On the role of metaheuristic optimization in bioinformatics

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

Learning FCMs with multi-local and balanced memetic algorithms for forecasting industrial drying processes

In this paper, we propose a Fuzzy Cognitive Map (FCM) learning approach with a multi-local search in balanced memetic algorithms for forecasting industrial drying processes. The first contribution of this paper is to propose a FCM model by an Evolutionary Algorithm (EA), but the resulted FCM model is improved by a multi-local and balanced local search algorithm. Memetic algorithms can be tuned with different local search strategies (CMA-ES, SW, SSW and Simplex) and the balance of the effort between global and local search. To do this, we applied the proposed approach to the forecasting of moisture loss in industrial drying process. The thermal drying process is a relevant one used in many industrial processes such as food industry, biofuels production, detergents and dyes in powder production, pharmaceutical industry, reprography applications, textile industries, and others. This research also shows that exploration of the search space is more relevant than finding local optima in the FCM models tested

Preventing premature convergence and proving the optimality in evolutionary algorithms

http://ea2013.inria.fr//proceedings.pdfInternational audienceEvolutionary Algorithms (EA) usually carry out an efficient exploration of the search-space, but get often trapped in local minima and do not prove the optimality of the solution. Interval-based techniques, on the other hand, yield a numerical proof of optimality of the solution. However, they may fail to converge within a reasonable time due to their inability to quickly compute a good approximation of the global minimum and their exponential complexity. The contribution of this paper is a hybrid algorithm called Charibde in which a particular EA, Differential Evolution, cooperates with a Branch and Bound algorithm endowed with interval propagation techniques. It prevents premature convergence toward local optima and outperforms both deterministic and stochastic existing approaches. We demonstrate its efficiency on a benchmark of highly multimodal problems, for which we provide previously unknown global minima and certification of optimality