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

A comprehensive comparison of metaheuristics for the repetition-free longest common subsequence problem

This paper deals with an NP-hard string problem from the bio-informatics field: the repetition-free longest common subsequence problem. This problem has enjoyed an increasing interest in recent years, which has resulted in the application of several pure as well as hybrid metaheuristics. However, the literature lacks a comprehensive comparison between those approaches. Moreover, it has been shown that general purpose integer linear programming solvers are very efficient for solving many of the problem instances that were used so far in the literature. Therefore, in this work we extend the available benchmark set, adding larger instances to which integer linear programming solvers cannot be applied anymore. Moreover, we provide a comprehensive comparison of the approaches found in the literature. Based on the results we propose a hybrid between two of the best methods which turns out to inherit the complementary strengths of both methods.Peer ReviewedPostprint (author's final draft

Offline Learning for Sequence-based Selection Hyper-heuristics

This thesis is concerned with finding solutions to discrete NP-hard problems. Such problems occur in a wide range of real-world applications, such as bin packing, industrial flow shop problems, determining Boolean satisfiability, the traveling salesman and vehicle routing problems, course timetabling, personnel scheduling, and the optimisation of water distribution networks. They are typically represented as optimisation problems where the goal is to find a ``best'' solution from a given space of feasible solutions. As no known polynomial-time algorithmic solution exists for NP-hard problems, they are usually solved by applying heuristic methods. Selection hyper-heuristics are algorithms that organise and combine a number of individual low level heuristics into a higher level framework with the objective of improving optimisation performance. Many selection hyper-heuristics employ learning algorithms in order to enhance optimisation performance by improving the selection of single heuristics, and this learning may be classified as either online or offline. This thesis presents a novel statistical framework for the offline learning of subsequences of low level heuristics in order to improve the optimisation performance of sequenced-based selection hyper-heuristics. A selection hyper-heuristic is used to optimise the HyFlex set of discrete benchmark problems. The resulting sequences of low level heuristic selections and objective function values are used to generate an offline learning database of heuristic selections. The sequences in the database are broken down into subsequences and the mathematical concept of a logarithmic return is used to discriminate between ``effective'' subsequences, that tend to lead to improvements in optimisation performance, and ``disruptive'' subsequences that tend to lead to worsening performance. Effective subsequences are used to improve hyper-heuristics performance directly, by embedding them in a simple hyper-heuristic design, and indirectly as the inputs to an appropriate hyper-heuristic learning algorithm. Furthermore, by comparing effective subsequences across different problem domains it is possible to investigate the potential for cross-domain learning. The results presented here demonstrates that the use of well chosen subsequences of heuristics can lead to small, but statistically significant, improvements in optimisation performance

The Weighted Independent Domination Problem: ILP Model and Algorithmic Approaches

This work deals with the so-called weighted independent domination problem, which is an $NP$-hard combinatorial optimization problem in graphs. In contrast to previous work, this paper considers the problem from a non-theoretical perspective. The first contribution consists in the development of three integer linear programming models. Second, two greedy heuristics are proposed. Finally, the last contribution is a population-based iterated greedy metaheuristic which is applied in two different ways: (1) the metaheuristic is applied directly to each problem instance, and (2) the metaheuristic is applied at each iteration of a higher-level framework---known as construct, merge, solve \& adapt---to sub-instances of the tackled problem instances. The results of the considered algorithmic approaches show that integer linear programming approaches can only compete with the developed metaheuristics in the context of graphs with up to 100 nodes. When larger graphs are concerned, the application of the populated-based iterated greedy algorithm within the higher-level framework works generally best. The experimental evaluation considers graphs of different types, sizes, densities, and ways of generating the node and edge weights

Construct, Merge, Solve & Adapt A new general algorithm for combinatorial optimization

[EN]This paper describes a general hybrid metaheuristic for combinatorial optimization labelled Construct,Merge, Solve & Adapt. The proposed algorithm is a specific instantiation of a framework known from theliterature as Generate-And-Solve, which is based on the following general idea. First, generate a reducedsub-instance of the original problem instance, in a way such that a solution to the sub-instance is also asolution to the original problem instance. Second, apply an exact solver to the reduced sub-instance inorder to obtain a (possibly) high quality solution to the original problem instance. And third, make use ofthe results of the exact solver as feedback for the next algorithm iteration. The minimum common stringpartition problem and the minimum covering arborescence problem are chosen as test cases in order todemonstrate the application of the proposed algorithm. The obtained results show that the algorithm iscompetitive with the exact solver for small to medium size problem instances, while it significantlyoutperforms the exact solver for larger problem instancesC. Blum was supported by project TIN2012-37930-02 of the Spanish Government. In addition, support is acknowledged from IKERBASQUE (Basque Foundation for Science). J.A. Lozano was partially supported by the IT609-13 program (Basque Government) and project TIN2013-41272P (Spanish Ministry of Science and Innovation)Peer reviewe