A Biased Random Key Genetic Algorithm for Solving the Longest Run Subsequence Problem
This work addresses a combinatorial optimization problem in bioinformatics, specifically for genome reassembly, but is incremental as it applies an existing algorithm variant to a known problem.
The authors tackled the NP-hard longest run subsequence problem, which is relevant for genome reassembly, by proposing a Biased Random Key Genetic Algorithm (BRKGA) that achieved state-of-the-art performance compared to Max-Min Ant System and CPLEX, though improvements are needed for large alphabet sizes.
The longest run subsequence (LRS) problem is an NP-hard combinatorial optimization problem belonging to the class of subsequence problems from bioinformatics. In particular, the problem plays a role in genome reassembly. In this paper, we present a solution to the LRS problem using a Biased Random Key Genetic Algorithm (BRKGA). Our approach places particular focus on the computational efficiency of evaluating individuals, which involves converting vectors of gray values into valid solutions to the problem. For comparison purposes, a Max-Min Ant System is developed and implemented. This is in addition to the application of the integer linear programming solver CPLEX for solving all considered problem instances. The computation results show that the proposed BRKGA is currently a state-of-the-art technique for the LRS problem. Nevertheless, the results also show that there is room for improvement, especially in the context of input strings based on large alphabet sizes.