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 recover the first and zero-th homology of the gluing from the respective homologies of the components.
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.
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）
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 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…
We prove a Kunneth theorem for the Vietoris-Rips homology and cohomology of a semi-uniform space. We then interpret this result for graphs, where we show that the Kunneth theorem holds for graphs with respect to the strong graph product. We finish by computing the Vietoris-Rips cohomology of the torus endowed with diferent semi-uniform structures.
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…
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…
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…
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…
We formalize an equivariant version of Bestvina-Brady discrete Morse theory, and apply it to Vietoris-Rips complexes in order to exhibit finite universal spaces for proper actions for all asymptotically CAT(0) groups.
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…
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.
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 Geometry of Cochains on Sampled Vietoris-Rips Complexes
University of Edinburgh（爱丁堡大学）；Max Planck Institute of Molecular Cell Biology and Genetics（马克斯·普朗克分子细胞生物学与遗传学研究所）；Center for Systems Biology（系统生物学中心）；Technische Universitat Dresden（德累斯顿工业大学）
Vietoris--Rips Contractibility for Dense Subsets of Finite-Dimensional Normed Spaces
Halıcıoğlu Data Science Institute, University of California San Diego（加州大学圣地亚哥分校哈奇奥格鲁数据科学研究所）；Department of Mathematics, University of Oklahoma（俄克拉荷马大学数学系）
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…
The so called Čech and Vietoris-Rips simplicial filtrations are designed to capture information about the topological structure of metric datasets. These filtrations are two of the workhorses in the field of topological data analysis. They enjoy stability with respect to the Gromov-Hausdorff (GH) distance, and this stability property allows us to estimate the GH distance between finite metric space representations of the underlying datasets. Via the concept of Gromov's curvature sets we construct a rich theoretical framework of valuation-induced stable filtration functors. This framework inclu…
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…
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.
Many simplicial complexes arising in practice have an associated metric space structure on the vertex set but not on the complex, e.g. the Vietoris-Rips complex in applied topology. We formalize a remedy by introducing a category of simplicial metric thickenings whose objects have a natural realization as metric spaces. The properties of this category allow us to prove that, for a large class of thickenings including Vietoris-Rips and Cech thickenings, the product of metric thickenings is homotopy equivalent to the metric thickenings of product spaces, and similarly for wedge sums.
The efficiency of extracting topological information from point data depends largely on the complex that is built on top of the data points. From a computational viewpoint, the most favored complexes for this purpose have so far been Vietoris-Rips and witness complexes. While the Vietoris-Rips complex is simple to compute and is a good vehicle for extracting topology of sampled spaces, its size is huge--particularly in high dimensions. The witness complex on the other hand enjoys a smaller size because of a subsampling, but fails to capture the topology in high dimensions unless imposed with e…
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…
We study the relationship between metric thickenings and simplicial complexes associated to coverings of metric spaces. Let $\mathcal{U}$ be a cover of a separable metric space $X$ by open sets with a uniform diameter bound. The Vietoris complex contains all simplices with vertex set contained in some $U \in \mathcal{U}$, and the Vietoris metric thickening is the space of probability measures with support in some $U \in \mathcal{U}$, equipped with an optimal transport metric. We show that the Vietoris metric thickening and the Vietoris complex have isomorphic homotopy groups in all dimensions.…
We construct a nerve functor parametrized by a choice of quantale, exhibiting both the Vietoris-Rips complex and the magnitude nerve as instances of this nerve for different choices of monoidal structure on $\mathbb{R}$. Furthermore, the difference between how persistent homology processes the Vietoris-Rips complex and how magnitude homology processes the magnitude nerve is cast as a choice of whether or not to "localize" the corresponding nerves along $\mathbb{R}$ in a precise sense. Lastly, we mention some application-oriented observations naturally suggested by the perspective mentioned abo…
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…
