Added Example 4.15 (in Section 4.3) to show that persistence sets and persistent homology distinguish different spaces, and added more running time comparisons to Section 4.4
We study a family of invariants of compact metric spaces that combines the Curvature Sets defined by Gromov in the 1980s with Vietoris-Rips Persistent Homology. For given integers $k\geq 0$ and $n\geq 1$ we consider the dimension $k$ Vietoris-Rips persistence diagrams of \emph{all} subsets of a given metric space with cardinality at most $n$. We call these invariants \emph{persistence sets} and denote them as $\mathbf{D}_{n,k}^\textrm{VR}$. We establish that (1) computing these invariants is often significantly more efficient than computing the usual Vietoris-Rips persistence diagrams, (2) these invariants have very good discriminating power and, in many cases, capture information that is imperceptible through standard Vietoris-Rips persistence diagrams, and (3) they enjoy stability properties. We precisely characterize some of them in the case of spheres and surfaces with constant curvature using a generalization of Ptolemy's inequality. We also identify a rich family of metric graphs for which $\mathbf{D}_{4,1}^\textrm{VR}$ fully recovers their homotopy type by studying split-metric decompositions. Along the way we prove some useful properties of Vietoris-Rips persistence diagrams using Mayer-Vietoris sequences. These yield a geometric algorithm for computing the Vietoris-Rips persistence diagram of a space $X$ with cardinality $2k+2$ with quadratic time complexity as opposed to the much higher cost incurred by the usual algebraic algorithms relying on matrix reduction.
We introduce a refinement of the persistence diagram, the graded persistence diagram. It is the Mobius inversion of the graded rank function, which is obtained from the rank function using the unary numeral system. Both persistence diagrams and graded persistence diagrams are integer-valued functions on the Cartesian plane. Whereas the persistence diagram takes non-negative values, the graded persistence diagram takes values of 0, 1, or -1. The sum of the graded persistence diagrams is the persistence diagram. We show that the positive and negative points in the k-th graded persistence diagram…
We generalize the persistence diagram of Cohen-Steiner, Edelsbrunner, and Harer to the setting of constructible persistence modules valued in a symmetric monoidal category. We call this the type A persistence diagram of a persistence module. If the category is also abelian, then we define a second type B persistence diagram. In addition, we show that both diagrams are stable to all sufficiently small perturbations of the module.
It is known that for a variety of choices of metrics, including the standard bottleneck distance, the space of persistence diagrams admits geodesics. Typically these existence results produce geodesics that have the form of a convex combination. More specifically, given two persistence diagrams and a choice of metric, one obtains a bijection realizing the distance between the diagrams, and uses this bijection to linearly interpolate from one diagram to another. We prove that for several families of metrics, every geodesic in persistence diagram space arises as such a convex combination. For ce…
Persistence diagrams do not admit an inner product structure compatible with any Wasserstein metric. Hence, when applying kernel methods to persistence diagrams, the underlying feature map necessarily causes distortion. We prove persistence diagrams with the p-Wasserstein metric do not admit a coarse embedding into a Hilbert space when p > 2.
We prove that the space of persistence diagrams on $n$ points (with the bottleneck or a Wasserstein distance) coarsely embeds into Hilbert space by showing it is of asymptotic dimension $2n$. Such an embedding enables utilisation of Hilbert space techniques on the space of persistence diagrams. We also prove that when the number of points is not bounded, the corresponding spaces of persistence diagrams do not have finite asymptotic dimension. Furthermore, in the case of the bottleneck distance, the corresponding space does not coarsely embed into Hilbert space.
Since persistence diagrams do not admit an inner product structure, a map into a Hilbert space is needed in order to use kernel methods. It is natural to ask if such maps necessarily distort the metric on persistence diagrams. We show that persistence diagrams with the bottleneck distance do not even admit a coarse embedding into a Hilbert space. As part of our proof, we show that any separable, bounded metric space isometrically embeds into the space of persistence diagrams with the bottleneck distance. As corollaries, we obtain the generalized roundness, negative type, and asymptotic dimensi…
In this paper, we extend bottleneck stability to the setting of one dimensional constructible persistences module valued in any small abelian category.
In topological data analysis, persistent homology characterizes robust topological features in data and it has a summary representation, called a persistence diagram. Statistical research for persistence diagrams have been actively developed, and the persistence weighted kernel shows several advantages over other statistical methods for persistence diagrams. If data is drawn from some probability distribution, the corresponding persistence diagram have randomness. Then, the expectation of the persistence diagram by the persistence weighted kernel is well-defined. In this paper, we study relati…
Metric graphs are special types of metric spaces used to model and represent simple, ubiquitous, geometric relations in data such as biological networks, social networks, and road networks. We are interested in giving a qualitative description of metric graphs using topological summaries. In particular, we provide a complete characterization of the 1-dimensional intrinsic Cech persistence diagrams for metric graphs using persistent homology. Together with complementary results by Adamaszek et. al, which imply results on intrinsic Cech persistence diagrams in all dimensions for a single cycle, …
The natural pseudo-distance of spaces endowed with filtering functions is precious for shape classification and retrieval; its optimal estimate coming from persistence diagrams is the bottleneck distance, which unfortunately suffers from combinatorial explosion. A possible algebraic representation of persistence diagrams is offered by complex polynomials; since far polynomials represent far persistence diagrams, a fast comparison of the coefficient vectors can reduce the size of the database to be classified by the bottleneck distance. This article explores experimentally three transformations…
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…
Persistence diagrams are important descriptors in Topological Data Analysis. Due to the nonlinearity of the space of persistence diagrams equipped with their {\em diagram distances}, most of the recent attempts at using persistence diagrams in machine learning have been done through kernel methods, i.e., embeddings of persistence diagrams into Reproducing Kernel Hilbert Spaces, in which all computations can be performed easily. Since persistence diagrams enjoy theoretical stability guarantees for the diagram distances, the {\em metric properties} of the feature map, i.e., the relationship betw…
Persistent homology studies the birth and death of cycles in a parameterized family of spaces. In this paper, we study the birth and death of cycles in a multifiltration of a chain complex with the goal of producing a persistence diagram that satisfies bottleneck stability.
The persistent homology of a stationary point process on ${\bf R}^N$ is studied in this paper. As a generalization of continuum percolation theory, we study higher dimensional topological features of the point process such as loops, cavities, etc. in a multiscale way. The key ingredient is the persistence diagram, which is an expression of the persistent homology. We prove the strong law of large numbers for persistence diagrams as the window size tends to infinity and give a sufficient condition for the limiting persistence diagram to have the full support. We also discuss a central limit the…
The objective of this paper is to examine the asymptotic behavior of persistence diagrams associated with Čech filtration. A persistence diagram is a graphical descriptor of a topological and algebraic structure of geometric objects. We consider Čech filtration over a scaled random sample $r_n^{-1}\mathcal X_n = \{ r_n^{-1}X_1,\dots, r_n^{-1}X_n \}$, such that $r_n\to 0$ as $n\to\infty$. We treat persistence diagrams as a point process and establish their limit theorems in the sparse regime: $nr_n^d\to0$, $n\to\infty$. In this setting, we show that the asymptotics of the $k$th persistence diag…
Persistence diagrams are common objects in the field of Topological Data Analysis. They are topological summaries that capture both topological and geometric structure within data. Recently there has been a surge of interest in developing tools to statistically analyse populations of persistence diagrams, a process hampered by the complicated geometry of the space of persistence diagrams. In this paper we study the median of a set of diagrams, defined as the minimizer of an appropriate cost function analogous to the sum of distances used for samples of real numbers. We then characterize the lo…
We prove that the existence of a $1$-Lipschitz retraction (a contraction) from a space $X$ onto its subspace $A$ implies the persistence diagram of $A$ embeds into the persistence diagram of $X$. As a tool we introduce tight injections of persistence modules as maps inducing the said embeddings. We show contractions always exist onto shortest loops in metric graphs and conjecture on existence of contractions in planar metric graphs onto all loops of a shortest homology basis. Of primary interest are contractions onto loops in geodesic spaces. These act as ideal circular coordinates. Furthermor…
University of North Carolina at Greensboro（北卡罗来纳大学格林斯伯勒分校）；Eli Lilly and Company（礼来公司）
Persistence diagrams are one of the main tools in the field of Topological Data Analysis (TDA). They contain fruitful information about the shape of data. The use of machine learning algorithms on the space of persistence diagrams proves to be challenging as the space lacks an inner product. For that reason, transforming these diagrams in a way that is compatible with machine learning is an important topic currently researched in TDA. In this paper, our main contribution consists of three components. First, we develop a general and unifying framework of vectorizing diagrams that we call the \t…
Topological data analysis is an emerging mathematical concept for characterizing shapes in multi-scale data. In this field, persistence diagrams are widely used as a descriptor of the input data, and can distinguish robust and noisy topological properties. Nowadays, it is highly desired to develop a statistical framework on persistence diagrams to deal with practical data. This paper proposes a kernel method on persistence diagrams. A theoretical contribution of our method is that the proposed kernel allows one to control the effect of persistence, and, if necessary, noisy topological properti…
We develop a novel hierarchy for zero-dimensional persistence pairs, i.e., connected components, which is capable of capturing more fine-grained spatial relations between persistence pairs. Our work is motivated by a lack of spatial relationships between features in persistence diagrams, leading to a limited expressive power. We build upon a recently-introduced hierarchy of pairs in persistence diagrams that augments the pairing stored in persistence diagrams with information about which components merge. Our proposed hierarchy captures differences in branching structure. Moreover, we show how…
Persistence diagrams, the most common descriptors of Topological Data Analysis, encode topological properties of data and have already proved pivotal in many different applications of data science. However, since the (metric) space of persistence diagrams is not Hilbert, they end up being difficult inputs for most Machine Learning techniques. To address this concern, several vectorization methods have been put forward that embed persistence diagrams into either finite-dimensional Euclidean space or (implicit) infinite dimensional Hilbert space with kernels. In this work, we focus on persistenc…
Continuation of Point Clouds via Persistence Diagrams
Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo（圣保罗大学数学与计算科学学院）；WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University（东北大学世界顶尖研究中心材料研究高级研究所）
The Pennsylvania State University（宾夕法尼亚州立大学）；The Institute of Statistical Mathematics（统计数学研究所）
Persistent homology has become an important tool for extracting geometric and topological features from data, whose multi-scale features are summarized in a persistence diagram. From a statistical perspective, however, persistence diagrams are very sensitive to perturbations in the input space. In this work, we develop a framework for constructing robust persistence diagrams from superlevel filtrations of robust density estimators constructed using reproducing kernels. Using an analogue of the influence function on the space of persistence diagrams, we establish the proposed framework to be le…
We consider random filtered complexes built over marked point processes on Euclidean spaces. Examples of our filtered complexes include a filtration of $\check{\textrm{C}}$ech complexes of a family of sets with various sizes, growths, and shapes. We establish the law of large numbers for persistence diagrams as the size of the convex window observing a marked point process tends to infinity.
One of the most elusive challenges within the area of topological data analysis is understanding the distribution of persistence diagrams. Despite much effort, this is still largely an open problem. In this paper, we present a series of novel conjectures regarding the behavior of persistence diagrams arising from random point-clouds. We claim that these diagrams obey a universal probability law, and include an explicit expression as a candidate for what this law is. We back these conjectures with an exhaustive set of experiments, including both simulated and real data. We demonstrate the power…
Topological Data Analysis (TDA) studies the shape of data. A common topological descriptor is the persistence diagram, which encodes topological features in a topological space at different scales. Turner, Mukeherjee, and Boyer showed that one can reconstruct a simplicial complex embedded in R^3 using persistence diagrams generated from all possible height filtrations (an uncountably infinite number of directions). In this paper, we present an algorithm for reconstructing plane graphs K=(V,E) in R^2 , i.e., a planar graph with vertices in general position and a straight-line embedding, from a …
Topological data analysis (TDA) is an emerging mathematical concept for characterizing shapes in complex data. In TDA, persistence diagrams are widely recognized as a useful descriptor of data, and can distinguish robust and noisy topological properties. This paper proposes a kernel method on persistence diagrams to develop a statistical framework in TDA. The proposed kernel satisfies the stability property and provides explicit control on the effect of persistence. Furthermore, the method allows a fast approximation technique. The method is applied into practical data on proteins and oxide gl…
Advanced Institute for Materials Research (WPI-AIMR), Tohoku University（东北大学材料科学高等研究所）；Center for Materials research by Information Integration (CMI2), Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS)（日本国立材料科学研究所材料信息集成研究中心材料数据与综合系统研究服务部）
Persistence diagrams have been widely recognized as a compact descriptor for characterizing multiscale topological features in data. When many datasets are available, statistical features embedded in those persistence diagrams can be extracted by applying machine learnings. In particular, the ability for explicitly analyzing the inverse in the original data space from those statistical features of persistence diagrams is significantly important for practical applications. In this paper, we propose a unified method for the inverse analysis by combining linear machine learning models with persis…
Persistent homology probes topological properties from point clouds and functions. By looking at multiple scales simultaneously, one can record the births and deaths of topological features as the scale varies. In this paper we use a statistical technique, the empirical bootstrap, to separate topological signal from topological noise. In particular, we derive confidence sets for persistence diagrams and confidence bands for persistence landscapes.
In order to use persistence diagrams as a true statistical tool, it would be very useful to have a good notion of mean and variance for a set of diagrams. In 2011, Mileyko and his collaborators made the first study of the properties of the Fréchet mean in $(\mathcal{D}_p,W_p)$, the space of persistence diagrams equipped with the p-th Wasserstein metric. In particular, they showed that the Fréchet mean of a finite set of diagrams always exists, but is not necessarily unique. The means of a continuously-varying set of diagrams do not themselves (necessarily) vary continuously, which presents obv…
We describe a method for approximating a single-variable function $f$ using persistence diagrams of sublevel sets of $f$ from height functions in different directions. We provide algorithms for the piecewise linear case and for the smooth case. Three directions suffice to locate all local maxima and minima of a piecewise linear continuous function from its collection of directional persistence diagrams, while five directions are needed in the case of smooth functions with non-degenerate critical points. Our approximation of functions by means of persistence diagrams is motivated by a study of …
We first introduce the notion of meta-rank for a 2-parameter persistence module, an invariant that captures the information behind images of morphisms between 1D slices of the module. We then define the meta-diagram of a 2-parameter persistence module to be the Möbius inversion of the meta-rank, resulting in a function that takes values from signed 1-parameter persistence modules. We show that the meta-rank and meta-diagram contain information equivalent to the rank invariant and the signed barcode. This equivalence leads to computational benefits, as we introduce an algorithm for computing th…
Many attempts have been made in recent decades to integrate machine learning (ML) and topological data analysis. A prominent problem in applying persistent homology to ML tasks is finding a vector representation of a persistence diagram (PD), which is a summary diagram for representing topological features. From the perspective of data fitting, a stable vector representation, namely, persistence B-spline grid (PBSG), is proposed based on the efficient technique of progressive-iterative approximation for least-squares B-spline function fitting. We theoretically prove that the PBSG method is sta…
The persistence diagram is an increasingly useful tool from Topological Data Analysis, but its use alongside typical machine learning techniques requires mathematical finesse. The most success to date has come from methods that map persistence diagrams into vector spaces, in a way which maximizes the structure preserved. This process is commonly referred to as featurization. In this paper, we describe a mathematical framework for featurization called \emph{template functions}, and we show that it addresses the problem of approximating continuous functions on compact subsets of the space of per…
Topological data analysis (TDA) is a rising field in the intersection of mathematics, statistics, and computer science/data science. The cornerstone of TDA is persistent homology, which produces a summary of topological information called a persistence diagram. To utilize machine and deep learning methods on persistence diagrams, These diagrams are further summarized by transforming them into functions. In this paper we investigate the stability and injectivity of a class of smooth, one-dimensional functional summaries called Gaussian persistence curves.
