Evolutionary Multi-Objective Design of SARS-CoV-2 Protease Inhibitor Candidates

Computational drug design based on artificial intelligence is an emerging research area. At the time of writing this paper, the world suffers from an outbreak of the coronavirus SARS-CoV-2. A promising way to stop the virus replication is via protease inhibition. We propose an evolutionary multi-objective algorithm (EMOA) to design potential protease inhibitors for SARS-CoV-2's main protease. Based on the SELFIES representation the EMOA maximizes the binding of candidate ligands to the protein using the docking tool QuickVina 2, while at the same time taking into account further objectives like drug-likeliness or the fulfillment of filter constraints. The experimental part analyzes the evolutionary process and discusses the inhibitor candidates.Comment: 15 pages, 7 figures, submitted to PPSN 202

Metaheuristic design of feedforward neural networks: a review of two decades of research

Over the past two decades, the feedforward neural network (FNN) optimization has been a key interest among the researchers and practitioners of multiple disciplines. The FNN optimization is often viewed from the various perspectives: the optimization of weights, network architecture, activation nodes, learning parameters, learning environment, etc. Researchers adopted such different viewpoints mainly to improve the FNN's generalization ability. The gradient-descent algorithm such as backpropagation has been widely applied to optimize the FNNs. Its success is evident from the FNN's application to numerous real-world problems. However, due to the limitations of the gradient-based optimization methods, the metaheuristic algorithms including the evolutionary algorithms, swarm intelligence, etc., are still being widely explored by the researchers aiming to obtain generalized FNN for a given problem. This article attempts to summarize a broad spectrum of FNN optimization methodologies including conventional and metaheuristic approaches. This article also tries to connect various research directions emerged out of the FNN optimization practices, such as evolving neural network (NN), cooperative coevolution NN, complex-valued NN, deep learning, extreme learning machine, quantum NN, etc. Additionally, it provides interesting research challenges for future research to cope-up with the present information processing era

Controller tuning by means of evolutionary multiobjective optimization: current trends and applications

Control engineering problems are generally multi-objective problems; meaning that there are several specifications and requirements that must be fulfilled. A traditional approach for calculating a solution with the desired trade-off is to define an optimisation statement. Multi-objective optimisation techniques deal with this problem from a particular perspective and search for a set of potentially preferable solutions; the designer may then analyse the trade-offs among them, and select the best solution according to his/her preferences. In this paper, this design procedure based on evolutionary multiobjective optimisation (EMO) is presented and significant applications on controller tuning are discussed. Throughout this paper it is noticeable that EMO research has been developing towards different optimisation statements, but these statements are not commonly used in controller tuning. Gaps between EMO research and EMO applications on controller tuning are therefore detected and suggested as potential trends for research.The first author is grateful for the hospitality and availability of the UTC at the University of Sheffield during his academic research stay at 2011; especially to Dr. P.J. Fleming for his valuable comments and insights in the development of this paper. This work was partially supported by Grant FPI-2010/19 and project PAID-2011/2732 from the Universitat Politecnica de Valencia and projects TIN2011-28082 and ENE2011-25900 from the Spanish Ministry of Economy and Competitiveness.Reynoso Meza, G.; Blasco Ferragud, FX.; Sanchís Saez, J.; Martínez Iranzo, MA. (2014). Controller tuning by means of evolutionary multiobjective optimization: current trends and applications. Control Engineering Practice. 28:58-73. https://doi.org/10.1016/j.conengprac.2014.03.003S58732

Advances and applications in high-dimensional heuristic optimization

“Applicable to most real-world decision scenarios, multiobjective optimization is an area of multicriteria decision-making that seeks to simultaneously optimize two or more conflicting objectives. In contrast to single-objective scenarios, nontrivial multiobjective optimization problems are characterized by a set of Pareto optimal solutions wherein no solution unanimously optimizes all objectives. Evolutionary algorithms have emerged as a standard approach to determine a set of these Pareto optimal solutions, from which a decision-maker can select a vetted alternative. While easy to implement and having demonstrated great efficacy, these evolutionary approaches have been criticized for their runtime complexity when dealing with many alternatives or a high number of objectives, effectively limiting the range of scenarios to which they may be applied. This research introduces mechanisms to improve the runtime complexity of many multiobjective evolutionary algorithms, achieving state-of-the-art performance, as compared to many prominent methods from the literature. Further, the investigations here presented demonstrate the capability of multiobjective evolutionary algorithms in a complex, large-scale optimization scenario. Showcasing the approach’s ability to intelligently generate well-performing solutions to a meaningful optimization problem. These investigations advance the concept of multiobjective evolutionary algorithms by addressing a key limitation and demonstrating their efficacy in a challenging real-world scenario. Through enhanced computational efficiency and exhibited specialized application, the utility of this powerful heuristic strategy is made more robust and evident”--Abstract, page iv

On green routing and scheduling problem

The vehicle routing and scheduling problem has been studied with much interest within the last four decades. In this paper, some of the existing literature dealing with routing and scheduling problems with environmental issues is reviewed, and a description is provided of the problems that have been investigated and how they are treated using combinatorial optimization tools

A System for Accessible Artificial Intelligence

While artificial intelligence (AI) has become widespread, many commercial AI systems are not yet accessible to individual researchers nor the general public due to the deep knowledge of the systems required to use them. We believe that AI has matured to the point where it should be an accessible technology for everyone. We present an ongoing project whose ultimate goal is to deliver an open source, user-friendly AI system that is specialized for machine learning analysis of complex data in the biomedical and health care domains. We discuss how genetic programming can aid in this endeavor, and highlight specific examples where genetic programming has automated machine learning analyses in previous projects.Comment: 14 pages, 5 figures, submitted to Genetic Programming Theory and Practice 2017 worksho

A Practical Guide to Multi-Objective Reinforcement Learning and Planning

Real-world decision-making tasks are generally complex, requiring trade-offs between multiple, often conflicting, objectives. Despite this, the majority of research in reinforcement learning and decision-theoretic planning either assumes only a single objective, or that multiple objectives can be adequately handled via a simple linear combination. Such approaches may oversimplify the underlying problem and hence produce suboptimal results. This paper serves as a guide to the application of multi-objective methods to difficult problems, and is aimed at researchers who are already familiar with single-objective reinforcement learning and planning methods who wish to adopt a multi-objective perspective on their research, as well as practitioners who encounter multi-objective decision problems in practice. It identifies the factors that may influence the nature of the desired solution, and illustrates by example how these influence the design of multi-objective decision-making systems for complex problems