DTM-based Filtrations

Despite strong stability properties, the persistent homology of filtrations classically used in Topological Data Analysis, such as, e.g. the Cech or Vietoris-Rips filtrations, are very sensitive to the presence of outliers in the data from which they are computed. In this paper, we introduce and study a new family of filtrations, the DTM-filtrations, built on top of point clouds in the Euclidean space which are more robust to noise and outliers. The approach adopted in this work relies on the notion of distance-to-measure functions, and extends some previous work on the approximation of such functions.Comment: Abel Symposia, Springer, In press, Topological Data Analysi

DTM-Based Filtrations

Despite strong stability properties, the persistent homology of filtrations classically used in Topological Data Analysis, such as, e.g. the Cech or Vietoris-Rips filtrations, are very sensitive to the presence of outliers in the data from which they are computed. In this paper, we introduce and study a new family of filtrations, the DTM-filtrations, built on top of point clouds in the Euclidean space which are more robust to noise and outliers. The approach adopted in this work relies on the notion of distance-to-measure functions and extends some previous work on the approximation of such functions

DTM-based Filtrations

International audienceDespite strong stability properties, the persistent homology of filtrations classically used in Topological Data Analysis, such as, e.g. the Cech or Vietoris-Rips filtrations, are very sensitive to the presence of outliers in the data from which they are computed. In this paper, we introduce and study a new family of filtrations, the DTM-filtrations, built on top of point clouds in the Euclidean space which are more robust to noise and outliers. The approach adopted in this work relies on the notion of distance-to-measure functions, and extends some previous work on the approximation of such functions

The Persistence of Large Scale Structures I: Primordial non-Gaussianity

We develop an analysis pipeline for characterizing the topology of large scale structure and extracting cosmological constraints based on persistent homology. Persistent homology is a technique from topological data analysis that quantifies the multiscale topology of a data set, in our context unifying the contributions of clusters, filament loops, and cosmic voids to cosmological constraints. We describe how this method captures the imprint of primordial local non-Gaussianity on the late-time distribution of dark matter halos, using a set of N-body simulations as a proxy for real data analysis. For our best single statistic, running the pipeline on several cubic volumes of size $40~(\rm{Gpc/h})^{3}$, we detect $f_{\rm NL}^{\rm loc}=10$ at $97.5\%$ confidence on $\sim 85\%$ of the volumes. Additionally we test our ability to resolve degeneracies between the topological signature of $f_{\rm NL}^{\rm loc}$ and variation of $\sigma_8$ and argue that correctly identifying nonzero $f_{\rm NL}^{\rm loc}$ in this case is possible via an optimal template method. Our method relies on information living at $\mathcal{O}(10)$ Mpc/h, a complementary scale with respect to commonly used methods such as the scale-dependent bias in the halo/galaxy power spectrum. Therefore, while still requiring a large volume, our method does not require sampling long-wavelength modes to constrain primordial non-Gaussianity. Moreover, our statistics are interpretable: we are able to reproduce previous results in certain limits and we make new predictions for unexplored observables, such as filament loops formed by dark matter halos in a simulation box.Comment: 33+11 pages, 19 figures, code available at https://gitlab.com/mbiagetti/persistent_homology_ls

Recovering the homology of immersed manifolds

Given a sample of an abstract manifold immersed in some Euclidean space, we describe a way to recover the singular homology of the original manifold. It consists in estimating its tangent bundle---seen as subset of another Euclidean space---in a measure theoretic point of view, and in applying measure-based filtrations for persistent homology. The construction we propose is consistent and stable, and does not involve the knowledge of the dimension of the manifold.In order to obtain quantitative results, we introduce the normal reach, which is a notion of reach suitable for an immersed manifold

Adaptive Topological Feature via Persistent Homology: Filtration Learning for Point Clouds

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. To enhance the accuracy of such machine learning methods, it is known to be effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we need to choose a filtration for the point clouds, an increasing sequence of spaces. Because the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we theoretically show a finite-dimensional approximation result that justifies our architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.Comment: 17 pages with 4 figure

Sparse Higher Order ?ech Filtrations

For a finite set of balls of radius r, the k-fold cover is the space covered by at least k balls. Fixing the ball centers and varying the radius, we obtain a nested sequence of spaces that is called the k-fold filtration of the centers. For k = 1, the construction is the union-of-balls filtration that is popular in topological data analysis. For larger k, it yields a cleaner shape reconstruction in the presence of outliers. We contribute a sparsification algorithm to approximate the topology of the k-fold filtration. Our method is a combination and adaptation of several techniques from the well-studied case k = 1, resulting in a sparsification of linear size that can be computed in expected near-linear time with respect to the number of input points

Detection of Small Holes by the Scale-Invariant Robust Density-Aware Distance (RDAD) Filtration

A novel topological-data-analytical (TDA) method is proposed to distinguish, from noise, small holes surrounded by high-density regions of a probability density function whose mass is concentrated near a manifold (or more generally, a CW complex) embedded in a high-dimensional Euclidean space. The proposed method is robust against additive noise and outliers. In particular, sample points are allowed to be perturbed away from the manifold. Traditional TDA tools, like those based on the distance filtration, often struggle to distinguish small features from noise, because of their short persistence. An alternative filtration, called Robust Density-Aware Distance (RDAD) filtration, is proposed to prolong the persistence of small holes surrounded by high-density regions. This is achieved by weighting the distance function by the density in the sense of Bell et al. Distance-to-measure is incorporated to enhance stability and mitigate noise due to the density estimation. The utility of the proposed filtration in identifying small holes, as well as its robustness against noise, are illustrated through an analytical example and extensive numerical experiments. Basic mathematical properties of the proposed filtration are proven.Comment: 47 pages, 60 figures, GitHub repo: https://github.com/c-siu/RDA