A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem

The Twelfth Workshop on Algorithm Engineering and Experiments

Stefan Canzar

Others  :  http://www.siam.org/proceedings/alenex/2010/alx10_003_canzars.pdf
PID  :  38126

来源: CEUR

【 摘 要 】

We study the interval constrained coloring problem, a combinatorial problem arising in the interpretation of data on protein structure emanating from experiments based on hydrogen/deuterium exchange and mass spectrometry. The problem captures the challenging task of increasing the spatial resolution of experimental data in order to get a better picture of the protein structure. Since solutions proposed by any algorithmic framework have to ultimately be veried by biochemists, it is important to provide not just a single solution, but a valuable set of candidate solutions. Our contribution is a polynomial-delay polynomial-space algorithm for enumerating all exact solutions plus further approximate solutions, whose components are guaranteed to be within an absolute error of one of the optimum. Our experiments indicate that these approximate solutions are reasonably close to the optimal ones, in terms of the accumulative error. In addition, the experiments also conrm the eectiveness of the method in reducing the delay between two consecutive solutions considerably, compared to what it takes an integer programming solver to produce the next exact solution.