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Authors: Miloš Chromý and Markus Sinnl

Affiliation: Institute of Production and Logistics Management/JKU Business School, Johannes Kepler University Linz, Altenberger Straße 69, 4040 Linz, Austria

Keyword(s): Decision Diagram, Bioinformatics, Computational Biology, Minimum Common String Partition Problem.

Abstract: In the Minimum Common String Partition Problem (MCSP), we are given two strings on input, and we want to partition both into the same collection of substrings, minimizing the number of the substrings in the partition. This combinatorial optimization problem has applications in computational biology and is NP-hard. Many different heuristic and exact methods exist for this problem, such as a Greedy approach, Ant Colony Optimization, or Integer Linear Programming. In this paper, we formulate the MCSP as a Dynamic Program and develop an exact solution algorithm based on Decision Diagrams for it. We also introduce a restricted Decision Diagram that allows to compute heuristic solutions to the MCSP and compare the quality of solution and runtime on instances from literature with existing approaches. Our approach scales well and is suitable for heuristic solutions of large-scale instances.

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Paper citation in several formats:
Chromý, M. and Sinnl, M. (2022). On Solving the Minimum Common String Partition Problem by Decision Diagrams. In Proceedings of the 11th International Conference on Operations Research and Enterprise Systems - ICORES; ISBN 978-989-758-548-7; ISSN 2184-4372, SciTePress, pages 177-184. DOI: 10.5220/0010830200003117

@conference{icores22,
author={Miloš Chromý. and Markus Sinnl.},
title={On Solving the Minimum Common String Partition Problem by Decision Diagrams},
booktitle={Proceedings of the 11th International Conference on Operations Research and Enterprise Systems - ICORES},
year={2022},
pages={177-184},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0010830200003117},
isbn={978-989-758-548-7},
issn={2184-4372},
}

TY - CONF

JO - Proceedings of the 11th International Conference on Operations Research and Enterprise Systems - ICORES
TI - On Solving the Minimum Common String Partition Problem by Decision Diagrams
SN - 978-989-758-548-7
IS - 2184-4372
AU - Chromý, M.
AU - Sinnl, M.
PY - 2022
SP - 177
EP - 184
DO - 10.5220/0010830200003117
PB - SciTePress

- Science and Technology Publications, Lda.
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