Multi-objectivization, fitness landscape transformation and search performance: A case of study on the hp model for protein structure prediction

Multi-objectivization represents a current and promising research direction which has led to the development of more competitive search mechanisms. This concept involves the restatement of a single-objective problem in an alternative multi-objective form, which can facilitate the process of finding a solution to the original problem. Recently, this transformation was applied with success to the HP model, a simplified yet challenging representation of the protein structure prediction problem. The use of alternative multi-objective formulations, based on the decomposition of the original objective function of the problem, has significantly increased the performance of search algorithms. The present study goes further on this topic. With the primary aim of understanding and quantifying the potential effects of multi-objectivization, a detailed analysis is first conducted to evaluate the extent to which this problem transformation impacts on an important characteristic of the fitness landscape, neutrality. To the authors’ knowledge, the effects of multi-objectivization have not been previously investigated by explicitly sampling and evaluating the neutrality of the fitness landscape. Although focused on the HP model, most of the findings of such an analysis can be extrapolated to other problem domains, contributing thus to the general understanding of multi-objectivization. Finally, this study presents a comparative analysis where the advantages of multi-objectivization are evaluated in terms of the performance of a basic evolutionary algorithm. Both the two- and three-dimensional variants of the HP model (based on the square and cubic lattices, respectively) are considered.