Now showing items 1-10 of 32
User's Guide for LMaFit: Low-rank Matrix Fitting
This User's Guide describes the functionality and basic usage of the Matlab package LMaFit for low-rank matrix optimization. It also briefly explains the formulations and algorithms used.
Simultaneous Structure Factor and Contrast Transfer Function Parameter Determination in Transmission Electron Microscopy
We present a new method that allows a fully automated simultaneous determination of the structure factor and the parameters of the Contrast Transfer Function (CTF) and noise function. No previous knowledge of the structure ...
A Computational Study of a Gradient-Based Log-Barrier Algorithm for a Class of Large-Scale SDPs
The authors of this paper recently introduced a transformation that converts a class of semidefinite programs (SDPs) into nonlinear optimization problems free of matrix-valued constraints and variables. This transformation ...
Solving the Double Digestion Problem as a Mixed-Integer Linear Program
The double digestion problem for DNA restriction mapping is known to be NP-complete. Several approaches to the problem have been used including exhaustive search, simulated annealing, branch-and-bound. In this paper, we ...
User's Guide For YALL1: Your Algorithms for L1 Optimization
This User's Guide describes the functionality and basic usage of the Matlab package YALL1 for L1 minimization. The one-for-six algorithm used in the YALL1 solver is briefly introduced in the appendix.
Variationally Constrained Numerical Solution of Electrical Impedance Tomography
We propose a novel, variational inversion methodology for the electrical impedance tomography problem, where we seek electrical conductivity σ inside a bounded, simply connected domain Ω, given simultaneous measurements ...
Computational Experience with Lenstra's Algorithm
Integer programming is an important mathematical approach for many decision-making problems. In this field, a major theoretical breakthrough came in 1983 when H. W. Lenstra, Jr. proposed a polynomial-time algorithm for a ...
A Global Optimization Method for the Molecular Replacement Problem in X-ray Crystallography
The primary technique for determining the three-dimensional structure of a protein molecule is X-ray crystallography, from which the molecular replacement (MR) problem often arises as a critical step. The MR problem is a ...
Case Studies For a First-Order Fobust Nonlinear Programming
In this paper, we conduct three case studies to assess the effectiveness of a recently proposed first-order method for robust nonlinear programming (Ref. 1). Three robust nonlinear programming problems were chosen from the ...
On the Equivalence Between a Commonly Used Correlation Coefficient and a Least Squares Function
Many objective functions have been proposed in X-ray crystallography to solve the molecular replacement (MR) problem and other optimization problems. In this paper, we establish the equivalence between optimizing two target ...