Mathematical Programming Strategies for Solving the Minimum Common String Partition Problem
This work addresses a combinatorial optimization problem in computational biology, offering incremental improvements with new methods for known bottlenecks.
The authors tackled the NP-hard minimum common string partition problem by proposing the first integer linear programming model and a deterministic 2-phase heuristic, achieving provenly optimal solutions for small to medium instances and new best-known solutions for all considered instances.
The minimum common string partition problem is an NP-hard combinatorial optimization problem with applications in computational biology. In this work we propose the first integer linear programming model for solving this problem. Moreover, on the basis of the integer linear programming model we develop a deterministic 2-phase heuristic which is applicable to larger problem instances. The results show that provenly optimal solutions can be obtained for problem instances of small and medium size from the literature by solving the proposed integer linear programming model with CPLEX. Furthermore, new best-known solutions are obtained for all considered problem instances from the literature. Concerning the heuristic, we were able to show that it outperforms heuristic competitors from the related literature.