Tight Bounds for the Maximum Distance Over a Polytope to a Given Point

In this paper we study the problem of maximizing the distance to a given point $C_0$ over a polytope $\mathcal{P}$. Assuming that the polytope is circumscribed by a known ball we construct an intersection of balls which preserves the vertices of the polytope on the boundary of this ball, and show that the intersection of balls approximates the polytope arbitrarily well. Then, we use some known results regarding the maximization of distances to a given point over an intersection of balls to create a new polytope which preserves the maximizers to the original problem. Next, a new intersection of balls is obtained in a similar fashion, and as such, after a finite number of iterations, we conjecture, we end up with an intersection of balls over which we can maximize the distance to the given point. The obtained distance is shown to be a non trivial upper bound to the original distance. Tests are made with maximizing the distance to a random point over the unit hypercube up to dimension $n = 100$. Several detailed 2-d examples are also shown.Comment: arXiv admin note: text overlap with arXiv:2308.1505

On Khachiyan's algorithm for the computation of minimum-volume enclosing ellipsoids

Cataloged from PDF version of article.Given A := {a(1),..., a(m)} subset of R(d) whose affine hull is R(d), we study the problems of computing an approximate rounding of the convex hull of A and an approximation to the minimum-volume enclosing ellipsoid of V. In the case of centrally symmetric sets, we first establish that Khachiyan's barycentric coordinate descent (BCD) method is exactly the polar of the deepest cut ellipsoid method using two-sided symmetric cuts. This observation gives further insight into the efficient implementation of the BCD method. We then propose a variant algorithm which computes an approximate rounding of the convex hull of,91, and which can also be used to compute an approximation to the minimum-volume enclosing ellipsoid of A.. Our algorithm is a modification of the algorithm of Kumar and Yildirim, which combines Khachiyan's BCD method with a simple initialization scheme to achieve a slightly improved polynomial complexity result, and which returns a small "core set." We establish that our algorithm computes an approximate solution to the dual optimization formulation of the minimum-volume enclosing ellipsoid problem that satisfies a more complete set of approximate optimality conditions than either of the two previous algorithms. Furthermore, this added benefit is achieved without any increase in the improved asymptotic complexity bound of the algorithm of Kumar and Yildirim or any increase in the bound on the size of the computed core set. In addition, the "dropping idea" used in our algorithm has the potential of computing smaller core sets in practice. We also discuss several possible variants of this dropping technique. (C) 2007 Elsevier B.V. All rights reserved

On Khachiyan's Algorithm for the Computation of Minimum Volume Enclosing Ellipsoids

On Khachiyan's Algorithm for the Computation of Minimum Volume Enclosing Ellipsoid

Minimizing Convex Functions with Integral Minimizers

Given a separation oracle $\mathsf{SO}$ for a convex function $f$ that has an integral minimizer inside a box with radius $R$, we show how to find an exact minimizer of $f$ using at most (a) $O(n (n + \log(R)))$ calls to $\mathsf{SO}$ and $\mathsf{poly}(n, \log(R))$ arithmetic operations, or (b) $O(n \log(nR))$ calls to $\mathsf{SO}$ and $\exp(n) \cdot \mathsf{poly}(\log(R))$ arithmetic operations. When the set of minimizers of $f$ has integral extreme points, our algorithm outputs an integral minimizer of $f$. This improves upon the previously best oracle complexity of $O(n^2 (n + \log(R)))$ for polynomial time algorithms obtained by [Gr\"otschel, Lov\'asz and Schrijver, Prog. Comb. Opt. 1984, Springer 1988] over thirty years ago. For the Submodular Function Minimization problem, our result immediately implies a strongly polynomial algorithm that makes at most $O(n^3)$ calls to an evaluation oracle, and an exponential time algorithm that makes at most $O(n^2 \log(n))$ calls to an evaluation oracle. These improve upon the previously best $O(n^3 \log^2(n))$ oracle complexity for strongly polynomial algorithms given in [Lee, Sidford and Wong, FOCS 2015] and [Dadush, V\'egh and Zambelli, SODA 2018], and an exponential time algorithm with oracle complexity $O(n^3 \log(n))$ given in the former work. Our result is achieved via a reduction to the Shortest Vector Problem in lattices. We show how an approximately shortest vector of certain lattice can be used to effectively reduce the dimension of the problem. Our analysis of the oracle complexity is based on a potential function that captures simultaneously the size of the search set and the density of the lattice, which we analyze via technical tools from convex geometry.Comment: This version of the paper simplifies and generalizes the results in an earlier version which will appear in SODA 202

GOGMA: Globally-Optimal Gaussian Mixture Alignment

Gaussian mixture alignment is a family of approaches that are frequently used for robustly solving the point-set registration problem. However, since they use local optimisation, they are susceptible to local minima and can only guarantee local optimality. Consequently, their accuracy is strongly dependent on the quality of the initialisation. This paper presents the first globally-optimal solution to the 3D rigid Gaussian mixture alignment problem under the L2 distance between mixtures. The algorithm, named GOGMA, employs a branch-and-bound approach to search the space of 3D rigid motions SE(3), guaranteeing global optimality regardless of the initialisation. The geometry of SE(3) was used to find novel upper and lower bounds for the objective function and local optimisation was integrated into the scheme to accelerate convergence without voiding the optimality guarantee. The evaluation empirically supported the optimality proof and showed that the method performed much more robustly on two challenging datasets than an existing globally-optimal registration solution.Comment: Manuscript in press 2016 IEEE Conference on Computer Vision and Pattern Recognitio

Minkowski Centers via Robust Optimization: Computation and Applications

Centers of convex sets are geometric objects that have received extensive attention in the mathematical and optimization literature, both from a theoretical and practical standpoint. For instance, they serve as initialization points for many algorithms such as interior-point, hit-and-run, or cutting-planes methods. First, we observe that computing a Minkowski center of a convex set can be formulated as the solution of a robust optimization problem. As such, we can derive tractable formulations for computing Minkowski centers of polyhedra and convex hulls. Computationally, we illustrate that using Minkowski centers, instead of analytic or Chebyshev centers, improves the convergence of hit-and-run and cutting-plane algorithms. We also provide efficient numerical strategies for computing centers of the projection of polyhedra and of the intersection of two ellipsoids

Geometric algorithms for cavity detection on protein surfaces

Macromolecular structures such as proteins heavily empower cellular processes or functions. These biological functions result from interactions between proteins and peptides, catalytic substrates, nucleotides or even human-made chemicals. Thus, several interactions can be distinguished: protein-ligand, protein-protein, protein-DNA, and so on. Furthermore, those interactions only happen under chemical- and shapecomplementarity conditions, and usually take place in regions known as binding sites. Typically, a protein consists of four structural levels. The primary structure of a protein is made up of its amino acid sequences (or chains). Its secondary structure essentially comprises -helices and -sheets, which are sub-sequences (or sub-domains) of amino acids of the primary structure. Its tertiary structure results from the composition of sub-domains into domains, which represent the geometric shape of the protein. Finally, the quaternary structure of a protein results from the aggregate of two or more tertiary structures, usually known as a protein complex. This thesis fits in the scope of structure-based drug design and protein docking. Specifically, one addresses the fundamental problem of detecting and identifying protein cavities, which are often seen as tentative binding sites for ligands in protein-ligand interactions. In general, cavity prediction algorithms split into three main categories: energy-based, geometry-based, and evolution-based. Evolutionary methods build upon evolutionary sequence conservation estimates; that is, these methods allow us to detect functional sites through the computation of the evolutionary conservation of the positions of amino acids in proteins. Energy-based methods build upon the computation of interaction energies between protein and ligand atoms. In turn, geometry-based algorithms build upon the analysis of the geometric shape of the protein (i.e., its tertiary structure) to identify cavities. This thesis focuses on geometric methods. We introduce here three new geometric-based algorithms for protein cavity detection. The main contribution of this thesis lies in the use of computer graphics techniques in the analysis and recognition of cavities in proteins, much in the spirit of molecular graphics and modeling. As seen further ahead, these techniques include field-of-view (FoV), voxel ray casting, back-face culling, shape diameter functions, Morse theory, and critical points. The leading idea is to come up with protein shape segmentation, much like we commonly do in mesh segmentation in computer graphics. In practice, protein cavity algorithms are nothing more than segmentation algorithms designed for proteins.Estruturas macromoleculares tais como as proteínas potencializam processos ou funções celulares. Estas funções resultam das interações entre proteínas e peptídeos, substratos catalíticos, nucleótideos, ou até mesmo substâncias químicas produzidas pelo homem. Assim, há vários tipos de interacções: proteína-ligante, proteína-proteína, proteína-DNA e assim por diante. Além disso, estas interações geralmente ocorrem em regiões conhecidas como locais de ligação (binding sites, do inglês) e só acontecem sob condições de complementaridade química e de forma. É também importante referir que uma proteína pode ser estruturada em quatro níveis. A estrutura primária que consiste em sequências de aminoácidos (ou cadeias), a estrutura secundária que compreende essencialmente por hélices e folhas , que são subsequências (ou subdomínios) dos aminoácidos da estrutura primária, a estrutura terciária que resulta da composição de subdomínios em domínios, que por sua vez representa a forma geométrica da proteína, e por fim a estrutura quaternária que é o resultado da agregação de duas ou mais estruturas terciárias. Este último nível estrutural é frequentemente conhecido por um complexo proteico. Esta tese enquadra-se no âmbito da conceção de fármacos baseados em estrutura e no acoplamento de proteínas. Mais especificamente, aborda-se o problema fundamental da deteção e identificação de cavidades que são frequentemente vistos como possíveis locais de ligação (putative binding sites, do inglês) para os seus ligantes (ligands, do inglês). De forma geral, os algoritmos de identificação de cavidades dividem-se em três categorias principais: baseados em energia, geometria ou evolução. Os métodos evolutivos baseiam-se em estimativas de conservação das sequências evolucionárias. Isto é, estes métodos permitem detectar locais funcionais através do cálculo da conservação evolutiva das posições dos aminoácidos das proteínas. Em relação aos métodos baseados em energia estes baseiam-se no cálculo das energias de interação entre átomos da proteína e do ligante. Por fim, os algoritmos geométricos baseiam-se na análise da forma geométrica da proteína para identificar cavidades. Esta tese foca-se nos métodos geométricos. Apresentamos nesta tese três novos algoritmos geométricos para detecção de cavidades em proteínas. A principal contribuição desta tese está no uso de técnicas de computação gráfica na análise e reconhecimento de cavidades em proteínas, muito no espírito da modelação e visualização molecular. Como pode ser visto mais à frente, estas técnicas incluem o field-of-view (FoV), voxel ray casting, back-face culling, funções de diâmetro de forma, a teoria de Morse, e os pontos críticos. A ideia principal é segmentar a proteína, à semelhança do que acontece na segmentação de malhas em computação gráfica. Na prática, os algoritmos de detecção de cavidades não são nada mais que algoritmos de segmentação de proteínas

Exploiting Sparse Structures in Source Localization and Tracking

This thesis deals with the modeling of structured signals under different sparsity constraints. Many phenomena exhibit an inherent structure that may be exploited when setting up models, examples include audio waves, radar, sonar, and image objects. These structures allow us to model, identify, and classify the processes, enabling parameter estimation for, e.g., identification, localisation, and tracking.In this work, such structures are exploited, with the goal to achieve efficient localisation and tracking of a structured source signal. Specifically, two scenarios are considered. In papers A and B, the aim is to find a sparse subset of a structured signal such that the signal parameters and source locations maybe estimated in an optimal way. For the sparse subset selection, a combinatorial optimization problem is approximately solved by means of convex relaxation, with the results of allowing for different types of a priori information to be incorporated in the optimization. In paper C, a sparse subset of data is provided, and a generative model is used to find the location of an unknown number of jammers in a wireless network, with the jammers’ movement in the network being tracked as additional observations become available