Optimization-based search for Nordsieck methods of high order with quadratic stability

We describe the search for explicit general linear methods in Nordsieck form for which the stability function has only two nonzero roots. This search is based on state-of-the-art optimization software. Examples of methods found in this way are given for order p = 5, p = 6, and p = 7. Article Download View Optimization-based … Read more

On Computation of Performance Bounds of Optimal Index Assignment

Channel-optimized index assignment of source codewords is arguably the simplest way of improving transmission error resilience, while keeping the source and/or channel codes intact. But optimal design of index assignment is an in- stance of quadratic assignment problem (QAP), one of the hardest optimization problems in the NP-complete class. In this paper we make a … Read more

MultiRTA: A simple yet accurate method for predicting peptide binding affinities for multiple class II MHC allotypes

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

The state-of-the-art in conic optimization software

This work gives an overview over the major codes available for the solution of linear semidefinite (SDP) and second-order cone (SOCP) programs. Some developments since the 7th DIMACS Challenge [9, 17] are pointed out as well as some currently under way. Instead of presenting per- formance tables, reference is made to the ongoing benchmark [19] … Read more

Semidefinite code bounds based on quadruple distances

Let A(n, d) be the maximum number of 0, 1 words of length n, any two having Hamming distance at least d. We prove A(20, 8) = 256, which implies that the quadruply shortened Golay code is optimal. Moreover, we show A(18, 6) ≤ 673, A(19, 6) ≤ 1237, A(20, 6) ≤ 2279, A(23, 6) … Read more

On Computation of Performance Bounds of Optimal Index Assignment

Channel-optimized index assignment of source codewords is arguably the simplest way of improving transmission error resilience, while keeping the source and/or channel codes intact. But optimal design of index assignment is an in- stance of quadratic assignment problem (QAP), one of the hardest optimization problems in the NP-complete class. In this paper we make a … Read more

Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

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

High accuracy semidefinite programming bounds for kissing numbers

The kissing number in n-dimensional Euclidean space is the maximal number of non-overlapping unit spheres which simultaneously can touch a central unit sphere. Bachoc and Vallentin developed a method to find upper bounds for the kissing number based on semidefinite programming. This paper is a report on high accuracy calculations of these upper bounds for … Read more

High accuracy semidefinite programming bounds for kissing numbers

The kissing number in n-dimensional Euclidean space is the maximal number of non-overlapping unit spheres which simultaneously can touch a central unit sphere. Bachoc and Vallentin developed a method to find upper bounds for the kissing number based on semidefinite programming. This paper is a report on high accuracy calculations of these upper bounds for … Read more

A New Relaxation Framework for Quadratic Assignment Problems based on Matrix Splitting

Quadratic assignment problems (QAPs) are among the hardest discrete optimization problems. Recent study shows that even obtaining a strong lower bound for QAPs is a computational challenge. In this paper, we first discuss how to construct new simple convex relaxations of QAPs based on various matrix splitting schemes. Then we introduce the so-called symmetric mappings … Read more