Alignment of molecular networks by integer quadratic programming

Alignment of molecular networks by integer quadratic programming

MOTIVATION With more and more data on molecular networks (e.g. protein interaction networks, gene regulatory networks and metabolic networks) available, the discovery of conserved patterns or signaling pathways by comparing various kinds of networks among different species or within a species becomes an increasingly important problem. However, most of the conventional approaches either restrict...

Quadratic Integer Programming: Complexity and Equivalent Forms

Integer Quadratic Programming Models in Computational Biology

This presentation has two purposes: (1) show operations researchers how they can apply quadratic binary programming to current problems in molecular biology, and (2) show formulations of some combinatorial optimization problems as integer programs. The former purpose is primary, and I wish to persuade researchers to enter this exciting frontier. The latter purpose is part of a work in progress....

Parameterized Integer Quadratic Programming: Variables and Coefficients

In the Integer Quadratic Programming problem input is an n× n integer matrix Q, an m × n integer matrix A and an m-dimensional integer vector b. The task is to find a vector x ∈ Z minimizing xQx, subject to Ax ≤ b. We give a fixed parameter tractable algorithm for Integer Quadratic Programming parameterized by n+α. Here α is the largest absolute value of an entry of Q and A. As an application o...

Integer Quadratic Programming for Control and Communication

The main topic of this thesis is integer quadratic programming with applications to prob-lems arising in the areas of automatic control and communication. One of the mostwidespread modern control methods is Model Predictive Control (MPC). In each sam-pling time, MPC requires the solution of a Quadratic Programming (QP) problem. Tobe able to use MPC for large systems, and at high...