21 pages. This is a new version of this preprint. The proof of Lemma 19 of the previous version had an error that rendered the proof of the former Theorem 23 invalid. No statement of that form is now claimed
Vietoris-Rips and degree Rips complexes are represented as homotopy types by their underlying posets of simplices, and basic homotopy stability theorems are recast in these terms. These homotopy types are viewed as systems (or functors), which are defined on a parameter space. The category of systems of spaces admits a partial homotopy theory that is based on controlled equivalences, suitably defined, that are the output of homotopy stability results.
Computation of degree-1 persistent homology on larger point-clouds using the Reduced Vietoris-Rips filtration
Australian National University（澳大利亚国立大学）；Centre for Systems Biology Dresden（德累斯顿系统生物学中心）；Max Planck Institute of Cell Biology and Genetics（马克斯·普朗克细胞生物学与遗传学研究所）；Max Planck institute for the Physics of Complex Systems（马克斯·普朗克复杂系统物理研究所）
Motivated by applications in Topological Data Analysis, we consider decompositions of a simplicial complex induced by a cover of its vertices. We study how the homotopy type of such decompositions approximates the homotopy of the simplicial complex itself. The difference between the simplicial complex and such an approximation is quantitatively measured by means of the so called obstruction complexes. Our general machinery is then specialized to clique complexes, Vietoris-Rips complexes and Vietoris-Rips complexes of metric gluings. For the latter we give metric conditions which allow to recov…
The Rips complex at scale r of a set of points X in a metric space is the abstract simplicial complex whose faces are determined by finite subsets of X of diameter less than r. We prove that for X in the Euclidean 3-space R^3 the natural projection map from the Rips complex of X to its shadow in R^3 induces a surjection on fundamental groups. This partially answers a question of Chambers, de Silva, Erickson and Ghrist who studied this projection for subsets of R^2. We further show that Rips complexes of finite subsets of R^n are universal, in that they model all homotopy types of simplicial co…
We derive conditions under which the reconstruction of a target space is topologically correct via the Čech complex or the Vietoris-Rips complex obtained from possibly noisy point cloud data. We provide two novel theoretical results. First, we describe sufficient conditions under which any non-empty intersection of finitely many Euclidean balls intersected with a positive reach set is contractible, so that the Nerve theorem applies for the restricted Čech complex. Second, we demonstrate the homotopy equivalence of a positive $μ$-reach set and its offsets. Applying these results to the restrict…
Persistence diagrams are useful displays that give a summary information regarding the topological features of some phenomenon. Usually, only one persistence diagram is available, and replicated persistence diagrams are needed for statistical inference. One option for generating these replications is to fit a distribution for the points on the persistence diagram. The type of the relevant distribution depends on the way the persistence diagram is builded. There are two approaches for building the persistence diagram, one is based on the Vietoris-Rips complex, and the second is based on some fi…
We introduce weighted versions of the classical Čech and Vietoris-Rips complexes. We show that a version of the Vietoris-Rips Lemma holds for these weighted complexes and that they enjoy appropriate stability properties. We also give some preliminary applications of these weighted complexes.
We describe the homotopy types of Vietoris-Rips complexes of hypercube graphs at small scale parameters. In more detail, let $Q_n$ be the vertex set of the hypercube graph with $2^n$ vertices, equipped with the shortest path metric. Equivalently, $Q_n$ is the set of all binary strings of length $n$, equipped with the Hamming distance. The Vietoris-Rips complex of $Q_n$ at scale parameter zero is $2^n$ points, and the Vietoris-Rips complex of $Q_n$ at scale parameter one is the hypercube graph, which is homotopy equivalent to a wedge sum of circles. We show that the Vietoris-Rips complex of $Q_…
Vietoris-Rips metric thickenings have previously been proposed as an alternate approach to understanding Vietoris-Rips simplicial complexes and their persistent homology. Recent work has shown that for totally bounded metric spaces, Vietoris-Rips metric thickenings have persistent homology barcodes that agree with those of Vietoris-Rips simplicial complexes, ignoring whether endpoints of bars are open or closed. Combining this result with the known homotopy types and barcodes of the Vietoris-Rips simplicial complexes of the circle, the barcodes of the Vietoris-Rips metric thickenings of the ci…
While the Vietoris-Rips complex is now widely used in both topological data analysis and the theory of hyperbolic groups, many of the fundamental properties of its homology have remained elusive. In this article, we define the Vietoris-Rips homology for semi-uniform spaces, which generalizes the classical theory for graphs and metric spaces, and provides a natural, general setting for the construction. We then prove a version of the Eilenberg-Steenrod axioms in this setting, giving a natural definition of homotopy for semi-uniform spaces in the process.
Given a metric space X and a distance threshold r>0, the Vietoris-Rips simplicial complex has as its simplices the finite subsets of X of diameter less than r. A theorem of Jean-Claude Hausmann states that if X is a Riemannian manifold and r is sufficiently small, then the Vietoris-Rips complex is homotopy equivalent to the original manifold. Little is known about the behavior of Vietoris-Rips complexes for larger values of r, even though these complexes arise naturally in applications using persistent homology. We show that as r increases, the Vietoris-Rips complex of the circle obtains the h…
Universidade Federal do ABC（阿贝克联邦大学）；Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales（布宜诺斯艾利斯大学理学院）；CONICET-Universidad de Buenos Aires. Instituto de Ciencias de la Compuatción (ICC)（阿根廷国家科学研究委员会-布宜诺斯艾利斯大学计算机科学研究所）
In this paper we define, implement, and investigate a simplicial complex construction for computing persistent homology of Euclidean point cloud data, which we call the Delaunay-Rips complex (DR). Assigning the Vietoris-Rips weights to simplices, DR experiences speed-up in the persistence calculations by only considering simplices that appear in the Delaunay triangulation of the point cloud. We document and compare a Python implementation of DR with other simplicial complex constructions for generating persistence diagrams. By imposing sufficient conditions on point cloud data, we are able to …
The degree-Rips bifiltration is the most computable of the parameter-free, density-sensitive bifiltrations in topological data analysis. It is known that this construction is stable to small perturbations of the input data, but its robustness to outliers is not well understood. In recent work, Blumberg-Lesnick prove a result in this direction using the Prokhorov distance and homotopy interleavings. Based on experimental evaluation, they argue that a more refined approach is desirable, and suggest the framework of homology inference. Motivated by these experiments, we consider a probability mea…
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…
This paper presents explicit assumptions for the existence of interleaving homotopy equivalences of both Vietoris-Rips and Lesnick complexes associated to an inclusion of data sets. Consequences of these assumptions are investigated on the space level, and for corresponding hierarchies of clusters and their sub-posets of branch points. Hierarchy posets and branch point posets admit a calculus of least upper bounds, which is used to show that the map of branch points associated to the inclusion of data sets is a controlled homotopy equivalence.
Given a sample of points $X$ in a metric space $M$ and a scale $r>0$, the Vietoris-Rips simplicial complex $\mathrm{VR}(X;r)$ is a standard construction to attempt to recover $M$ from $X$ up to homotopy type. A deficiency of this approach is that $\mathrm{VR}(X;r)$ is not metrizable if it is not locally finite, and thus does not recover metric information about $M$. We attempt to remedy this shortcoming by defining a metric space thickening of $X$, which we call the \emph{Vietoris-Rips thickening} $\mathrm{VR}^m(X;r)$, via the theory of optimal transport. When $M$ is a complete Riemannian mani…
We study two methods for computing network features with topological underpinnings: the Rips and Dowker persistent homology diagrams. Our formulations work for general networks, which may be asymmetric and may have any real number as an edge weight. We study the sensitivity of Dowker persistence diagrams to asymmetry via numerous theoretical examples, including a family of highly asymmetric cycle networks that have interesting connections to the existing literature. In particular, we characterize the Dowker persistence diagrams arising from asymmetric cycle networks. We investigate the stabili…
This paper is a survey of persistent homology, primarily as it is used in topological data analysis. It includes the theory of persistence modules, as well as stability theorems for persistence barcodes, generalized persistence, vectorization of persistence barcodes, as well as some applications.
Using ideas of the Dowker duality we prove that the Rips complex at scale $r$ is homotopy equivalent to the nerve of a cover consisting of sets of prescribed diameter. We then develop a functorial version of the Nerve theorem coupled with the Dowker duality, which is presented as a Functorial Dowker-Nerve Diagram. These results are incorporated into a systematic theory of filtrations arising from covers. As a result we provide a general framework for reconstruction of spaces by Rips complexes, a short proof of the reconstruction result of Hausmann, and completely classify reconstruction scales…
Motivated by computational aspects of persistent homology for Vietoris-Rips filtrations, we generalize a result of Eliyahu Rips on the contractibility of Vietoris-Rips complexes of geodesic spaces for a suitable parameter depending on the hyperbolicity of the space. We consider the notion of geodesic defect to extend this result to general metric spaces in a way that is also compatible with the filtration. We further show that for finite tree metrics the Vietoris-Rips complexes collapse to their corresponding subforests. We relate our result to modern computational methods by showing that thes…
A challenge in computational topology is to deal with large filtered geometric complexes built from point cloud data such as Vietoris-Rips filtrations. This has led to the development of schemes for parallel computation and compression which restrict simplices to lie in open sets in a cover of the data. We extend the method of acyclic carriers to the setting of persistent homology to give detailed bounds on the relationship between Vietoris-Rips filtrations restricted to covers and the full construction. We show how these complexes can be used to study data over a base space and use our result…
By analogy with methods of Spivak, there is a realization functor which takes a persistence diagram $Y$ in simplicial sets to an extended pseudo-metric space (or ep-metric space) $Re(Y)$. The functor $Re$ has a right adjoint, called the singular functor, which takes an ep-metric space $Z$ to a persistence diagram $S(Z)$. We give an explicit description of $Re(Y)$, and show that it depends only on the $1$-skeleton $sk_{1}Y$ of $Y$. If $X$ is a totally ordered ep-metric space, then there is an isomorphism $Re(V_{\ast}(X)) \cong X$, between the realization of the Vietoris-Rips diagram $V_{\ast}(X…
The Rips filtration over a finite metric space and its corresponding persistent homology are prominent methods in TDA to summarise the shape of data. Crucial to their use is the bottleneck stability result. A generalisation of the Rips filtration to any symmetric function $f:X\times X\to \mathbb{R}$ was defined by Chazal, De Silva and Oudot, and they showed it was stable with respect to the correspondence distortion distance. Allowing asymmetry, we consider four different persistence modules. The first method is through symmetrisation. For $a\in [0,1]$ we can construct a symmetric function $sy…
Let $G$ be a group acting properly and by isometries on a metric space $X$; it follows that the quotient or orbit space $X/G$ is also a metric space. We study the Vietoris-Rips and Čech complexes of $X/G$. Whereas (co)homology theories for metric spaces let the scale parameter of a Vietoris-Rips or Čech complex go to zero, and whereas geometric group theory requires the scale parameter to be sufficiently large, we instead consider intermediate scale parameters (neither tending to zero nor to infinity). As a particular case, we study the Vietoris-Rips and Čech thickenings of projective spaces a…
Given a sample $Y$ from an unknown manifold $X$ embedded in Euclidean space, it is possible to recover the homology groups of $X$ by building a Vietoris--Rips or Čech simplicial complex on top of the vertex set $Y$. However, these simplicial complexes need not inherit the metric structure of the manifold, in particular when $Y$ is infinite. Indeed, a simplicial complex is not even metrizable if it is not locally finite. We instead consider metric thickenings, called the \emph{Vietoris--Rips} and \emph{Čech thickenings}, which are equipped with the 1-Wasserstein metric in place of the simplicia…
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…
We study notions of persistent homotopy groups of compact metric spaces together with their stability properties in the Gromov-Hausdorff sense. We pay particular attention to the case of fundamental groups, for which we obtain a more precise description. Under fairly mild assumptions on the spaces, we proved that the classical fundamental group has an underlying tree-like structure (i.e. a dendrogram) and an associated ultra-metric.
Consider the space of continuous functions on a geometric tree $X$ whose persistent homology gives rise to a finite generic barcode $D$. We show that there are exactly as many path connected components in this space as there are merge trees whose barcode is $D$. We find that each component is homotopy equivalent to a configuration space on $X$ with specialized constraints encoded by the merge tree. For barcodes $D$ with either one or two intervals, our method also allows us to compute the homotopy type of this space of functions.
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…
For a fixed $N$, we analyze the space of all sequences $z=(z_1,\dots,z_N)$, approximating a continuous function on the circle, with a given persistence diagram $P$, and show that the typical components of this space are homotopy equivalent to $S^1$. We also consider the space of functions on $Y$-shaped (resp., star-shaped) trees with a 2-point persistence diagram, and show that this space is homotopy equivalent to $S^1$ (resp., to a bouquet of circles).
