TY - GEN

T1 - A polynomial delay algorithm for enumerating approximate solutions to the interval Constrained Coloring problem

AU - Canzar, Stefan

AU - Elbassioni, Khaled

AU - Mestre, Julián

PY - 2010

Y1 - 2010

N2 - 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 verified 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 confirm the effectiveness 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.

AB - 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 verified 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 confirm the effectiveness 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.

UR - http://www.scopus.com/inward/record.url?scp=78650895998&partnerID=8YFLogxK

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U2 - 10.1137/1.9781611972900.3

DO - 10.1137/1.9781611972900.3

M3 - Conference contribution

AN - SCOPUS:78650895998

SN - 9780898719314

T3 - 2010 Proceedings of the 12th Workshop on Algorithm Engineering and Experiments, ALENEX 2010

SP - 23

EP - 33

BT - 2010 Proceedings of the 12th Workshop on Algorithm Engineering and Experiments, ALENEX 2010

PB - Society for Industrial and Applied Mathematics Publications

T2 - 12th Annual Workshop on Algorithm Engineering and Experiments, ALENEX 2010

Y2 - 16 January 2010 through 16 January 2010

ER -