NodEO, a multi-paradigm distributed evolutionary algorithm platform in JavaScript

In this paper we measure the speed of several popular and recent programming languages performing the most usual operators in the canonical evolutionary algorithm, mutation and crossover, as well as an usual fitness function, OneMax. These three operations are representative of the kind of the ones performed in binary chromosomes. Our main objectives are, first, to create programs in programming languages that use the fastest available implementation. Second, to find out the differences in speeds for the different languages. Third, to find out whether the usual assumptions about the speed of languages really holds. And, finally, to find if the assumed order of speed in languages used in evolutionary algorithms holds true for all kinds of operations. In order to do that, we use available implementations or perform our own, concluding that the evolutionary algorithm scenario is more complex than usually assumed and finding out some surprising winners and losers among the languages tested.

Evolutionary algorithms (EAs), as global search methods, are proved to be more robust than their counterpart local heuristics for detecting protein complexes in protein-protein interaction (PPI) networks. Typically, the source of robustness of these EAs comes from their components and parameters. These components are solution representation, selection, crossover, and mutation. Unfortunately, almost all EA based complex detection methods suggested in the literature were designed with only canonical or traditional components. Further, topological structure of the protein network is the main information that is used in the design of almost all such components. The main contribution of this paper is to formulate a more robust EA with more biological consistency. For this purpose, a new crossover operator is suggested where biological information in terms of both gene semantic similarity and protein functional similarity is fed into its design. To reflect the heuristic roles of both semantic and functional similarities, this paper introduces two gene ontology (GO) aware crossover operators. These are direct annotation-aware and inherited annotation-aware crossover operators. The first strategy is handled with the direct gene ontology annotation of the proteins, while the second strategy is handled with the directed acyclic graph (DAG) of each gene ontology term in the gene product. To conduct our experiments, the proposed EAs with GO-aware crossover operators are compared against the state-of-the-art heuristic, canonical EAs with the traditional crossover operator, and GO-based EAs. Simulation results are evaluated in terms of recall, precision, and F measure at both complex level and protein level. The results prove that the new EA design encourages a more reliable treatment of exploration and exploitation and, thus, improves the detection ability for more accurate protein complex structures.

The paper presents an approach to design optimization using parallel evolutionary algorithms. The only use of a simple evolutionary algorithm in order to generate the optimal solution for complex problems can be ineffective due to long calculation time. Thus a tournament evolutionary algorithm (EA) and a parallel computation method are proposed and used. The proposed EA does not require an analysis of the optimization model for each potential solution from evolutionary populations. The second element of the method consists in parallel running of evolutionary algorithms using multi-threads approach. The experiments were carried out for many different single design optimization problems and two of them are presented in the paper. The first problem considers a task of robot gripper mechanism optimization and the second one deals with the optimization of a shaft based on Finite Element Method analysis. From the generated results it is clear that proposed approach is a very effective tool for solving fairly complicated tasks considering both the accuracy and the time of calculation.

This paper presents a general methodology for the conversion of the sequential evolutionary algorithms into parallel evolutionary algorithms using MPI. The methodology is showed by applying it to a combinatorial optimization problem well-known as Water Distribution Networks. Also a comparison of two parallelization approaches is done, showing the advantages and disadvantages of each approach. The implementation of this parallel algorithm reduces the necessary time to obtain good solutions for NP-Complete problems as Water Distribution Networks.

Analysis of speedups in parallel evolutionary algorithms and [formula omitted] EAs for combinatorial optimization

This work presents sequential and parallel evolutionary algorithms (EAs) applied to the scheduling problem in heterogeneous computing environments, a NP-hard problem with capital relevance in distributed computing. These methods have been specifically designed to provide accurate and efficient solutions by using simple operators that allow them to be later extended for solving realistic problem instances arising in distributed heterogeneous computing (HC) and grid systems. The EAs were codified over MALLBA, a general-purpose library for combinatorial optimization. Efficient numerical results are reported in the experimental analysis performed on well-known problem instances. The comparative study of scheduling methods shows that the parallel versions of the implemented evolutionary algorithms are able to achieve high problem solving efficacy, outperforming traditional scheduling heuristics and also improving over previous results already reported in the related literature.

This paper proposes Extreme Learning Surrogate assisted Asynchronous Multi-Objective Optimization Based on Decomposition (AELMOEA/D) that solves multi-objective optimization problems with expensive and different evaluation time by integrating a surrogate evaluation model and an asynchronous evolution method. Extreme Learning Surrogate assisted Multi-Objective Optimization Based on Decomposition (ELMOEA/D), which is a surrogate-assisted MOEA/D, was proposed to reduce the number of actual evaluations, while asynchronous evolution methods were proposed to reduce the waiting time for evaluation of solutions in a parallel evolutionary algorithm. This paper employs ELMOEA/D as a surrogate assisted EA and introduces an asynchronous manner into it. Our experiment proves that our proposed AELMOEA/D can obtain optimal solutions faster than ELMOEA/D without performance deterioration.

In this paper a parallel evolutionary algorithm (PEA) for coloring graph vertices is investigated. In the algorithm we apply a diffusion model of parallelism (DM). Evolutionary computations are performed in a regular mesh with either a constant size global population or a constant subpopulation in a single node. The performance of the PEA-DM is verified by computer experiments on standard DIMACS graph coloring instances. For recombination well known crossover and mutation operators are chosen. Selection mechanisms include standard roulette and tournament. The results obtained by PEA-DM are compared with a classical evolutionary algorithm. It is possible to define dimensions of the rectangular mesh and two types of additional local connections: boundary enclosures (cyclic mesh) and diagonal links. The problem of optimal selection of the mesh configuration as well as global population and subpopulation sizes is adressed.

This article presents the application of a parallel evolutionary algorithm implemented in both CPU and Graphic Processing Units (GPU), to solve large instances of the noisy OneMax problem with up to one billion variables. Actually, new GPU platforms provide the computing power needed to apply massively parallel strategies to solve large problems. We report here the experimental evaluation of both CPU and GPU implementations for a compact evolutionary algorithm. the proposed method demonstrates a high problem solving efficacy and shows a good scalability behavior when facing high dimension instances of the noisy OneMax problem, improving the computational efficiency and the results reported in previous similar approaches developed on CPU.

Evolutionary Algorithms are good optimizing agents that use the evolutionary concepts to evolve systems. The complex fitness landscapes are a problem that restricts the performance of these algorithms. Besides specifying the correct parameter is always very important. In this chapter we study the means by which we can execute a number of evolutionary algorithms in a variety of models to give an overall optimal performance to the entire network. We first discuss the Island Model Algorithm where the individuals are evolved in multiple islands with regular interaction. We then study a related algorithm called the Hierarchical Fair Competition algorithm. Here we would separate the various individuals into classes as per their fitness values. Each of these would have a separate evolution. We would then discuss the Nested Evolutionary Strategies where we fix the parameters of an Evolutionary Strategy by some technique. Towards the end we discuss the Hybrid Genetic Algorithm Particle Swarm Optimization. This algorithm generates individuals by twin usage of Genetic Algorithm and Particle Swarm Optimization.

In this article, evolutionary algorithms (EAs) are applied to solve the radio network design problem (RND). The task is to find the best set of transmitter locations in order to cover a given geographical region at an optimal cost. Usually, parallel EAs are needed to cope with the high computational requirements of such a problem. Here, we develop and evaluate a set of sequential and parallel genetic algorithms (GAs) to solve the RND problem efficiently. The results show that our distributed steady state GA is an efficient and accurate tool for solving RND that even outperforms existing parallel solutions. The sequential algorithm performs very efficiently from a numerical point of view, although the distributed version is much faster.

The task planning of satellite-ground time synchronization (SGTSTP) is a complex many-objective ground station scheduling problem. In this paper, we first provide a mathematical formulation of SGTSTP. To solve this problem, we propose a decomposition-and-integration (DI) based method. In DI method, the plan horizon is evenly divided into many disjoint plan periods and all time windows are distributed to each period, based on which the task planning problem turns into a multi-period 0-1 programming problem. Then we embed DI method into evolutionary algorithm framework and propose DI based evolutionary many-objective algorithm (DI-EMOA). At last, the computational results show that the DI-EMOAs have obvious performance promotion compared with heuristic algorithm.

One of the recent significant but challenging research studies in computational biology and bioinformatics is to unveil protein complexes from protein-protein interaction networks (PPINs). However, the development of a reliable algorithm to detect more complexes with high quality is still ongoing in many studies. The main contribution of this paper is to improve the effectiveness of the well-known modularity density ( ) model when used as a single objective optimization function in the framework of the canonical evolutionary algorithm (EA). To this end, the design of the EA is modified with a gene ontology-based mutation operator, where the aim is to make a positive collaboration between the modularity density model and the proposed gene ontology-based mutation operator. The performance of the proposed EA to have a high quantity and quality of the detected complexes is assessed on two yeast PPINs and compared with two benchmarking gold complex sets. The reported results reveal the ability of modularity density to be more productive in detecting more complexes with high quality when teamed up with a gene ontology-based mutation operator.

The theory of evolutionary computation (EC) has experienced rapid and productive growth in recent years. New proof techniques and novel theoretical frameworks have allowed advances in our understanding of the processes and structures inherent in evolutionary optimization. As a result, the frontiers of our knowledge have been expanded further than ever before. Some recent trends in this field, which are covered in this issue, include developments in the understanding of the behavior of evolutionary algorithms (EAs) in dynamic environments rather than just static settings, a theoretical appreciation of the advantages arising from the parallelization of evolutionary algorithms through a greater comprehension of the underlying dynamics, and an understanding of algorithm behavior on broad function classes, including -hard problems.The primary goal of this special issue is to provide extended and polished versions of diverse examples of the best theoretical work presented at conferences in 2014, and to serve as a forum for researchers to advance the theoretical understanding of evolutionary computation methods. The papers included in this special issue span a plurality of topics and offer the reader a cross section of recent outstanding work in EC theory.In dynamic optimization the objective function changes over time, and optimization algorithms face the additional challenge of tracking these changes to be successful. The article “Analysis of Randomised Search Heuristics for Dynamic Optimisation,” by Thomas Jansen and Christine Zarges, presents a novel analytical framework for the analysis of randomized search heuristics on dynamic problems inspired by the fixed-budget computations perspective. The authors introduce a new interesting class of bi-stable dynamic functions where the optimum oscillates between two complementary strings, and apply the framework to analyze and compare the performance of evolutionary algorithms and artificial immune systems on the novel class of functions.Over three decades ago, László Lovász observed that in discrete optimization, submodularity is the counterpart to convexity. However, in contrast to the focus on convex functions in continuous evolutionary optimization, so far submodular functions have received comparatively little attention from EC theoreticians studying discrete functions. The article “Maximizing Submodular Functions under Matroid Constraints by Evolutionary Algorithms,” by Tobias Friedrich and Frank Neumann, addresses this gap by analyzing the performance of evolutionary algorithms on different classes of submodular functions. The maximization of submodular functions is -hard in general, and the authors present several approximation results for monotone submodular and nonmonotone symmetric submodular functions under different kinds of matroid constraints.The idea behind parallel evolutionary algorithms is to evolve multiple subpopulations in parallel and allow interprocess communication at given time intervals. During these migration phases, fractions of each subpopulation can be shared among the subpopulations. There is very little understanding of how the migration frequency affects algorithmic performance, so setting the migration interval parameter appropriately may be difficult. In the article “Design and Analysis of Schemes for Adapting Migration Intervals in Parallel Evolutionary Algorithms,” Andrea Mambrini and Dirk Sudholt propose two schemes to automatically adapt the migration interval of parallel EAs during execution and provide a rigorous analytical framework that yields upper bounds on the expected runtime and expected communication effort of the parallel EAs with different migration topologies for various function classes.In the field of genetic programming, a long-standing open problem is how to address the issue of bloat, the emergence during evolution of solution elements that do not contribute significantly or at all to program fitness or semantics but increase program complexity. The article “On the Performance of Different Genetic Programming Approaches for the SORTING Problem,” by Markus Wagner, Frank Neumann, and Tommaso Urli, tackles the issue of bloat control in the context of sorting. As a basis for their study, they consider program trees and use some measure of sortedness of an in-order traversal to evaluate their fitness. The authors investigate single- and multiobjective variants of genetic programming algorithms with and without bloat control mechanisms, give rigorous upper bounds on their running times, and complement the study with experiments.The topic of constraint handling has recently gained traction in the continuous domain. The article “Markov Chain Analysis of Cumulative Step-Size Adaptation on a Linear Constrained Problem,” by Alexandre Chotard, Anne Auger, and Nikolaus Hansen, presents a rigorous analysis of a (1,)-Evolution Strategy using resampling on a linear function with a linear constraint. The authors prove the previously assumed property that a Markov chain, describing the behavior of the algorithm, exhibits stability in cases with constant step-size and with cumulative step-size adaptation with cumulation parameter equal to 1. This property characterizes the divergence of the algorithm with constant step-size and the geometric divergence or convergence with step-size adaptation, implying fast convergence of Monte Carlo simulations of the divergence rate.In their seminal 2006 paper, Droste, Jansen, and Wegener introduced the concept of black box complexity in order to establish a complexity theory for general-purpose randomized search heuristics. Generally speaking, the black box complexity of a problem is a lower bound on the number of function evaluations needed by any black box algorithm to solve it. Recently, black box models have been refined and developed extensively, allowing the hardness of objective function classes to be more precisely understood. The article “Unbiased Black Box Complexities of Jump Functions,” by Benjamin Doerr, Carola Doerr, and Timo Kötzing, analyzes the unbiased black box complexity of a Jump function class where in each function a local optimum is k bits in distance from the global optimum. The authors provide polynomial upper bounds on the black box complexity of Jump for different sizes of the gap. In particular, they show that an unbiased polynomial-time black box algorithm exists even when almost all of the search space is a plateau of constant fitness.The guest editors would like to thank the authors for their contributions, the referees for their careful reviewing and constructive comments, and the editor-in-chief, Hans-Georg Beyer, for his support in preparing this special issue.

How to discover high-level knowledge modeled by complicated functions, ordinary differential equations and difference equations in databases automatically is a very important and difficult task in KDD research. In this paper, high-level knowledge modeled by ordinary differential equations (ODEs) is discovered in dynamic data automatically by an asynchronous parallel evolutionary modeling algorithm (APHEMA). A numerical example is used to demonstrate the potential of APEA. The results show that the dynamic models discovered automatically in dynamic data by computer sometimes can compare with the models discovered by human.