Abstract
This study is motivated by the Discretizable Molecular Distance Geometry Problem (DMDGP), a specific category in Distance Geometry, where the search space is discrete. We address the challenge of ordering the DMDGP constraints, a critical factor in the performance of the state-of-the-art SBBU algorithm. To this end, we formalize the constraint ordering problem as a vertex cover problem, which diverges from traditional covering problems due to the substantial importance of the sequence of vertices in the covering. In order to solve the covering problem, we propose a greedy heuristic and compare it to the ordering of the SBBU. The computational results indicate that the greedy heuristic outperforms the SBBU ordering by an average factor of 1,300\(\times \).
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Acknowledgements
We thank the Brazilian research agencies FAPESP and CNPq, and the comments made by the reviewers.
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Souza, M., Maia, N., Lavor, C. (2023). The Ordered Covering Problem in Distance Geometry. In: Guo, X., Mangul, S., Patterson, M., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Computer Science(), vol 14248. Springer, Singapore. https://doi.org/10.1007/978-981-99-7074-2_20
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DOI: https://doi.org/10.1007/978-981-99-7074-2_20
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