Computing Longest Common Subsequences with the B-Cell Algorithm

Computing a longest common subsequence of a number of strings is a classical combinatorial optimisation problem with many applications in computer science and bioinformatics. It is a hard problem in the general case so that the use of heuristics is motivated. Evolutionary algorithms have been reported to be successful heuristics in practice but a theoretical analysis has proven that a large class of evolutionary algorithms using mutation and crossover fail to solve and even approximate the problem efficiently. This was done using hard instances. We reconsider the very same hard instances and prove that the B-cell algorithm outperforms these evolutionary algorithms by far. The advantage stems from the use of contiguous hypermutations. The result is another demonstration that relatively simple artificial immune systems can excel over more complex evolutionary algorithms in the domain of optimisation.