A Study of Archiving Strategies in Multi-Objective PSO for Molecular Docking

Molecular docking is a complex optimization problem aimed at predicting the position of a ligand molecule in the active site of a receptor with the lowest binding energy. This problem can be formulated as a bi-objective optimization problem by minimizing the binding energy and the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands. In this context, the SMPSO multi-objective swarm-intelligence algorithm has shown a remarkable performance. SMPSO is characterized by having an external archive used to store the non-dominated solutions and also as the basis of the leader selection strategy. In this paper, we analyze several SMPSO variants based on different archiving strategies in the scope of a benchmark of molecular docking instances. Our study reveals that the SMPSOhv, which uses an hypervolume contribution based archive, shows the overall best performance.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Local Optimal Sets and Bounded Archiving on Multi-objective NK-Landscapes with Correlated Objectives

The properties of local optimal solutions in multi-objective combinatorial optimization problems are crucial for the effectiveness of local search algorithms, particularly when these algorithms are based on Pareto dominance. Such local search algorithms typically return a set of mutually nondominated Pareto local optimal (PLO) solutions, that is, a PLO-set. This paper investigates two aspects of PLO-sets by means of experiments with Pareto local search (PLS). First, we examine the impact of several problem characteristics on the properties of PLO-sets for multi-objective NK-landscapes with correlated objectives. In particular, we report that either increasing the number of objectives or decreasing the correlation between objectives leads to an exponential increment on the size of PLO-sets, whereas the variable correlation has only a minor effect. Second, we study the running time and the quality reached when using bounding archiving methods to limit the size of the archive handled by PLS, and thus, the maximum size of the PLO-set found. We argue that there is a clear relationship between the running time of PLS and the difficulty of a problem instance.Comment: appears in Parallel Problem Solving from Nature - PPSN XIII, Ljubljana : Slovenia (2014

Local Optimal Sets and Bounded Archiving on Multi-objective NK-Landscapes with Correlated Objectives

The properties of local optimal solutions in multi-objective combinatorial optimization problems are crucial for the effectiveness of local search algorithms, particularly when these algorithms are based on Pareto dominance. Such local search algorithms typically return a set of mutually nondominated Pareto local optimal (PLO) solutions, that is, a PLO-set. This paper investigates two aspects of PLO-sets by means of experiments with Pareto local search (PLS). First, we examine the impact of several problem characteristics on the properties of PLO-sets for multi-objective NK-landscapes with correlated objectives. In particular, we report that either increasing the number of objectives or decreasing the correlation between objectives leads to an exponential increment on the size of PLO-sets, whereas the variable correlation has only a minor effect. Second, we study the running time and the quality reached when using bounding archiving methods to limit the size of the archive handled by PLS, and thus, the maximum size of the PLO-set found. We argue that there is a clear relationship between the running time of PLS and the difficulty of a problem instance.Comment: appears in Parallel Problem Solving from Nature - PPSN XIII, Ljubljana : Slovenia (2014

Multi-Objective Archiving

Most multi-objective optimisation algorithms maintain an archive explicitly or implicitly during their search. Such an archive can be solely used to store high-quality solutions presented to the decision maker, but in many cases may participate in the search process (e.g., as the population in evolutionary computation). Over the last two decades, archiving, the process of comparing new solutions with previous ones and deciding how to update the archive/population, stands as an important issue in evolutionary multi-objective optimisation (EMO). This is evidenced by constant efforts from the community on developing various effective archiving methods, ranging from conventional Pareto-based methods to more recent indicator-based and decomposition-based ones. However, the focus of these efforts is on empirical performance comparison in terms of specific quality indicators; there is lack of systematic study of archiving methods from a general theoretical perspective. In this paper, we attempt to conduct a systematic overview of multi-objective archiving, in the hope of paving the way to understand archiving algorithms from a holistic perspective of theory and practice, and more importantly providing a guidance on how to design theoretically desirable and practically useful archiving algorithms. In doing so, we also present that archiving algorithms based on weakly Pareto compliant indicators (e.g., epsilon-indicator), as long as designed properly, can achieve the same theoretical desirables as archivers based on Pareto compliant indicators (e.g., hypervolume indicator). Such desirables include the property limit-optimal, the limit form of the possible optimal property that a bounded archiving algorithm can have with respect to the most general form of superiority between solution sets.Comment: 21 pages, 4 figures, journa

Investigation of Archiving Techniques for Evolutionary Multi-objective Optimizers

Abstract: The optimization of multi-objective problems from the Pareto dominance viewpoint can lead to huge sets of incomparable solutions. Many heuristic techniques proposed to these problems have to deal with approximation sets that can be limited or not. Usually, a new solution generated by a heuristic is compared with other archived non-dominated solutions generated previously. Many techniques deal with limited size archives, since comparisons within unlimited archives may require significant computational effort. To maintain limited archives, solutions need to be discarded. Several techniques were proposed to deal with the problem of deciding which solutions remain in the archive and which are discarded. Previous investigations showed that those techniques might not prevent deterioration of the archives. In this study, we propose to store discarded solutions in a secondary archive and, periodically, recycle them, bringing them back to the optimization process. Three recycling techniques were investigated for three known methods. The datasets for the experiments consisted of 91 instances of discrete and continuous problems with 2, 3 and 4 objectives. The results showed that the recycling method can benefit the tested optimizers on many problem classes

An Approach for the Generation of Multi-Objective Algorithms Applied to the Integration and Test Order Problem

Multi-Objective Evolutionary Algorithms (MOEAs) have been successfully applied to solve hard real software engineering problems. However, to choose and design a MOEA is considered a difficult task, since there are several parameters and components to be configured. These aspects directly impact the generated solutions and the performance of MOEAs. In this sense, this paper proposes an approach for the automatic generation of MOEAs applied to the Integration and Test Order (ITO) problem. Such a problem refers to the generation of optimal sequences of units for integration testing. The approach includes a set of parameters and components of different MOEAs, and is implemented with two design algorithms: Grammatical Evolution (GE) and Iterated Racing (irace). Evaluation results are presented, comparing the MOEAs generated by both design algorithms. Furthermore, the generated MOEAs are compared to two well-known MOEAs used in the literature to solve the ITO problem. Results show that the MOEAs generated with GE and irace perform similarly, and both outperform traditional MOEAs. The approach can reduce efforts spent to design and configure MOEAs, and serves as basis for implementing solutions to other software engineering problems

PasMoQAP: A Parallel Asynchronous Memetic Algorithm for solving the Multi-Objective Quadratic Assignment Problem

Multi-Objective Optimization Problems (MOPs) have attracted growing attention during the last decades. Multi-Objective Evolutionary Algorithms (MOEAs) have been extensively used to address MOPs because are able to approximate a set of non-dominated high-quality solutions. The Multi-Objective Quadratic Assignment Problem (mQAP) is a MOP. The mQAP is a generalization of the classical QAP which has been extensively studied, and used in several real-life applications. The mQAP is defined as having as input several flows between the facilities which generate multiple cost functions that must be optimized simultaneously. In this study, we propose PasMoQAP, a parallel asynchronous memetic algorithm to solve the Multi-Objective Quadratic Assignment Problem. PasMoQAP is based on an island model that structures the population by creating sub-populations. The memetic algorithm on each island individually evolve a reduced population of solutions, and they asynchronously cooperate by sending selected solutions to the neighboring islands. The experimental results show that our approach significatively outperforms all the island-based variants of the multi-objective evolutionary algorithm NSGA-II. We show that PasMoQAP is a suitable alternative to solve the Multi-Objective Quadratic Assignment Problem.Comment: 8 pages, 3 figures, 2 tables. Accepted at Conference on Evolutionary Computation 2017 (CEC 2017