Bio-inspired computation: where we stand and what's next

In recent years, the research community has witnessed an explosion of literature dealing with the adaptation of behavioral patterns and social phenomena observed in nature towards efficiently solving complex computational tasks. This trend has been especially dramatic in what relates to optimization problems, mainly due to the unprecedented complexity of problem instances, arising from a diverse spectrum of domains such as transportation, logistics, energy, climate, social networks, health and industry 4.0, among many others. Notwithstanding this upsurge of activity, research in this vibrant topic should be steered towards certain areas that, despite their eventual value and impact on the field of bio-inspired computation, still remain insufficiently explored to date. The main purpose of this paper is to outline the state of the art and to identify open challenges concerning the most relevant areas within bio-inspired optimization. An analysis and discussion are also carried out over the general trajectory followed in recent years by the community working in this field, thereby highlighting the need for reaching a consensus and joining forces towards achieving valuable insights into the understanding of this family of optimization techniques

Bio-inspired computation: where we stand and what's next

In recent years, the research community has witnessed an explosion of literature dealing with the adaptation of behavioral patterns and social phenomena observed in nature towards efficiently solving complex computational tasks. This trend has been especially dramatic in what relates to optimization problems, mainly due to the unprecedented complexity of problem instances, arising from a diverse spectrum of domains such as transportation, logistics, energy, climate, social networks, health and industry 4.0, among many others. Notwithstanding this upsurge of activity, research in this vibrant topic should be steered towards certain areas that, despite their eventual value and impact on the field of bio-inspired computation, still remain insufficiently explored to date. The main purpose of this paper is to outline the state of the art and to identify open challenges concerning the most relevant areas within bio-inspired optimization. An analysis and discussion are also carried out over the general trajectory followed in recent years by the community working in this field, thereby highlighting the need for reaching a consensus and joining forces towards achieving valuable insights into the understanding of this family of optimization techniques

A Comprehensive Survey on Particle Swarm Optimization Algorithm and Its Applications

Particle swarm optimization (PSO) is a heuristic global optimization method, proposed originally by Kennedy and Eberhart in 1995. It is now one of the most commonly used optimization techniques. This survey presented a comprehensive investigation of PSO. On one hand, we provided advances with PSO, including its modifications (including quantum-behaved PSO, bare-bones PSO, chaotic PSO, and fuzzy PSO), population topology (as fully connected, von Neumann, ring, star, random, etc.), hybridization (with genetic algorithm, simulated annealing, Tabu search, artificial immune system, ant colony algorithm, artificial bee colony, differential evolution, harmonic search, and biogeography-based optimization), extensions (to multiobjective, constrained, discrete, and binary optimization), theoretical analysis (parameter selection and tuning, and convergence analysis), and parallel implementation (in multicore, multiprocessor, GPU, and cloud computing forms). On the other hand, we offered a survey on applications of PSO to the following eight fields: electrical and electronic engineering, automation control systems, communication theory, operations research, mechanical engineering, fuel and energy, medicine, chemistry, and biology. It is hoped that this survey would be beneficial for the researchers studying PSO algorithms

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

Reducing the Size of Combinatorial Optimization Problems Using the Operator Vaccine by Fuzzy Selector with Adaptive Heuristics

Nowadays, solving optimally combinatorial problems is an open problem. Determining the best arrangement of elements proves being a very complex task that becomes critical when the problem size increases. Researchers have proposed various algorithms for solving Combinatorial Optimization Problems (COPs) that take into account the scalability; however, issues are still presented with larger COPs concerning hardware limitations such as memory and CPU speed. It has been shown that the Reduce-Optimize-Expand (ROE) method can solve COPs faster with the same resources; in this methodology, the reduction step is the most important procedure since inappropriate reductions, applied to the problem, will produce suboptimal results on the subsequent stages. In this work, an algorithm to improve the reduction step is proposed. It is based on a fuzzy inference system to classify portions of the problem and remove them, allowing COPs solving algorithms to utilize better the hardware resources by dealing with smaller problem sizes, and the use of metadata and adaptive heuristics. The Travelling Salesman Problem has been used as a case of study; instances that range from 343 to 3056 cities were used to prove that the fuzzy logic approach produces a higher percentage of successful reductions

Bioinformatics Applications Based On Machine Learning

The great advances in information technology (IT) have implications for many sectors, such as bioinformatics, and has considerably increased their possibilities. This book presents a collection of 11 original research papers, all of them related to the application of IT-related techniques within the bioinformatics sector: from new applications created from the adaptation and application of existing techniques to the creation of new methodologies to solve existing problems

Benchmarking B-Cell Epitope Prediction for the Design of Peptide-Based Vaccines: Problems and Prospects

To better support the design of peptide-based vaccines, refinement of methods to predict B-cell epitopes necessitates meaningful benchmarking against empirical data on the cross-reactivity of polyclonal antipeptide antibodies with proteins, such that the positive data reflect functionally relevant cross-reactivity (which is consistent with antibody-mediated change in protein function) and the negative data reflect genuine absence of cross-reactivity (rather than apparent absence of cross-reactivity due to artifactual masking of B-cell epitopes in immunoassays). These data are heterogeneous in view of multiple factors that complicate B-cell epitope prediction, notably physicochemical factors that define key structural differences between immunizing peptides and their cognate proteins (e.g., unmatched electrical charges along the peptide-protein sequence alignments). If the data are partitioned with respect to these factors, iterative parallel benchmarking against the resulting subsets of data provides a basis for systematically identifying and addressing the limitations of methods for B-cell epitope prediction as applied to vaccine design

Optimization Algorithm Based on Novelty Search Applied to the Treatment of Uncertainty in Models

[ES] La búsqueda novedosa es un nuevo paradigma de los algoritmos de optimización, evolucionarios y bioinspirados, que está basado en la idea de forzar la búsqueda del óptimo global en aquellas partes inexploradas del dominio de la función que no son atractivas para el algoritmo, con la intención de evitar estancamientos en óptimos locales. La búsqueda novedosa se ha aplicado al algoritmo de optimización de enjambre de partículas, obteniendo un nuevo algoritmo denominado algoritmo de enjambre novedoso (NS). NS se ha aplicado al conjunto de pruebas sintéticas CEC2005, comparando los resultados con los obtenidos por otros algoritmos del estado del arte. Los resultados muestran un mejor comportamiento de NS en funciones altamente no lineales, a cambio de un aumento en la complejidad computacional. En lo que resta de trabajo, el algoritmo NS se ha aplicado en diferentes modelos, específicamente en el diseño de un motor de combustión interna, en la estimación de demanda de energía mediante gramáticas de enjambre, en la evolución del cáncer de vejiga de un paciente concreto y en la evolución del COVID-19. Cabe remarcar que, en el estudio de los modelos de COVID-19, se ha tenido en cuenta la incertidumbre, tanto de los datos como de la evolución de la enfermedad.[CA] La cerca nova és un nou paradigma dels algoritmes d'optimització, evolucionaris i bioinspirats, que està basat en la idea de forçar la cerca de l'òptim global en les parts inexplorades del domini de la funció que no són atractives per a l'algoritme, amb la intenció d'evitar estancaments en òptims locals. La cerca nova s'ha aplicat a l'algoritme d'optimització d'eixam de partícules, obtenint un nou algoritme denominat algoritme d'eixam nou (NS). NS s'ha aplicat al conjunt de proves sintètiques CEC2005, comparant els resultats amb els obtinguts per altres algoritmes de l'estat de l'art. Els resultats mostren un millor comportament de NS en funcions altament no lineals, a canvi d'un augment en la complexitat computacional. En el que resta de treball, l'algoritme NS s'ha aplicat en diferents models, específicament en el disseny d'un motor de combustió interna, en l'estimació de demanda d'energia mitjançant gramàtiques d'eixam, en l'evolució del càncer de bufeta d'un pacient concret i en l'evolució del COVID-19. Cal remarcar que, en l'estudi dels models de COVID-19, s'ha tingut en compte la incertesa, tant de les dades com de l'evolució de la malaltia.[EN] Novelty Search is a recent paradigm in evolutionary and bio-inspired optimization algorithms, based on the idea of forcing to look for those unexplored parts of the domain of the function that might be unattractive for the algorithm, with the aim of avoiding stagnation in local optima. Novelty Search has been applied to the Particle Swarm Optimization algorithm, obtaining a new algorithm named Novelty Swarm (NS). NS has been applied to the CEC2005 benchmark, comparing its results with other state of the art algorithms. The results show better behaviour in high nonlinear functions at the cost of increasing the computational complexity. During the rest of the thesis, the NS algorithm has been used in different models, specifically the design of an Internal Combustion Engine, the prediction of energy demand estimation with Grammatical Swarm, the evolution of the bladder cancer of a specific patient and the evolution of COVID-19. It is also remarkable that, in the study of COVID-19 models, uncertainty of the data and the evolution of the disease has been taken in account.Martínez Rodríguez, D. (2021). Optimization Algorithm Based on Novelty Search Applied to the Treatment of Uncertainty in Models [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/17899

2017 EURēCA Abstract Book

Listing of student participant abstracts