An Integer Programming Formulation of the Minimum Common String Partition Problem

Ferdous, S. M.; Rahman, M. Sohel

doi:10.1371/journal.pone.0130266

Cited by 6 publications

(3 citation statements)

References 18 publications

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“…Blum et al (2015) present the first integer linear programming (ILP) model for this problem, as well as an ILP-based heuristic. More efficient ILP models have been later proposed by Blum and Raidl (2016) and Ferdous and Rahman (2015). A list of recent articles on the MCSP problem is shown in Table 11.…”

Section: Unbalanced Minimum Common String Partition Problemmentioning

confidence: 99%

On the role of metaheuristic optimization in bioinformatics

Calvet

Benito

Juan

et al. 2022

Int Trans Operational Res

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Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics.

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Section: Unbalanced Minimum Common String Partition Problemmentioning

confidence: 99%

On the role of metaheuristic optimization in bioinformatics

Calvet

Benito

Juan

et al. 2022

Int Trans Operational Res

View full text Add to dashboard Cite

show abstract

“…Finally, both original and modified models are applied to a wide range of problem instances. Note that the third existing ILP model from Ferdous and Sohel Rahman () is not considered here because a corresponding modification is not as straightforward as for the other two models.…”

Section: Modification Of the Ilp Modelsmentioning

confidence: 99%

“…(), together with a deterministic 2‐phase heuristic based on the ILP model. Later on, improved ILP models were presented in Ferdous and Sohel Rahman () and Blum and Raidl (). The current state‐of‐the‐art technique is a construct, merge, solve, and adapt (CMSA) approach from Blum et al.…”

Section: Introductionmentioning

confidence: 99%

Minimum common string partition: on solving large‐scale problem instances

Blum

2018

Int Trans Operational Res

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Minimum common string partition is an NP‐hard combinatorial optimization problem from the bioinformatics field. The current state‐of‐the‐art algorithm is a hybrid technique known as construct, merge, solve, and adapt (CMSA). This algorithm combines two main algorithmic components: generating solutions in a probabilistic way and solving reduced subinstances obtained from the tackled problem instances, if possible, to optimality. However, the CMSA algorithm was not intended for application to very large problem instances. Therefore, in this paper we present a technique that makes CMSA, and other available algorithms for this problem, applicable to problem instances that are about one order of magnitude larger than the largest problem instances considered so far. Moreover, a reduced variable neighborhood search (RVNS) for solving the tackled problem, based on integer programming, is introduced. The experimental results show that the modified CMSA algorithm is very strong for problem instances based on rather small alphabets. With growing alphabet size, it turns out that RVNS has a growing advantage over CMSA.

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2016

Metaheuristics for String Problems in Bio‐Informatics

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An Integer Programming Formulation of the Minimum Common String Partition Problem

Cited by 6 publications

References 18 publications

On the role of metaheuristic optimization in bioinformatics

On the role of metaheuristic optimization in bioinformatics

Minimum common string partition: on solving large‐scale problem instances

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