can provide. Instead, our approach compares between two topological representations directly in the data space. We do so by defining a correspondence relation betwe…
The present lack of a stable method to compare persistent homology groups with torsion is a relevant problem in current research about Persistent Homology and its applications in Pattern Recognition. In this paper we introduce a pseudo-distance d_T that represents a possible solution to this problem. Indeed, d_T is a pseudo-distance between multidimensional persistent homology groups with coefficients in an Abelian group, hence possibly having torsion. Our main theorem proves the stability of the new pseudo-distance with respect to the change of the filtering function, expressed both with resp…
We introduce a fractal dimension for a metric space defined in terms of the persistent homology of extremal subsets of that space. We exhibit hypotheses under which this dimension is comparable to the upper box dimension; in particular, the dimensions coincide for subsets of $\mathbb{R}^2$ whose upper box dimension exceeds $1.5.$ These results are related to extremal questions about the number of persistent homology intervals of a set of $n$ points in a metric space.
We define persistent homology groups over any set of spaces which have inclusions defined so that the corresponding directed graph between the spaces is acyclic, as well as along any subgraph of this directed graph. This method simultaneously generalizes standard persistent homology, zigzag persistence and multidimensional persistence to arbitrary directed acyclic graphs, and it also allows the study of more general families of topological spaces or point-cloud data. We give an algorithm to compute the persistent homology groups simultaneously for all subgraphs which contain a single source an…
Classical persistent homology is a powerful mathematical tool for shape comparison. Unfortunately, it is not tailored to study the action of transformation groups that are different from the group Homeo(X) of all self-homeomorphisms of a topological space X. This fact restricts its use in applications. In order to obtain better lower bounds for the natural pseudo-distance d_G associated with a subgroup G of Homeo(X), we need to adapt persistent homology and consider G-invariant persistent homology. Roughly speaking, the main idea consists in defining persistent homology by means of a set of ch…
Persistent homology is a popular tool in Topological Data Analysis. It provides numerical characteristics of data sets which reflect global geometric properties. In order to be useful in practice, for example for feature generation in machine learning, it needs to be effectively computable. Classical homology is a computable topological invariant because of the Mayer-Vietoris exact and spectral sequences associated to coverings of a space. We state and prove versions of the Mayer-Vietoris theorem for persistent homology under mild and commonplace assumptions. This is done through the use of a …
The subject of persistent homology has vitalized applications of algebraic topology to point cloud data and to application fields far outside the realm of pure mathematics. The area has seen several fundamentally important results that are rooted in choosing a particular algebraic foundational theory to describe persistent homology, and applying results from that theory to prove useful and important results. In this survey paper, we shall examine the various choices in use, and what they allow us to prove. We shall also discuss the inherent differences between the choices people use, and specu…
The Čech and Rips constructions of persistent homology are stable with respect to perturbations of the input data. However, neither is robust to outliers, and both can be insensitive to topological structure of high-density regions of the data. A natural solution is to consider 2-parameter persistence. This paper studies the stability of 2-parameter persistent homology: We show that several related density-sensitive constructions of bifiltrations from data satisfy stability properties accommodating the addition and removal of outliers. Specifically, we consider the multicover bifiltration, She…
Topological data analysis is an emerging area in exploratory data analysis and data mining. Its main tool, persistent homology, has become a popular technique to study the structure of complex, high-dimensional data. In this paper, we propose a novel method using persistent homology to quantify structural changes in time-varying graphs. Specifically, we transform each instance of the time-varying graph into metric spaces, extract topological features using persistent homology, and compare those features over time. We provide a visualization that assists in time-varying graph exploration and he…
We consider generic curves in R^2, i.e. generic C^1 functions f from S^1 to R^2. We analyze these curves through the persistent homology groups of a filtration induced on S^1 by f. In particular, we consider the question whether these persistent homology groups uniquely characterize f, at least up to re-parameterizations of S^1. We give a partially positive answer to this question. More precisely, we prove that f=goh, where h:S^1-> S^1 is a C^1-diffeomorphism, if and only if the persistent homology groups of sof and sog coincide, for every s belonging to the group Sigma_2 generated by reflecti…
We introduce a homology-based technique for the analysis of multiqubit state vectors. In our approach, we associate state vectors to data sets by introducing a metric-like measure in terms of bipartite entanglement, and investigate the persistence of homologies at different scales. This leads to a novel classification of multiqubit entanglement. The relative occurrence frequency of various classes of entangled states is also shown.
Michigan State University（密歇根州立大学）；University of South Florida（南佛罗里达大学）
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.
EPFL（洛桑联邦理工学院）；IST Austria (Institute of Science and Technology Austria)（奥地利科学技术研究所）；Mathematical Sciences Institute, The Australian National University（澳大利亚国立大学数学科学研究所）；University of New England（新英格兰大学）；Research School of Physics, The Australian National University（澳大利亚国立大学物理研究学院）
We derive the relationship between the persistent homology barcodes of two dual filtered CW complexes. Applied to greyscale digital images, we obtain an algorithm to convert barcodes between the two different (dual) topological models of pixel connectivity.
Persistent Homology of Music Network with Three Different Distances
Department of Mathematics, Pohang University of Science & Technology（POSTECH数学系）；POSTECH Mathematical Institute for Data Science (MINDS)（POSTECH数据科学数学研究所）；Korea Institute for Advanced Study (KIAS)（韩国高级研究院）
Computing persistent homology using Gaussian kernels is useful in the domains of topological data analysis and machine learning as shown by Phillips, Wang and Zheng [SoCG 2015]. However, contrary to the case of computing persistent homology using the Euclidean distance or even the $k$-distance, it is not known how to compute the persistent homology of high dimensional data using Gaussian kernels. In this paper, we consider a power distance version of the Gaussian kernel distance (GKPD) given by Phillips, Wang and Zheng, and show that the persistent homology of the Čech filtration of $P$ comput…
Persistent Topology studies topological features of shapes by analyzing the lower level sets of suitable functions, called filtering functions, and encoding the arising information in a parameterized version of the Betti numbers, i.e. the ranks of persistent homology groups. Initially introduced by considering real-valued filtering functions, Persistent Topology has been subsequently generalized to a multidimensional setting, i.e. to the case of $\R^n$-valued filtering functions, leading to studying the ranks of multidimensional homology groups. In particular, a multidimensional matching dista…
Arizona State University（亚利桑那州立大学）；IBM Thomas J. Watson Research Center（IBM托马斯·J·沃森研究中心）
In this paper, we propose a novel framework for dynamical analysis of human actions from 3D motion capture data using topological data analysis. We model human actions using the topological features of the attractor of the dynamical system. We reconstruct the phase-space of time series corresponding to actions using time-delay embedding, and compute the persistent homology of the phase-space reconstruction. In order to better represent the topological properties of the phase-space, we incorporate the temporal adjacency information when computing the homology groups. The persistence of these ho…
Force-directed layouts belong to a popular class of methods used to position nodes in a node-link diagram. However, they typically lack direct consideration of global structures, which can result in visual clutter and the overlap of unrelated structures. In this paper, we use the principles of persistent homology to untangle force-directed layouts thus mitigating these issues. First, we devise a new method to use 0-dimensional persistent homology to efficiently generate an initial graph layout. The approach results in faster convergence and better quality graph layouts. Second, we provide a ne…
Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically -- as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems, we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits th…
In this paper we propose a computationally efficient multiple hypothesis testing procedure for persistent homology. The computational efficiency of our procedure is based on the observation that one can empirically simulate a null distribution that is universal across many hypothesis testing applications involving persistence homology. Our observation suggests that one can simulate the null distribution efficiently based on a small number of summaries of the collected data and use this null in the same way that p-value tables were used in classical statistics. To illustrate the efficiency and …
This paper shows a mathematical formalization, algorithms and computation software of volume optimal cycles, which are useful to understand geometric features shown in a persistence diagram. Volume optimal cycles give us concrete and optimal homologous structures, such as rings or cavities, on a given data. The key idea is the optimality on $(q + 1)$-chain complex for a $q$th homology generator. This optimality formalization is suitable for persistent homology. We can solve the optimization problem using linear programming. For an alpha filtration on $\mathbb{R}^n$, volume optimal cycles on an…
Over the past two decades, topological data analysis has emerged as a field of applied mathematics with new applications and algorithmic developments appearing rapidly. Two fundamental computations in this field are persistent homology and zigzag homology. In this paper, we show how these computations in the most general case reduce to finding a canonical form of a matrix associated with a type A quiver representation, which in turn can be computed using factorizations of associated matrices. We show how to use arbitrary induced maps on homology for computation, providing a framework that goes…
In this paper we study the relationship between a very classical algebraic object associated to a filtration of spaces, namely a spectral sequence introduced by Leray in the 1940's, and a more recently invented object that has found many applications -- namely, its persistent homology groups. We show the existence of a long exact sequence of groups linking these two objects and using it derive formulas expressing the dimensions of each individual groups of one object in terms of the dimensions of the groups in the other object. The main tool used to mediate between these objects is the notion …
We give an $O(n^2(k+\log n))$ algorithm for computing the $k$-dimensional persistent homology of a filtration of clique complexes of cyclic graphs on $n$ vertices. This is nearly quadratic in the number of vertices $n$, and therefore a large improvement upon the traditional persistent homology algorithm, which is cubic in the number of simplices of dimension at most $k+1$, and hence of running time $O(n^{3(k+2)})$ in the number of vertices $n$. Our algorithm applies, for example, to Vietoris--Rips complexes of points sampled from a curve in $\mathbb{R}^d$ when the scale is bounded depending on…
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…
The Vietoris-Rips filtration for an $n$-point metric space is a sequence of large simplicial complexes adding a topological structure to the otherwise disconnected space. The persistent homology is a key tool in topological data analysis and studies topological features of data that persist over many scales. The fastest algorithm for computing persistent homology of a filtration has time $O(M(u)+u^2\log^2 u)$, where $u$ is the number of updates (additions or deletions of simplices), $M(u)=O(u^{2.376})$ is the time for multiplication of $u\times u$ matrices. For a space of $n$ points given by t…
A crucial step in the analysis of persistent homology is the transformation of data into an appropriate topological object (in our case, a simplicial complex). Modern packages for persistent homology often construct Vietoris--Rips or other distance-based simplicial complexes on point clouds because they are relatively easy to compute. We investigate alternative methods of constructing these complexes and the effects of making associated choices during simplicial-complex construction on the output of persistent-homology algorithms. We present two new methods for constructing simplicial complexe…
Motivated by the problem of dealing with incomplete or imprecise acquisition of data in computer vision and computer graphics, we extend results concerning the stability of persistent homology with respect to function perturbations to results concerning the stability with respect to domain perturbations. Domain perturbations can be measured in a number of different ways. An important method to compare domains is the Hausdorff distance. We show that by encoding sets using the distance function, the multidimensional matching distance between rank invariants of persistent homology groups is alway…
