Versions of Intersection and Local Homology

Arxiv preprint arXiv: …, 2009

Multidimensional persistence studies topological features of shapes by analyzing the lower level sets of vector-valued functions. The rank invariant completely determines the multidimensional analogue of persistent homology groups. We prove that multidimensional rank invariants are stable with respect to function perturbations. More precisely, we construct a distance between rank invariants such that small changes of the function imply only small changes of the rank invariant. This result can be obtained by assuming the function to be just continuous. Multidimensional stability opens the way to a stable shape comparison methodology based on multidimensional persistence.

Proceedings of The American Mathematical Society, 2010

A recent result on size functions is extended to higher homology modules: the persistent homology based on a multidimensional measuring function is reduced to a 1-dimensional one. This leads to a stable distance for multidimensional persistent homology. Some reflections on i-essentiality of homological critical values conclude the paper.

Computers & Graphics: X

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 oneparameter persistent homology have been established to connect persistent homology with machine learning techniques with applicability on shape analysis, recognition and classification. 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 multivariate data analysis.

2020

In this article, we show that hierarchical clustering and the zeroth persistent homology do deliver the same topological information about a given data set. We show this fact using cophenetic matrices constructed out of the filtered Vietoris-Rips complex of the data set at hand. As in any cophenetic matrix, one can also display the inter-relations of zeroth homology classes via a rooted tree, also known as a dendogram. Since homological cophenetic matrices can be calculated for higher homologies, one can also sketch similar dendograms for higher persistent homology classes.

Discrete & Computational Geometry, 2009

Persistent homology captures the topology of a filtration-a oneparameter family of increasing spaces-in terms of a complete discrete invariant. This invariant is a multiset of intervals that denote the lifetimes of the topological entities within the filtration. In many applications of topology, we need to study a multifiltration: a family of spaces parameterized along multiple geometric dimensions. In this paper, we show that no similar complete discrete invariant exists for multidimensional persistence. Instead, we propose the rank invariant, a discrete invariant for the robust estimation of Betti numbers in a multifiltration, and prove its completeness in one dimension.

Persistent homology (PH) is a method used in topological data analysis (TDA) to study qualitative features of data that persist across multiple scales. It is robust to perturbations of input data, independent of dimensions and coordinates, and provides a compact representation of the qualitative features of the input. Despite recent progress, the computation of PH remains a wide open area with numerous important and fascinating challenges. The field of PH computation is evolving rapidly, and new algorithms and software implementations are being updated and released at a rapid pace. The purposes of our article are to (1) introduce theory and computational methods for PH to a broad range of applied mathematicians and computational scientists and (2) provide benchmarks of state-of-the-art implementations for the computation of PH. We give a friendly introduction to PH, navigate the pipeline for the computation of PH with an eye towards applications, and use a range of synthetic and real-world data sets to evaluate currently available open-source implementations for the computation of PH. Based on our benchmarking, we indicate which algorithms and implementations are best suited to different types of data sets. In an accompanying tutorial, we provide guidelines for the computation of PH. We make publicly available all scripts that we wrote for the tutorial, and we make available the processed version of the data sets used in the benchmarking.

arXiv (Cornell University), 2020

In this paper we present an efficient algorithm to produce a provably dense sample of a smooth compact variety. The procedure is partly based on computing bottlenecks of the variety. Using geometric information such as the bottlenecks and the local reach we also provide bounds on the density of the sample needed in order to guarantee that the homology of the variety can be recovered from the sample. An implementation of the algorithm is provided together with numerical experiments and a computational comparison to the algorithm by Dufresne et. al. [17].

Discrete & Computational Geometry, 2005

We study the homology of a filtered d-dimensional simplicial complex K as a single algebraic entity and establish a correspondence that provides a simple description over fields. Our analysis enables us to derive a natural algorithm for computing persistent homology over an arbitrary field in any dimension. Our study also implies the lack of a simple classification over non-fields. Instead, we give an algorithm for computing individual persistent homology groups over an arbitrary PIDs in any dimension.

Arxiv preprint arXiv:1001.1078, 2010

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 always upperly bounded by the Hausdorff distance between sets. Moreover, we prove that our construction maintains information about the original set.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2013

Multidimensional persistent modules do not admit a concise representation analogous to that provided by persistence diagrams for real-valued functions. However, there is no obstruction for multidimensional persistent Betti numbers to admit one. Therefore, it is reasonable to look for a generalization of persistence diagrams concerning those properties that are related only to persistent Betti numbers. In this paper, the persistence space of a vector-valued continuous function is introduced to generalize the concept of persistence diagram in this sense. Furthermore, it is presented a method to visualize topological features of a shape via persistence spaces. Finally, it is shown that this method is resistant to perturbations of the input data.

2013

Proceedings of the Twentieth Annual ACM-SIAM Symposium on Discrete Algorithms, 2009

Motivated by the measurement of local homology and of functions on noisy domains, we extend the notion of persistent homology to sequences of kernels, images, and cokernels of maps induced by inclusions in a filtration of pairs of spaces. Specifically, we note that persistence in this context is well defined, we prove that the persistence diagrams are stable, and we explain how to compute them.

Advances in Applied Mathematics

Real data is often given as a point cloud, i.e. a finite set of points with pairwise distances between them. An important problem is to detect the topological shape of data-for example, to approximate a point cloud by a low-dimensional non-linear subspace such as an embedded graph or a simplicial complex. Classical clustering methods and principal component analysis work well when given data points split into well-separated clusters or lie near linear subspaces of a Euclidean space. Methods from topological data analysis in general metric spaces detect more complicated patterns such as holes and voids that persist for a long time in a 1-parameter family of shapes associated to a cloud. These features can be visualized in the form of a 1-dimensional homologically persistent skeleton, which optimally extends a minimal spanning tree of a point cloud to a graph with cycles. We generalize this skeleton to higher dimensions and prove its optimality among all complexes that preserve topological features of data at any scale.

arXiv (Cornell University), 2021

Persistence landscapes are functional summaries of persistence diagrams designed to enable analysis of the diagrams using tools from functional data analysis. They comprise a collection of scalar functions such that birth and death times of topological features in persistence diagrams map to extrema of functions and intervals where they are non-zero. As a consequence, variation in persistence diagrams is encoded in both amplitude and phase components of persistence landscapes. Through functional data analysis of persistence landscapes, under an elastic Riemannian metric, we show how meaningful statistical summaries of persistence landscapes (e.g., mean, dominant directions of variation) can be obtained by decoupling their amplitude and phase variations. This decoupling is achieved via optimal alignment, with respect to the elastic metric, of the persistence landscapes. The estimated phase functions are tied to the resolution parameter that determines the filtration of simplicial complexes used to construct persistence diagrams. For a dataset obtained under geometric, scale and sampling variabilities, the phase function prescribes an optimal rate of increase of the resolution parameter for enhancing the topological signal in a persistence diagram. The proposed approach adds substantially to the statistical analysis of data objects with rich structure compared to past studies. In particular, we focus on two sets of data that have been analyzed in the past, brain artery trees and images of prostate cancer cells, and show that separation of amplitude and phase of persistence landscapes is beneficial in both settings.

Computers and Mathematics with Applications, 2013

The theory of multidimensional persistent homology was initially developed in the discrete setting, and involved the study of simplicial complexes filtered through an ordering of the simplices. Later, stability properties of multidimensional persistence have been proved to hold when topological spaces are filtered by continuous functions, i.e. for continuous data. This paper aims to provide a bridge between the continuous setting, where stability properties hold, and the discrete setting, where actual computations are carried out. More precisely, a stability preserving method is developed to compare rank invariants of vector functions obtained from discrete data. These advances confirm that multidimensional persistent homology is an appropriate tool for shape comparison in computer vision and computer graphics applications. The results are supported by numerical tests.