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Efficient Search Algorithms for the Restricted Longest Common Subsequence Problem

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Computational Science – ICCS 2024 (ICCS 2024)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 14836))

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Abstract

This paper deals with the restricted longest common subsequence (RLCS) problem, an extension of the well-studied longest common subsequence problem involving two sets of strings: the input strings and the restricted strings. This problem has applications in bioinformatics, particularly in identifying similarities and discovering mutual patterns and motifs among DNA, RNA, and protein molecules. We introduce a general search framework to tackle the RLCS problem. Based on this, we present an exact best-first search algorithm and a meta-heuristic Beam Search algorithm. To evaluate the effectiveness of these algorithms, we compare them with two exact algorithms and two approximate algorithms from the literature along with a greedy approach. Our experimental results show the superior performance of our proposed approaches. In particular, our exact approach outperforms the other exact methods in terms of significantly shorter computation times, often reaching an order of magnitude compared to the second-best approach. Moreover, it successfully solves all problem instances, which was not the case with the other approaches. In addition, Beam Search provides close-to-optimal solutions with remarkably short computation times.

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Acknowledgements

The research of M. Djukanović is partially supported by the Ministry for Scientific and Technological Development and Higher Education of the Republic of Srpska, B &H in the course of the bilateral research project between B &H and Slovenia entitled “Theoretical and computational aspects of some graph problems with the application to graph network information spreading” and the COST Action ROAR-NET under no. CA22137. A. Kartelj was supported by grant 451-03-47/2023-01/200104 funded by the Ministry of Science Technological Development and Innovations of the Republic of Serbia. J. Reixach and C. Blum are supported by grants TED2021-129319B-I00 and PID2022-136787NB-I00 funded by MCIN/AEI/10.13039/501100011033. The authors would like to thank the Compute Cluster Unit of the Institute of Logic and Computation at the Vienna University of Technology for providing computing resources for this research project.

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Authors and Affiliations

  1. Faculty of Natural Sciences and Mathematics, University of Banja Luka, Banja Luka, Bosnia and Herzegovina

    Marko Djukanović

  2. Faculty of Mathematics, University of Belgrade, Belgrade, Serbia

    Aleksandar Kartelj

  3. Computer Systems, Jožef Stefan Institute, Ljubljana, Slovenia

    Tome Eftimov

  4. Artificial Intelligence Research Institute (IIIA-CSIC), Campus of the UAB, Bellaterra, Spain

    Jaume Reixach & Christian Blum

Authors
  1. Marko Djukanović
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  2. Aleksandar Kartelj
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  3. Tome Eftimov
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  4. Jaume Reixach
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  5. Christian Blum
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Corresponding author

Correspondence to Marko Djukanović .

Editor information

Editors and Affiliations

  1. University of Malaga, Malaga, Spain

    Leonardo Franco

  2. University of Amsterdam, Amsterdam, The Netherlands

    Clélia de Mulatier

  3. AGH University of Science and Technology, Krakow, Poland

    Maciej Paszynski

  4. University of Amsterdam, Amsterdam, The Netherlands

    Valeria V. Krzhizhanovskaya

  5. University of Tennessee, Knoxville, TN, USA

    Jack J. Dongarra

  6. University of Amsterdam, Amsterdam, The Netherlands

    Peter M. A. Sloot

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Djukanović, M., Kartelj, A., Eftimov, T., Reixach, J., Blum, C. (2024). Efficient Search Algorithms for the Restricted Longest Common Subsequence Problem. In: Franco, L., de Mulatier, C., Paszynski, M., Krzhizhanovskaya, V.V., Dongarra, J.J., Sloot, P.M.A. (eds) Computational Science – ICCS 2024. ICCS 2024. Lecture Notes in Computer Science, vol 14836. Springer, Cham. https://doi.org/10.1007/978-3-031-63775-9_5

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  • DOI: https://doi.org/10.1007/978-3-031-63775-9_5

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