Related papers: Quadratic Programming Approach to Fit Protein Comp…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
The matching problem between two adjacency matrices can be formulated as the NP-hard quadratic assignment problem (QAP). Previous work on semidefinite programming (SDP) relaxations to the QAP have produced solutions that are often tight in…
Binary quadratic programming problems have attracted much attention in the last few decades due to their potential applications. This type of problems are NP-hard in general, and still considered a challenge in the design of efficient…
In this paper, we introduce the Maximum Matrix Contraction problem, where we aim to contract as much as possible a binary matrix in order to maximize its density. We study the complexity and the polynomial approximability of the problem.…
We consider optimization problems involving the multiplication of variable matrices to be selected from a given family, which might be a discrete set, a continuous set or a combination of both. Such nonlinear, and possibly discrete,…
A standard quadratic program is an optimization problem that consists of minimizing a (nonconvex) quadratic form over the unit simplex. We focus on reformulating a standard quadratic program as a mixed integer linear programming problem. We…
Mixed-integer quadratic programming is the problem of optimizing a quadratic function over points in a polyhedral set where some of the components are restricted to be integral. In this paper, we prove that the decision version of…
Solution and analysis of mathematical programming problems may be simplified when these problems are symmetric under appropriate linear transformations. In particular, a knowledge of the symmetries may help reduce the problem dimension, cut…
The peptide-protein docking problem is an important problem in structural biology that facilitates rational and efficient drug design. In this work, we explore modeling and solving this problem with the quantum-amenable quadratic…
The paper covers a formulation of the inverse quadratic programming problem in terms of unconstrained optimization where it is required to find the unknown parameters (the matrix of the quadratic form and the vector of the quasi-linear part…
Correspondence problems are often modelled as quadratic optimization problems over permutations. Common scalable methods for approximating solutions of these NP-hard problems are the spectral relaxation for non-convex energies and the…
Quadratic Programming (QP) is the well-studied problem of maximizing over {-1,1} values the quadratic form \sum_{i \ne j} a_{ij} x_i x_j. QP captures many known combinatorial optimization problems, and assuming the unique games conjecture,…
Matching problems on 3D shapes and images are challenging as they are frequently formulated as combinatorial quadratic assignment problems (QAPs) with permutation matrix constraints, which are NP-hard. In this work, we address such problems…
We consider the problem of solving a large-scale Quadratically Constrained Quadratic Program. Such problems occur naturally in many scientific and web applications. Although there are efficient methods which tackle this problem, they are…
In this paper we propose a fast optimization algorithm for approximately minimizing convex quadratic functions over the intersection of affine and separable constraints (i.e., the Cartesian product of possibly nonconvex real sets). This…
The problem of minimizing a polynomial over a set of polynomial inequalities is an NP-hard non-convex problem. Thanks to powerful results from real algebraic geometry, one can convert this problem into a nested sequence of…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
In this paper, we solve a maximization problem where the objective function is quadratic and convex or concave and the constraints set is the reachable value set of a convergent discrete-time affine system. Moreover, we assume that the…
Multigraph matching is a recent variant of the graph matching problem. In this framework, the optimization procedure considers several graphs and enforces the consistency of the matches along the graphs. This constraint can be formalized as…
Particle swarm optimization is used in several combinatorial optimization problems. In this work, particle swarms are used to solve quadratic programming problems with quadratic constraints. The approach of particle swarms is an example for…