TY - JOUR AB - We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f:K→ ℝn on a finite simplicial complex K and α > 0, it holds that each function g: K → ℝn such that ||g - f || ∞ < α, has a root in K. Via a reduction to the extension problem of maps into a sphere, we particularly show that this problem is decidable in polynomial time for every fixed n, assuming dimK ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction, we prove that the problem is undecidable when dim K > 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is simplexwise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings. AU - Franek, Peter AU - Krcál, Marek ID - 1682 IS - 4 JF - Journal of the ACM TI - Robust satisfiability of systems of equations VL - 62 ER - TY - JOUR AB - We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞. AU - Akopyan, Arseniy AU - Plakhov, Alexander ID - 1710 IS - 4 JF - Society for Industrial and Applied Mathematics TI - Minimal resistance of curves under the single impact assumption VL - 47 ER - TY - JOUR AB - We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory. AU - Akopyan, Arseniy AU - Pirogov, Sergey AU - Rybko, Aleksandr ID - 1828 IS - 1 JF - Journal of Statistical Physics TI - Invariant measures of genetic recombination process VL - 160 ER - TY - JOUR AB - We numerically investigate the distribution of extrema of 'chaotic' Laplacian eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a) we count extrema on grid graphs with a small number of randomly added edges and show the behavior to coincide with the 1957 prediction of Longuet-Higgins for the continuous case and (b) we compute the regularity of their spatial distribution using discrepancy, which is a classical measure from the theory of Monte Carlo integration. The first part suggests that grid graphs with randomly added edges should behave like two-dimensional surfaces with ergodic geodesic flow; in the second part we show that the extrema are more regularly distributed in space than the grid Z2. AU - Pausinger, Florian AU - Steinerberger, Stefan ID - 1938 IS - 6 JF - Physics Letters, Section A TI - On the distribution of local extrema in quantum chaos VL - 379 ER - TY - JOUR AB - Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility. AU - Edelsbrunner, Herbert AU - Jablonski, Grzegorz AU - Mrozek, Marian ID - 2035 IS - 5 JF - Foundations of Computational Mathematics TI - The persistent homology of a self-map VL - 15 ER - TY - JOUR AB - We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard. AU - Attali, Dominique AU - Bauer, Ulrich AU - Devillers, Olivier AU - Glisse, Marc AU - Lieutier, André ID - 1805 IS - 8 JF - Computational Geometry: Theory and Applications TI - Homological reconstruction and simplification in R3 VL - 48 ER - TY - JOUR AB - We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth. AU - Symonova, Olga AU - Topp, Christopher AU - Edelsbrunner, Herbert ID - 1793 IS - 6 JF - PLoS One TI - DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots VL - 10 ER - TY - GEN AU - Symonova, Olga AU - Topp, Christopher AU - Edelsbrunner, Herbert ID - 9737 TI - Root traits computed by DynamicRoots for the maize root shown in fig 2 ER - TY - JOUR AB - Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology. AU - Pausinger, Florian AU - Svane, Anne ID - 1792 IS - 6 JF - Journal of Complexity TI - A Koksma-Hlawka inequality for general discrepancy systems VL - 31 ER - TY - THES AB - This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold. AU - Pausinger, Florian ID - 1399 SN - 2663-337X TI - On the approximation of intrinsic volumes ER - TY - CHAP AB - Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data. AU - Kasten, Jens AU - Reininghaus, Jan AU - Reich, Wieland AU - Scheuermann, Gerik ED - Bremer, Peer-Timo ED - Hotz, Ingrid ED - Pascucci, Valerio ED - Peikert, Ronald ID - 10893 SN - 1612-3786 T2 - Topological Methods in Data Analysis and Visualization III TI - Toward the extraction of saddle periodic orbits VL - 1 ER - TY - JOUR AB - Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques. AU - Huber, Stefan AU - Held, Martin AU - Meerwald, Peter AU - Kwitt, Roland ID - 1816 IS - 1 JF - International Journal of Computational Geometry and Applications TI - Topology-preserving watermarking of vector graphics VL - 24 ER - TY - JOUR AB - We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices. AU - Cibulka, Josef AU - Gao, Pu AU - Krcál, Marek AU - Valla, Tomáš AU - Valtr, Pavel ID - 1842 IS - 1 JF - Discrete & Computational Geometry TI - On the geometric ramsey number of outerplanar graphs VL - 53 ER - TY - JOUR AB - We study densities of functionals over uniformly bounded triangulations of a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay triangulation if this is the case for finite sets. AU - Dolbilin, Nikolai AU - Edelsbrunner, Herbert AU - Glazyrin, Alexey AU - Musin, Oleg ID - 1876 IS - 3 JF - Moscow Mathematical Journal SN - 16093321 TI - Functionals on triangulations of delaunay sets VL - 14 ER - TY - JOUR AB - We propose an algorithm for the generalization of cartographic objects that can be used to represent maps on different scales. AU - Alexeev, V V AU - Bogaevskaya, V G AU - Preobrazhenskaya, M M AU - Ukhalov, A Y AU - Edelsbrunner, Herbert AU - Yakimova, Olga ID - 1929 IS - 6 JF - Journal of Mathematical Sciences SN - 1072-3374 TI - An algorithm for cartographic generalization that preserves global topology VL - 203 ER - TY - JOUR AB - (Figure Presented) Data acquisition, numerical inaccuracies, and sampling often introduce noise in measurements and simulations. Removing this noise is often necessary for efficient analysis and visualization of this data, yet many denoising techniques change the minima and maxima of a scalar field. For example, the extrema can appear or disappear, spatially move, and change their value. This can lead to wrong interpretations of the data, e.g., when the maximum temperature over an area is falsely reported being a few degrees cooler because the denoising method is unaware of these features. Recently, a topological denoising technique based on a global energy optimization was proposed, which allows the topology-controlled denoising of 2D scalar fields. While this method preserves the minima and maxima, it is constrained by the size of the data. We extend this work to large 2D data and medium-sized 3D data by introducing a novel domain decomposition approach. It allows processing small patches of the domain independently while still avoiding the introduction of new critical points. Furthermore, we propose an iterative refinement of the solution, which decreases the optimization energy compared to the previous approach and therefore gives smoother results that are closer to the input. We illustrate our technique on synthetic and real-world 2D and 3D data sets that highlight potential applications. AU - Günther, David AU - Jacobson, Alec AU - Reininghaus, Jan AU - Seidel, Hans AU - Sorkine Hornung, Olga AU - Weinkauf, Tino ID - 1930 IS - 12 JF - IEEE Transactions on Visualization and Computer Graphics TI - Fast and memory-efficient topological denoising of 2D and 3D scalar fields VL - 20 ER - TY - CONF AB - Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node. AU - Bauer, Ulrich AU - Kerber, Michael AU - Reininghaus, Jan ED - McGeoch, Catherine ED - Meyer, Ulrich ID - 2043 T2 - Proceedings of the Workshop on Algorithm Engineering and Experiments TI - Distributed computation of persistent homology ER - TY - CHAP AB - We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation. AU - Bauer, Ulrich AU - Kerber, Michael AU - Reininghaus, Jan ED - Bremer, Peer-Timo ED - Hotz, Ingrid ED - Pascucci, Valerio ED - Peikert, Ronald ID - 2044 T2 - Topological Methods in Data Analysis and Visualization III TI - Clear and Compress: Computing Persistent Homology in Chunks ER - TY - CONF AB - We define a simple, explicit map sending a morphism f : M → N of pointwise finite dimensional persistence modules to a matching between the barcodes of M and N. Our main result is that, in a precise sense, the quality of this matching is tightly controlled by the lengths of the longest intervals in the barcodes of ker f and coker f . As an immediate corollary, we obtain a new proof of the algebraic stability theorem for persistence barcodes [5, 9], a fundamental result in the theory of persistent homology. In contrast to previous proofs, ours shows explicitly how a δ-interleaving morphism between two persistence modules induces a δ-matching between the barcodes of the two modules. Our main result also specializes to a structure theorem for submodules and quotients of persistence modules. Copyright is held by the owner/author(s). AU - Bauer, Ulrich AU - Lesnick, Michael ID - 2153 T2 - Proceedings of the Annual Symposium on Computational Geometry TI - Induced matchings of barcodes and the algebraic stability of persistence ER - TY - CONF AB - We propose a metric for Reeb graphs, called the functional distortion distance. Under this distance, the Reeb graph is stable against small changes of input functions. At the same time, it remains discriminative at differentiating input functions. In particular, the main result is that the functional distortion distance between two Reeb graphs is bounded from below by the bottleneck distance between both the ordinary and extended persistence diagrams for appropriate dimensions. As an application of our results, we analyze a natural simplification scheme for Reeb graphs, and show that persistent features in Reeb graph remains persistent under simplification. Understanding the stability of important features of the Reeb graph under simplification is an interesting problem on its own right, and critical to the practical usage of Reeb graphs. Copyright is held by the owner/author(s). AU - Bauer, Ulrich AU - Ge, Xiaoyin AU - Wang, Yusu ID - 2156 T2 - Proceedings of the Annual Symposium on Computational Geometry TI - Measuring distance between Reeb graphs ER - TY - CONF AB - Given a finite set of points in Rn and a positive radius, we study the Čech, Delaunay-Čech, alpha, and wrap complexes as instances of a generalized discrete Morse theory. We prove that the latter three complexes are simple-homotopy equivalent. Our results have applications in topological data analysis and in the reconstruction of shapes from sampled data. Copyright is held by the owner/author(s). AU - Bauer, Ulrich AU - Edelsbrunner, Herbert ID - 2155 T2 - Proceedings of the Annual Symposium on Computational Geometry TI - The morse theory of Čech and Delaunay filtrations ER - TY - CONF AB - We give evidence for the difficulty of computing Betti numbers of simplicial complexes over a finite field. We do this by reducing the rank computation for sparse matrices with to non-zero entries to computing Betti numbers of simplicial complexes consisting of at most a constant times to simplices. Together with the known reduction in the other direction, this implies that the two problems have the same computational complexity. AU - Edelsbrunner, Herbert AU - Parsa, Salman ID - 2177 T2 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms TI - On the computational complexity of betti numbers reductions from matrix rank ER - TY - JOUR AB - Given topological spaces X,Y, a fundamental problem of algebraic topology is understanding the structure of all continuous maps X→ Y. We consider a computational version, where X,Y are given as finite simplicial complexes, and the goal is to compute [X,Y], that is, all homotopy classes of suchmaps.We solve this problem in the stable range, where for some d ≥ 2, we have dim X ≤ 2d-2 and Y is (d-1)-connected; in particular, Y can be the d-dimensional sphere Sd. The algorithm combines classical tools and ideas from homotopy theory (obstruction theory, Postnikov systems, and simplicial sets) with algorithmic tools from effective algebraic topology (locally effective simplicial sets and objects with effective homology). In contrast, [X,Y] is known to be uncomputable for general X,Y, since for X = S1 it includes a well known undecidable problem: testing triviality of the fundamental group of Y. In follow-up papers, the algorithm is shown to run in polynomial time for d fixed, and extended to other problems, such as the extension problem, where we are given a subspace A ⊂ X and a map A→ Y and ask whether it extends to a map X → Y, or computing the Z2-index-everything in the stable range. Outside the stable range, the extension problem is undecidable. AU - Čadek, Martin AU - Krcál, Marek AU - Matoušek, Jiří AU - Sergeraert, Francis AU - Vokřínek, Lukáš AU - Wagner, Uli ID - 2184 IS - 3 JF - Journal of the ACM TI - Computing all maps into a sphere VL - 61 ER - TY - CONF AB - Persistent homology is a recent grandchild of homology that has found use in science and engineering as well as in mathematics. This paper surveys the method as well as the applications, neglecting completeness in favor of highlighting ideas and directions. AU - Edelsbrunner, Herbert AU - Morozovy, Dmitriy ID - 2905 TI - Persistent homology: Theory and practice ER - TY - CONF AB - In this paper, we introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings. AU - Biedl, Therese AU - Huber, Stefan AU - Palfrader, Peter ID - 10892 SN - 0302-9743 T2 - 25th International Symposium, ISAAC 2014 TI - Planar matchings for weighted straight skeletons VL - 8889 ER - TY - BOOK AB - This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields. AU - Edelsbrunner, Herbert ID - 6853 SN - 2191-530X TI - A Short Course in Computational Geometry and Topology ER - TY - CONF AB - We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set. AU - Zobel, Valentin AU - Reininghaus, Jan AU - Hotz, Ingrid ID - 10886 SN - 1612-3786 T2 - Topological Methods in Data Analysis and Visualization III TI - Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature ER - TY - CHAP AB - The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption. AU - Günther, David AU - Reininghaus, Jan AU - Seidel, Hans-Peter AU - Weinkauf, Tino ED - Bremer, Peer-Timo ED - Hotz, Ingrid ED - Pascucci, Valerio ED - Peikert, Ronald ID - 10817 SN - 1612-3786 T2 - Topological Methods in Data Analysis and Visualization III. TI - Notes on the simplification of the Morse-Smale complex ER - TY - JOUR AB - Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm. AU - Edelsbrunner, Herbert AU - Pausinger, Florian ID - 2255 IS - 1 JF - Journal of Mathematical Imaging and Vision SN - 09249907 TI - Stable length estimates of tube-like shapes VL - 50 ER - TY - CONF AB - PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations. AU - Bauer, Ulrich AU - Kerber, Michael AU - Reininghaus, Jan AU - Wagner, Hubert ID - 10894 SN - 0302-9743 T2 - ICMS 2014: International Congress on Mathematical Software TI - PHAT – Persistent Homology Algorithms Toolbox VL - 8592 ER - TY - GEN AB - The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice. AU - Iglesias Ham, Mabel AU - Kerber, Michael AU - Uhler, Caroline ID - 2012 T2 - arXiv TI - Sphere packing with limited overlap ER - TY - CONF AB - A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon or planar straight-line graph. In this paper, we ask the reverse question: Given the straight skeleton (in form of a planar straight-line graph, with some rays to infinity), can we reconstruct a planar straight-line graph for which this was the straight skeleton? We show how to reduce this problem to the problem of finding a line that intersects a set of convex polygons. We can find these convex polygons and all such lines in $O(nlog n)$ time in the Real RAM computer model, where $n$ denotes the number of edges of the input graph. We also explain how our approach can be used for recognizing Voronoi diagrams of points, thereby completing a partial solution provided by Ash and Bolker in 1985. AU - Biedl, Therese AU - Held, Martin AU - Huber, Stefan ID - 2209 TI - Recognizing straight skeletons and Voronoi diagrams and reconstructing their input ER - TY - CONF AB - A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon. In this paper, we ask the reverse question: Given the straight skeleton (in form of a tree with a drawing in the plane, but with the exact position of the leaves unspecified), can we reconstruct the polygon? We show that in most cases there exists at most one polygon; in the remaining case there is an infinite number of polygons determined by one angle that can range in an interval. We can find this (set of) polygon(s) in linear time in the Real RAM computer model. AU - Biedl, Therese AU - Held, Martin AU - Huber, Stefan ID - 2210 T2 - 29th European Workshop on Computational Geometry TI - Reconstructing polygons from embedded straight skeletons ER - TY - JOUR AB - This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter. AU - Pausinger, Florian ID - 2304 JF - Electronic Notes in Discrete Mathematics TI - Van der Corput sequences and linear permutations VL - 43 ER - TY - CONF AB - We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov's result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \no holes up to dimension k-1" (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. AU - Čadek, Martin AU - Krcál, Marek AU - Matoušek, Jiří AU - Vokřínek, Lukáš AU - Wagner, Uli ID - 2807 T2 - 45th Annual ACM Symposium on theory of computing TI - Extending continuous maps: Polynomiality and undecidability ER - TY - CONF AB - We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard. AU - Attali, Dominique AU - Bauer, Ulrich AU - Devillers, Olivier AU - Glisse, Marc AU - Lieutier, André ID - 2812 T2 - Proceedings of the 29th annual symposium on Computational Geometry TI - Homological reconstruction and simplification in R3 ER - TY - JOUR AB - Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops. AU - Topp, Christopher AU - Iyer Pascuzzi, Anjali AU - Anderson, Jill AU - Lee, Cheng AU - Zurek, Paul AU - Symonova, Olga AU - Zheng, Ying AU - Bucksch, Alexander AU - Mileyko, Yuriy AU - Galkovskyi, Taras AU - Moore, Brad AU - Harer, John AU - Edelsbrunner, Herbert AU - Mitchell Olds, Thomas AU - Weitz, Joshua AU - Benfey, Philip ID - 2822 IS - 18 JF - PNAS TI - 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture VL - 110 ER - TY - CONF AB - Mathematical objects can be measured unambiguously, but not so objects from our physical world. Even the total length of tubelike shapes has its difficulties. We introduce a combination of geometric, probabilistic, and topological methods to design a stable length estimate for tube-like shapes; that is: one that is insensitive to small shape changes. AU - Edelsbrunner, Herbert AU - Pausinger, Florian ID - 2843 T2 - 17th IAPR International Conference on Discrete Geometry for Computer Imagery TI - Stable length estimates of tube-like shapes VL - 7749 ER - TY - JOUR AB - Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization. AU - Bendich, Paul AU - Edelsbrunner, Herbert AU - Morozov, Dmitriy AU - Patel, Amit ID - 2859 IS - 1 JF - Homology, Homotopy and Applications TI - Homology and robustness of level and interlevel sets VL - 15 ER - TY - JOUR AB - Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes. AU - Fang, Suqin AU - Clark, Randy AU - Zheng, Ying AU - Iyer Pascuzzi, Anjali AU - Weitz, Joshua AU - Kochian, Leon AU - Edelsbrunner, Herbert AU - Liao, Hong AU - Benfey, Philip ID - 2887 IS - 7 JF - PNAS TI - Genotypic recognition and spatial responses by rice roots VL - 110 ER - TY - CONF AB - We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. AU - Chen, Chao AU - Kolmogorov, Vladimir AU - Yan, Zhu AU - Metaxas, Dimitris AU - Lampert, Christoph ID - 2901 TI - Computing the M most probable modes of a graphical model VL - 31 ER - TY - CONF AB - Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented using CGAL, following the exact geometric computation paradigm. We report on several techniques to accelerate the computation that turn our implementation applicable to the underlying biological problem. AU - Kerber, Michael AU - Edelsbrunner, Herbert ID - 2906 T2 - 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments TI - 3D kinetic alpha complexes and their implementation ER - TY - JOUR AB - The fact that a sum of isotropic Gaussian kernels can have more modes than kernels is surprising. Extra (ghost) modes do not exist in ℝ1 and are generally not well studied in higher dimensions. We study a configuration of n+1 Gaussian kernels for which there are exactly n+2 modes. We show that all modes lie on a finite set of lines, which we call axes, and study the restriction of the Gaussian mixture to these axes in order to discover that there are an exponential number of critical points in this configuration. Although the existence of ghost modes remained unknown due to the difficulty of finding examples in ℝ2, we show that the resilience of ghost modes grows like the square root of the dimension. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. AU - Edelsbrunner, Herbert AU - Fasy, Brittany Terese AU - Rote, Günter ID - 2815 IS - 4 JF - Discrete & Computational Geometry SN - 0179-5376 TI - Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions VL - 49 ER - TY - JOUR AB - In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ > 0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number of homology classes with persistence at least (1 - δ) Γ, n is the total number of simplices in the complex, d its dimension, and R d (n) is the complexity of computing the rank of an n × n matrix with O (d n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ) Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C (1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} > 0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n log n). AU - Chen, Chao AU - Kerber, Michael ID - 2939 IS - 4 JF - Computational Geometry: Theory and Applications TI - An output sensitive algorithm for persistent homology VL - 46 ER - TY - CONF AB - Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing. AU - Edelsbrunner, Herbert ID - 10897 SN - 0302-9743 T2 - Graph-Based Representations in Pattern Recognition TI - Persistent homology in image processing VL - 7877 ER - TY - JOUR AU - Edelsbrunner, Herbert AU - Strelkova, Nataliya ID - 2849 IS - 6 JF - Russian Mathematical Surveys TI - On the configuration space of Steiner minimal trees VL - 67 ER - TY - CONF AB - In order to enjoy a digital version of the Jordan Curve Theorem, it is common to use the closed topology for the foreground and the open topology for the background of a 2-dimensional binary image. In this paper, we introduce a single topology that enjoys this theorem for all thresholds decomposing a real-valued image into foreground and background. This topology is easy to construct and it generalizes to n-dimensional images. AU - Edelsbrunner, Herbert AU - Symonova, Olga ID - 2903 TI - The adaptive topology of a digital image ER - TY - JOUR AU - Dolbilin, Nikolai AU - Edelsbrunner, Herbert AU - Musin, Oleg ID - 2941 IS - 4 JF - Russian Mathematical Surveys TI - On the optimality of functionals over triangulations of Delaunay sets VL - 67 ER - TY - CONF AB - We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. AU - Zankl, Georg AU - Haxhimusa, Yll AU - Ion, Adrian ID - 2971 TI - Interactive labeling of image segmentation hierarchies VL - 7476 ER - TY - JOUR AB - We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica. AU - Brown, Gavin AU - Kerber, Michael AU - Reid, Miles ID - 3120 IS - 4 JF - Compositio Mathematica TI - Fano 3 folds in codimension 4 Tom and Jerry Part I VL - 148 ER -