Seeking multiple solutions:an updated survey on niching methods and their applications

Multi-Modal Optimization (MMO) aiming to locate multiple optimal (or near-optimal) solutions in a single simulation run has practical relevance to problem solving across many fields. Population-based meta-heuristics have been shown particularly effective in solving MMO problems, if equipped with specificallydesigned diversity-preserving mechanisms, commonly known as niching methods. This paper provides an updated survey on niching methods. The paper first revisits the fundamental concepts about niching and its most representative schemes, then reviews the most recent development of niching methods, including novel and hybrid methods, performance measures, and benchmarks for their assessment. Furthermore, the paper surveys previous attempts at leveraging the capabilities of niching to facilitate various optimization tasks (e.g., multi-objective and dynamic optimization) and machine learning tasks (e.g., clustering, feature selection, and learning ensembles). A list of successful applications of niching methods to real-world problems is presented to demonstrate the capabilities of niching methods in providing solutions that are difficult for other optimization methods to offer. The significant practical value of niching methods is clearly exemplified through these applications. Finally, the paper poses challenges and research questions on niching that are yet to be appropriately addressed. Providing answers to these questions is crucial before we can bring more fruitful benefits of niching to real-world problem solving

The application of multiobjective optimisation to protein-ligand docking

Despite the intense efforts that have been devoted to the development of scoring functions for protein-ligand docking, they are still limited in their ability to identify the correct binding pose of a ligand within a protein binding site. A deeper understanding of the intricacies of scoring functions is therefore essential in order to develop these effectively. The aim of the work described in this thesis is to analyse the individual interaction energy types which form the individual components of a force field-based scoring function. To do this, & protein-ligand docking algorithm that is based on multiobjective optimisation has been developed. Multiobjective optimisation allows for the optimisation of several objectives simultaneously and this has been applied to the individual interaction energy types of the GRID scoring function. Traditionally these interaction energy types are summed together and the total energy is used to guide the search. By using individual energy types during optimisation, their roles can be better understood. The interaction energy types that have been used here are the electrostatic and hydrogen bond interactions combined, and van der Waals interactions. The algorithm is first tested on two datasets containing twenty complexes. The results show that the different interaction energy types have varying influences when it comes to successfully docking certain complexes, and that it is important to fmd the right balance of interaction energy types so as to find correct solutions. Ofthe twenty complexes, the algorithm found correct solutions for fifteen. To improve the performance of the algorithm, a few enhancements were introduced. This includes a simplex minimisation process with a Lamarckian element. The algorithm was retested on the twenty complexes, and the newer version was found to outperform the original version, finding correct solutions for seventeen of the twenty complexes. To extensively study the capabilities of the algorithm, it was tested on varied datasets, including the FlexX dataset. The algoritlun's performance was also compared to a single-objective docking tool, Q-fit. The comparison betw~en the multiobjective and single-objective methodologies revealed that single-objective methods can sometimes fail at finding correct docked solutions because they are unable to correctly balance the interaction energy types comprising a scoring function. The study also showed that a multiobjective optimisation method can reveal the reasons why a given docking algorithm may fail at fmding a correct solution. Finally, the algorithm was extended to incorporate desolvation energy as a third objective. Though these results are preliminary, they revealed some interesting relationships between the different objectives.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Multi-and many-objective optimization: present and future in de novo drug design

de novo Drug Design (dnDD) aims to create new molecules that satisfy multiple conflicting objectives. Since several desired properties can be considered in the optimization process, dnDD is naturally categorized as a many-objective optimization problem (ManyOOP), where more than three objectives must be simultaneously optimized. However, a large number of objectives typically pose several challenges that affect the choice and the design of optimization methodologies. Herein, we cover the application of multi- and many-objective optimization methods, particularly those based on Evolutionary Computation and Machine Learning techniques, to enlighten their potential application in dnDD. Additionally, we comprehensively analyze how molecular properties used in the optimization process are applied as either objectives or constraints to the problem. Finally, we discuss future research in many-objective optimization for dnDD, highlighting two important possible impacts: i) its integration with the development of multi-target approaches to accelerate the discovery of innovative and more efficacious drug therapies and ii) its role as a catalyst for new developments in more fundamental and general methodological frameworks in the field

Evolutionary Computation

This book presents several recent advances on Evolutionary Computation, specially evolution-based optimization methods and hybrid algorithms for several applications, from optimization and learning to pattern recognition and bioinformatics. This book also presents new algorithms based on several analogies and metafores, where one of them is based on philosophy, specifically on the philosophy of praxis and dialectics. In this book it is also presented interesting applications on bioinformatics, specially the use of particle swarms to discover gene expression patterns in DNA microarrays. Therefore, this book features representative work on the field of evolutionary computation and applied sciences. The intended audience is graduate, undergraduate, researchers, and anyone who wishes to become familiar with the latest research work on this field

Evolution strategies for robust optimization

Real-world (black-box) optimization problems often involve various types of uncertainties and noise emerging in different parts of the optimization problem. When this is not accounted for, optimization may fail or may yield solutions that are optimal in the classical strict notion of optimality, but fail in practice. Robust optimization is the practice of optimization that actively accounts for uncertainties and/or noise. Evolutionary Algorithms form a class of optimization algorithms that use the principle of evolution to find good solutions to optimization problems. Because uncertainty and noise are indispensable parts of nature, this class of optimization algorithms seems to be a logical choice for robust optimization scenarios. This thesis provides a clear definition of the term robust optimization and a comparison and practical guidelines on how Evolution Strategies, a subclass of Evolutionary Algorithms for real-parameter optimization problems, should be adapted for such scenarios.UBL - phd migration 201

A complex systems approach to education in Switzerland

The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance

Proceedings of the XIII Global Optimization Workshop: GOW'16

[Excerpt] Preface: Past Global Optimization Workshop shave been held in Sopron (1985 and 1990), Szeged (WGO, 1995), Florence (GO’99, 1999), Hanmer Springs (Let’s GO, 2001), Santorini (Frontiers in GO, 2003), San José (Go’05, 2005), Mykonos (AGO’07, 2007), Skukuza (SAGO’08, 2008), Toulouse (TOGO’10, 2010), Natal (NAGO’12, 2012) and Málaga (MAGO’14, 2014) with the aim of stimulating discussion between senior and junior researchers on the topic of Global Optimization. In 2016, the XIII Global Optimization Workshop (GOW’16) takes place in Braga and is organized by three researchers from the University of Minho. Two of them belong to the Systems Engineering and Operational Research Group from the Algoritmi Research Centre and the other to the Statistics, Applied Probability and Operational Research Group from the Centre of Mathematics. The event received more than 50 submissions from 15 countries from Europe, South America and North America. We want to express our gratitude to the invited speaker Panos Pardalos for accepting the invitation and sharing his expertise, helping us to meet the workshop objectives. GOW’16 would not have been possible without the valuable contribution from the authors and the International Scientific Committee members. We thank you all. This proceedings book intends to present an overview of the topics that will be addressed in the workshop with the goal of contributing to interesting and fruitful discussions between the authors and participants. After the event, high quality papers can be submitted to a special issue of the Journal of Global Optimization dedicated to the workshop. [...

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Products and Services

Today’s global economy offers more opportunities, but is also more complex and competitive than ever before. This fact leads to a wide range of research activity in different fields of interest, especially in the so-called high-tech sectors. This book is a result of widespread research and development activity from many researchers worldwide, covering the aspects of development activities in general, as well as various aspects of the practical application of knowledge