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The \emph{strong collapse} of a simplicial complex, proposed by Barmak and Minian (\emph{Disc. Comp. Geom. 2012}), is a combinatorial collapse of a complex onto its sub-complex. Recently, it has received attention from computational topology researchers, owing to its empirically observed usefulness in simplification and size-reduction of the size of simplicial complexes while preserving the homotopy class. We consider the strong collapse process on random simplicial complexes. For the Erd\H{o}s-R\'enyi random clique complex $X(n,c/n)$ on $n$ vertices with edge probability $c/n$ with $c>1$, we show that after any maximal sequence of strong collapses the remaining subcomplex, or \emph{core} must have $(1-\gamma)(1-c\gamma) n+o(n)$ vertices asymptotically almost surely (a.a.s.), where $\gamma$ is the least non-negative fixed point of the function $f(x) = \exp\left(-c(1-x)\right)$ in the range $(0,1)$. These are the first theoretical results proved for strong collapses on random (or non-random) simplicial complexes.

Computing persistent homology using Gaussian kernels is useful in the domains of topological data analysis and machine learning as shown by Phillips, Wang and Zheng [SoCG 2015]. However, contrary to the case of computing persistent homology using the Euclidean distance or even the $k$-distance, it is not known how to compute the persistent homology of high dimensional data using Gaussian kernels. In this paper, we consider a power distance version of the Gaussian kernel distance (GKPD) given by Phillips, Wang and Zheng, and show that the persistent homology of the \v{C}ech filtration of $P$ computed using the GKPD is approximately preserved. For datasets in $d$-dimensional Euclidean space, under a relative error bound of $\varepsilon \in [0,1]$, we obtain a dimensionality of $(i)$ $O(\varepsilon^{-2}\log^2 n)$ for $n$-point datasets and $(ii)$ $O(D\varepsilon^{-2}\log (Dr/\varepsilon))$ for datasets having diameter $r$ (up to a scaling factor). We use two main ingredients. The first one is a new decomposition of the squared radii of \v{C}ech simplices using the kernel power distance, in terms of the pairwise GKPDs between the vertices, which we state and prove. The second one is the Random Fourier Features (RFF) map of Rahimi and Recht [NeurIPS 2007], as used by Chen and Phillips [ALT 2017].

Given a set P of n points and a constant k, we are interested in computing the persistent homology of the Cech filtration of P for the k-distance, and investigate the effectiveness of dimensionality reduction for this problem, answering an open question of Sheehy [Proc. SoCG, 2014]. We show that any linear transformation that preserves pairwise distances up to a (1 +/- e) multiplicative factor, must preserve the persistent homology of the Cech filtration up to a factor of (1-e)^(-1). Our results also show that the Vietoris-Rips and Delaunay filtrations for the k-distance, as well as the Cech filtration for the approximate k-distance of Buchet et al. [J. Comput. Geom., 2016] are preserved up to a (1 +/- e) factor. We also prove extensions of our main theorem, for point sets (i) lying in a region of bounded Gaussian width or (ii) on a low-dimensional submanifold, obtaining embeddings having the dimension bounds of Lotz [Proc. Roy. Soc., 2019] and Clarkson [Proc. SoCG, 2008] respectively. Our results also work in the terminal dimensionality reduction setting, where the distance of any point in the original ambient space, to any point in P, needs to be approximately preserved., Comment: 18 pages

This article introduces an algorithm to compute the persistent homology of a filtered complex with various coefficient fields in a single matrix reduction. The algorithm is output-sensitive in the total number of distinct persistent homological features in the diagrams for the different coefficient fields. This computation allows us to infer the prime divisors of the torsion coefficients of the integral homology groups of the topological space at any scale, hence furnishing a more informative description of topology than persistence in a single coefficient field. We provide theoretical complexity analysis as well as detailed experimental results. The code is part of the Gudhi software library.

This paper introduces a data structure, called simplex tree, to represent abstract simplicial complexes of any dimension. All faces of the simplicial complex are explicitly stored in a trie whose nodes are in bijection with the faces of the complex. This data structure allows to efficiently implement a large range of basic operations on simplicial complexes. We provide theoretical complexity analysis as well as detailed experimental results. We more specifically study Rips and witness complexes.

We introduce a fast and memory efficient approach to compute the persistent homology (PH) of a sequence of simplicial complexes. The basic idea is to simplify the complexes of the input sequence by using strong collapses, as introduced by J. Barmak and E. Miniam [DCG (2012)], and to compute the PH of an induced sequence of reduced simplicial complexes that has the same PH as the initial one. Our approach has several salient features that distinguishes it from previous work. It is not limited to filtrations (i.e. sequences of nested simplicial subcomplexes) but works for other types of sequences like towers and zigzags. To strong collapse a simplicial complex, we only need to store the maximal simplices of the complex, not the full set of all its simplices, which saves a lot of space and time. Moreover, the complexes in the sequence can be strong collapsed independently and in parallel. Finally, we can compromize between precision and time by choosing the number of simplicial complexes of the sequence we strong collapse. As a result and as demonstrated by numerous experiments on publicly available data sets, our approach is extremely fast and memory efficient in practice.

We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use., Comment: Extended abstract to appear in SoCG 2018

The construction of anisotropic triangulations is desirable for various applications, such as the numerical solving of partial differential equations and the representation of surfaces in graphics. To solve this notoriously difficult problem in a practical way, we introduce the discrete Riemannian Voronoi diagram, a discrete structure that approximates the Riemannian Voronoi diagram. This structure has been implemented and was shown to lead to good triangulations in $\mathbb{R}^2$ and on surfaces embedded in $\mathbb{R}^3$ as detailed in our experimental companion paper. In this paper, we study theoretical aspects of our structure. Given a finite set of points $\cal P$ in a domain $\Omega$ equipped with a Riemannian metric, we compare the discrete Riemannian Voronoi diagram of $\cal P$ to its Riemannian Voronoi diagram. Both diagrams have dual structures called the discrete Riemannian Delaunay and the Riemannian Delaunay complex. We provide conditions that guarantee that these dual structures are identical. It then follows from previous results that the discrete Riemannian Delaunay complex can be embedded in $\Omega$ under sufficient conditions, leading to an anisotropic triangulation with curved simplices. Furthermore, we show that, under similar conditions, the simplices of this triangulation can be straightened.

Delaunay has shown that the Delaunay complex of a finite set of points $P$ of Euclidean space $\mathbb{R}^m$ triangulates the convex hull of $P$, provided that $P$ satisfies a mild genericity property. Voronoi diagrams and Delaunay complexes can be defined for arbitrary Riemannian manifolds. However, Delaunay's genericity assumption no longer guarantees that the Delaunay complex will yield a triangulation; stronger assumptions on $P$ are required. A natural one is to assume that $P$ is sufficiently dense. Although results in this direction have been claimed, we show that sample density alone is insufficient to ensure that the Delaunay complex triangulates a manifold of dimension greater than 2., Comment: This is a revision and extension of a note that appeared as an appendix in the (otherwise unpublished) report arXiv:1303.6493

Air-ionization chambers have been used in radiotherapy and particle therapy for decades. However, fundamental parameters in action in the detector responses are sparsely studied. In this work we aimed to measure the electronic attachment, electrons and ions mobilities of an ionization chamber (IC) in air. The main idea is to extract these from the actual response of the IC to a single ionizing particle in order to insure that they were measured in the same condition they are to be used while neglecting undesired phenomena: recombination and space charge effect. The non-standard signal shape analysis performed here were also confronted to a more standard drift chamber measurements using time-of-flight. It was found that both detectors displayed compatible results concerning positive and negative ions drift velocities where literature data is well spread out. In the same time, electron attachment measurements sit in the middle of known measurements while electron drift velocities seemed to show an offset compared to the well known and modeled data.

A filtration over a simplicial complex $K$ is an ordering of the simplices of $K$ such that all prefixes in the ordering are subcomplexes of $K$. Filtrations are at the core of Persistent Homology, a major tool in Topological Data Analysis. In order to represent the filtration of a simplicial complex, the entire filtration can be appended to any data structure that explicitly stores all the simplices of the complex such as the Hasse diagram or the recently introduced Simplex Tree [Algorithmica '14]. However, with the popularity of various computational methods that need to handle simplicial complexes, and with the rapidly increasing size of the complexes, the task of finding a compact data structure that can still support efficient queries is of great interest. In this paper, we propose a new data structure called the Critical Simplex Diagram (CSD) which is a variant of the Simplex Array List (SAL) [Algorithmica '17]. Our data structure allows one to store in a compact way the filtration of a simplicial complex, and allows for the efficient implementation of a large range of basic operations. Moreover, we prove that our data structure is essentially optimal with respect to the requisite storage space. Finally, we show that the CSD representation admits fast construction algorithms for Flag complexes and relaxed Delaunay complexes., Comment: A preliminary version appeared in SODA 2017

Currently, radiobiology experiments using heavy ions at GANIL(Grand Accelerateur National d Ions Lourds) are conducted under the supervision of the CIMAP (Center for research on Ions, MAterials and Photonics). In this context, a new beam monitoring equipment named DOSION has been developed. It allows to perform measurements of accurate fluence and dose maps in near real time for each biological sample irradiated. In this paper, we present the detection system, its design, performances, calibration protocol and measurements performed during radiobiology experiments. This setup is currently available for any radiobiology experiments if one wishes to correlate one s own sample analysis to state of the art dosimetric references.

We give asymptotically tight estimates of tangent space variation on Riemannian submanifolds of Euclidean space with respect to the local feature size of the submanifolds. We show that the result follows directly from structural properties of local feature size of the Riemannian submanifold and some elementary Euclidean geometry. We also show that using the tangent variation result one can prove a new structural property of local feature size function. This structural property is a generalization of a result of Giesen and Wagner [GW04, Lem. 7]., Comment: 8 pages

Computing Delaunay triangulations in $\mathbb{R}^d$ involves evaluating the so-called in\_sphere predicate that determines if a point $x$ lies inside, on or outside the sphere circumscribing $d+1$ points $p_0,\ldots ,p_d$. This predicate reduces to evaluating the sign of a multivariate polynomial of degree $d+2$ in the coordinates of the points $x, \, p_0,\, \ldots,\, p_d$. Despite much progress on exact geometric computing, the fact that the degree of the polynomial increases with $d$ makes the evaluation of the sign of such a polynomial problematic except in very low dimensions. In this paper, we propose a new approach that is based on the witness complex, a weak form of the Delaunay complex introduced by Carlsson and de Silva. The witness complex $\mathrm{Wit} (L,W)$ is defined from two sets $L$ and $W$ in some metric space $X$: a finite set of points $L$ on which the complex is built, and a set $W$ of witnesses that serves as an approximation of $X$. A fundamental result of de Silva states that $\mathrm{Wit}(L,W)=\mathrm{Del} (L)$ if $W=X=\mathbb{R}^d$. In this paper, we give conditions on $L$ that ensure that the witness complex and the Delaunay triangulation coincide when $W$ is a finite set, and we introduce a new perturbation scheme to compute a perturbed set $L'$ close to $L$ such that $\mathrm{Del} (L')= \mathrm{wit} (L', W)$. Our perturbation algorithm is a geometric application of the Moser-Tardos constructive proof of the Lov\'asz local lemma. The only numerical operations we use are (squared) distance comparisons (i.e., predicates of degree 2). The time-complexity of the algorithm is sublinear in $|W|$. Interestingly, although the algorithm does not compute any measure of simplex quality, a lower bound on the thickness of the output simplices can be guaranteed., Comment: 24 pages

The Simplex Tree (ST) is a recently introduced data structure that can represent abstract simplicial complexes of any dimension and allows efficient implementation of a large range of basic operations on simplicial complexes. In this paper, we show how to optimally compress the Simplex Tree while retaining its functionalities. In addition, we propose two new data structures called the Maximal Simplex Tree (MxST) and the Simplex Array List (SAL). We analyze the compressed Simplex Tree, the Maximal Simplex Tree, and the Simplex Array List under various settings., Comment: An extended abstract appeared in the proceedings of SoCG 2015

In this paper, we give the first algorithm that outputs a faithful reconstruction of a submanifold of Euclidean space without maintaining or even constructing complicated data structures such as Voronoi diagrams or Delaunay complexes. Our algorithm uses the witness complex and relies on the stability of power protection, a notion introduced in this paper. The complexity of the algorithm depends exponentially on the intrinsic dimension of the manifold, rather than the dimension of ambient space, and linearly on the dimension of the ambient space. Another interesting feature of this work is that no explicit coordinates of the points in the point sample is needed. The algorithm only needs the distance matrix as input, i.e., only distance between points in the point sample as input., Comment: Major revision, 16 figures, 47 pages

We present an algorithm for producing Delaunay triangulations of manifolds. The algorithm can accommodate abstract manifolds that are not presented as submanifolds of Euclidean space. Given a set of sample points and an atlas on a compact manifold, a manifold Delaunay complex is produced provided the transition functions are bi-Lipschitz with a constant close to 1, and the sample points meet a local density requirement; no smoothness assumptions are required. If the transition functions are smooth, the output is a triangulation of the manifold. The output complex is naturally endowed with a piecewise flat metric which, when the original manifold is Riemannian, is a close approximation of the original Riemannian metric. In this case the ouput complex is also a Delaunay triangulation of its vertices with respect to this piecewise flat metric.

We present an algorithm that takes as input a finite point set in Euclidean space, and performs a perturbation that guarantees that the Delaunay triangulation of the resulting perturbed point set has quantifiable stability with respect to the metric and the point positions. There is also a guarantee on the quality of the simplices: they cannot be too flat. The algorithm provides an alternative tool to the weighting or refinement methods to remove poorly shaped simplices in Delaunay triangulations of arbitrary dimension, but in addition it provides a guarantee of stability for the resulting triangulation.

Every radiotherapy center has to be equipped with real-time beam monitoring devices. In 2008, the medical application group from the Laboratory of Corpuscular Physics (LPC Caen) developed an Ionization Chamber in collaboration with the company IBA (Ion Beam Applications). This monitoring device called IC2/3 was developed to be used in IBAs universal irradiation head for Pencil Beam Scanning (PBS). The objectives presented in this article are to characterize the IC2/3 monitor in the energy and ux ranges used in protontherapy. The equipment has been tested with an IBAs cyclotronable to deliver proton beams from 70 to 230 MeV. This beam monitoring device has been validated and is now installed at the Westdeutsches Protonentherapiezentrum Essen protontherapy center (WPE, Germany). The results obtained in both terms of spatial resolution and dose measurements are at least equal to the initials speci cations needed for PBS purposes. The detector measures the dose with a relative precision better than 1% in the range 0.5 Gy/min to 8 Gy/min while the spatial resolution is higher than 250 m. The technology has been patented and ve IC2/3 chambers were delivered to IBA. Nowadays, IBA produces the IC2/3 beam monitoring device as part of its Proteus 235 product

The persistent homology with coefficients in a field F coincides with the same for cohomology because of duality. We propose an implementation of a recently introduced algorithm for persistent cohomology that attaches annotation vectors with the simplices. We separate the representation of the simplicial complex from the representation of the cohomology groups, and introduce a new data structure for maintaining the annotation matrix, which is more compact and reduces substancially the amount of matrix operations. In addition, we propose heuristics to simplify further the representation of the cohomology groups and improve both time and space complexities. The paper provides a theoretical analysis, as well as a detailed experimental study of our implementation and comparison with state-of-the-art software for persistent homology and cohomology.

We introduce a parametrized notion of genericity for Delaunay triangulations which, in particular, implies that the Delaunay simplices of $\delta$-generic point sets are thick. Equipped with this notion, we study the stability of Delaunay triangulations under perturbations of the metric and of the vertex positions. We quantify the magnitude of the perturbations under which the Delaunay triangulation remains unchanged., Comment: Displayed expressions in the statements of Thm 3.14 and Cor 4.18 are missing a factor of the dimension (m) in the denominator of the version published in IJCGA: it is corrected here

We describe an algorithm to construct an intrinsic Delaunay triangulation of a smooth closed submanifold of Euclidean space. Using results established in a companion paper on the stability of Delaunay triangulations on $\delta$-generic point sets, we establish sampling criteria which ensure that the intrinsic Delaunay complex coincides with the restricted Delaunay complex and also with the recently introduced tangential Delaunay complex. The algorithm generates a point set that meets the required criteria while the tangential complex is being constructed. In this way the computation of geodesic distances is avoided, the runtime is only linearly dependent on the ambient dimension, and the Delaunay complexes are guaranteed to be triangulations of the manifold.

We consider the problem of reconstructing a compact 3-manifold (with boundary) embedded in $\mathbb{R}^3$ from its cross-sections $\mathcal S$ with a given set of cutting planes $\mathcal P$ having arbitrary orientations. Using the obvious fact that a point $x \in \mathcal P$ belongs to the original object if and only if it belongs to $\mathcal S$, we follow a very natural reconstruction strategy: we say that a point $x \in \mathbb{R}^3$ belongs to the reconstructed object if (at least one of) its nearest point(s) in $\mathcal P$ belongs to $\mathcal S$. This coincides with the algorithm presented by Liu et al. in \cite{LB+08}. In the present paper, we prove that under appropriate sampling conditions, the output of this algorithm preserves the homotopy type of the original object. Using the homotopy equivalence, we also show that the reconstructed object is homeomorphic (and isotopic) to the original object. This is the first time that 3-dimensional shape reconstruction from cross-sections comes with theoretical guarantees., Comment: 32 Pages, 21 Figure; appeared in Discrete & Computational Geometry: Volume 50, Issue 4, Page 821-856, 2013. Extended abstract appeared in the proceedings of the 26th Symposium on Computational Geometry 2010

The Voronoi diagram of a finite set of objects is a fundamental geometric structure that subdivides the embedding space into regions, each region consisting of the points that are closer to a given object than to the others. We may define many variants of Voronoi diagrams depending on the class of objects, the distance functions and the embedding space. In this paper, we investigate a framework for defining and building Voronoi diagrams for a broad class of distance functions called Bregman divergences. Bregman divergences include not only the traditional (squared) Euclidean distance but also various divergence measures based on entropic functions. Accordingly, Bregman Voronoi diagrams allow to define information-theoretic Voronoi diagrams in statistical parametric spaces based on the relative entropy of distributions. We define several types of Bregman diagrams, establish correspondences between those diagrams (using the Legendre transformation), and show how to compute them efficiently. We also introduce extensions of these diagrams, e.g. k-order and k-bag Bregman Voronoi diagrams, and introduce Bregman triangulations of a set of points and their connexion with Bregman Voronoi diagrams. We show that these triangulations capture many of the properties of the celebrated Delaunay triangulation. Finally, we give some applications of Bregman Voronoi diagrams which are of interest in the context of computational geometry and machine learning., Comment: Extend the proceedings abstract of SODA 2007 (46 pages, 15 figures)

Given a disk O in the plane called the objective, we want to find n small disks P_1,...,P_n called the pupils such that $\bigcup_{i,j=1}^n P_i \ominus P_j \supseteq O$, where $\ominus$ denotes the Minkowski difference operator, while minimizing the number of pupils, the sum of the radii or the total area of the pupils. This problem is motivated by the construction of very large telescopes from several smaller ones by so-called Optical Aperture Synthesis. In this paper, we provide exact, approximate and heuristic solutions to several variations of the problem., Comment: 10 pages, 8 figures

A circle $C$ separates two planar sets if it encloses one of the sets and its open interior disk does not meet the other set. A separating circle is a largest one if it cannot be locally increased while still separating the two given sets. An Theta(n log n) optimal algorithm is proposed to find all largest circles separating two given sets of line segments when line segments are allowed to meet only at their endpoints. In the general case, when line segments may intersect $\Omega(n^2)$ times, our algorithm can be adapted to work in O(n alpha(n) log n) time and O(n \alpha(n)) space, where alpha(n) represents the extremely slowly growing inverse of the Ackermann function., Comment: 14 pages, 3 figures, abstract presented at 8th Canadian Conference on Computational Geometry, 1996

We consider the motion planning problem for a point constrained to move along a smooth closed convex path of bounded curvature. The workspace of the moving point is bounded by a convex polygon with m vertices, containing an obstacle in a form of a simple polygon with $n$ vertices. We present an O(m+n) time algorithm finding the path, going around the obstacle, whose curvature is the smallest possible., Comment: 11 pages, 5 figures, abstract presented at European Symposium on Algorithms 1993

Two planar sets are circularly separable if there exists a circle enclosing one of the sets and whose open interior disk does not intersect the other set. This paper studies two problems related to circular separability. A linear-time algorithm is proposed to decide if two polygons are circularly separable. The algorithm outputs the smallest separating circle. The second problem asks for the largest circle included in a preprocessed, convex polygon, under some point and/or line constraints. The resulting circle must contain the query points and it must lie in the halfplanes delimited by the query lines., Comment: 23 pages, 7 figures, abstract presented at SODA95

We study the problem of computing the free space F of a simple legged robot called the spider robot. The body of this robot is a single point and the legs are attached to the body. The robot is subject to two constraints: each leg has a maximal extension R (accessibility constraint) and the body of the robot must lie above the convex hull of its feet (stability constraint). Moreover, the robot can only put its feet on some regions, called the foothold regions. The free space F is the set of positions of the body of the robot such that there exists a set of accessible footholds for which the robot is stable. We present an efficient algorithm that computes F in O(n2 log n) time using O(n2 alpha(n)) space for n discrete point footholds where alpha(n) is an extremely slowly growing function (alpha(n) <= 3 for any practical value of n). We also present an algorithm for computing F when the foothold regions are pairwise disjoint polygons with n edges in total. This algorithm computes F in O(n2 alpha8(n) log n) time using O(n2 alpha8(n)) space (alpha8(n) is also an extremely slowly growing function). These results are close to optimal since Omega(n2) is a lower bound for the size of F., Comment: 29 pages, 22 figures, prelininar results presented at WAFR94 and IEEE Robotics & Automation 94