Cooperative Coevolution for Non-Separable Large-Scale Black-Box Optimization: Convergence Analyses and Distributed Accelerations

Given the ubiquity of non-separable optimization problems in real worlds, in this paper we analyze and extend the large-scale version of the well-known cooperative coevolution (CC), a divide-and-conquer optimization framework, on non-separable functions. First, we reveal empirical reasons of why decomposition-based methods are preferred or not in practice on some non-separable large-scale problems, which have not been clearly pointed out in many previous CC papers. Then, we formalize CC to a continuous game model via simplification, but without losing its essential property. Different from previous evolutionary game theory for CC, our new model provides a much simpler but useful viewpoint to analyze its convergence, since only the pure Nash equilibrium concept is needed and more general fitness landscapes can be explicitly considered. Based on convergence analyses, we propose a hierarchical decomposition strategy for better generalization, as for any decomposition there is a risk of getting trapped into a suboptimal Nash equilibrium. Finally, we use powerful distributed computing to accelerate it under the multi-level learning framework, which combines the fine-tuning ability from decomposition with the invariance property of CMA-ES. Experiments on a set of high-dimensional functions validate both its search performance and scalability (w.r.t. CPU cores) on a clustering computing platform with 400 CPU cores

Composite Differential Evolution for Constrained Evolutionary Optimization

When solving constrained optimization problems (COPs) by evolutionary algorithms, the search algorithm plays a crucial role. In general, we expect that the search algorithm has the capability to balance not only diversity and convergence but also constraints and objective function during the evolution. For this purpose, this paper proposes a composite differential evolution (DE) for constrained optimization, which includes three different trial vector generation strategies with distinct advantages. In order to strike a balance between diversity and convergence, one of these three trial vector generation strategies is able to increase diversity, and the other two exhibit the property of convergence. In addition, to accomplish the tradeoff between constraints and objective function, one of the two trial vector generation strategies for convergence is guided by the individual with the least degree of constraint violation in the population, and the other is guided by the individual with the best objective function value in the population. After producing offspring by the proposed composite DE, the feasibility rule and the ϵ constrained method are combined elaborately for selection in this paper. Moreover, a restart scheme is proposed to help the population jump out of a local optimum in the infeasible region for some extremely complicated COPs. By assembling the above techniques together, a constrained composite DE is proposed. The experiments on two sets of benchmark test functions with various features, i.e., 24 test functions from IEEE CEC2006 and 18 test functions with 10 dimensions and 30 dimensions from IEEE CEC2010, have demonstrated that the proposed method shows better or at least competitive performance against other state-of-the-art methods

ABOUT THE COMPLEXITY OF LIVING SYSTEMS MODELS

In this paper we attempt an overview of the philosophical implications of complex systems thought, and investigate how this alternative viewpoint affects our attempts to design and utilise models for living systems. We classify the types of complex system that relate to self-organisation. The overall requirements for self-organising modeling are considered and some alternative ways of looking at some specific problems that may arise are explored. As a novelty, the paper proposes various ways of moving forward in the area of practical model design.complex systems, models, practical desing

`The frozen accident' as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms

We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks. The approach to most of these questions involves using elements of Shannon's rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure in proteins. This leads to the suggestion that the frozen accident may have been a type of evolutionary adaptation

DECMO2: a robust hybrid and adaptive multi-objective evolutionary algorithm.

We describe a hybrid and adaptive coevolutionary optimization method that can efficiently solve a wide range of multi-objective optimization problems (MOOPs) as it successfully combines positive traits from three main classes of multi-objective evolutionary algorithms (MOEAs): classical approaches that use Pareto-based selection for survival criteria, approaches that rely on differential evolution, and decomposition-based strategies. A key part of our hybrid evolutionary approach lies in the proposed fitness sharing mechanism that is able to smoothly transfer information between the coevolved subpopulations without negatively impacting the specific evolutionary process behavior that characterizes each subpopulation. The proposed MOEA also features an adaptive allocation of fitness evaluations between the coevolved populations to increase robustness and favor the evolutionary search strategy that proves more successful for solving the MOOP at hand. Apart from the new evolutionary algorithm, this paper also contains the description of a new hypervolume and racing-based methodology aimed at providing practitioners from the field of multi-objective optimization with a simple means of analyzing/reporting the general comparative run-time performance of multi-objective optimization algorithms over large problem sets

Integrated Analysis of Residue Coevolution and Protein Structure in ABC Transporters

Intraprotein side chain contacts can couple the evolutionary process of amino acid substitution at one position to that at another. This coupling, known as residue coevolution, may vary in strength. Conserved contacts thus not only define 3-dimensional protein structure, but also indicate which residue-residue interactions are crucial to a protein’s function. Therefore, prediction of strongly coevolving residue-pairs helps clarify molecular mechanisms underlying function. Previously, various coevolution detectors have been employed separately to predict these pairs purely from multiple sequence alignments, while disregarding available structural information. This study introduces an integrative framework that improves the accuracy of such predictions, relative to previous approaches, by combining multiple coevolution detectors and incorporating structural contact information. This framework is applied to the ABC-B and ABC-C transporter families, which include the drug exporter P-glycoprotein involved in multidrug resistance of cancer cells, as well as the CFTR chloride channel linked to cystic fibrosis disease. The predicted coevolving pairs are further analyzed based on conformational changes inferred from outward- and inward-facing transporter structures. The analysis suggests that some pairs coevolved to directly regulate conformational changes of the alternating-access transport mechanism, while others to stabilize rigid-body-like components of the protein structure. Moreover, some identified pairs correspond to residues previously implicated in cystic fibrosis

Evolutionary computation for expensive optimization: a survey

Expensive optimization problem (EOP) widely exists in various significant real-world applications. However, EOP requires expensive or even unaffordable costs for evaluating candidate solutions, which is expensive for the algorithm to find a satisfactory solution. Moreover, due to the fast-growing application demands in the economy and society, such as the emergence of the smart cities, the internet of things, and the big data era, solving EOP more efficiently has become increasingly essential in various fields, which poses great challenges on the problem-solving ability of optimization approach for EOP. Among various optimization approaches, evolutionary computation (EC) is a promising global optimization tool widely used for solving EOP efficiently in the past decades. Given the fruitful advancements of EC for EOP, it is essential to review these advancements in order to synthesize and give previous research experiences and references to aid the development of relevant research fields and real-world applications. Motivated by this, this paper aims to provide a comprehensive survey to show why and how EC can solve EOP efficiently. For this aim, this paper firstly analyzes the total optimization cost of EC in solving EOP. Then, based on the analysis, three promising research directions are pointed out for solving EOP, which are problem approximation and substitution, algorithm design and enhancement, and parallel and distributed computation. Note that, to the best of our knowledge, this paper is the first that outlines the possible directions for efficiently solving EOP by analyzing the total expensive cost. Based on this, existing works are reviewed comprehensively via a taxonomy with four parts, including the above three research directions and the real-world application part. Moreover, some future research directions are also discussed in this paper. It is believed that such a survey can attract attention, encourage discussions, and stimulate new EC research ideas for solving EOP and related real-world applications more efficiently