Applications – Science and Engineering

Transfer function restoration in 3D electron microscopy via iterative data refinement

  • J.M. Carazo
  • Yair Censor
  • C.O.S. Sorzano
  • Gabor T. Herman
  • R. Marabini
    • Categories Biomedical Applications Tags , ,

    Three-dimensional electron microscopy (3D-EM) is a powerful tool for visualizing complex biological systems. As any other imaging device, the electron microscope introduces a transfer function (called in this field the Contrast Transfer Function, CTF) into the image acquisition process that modulates the various frequencies of the signal. Thus, 3D reconstructions performed with these CTF-affected projections … Read more

    When LP is not a good idea – using structure in polyhedral optimization problems

  • Michael Osborne
    • Categories Convex Optimization, Linear Programming, Statistics Tags , , , , , , , , ,

    It has been known for almost 50 years that the discrete l_1 approximation problem can be solved effectively by linear programming. However, improved algorithms involve a step which can be interpreted as a line search, and which is not part of the standard LP solution procedures. l_1 provides the simplest example of a class of … Read more

    A New Computational Approach to Density Estimation with Semidefinite Programming

  • Tadayoshi Fushiki
  • Takashi Tsuchiya
  • Shingo Horiuchi
    • Categories Data-Mining, Semi-definite Programming, Statistics Tags , , , ,

    Density estimation is a classical and important problem in statistics. The aim of this paper is to develop a new computational approach to density estimation based on semidefinite programming (SDP), a new technology developed in optimization in the last decade. We express a density as the product of a nonnegative polynomial and a base density … Read more

    Quadratic interior-point methods in statistical disclosure control

  • Jordi Castro
    • Categories Network Optimization, Quadratic Programming, Statistics

    The safe dissemination of statistical tabular data is one of the main concerns of National Statistical Institutes (NSIs). Although each cell of the tables is made up of the aggregated information of several individuals, the statistical confidentiality can be violated. NSIs must guarantee that no individual information can be derived from the released tables. One … Read more

    Characterizing polynomials with roots in a semi-algebraic set

  • Jean-Bernard Lasserre
    • Categories Control Applications, Other Topics

    Consider a real polynomial $p$ and a semi-algebraic subset $S$ of the complex plane, defined by finitely many polynomial inequalities $g_k(z,\bar{z}) \geq 0$ for some complex polynomials $\{g_k\}$. We provide necessary and sufficient conditions on the coefficients of $p$ for the zeros of $p$ to be in $S$. Citation IEEE Trans. Automatic Control 49 (2004), … Read more

    The Reduced Density Matrix Method for Electronic Structure Calculations and the Role of Three-Index Representability Conditions

  • Bastiaan J. Braams
  • Mituhiro Fukuda
  • Michael L. Overton
  • Jerome K. Percus
  • Zhengji Zhao
    • Categories Basic Sciences Applications, Convex Optimization, Semi-definite Programming Tags

    The variational approach for electronic structure based on the two-body reduced density matrix is studied, incorporating two representability conditions beyond the previously used $P$, $Q$ and $G$ conditions. The additional conditions (called $T1$ and $T2$ here) are implicit in work of R.~M.~Erdahl [Int.\ J.\ Quantum Chem.\ {\bf13}, 697–718 (1978)] and extend the well-known three-index diagonal … Read more

    A GRASP/VND heuristic for the phylogeny problem using a new neighborhood structure

  • Celso C. Ribeiro
  • Dalessandro Vianna
    • Categories Biomedical Applications, Meta Heuristics Tags , , ,

    A phylogeny is a tree that relates taxonomic units, based on their similarity over a set of characters. The phylogeny problem consists in finding a phylogeny with the minimum number of evolutionary steps. We propose a new neighborhood structure for the phylogeny problem. A GRASP heuristic based on this neighborhood structure and using VND for … Read more

    Randomized Algorithms for Scene Recognition by Inexact Graph Matching

  • Isabelle Bloch
  • Celso C. Ribeiro
  • Maria Claudia Boeres
    • Categories Biomedical Applications, Graphs and Matroids, Meta Heuristics Tags , , ,

    We propose a new method for non-bijective graph matching for model-based pattern recognition. We formulate the search for the best correspondence between a model and an over-segmented image as a new combinatorial optimization problem, defined by the relational attributed graphs representing the model and the image where recognition has to be performed, together with the … Read more

    Heuristics for the Phylogeny Problem

  • Alexandre Andreatta
  • Celso C. Ribeiro
    • Categories Biomedical Applications, Meta Heuristics Tags , ,

    A phylogeny is a tree that relates taxonomic units, based on their similarity over a set of characters. The problem of finding a phylogeny with the minimum number of evolutionary steps (the so-called parsimony criterion) is one of the main problems in comparative biology. In this work, we study different heuristic approaches to the phylogeny … Read more

    Scheduling Workover Rigs for Onshore Oil Production

  • Daniel Aloise
  • Dario J. Aloise
  • Celso C. Ribeiro
  • Caroline Rocha
  • Luiz Moura
  • José Ribeiro Filho
    • Categories Facility Planning and Design, Meta Heuristics, Production and Logistics Tags , , , ,

    Many oil wells in Brazilian onshore fields rely on artificial lift methods. Maintenance services such as cleaning, reinstatement, stimulation and others are essential to these wells. These services are performed by workover rigs, which are avaliable on a limited number with respect to the number of wells demanding service. The decision of which workover rig … Read more