The Distance Geometry Problem in three dimensions consists in finding an embedding in R^3 of a given nonnegatively weighted simple undirected graph such that edge weights are equal to the corresponding Euclidean distances in the embedding. This is a continuous search problem that can be discretized under some assumptions on the minimum degree of the … Read more
Purpose: Iterative projection reconstruction algorithms are currently the preferred reconstruction method in proton computed tomography (pCT). However, due to inconsistencies in the measured data arising from proton energy straggling and multiple Coulomb scattering, noise in the reconstructed image increases with successive iterations. In the current work, we investigated the use of total variation superiorization (TVS) … Read more
Background: The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such peptide epitopes has potential applications in vaccine design and in better understanding autoimmune diseases and allergies. However, comprehensive experimental determination of peptide-MHC binding affinities is infeasible due … Read more
Iterative algorithms aimed at solving some problems are discussed. For certain problems, such as finding a common point in the intersection of a finite number of convex sets, there often exist iterative algorithms that impose very little demand on computer resources. For other problems, such as finding that point in the intersection at which the … Read more
Inferences need to be drawn in biological systems using experimental multivariate data. The number of samples collected in many such experiments is small, and the data is noisy. We present and study the performance of a robust optimization (RO) model for such situations. We adapt this model to generate a minimum and a maximum estimation … Read more
The effectiveness of projection methods for solving systems of linear inequalities is investigated. It is shown that they have a computational advantage over some alternatives and that this makes them successful in real-world applications. This is supported by experimental evidence provided in this paper on problems of various sizes (up to tens of thousands of … Read more
We consider penalized-likelihood reconstruction for X-ray computed tomography of objects that contain small metal structures. To reduce the beam hardening artefacts induced by these structures, we derive the reconstruction algorithm from a projection model that takes into account the photon emission spectrum and nonlinear variation of attenuation to photon energy. This algorithm requires excessively long … Read more
Distance geometry problems arise from the need to position entities in the Euclidean $K$-space given some of their respective distances. Entities may be atoms (molecular distance geometry), wireless sensors (sensor network localization), or abstract vertices of a graph(graph drawing). In the context of molecular distance geometry, the distances are usually known because of chemical properties … Read more
The binding of peptide fragments of extracellular peptides to class II MHC is a crucial event in the adaptive immune response. Each MHC allotype generally binds a distinct subset of peptides and the enormous number of possible peptide epitopes prevents their complete experimental characterization. Computational methods can utilize the limited experimental data to predict the … Read more
In a recent paper by Strohmer and Vershynin (J. Fourier Anal. Appl. 15:262–278, 2009) a “randomized Kaczmarz algorithm” is proposed for solving consistent systems of linear equations {ai, x = bi }m i=1. In that algorithm the next equation to be used in an iterative Kaczmarz process is selected with a probability proportional to ai2. … Read more