Extending Genetic Algorithms with Biological Life-Cycle Dynamics.

In this paper, we aim to enhance genetic algorithms (GAs) by integrating a dynamic model based on biological life cycles. This study addresses the challenge of maintaining diversity and adaptability in GAs by incorporating stages of birth, growth, reproduction, and death into the algorithm's framework. We consider an asynchronous execution of life cycle stages to individuals in the population, ensuring a steady-state evolution that preserves high-quality solutions while maintaining diversity. Experimental results demonstrate that the proposed extension outperforms traditional GAs and is as good or better than other well-known and well established algorithms like PSO and EvoSpace in various benchmark problems, particularly regarding convergence speed and solution qu/ality. The study concludes that incorporating biological life-cycle dynamics into GAs enhances their robustness and efficiency, offering a promising direction for future research in evolutionary computation.

Evolutionary algorithms guided by Erdos-Rényi complex networks.

This article proposes an evolutionary algorithm integrating Erdos-Rényi complex networks to regulate population crossovers, enhancing candidate solution refinement across generations. In this context, the population is conceptualized as a set of interrelated solutions, resembling a complex network. The algorithm enhances solutions by introducing new connections between them, thereby influencing population dynamics and optimizing the problem-solving process. The study conducts experiments comparing four instances of the traditional optimization problem known as the Traveling Salesman Problem (TSP). These experiments employ the traditional evolutionary algorithm, alternative algorithms utilizing different types of complex networks, and the proposed algorithm. The findings suggest that the approach guided by an Erdos-Rényi dynamic network surpasses the performance of the other algorithms. The proposed model exhibits improved convergence rates and shorter execution times. Thus, strategies based on complex networks reveal that network characteristics provide valuable information for solving optimization problems. Therefore, complex networks can regulate the decision-making process, similar to optimizing problems. This work emphasizes that the network structure is crucial in adding value to decision-making.

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.

Automatic Diagnosis of Diabetic Retinopathy from Fundus Images Using Neuro-Evolutionary Algorithms.

Due to the presence of high glucose levels, diabetes mellitus (DM) is a widespread disease that can damage blood vessels in the retina and lead to loss of the visual system. To combat this disease, called Diabetic Retinopathy (DR), retinography, using images of the fundus of the retina, is the most used method for the diagnosis of Diabetic Retinopathy. The Deep Learning (DL) area achieved high performance for the classification of retinal images and even achieved almost the same human performance in diagnostic tasks. However, the performance of DL architectures is highly dependent on the optimal configuration of the hyperparameters. In this article, we propose the use of Neuroevolutionary Algorithms to optimize the hyperparameters corresponding to the DL model for the diagnosis of DR. The results obtained prove that the proposed method outperforms the results obtained by the classical approach.

VSD-MOEA: A Dominance-Based Multiobjective Evolutionary Algorithm with Explicit Variable Space Diversity Management.

Most state-of-the-art Multiobjective Evolutionary Algorithms (moeas) promote the preservation of diversity of objective function space but neglect the diversity of decision variable space. The aim of this article is to show that explicitly managing the amount of diversity maintained in the decision variable space is useful to increase the quality of moeas when taking into account metrics of the objective space. Our novel Variable Space Diversity-based MOEA (vsd-moea) explicitly considers the diversity of both decision variable and objective function space. This information is used with the aim of properly adapting the balance between exploration and intensification during the optimization process. Particularly, at the initial stages, decisions made by the approach are more biased by the information on the diversity of the variable space, whereas it gradually grants more importance to the diversity of objective function space as the evolution progresses. The latter is achieved through a novel density estimator. The new method is compared with state-of-art moeas using several benchmarks with two and three objectives. This novel proposal yields much better results than state-of-the-art schemes when considering metrics applied on objective function space, exhibiting a more stable and robust behavior.

EvoSeg: Automated Electron Microscopy Segmentation through Random Forests and Evolutionary Optimization.

Electron Microscopy Maps are key in the study of bio-molecular structures, ranging from borderline atomic level to the sub-cellular range. These maps describe the envelopes that cover possibly a very large number of proteins that form molecular machines within the cell. Within those envelopes, we are interested to find what regions correspond to specific proteins so that we can understand how they function, and design drugs that can enhance or suppress a process that they are involved in, along with other experimental purposes. A classic approach by which we can begin the exploration of map regions is to apply a segmentation algorithm. This yields a mask where each voxel in 3D space is assigned an identifier that maps it to a segment; an ideal segmentation would map each segment to one protein unit, which is rarely the case. In this work, we present a method that uses bio-inspired optimization, through an Evolutionary-Optimized Segmentation algorithm, to iteratively improve upon baseline segments obtained from a classical approach, called watershed segmentation. The cost function used by the evolutionary optimization is based on an ideal segmentation classifier trained as part of this development, which uses basic structural information available to scientists, such as the number of expected units, volume and topology. We show that a basic initial segmentation with the additional information allows our evolutionary method to find better segmentation results, compared to the baseline generated by the watershed.

Modelo para otimização hidroenergética da operação de bombeamento em sistemas de distribuição de água / Hydro energy optimization model of pumping operation in water distribution systems

RESUMO Neste trabalho foi desenvolvido um modelo multiobjetivo para otimização da operação de sistemas de distribuição de água (SDAs), visando alcançar a eficiência hidroenergética considerando três objetivos: redução das perdas por vazamento; redução do custo de energia elétrica no bombeamento; e maximização da confiabilidade do sistema. O modelo de otimização foi concebido pela implementação de uma rotina computacional entre os algoritmos genéticos NSGAII e SPEA e o simulador hidráulico EPANET. O modelo foi aplicado a um SDA hipotético e demonstrou ser adequado para gerar um conjunto ótimo de regras operacionais. Dentre as soluções geradas pelos dois algoritmos, constatou-se que a diminuição do custo de energia elétrica no bombeamento não implicou, necessariamente, redução das perdas por vazamentos, ou seja, os dois objetivos podem ser conflitantes em SDAs caracterizados pela presença de reservatórios internos.

ABSTRACT In this work, a multi-objective model for operational optimization of water distribution systems has been developed in order to achieve hydro energy efficiency. Three objectives were considered: minimizing of leakage, minimizing of pumping energy costs, and maximizing system reliability. The optimization model was conceived by the implementation of a computational routine between a dyhraulic simulator (EPANET) and by genetic algorithms NSGAII and SPEA. The proposed model has been applied to the optimization of a hypothetical water distribution network to generate an optimal set of operational rules. Some solutions obtained by the two algorithms showed that a decrease in pumping energy costs did not necessarily imply in leakage reduction. This means that both objectives can be conflicting in water distribution systems with internal tanks.

Interaction-Transformation Evolutionary Algorithm for Symbolic Regression.

Interaction-Transformation (IT) is a new representation for Symbolic Regression that reduces the space of solutions to a set of expressions that follow a specific structure. The potential of this representation was illustrated in prior work with the algorithm called SymTree. This algorithm starts with a simple linear model and incrementally introduces new transformed features until a stop criterion is met. While the results obtained by this algorithm were competitive with the literature, it had the drawback of not scaling well with the problem dimension. This article introduces a mutation-only Evolutionary Algorithm, called ITEA, capable of evolving a population of IT expressions. One advantage of this algorithm is that it enables the user to specify the maximum number of terms in an expression. In order to verify the competitiveness of this approach, ITEA is compared to linear, nonlinear, and Symbolic Regression models from the literature. The results indicate that ITEA is capable of finding equal or better approximations than other Symbolic Regression models while being competitive to state-of-the-art nonlinear models. Additionally, since this representation follows a specific structure, it is possible to extract the importance of each original feature of a data set as an analytical function, enabling us to automate the explanation of any prediction. In conclusion, ITEA is competitive when comparing to regression models with the additional benefit of automating the extraction of additional information of the generated models.

A multi-objective approach for designing optimized operation sequence on binary image processing.

In binary image segmentation, the choice of the order of the operation sequence may yield to suboptimal results. In this work, we propose to tackle the associated optimization problem via multi-objective approach. Given the original image, in combination with a list of morphological, logical and stacking operations, the goal is to obtain the ideal output at the lowest computational cost. We compared the performance of two Multi-objective Evolutionary Algorithms (MOEAs): the Non-dominated Sorting Genetic Algorithm (NSGA-II) and the Strength Pareto Evolutionary Algorithm 2 (SPEA2). NSGA-II has better results in most cases, but the difference does not reach statistical significance. The results show that the similarity measure and the computational cost are objective functions in conflict, while the number of operations available and type of input images impact on the quality of Pareto set.

Automatically Designing State-of-the-Art Multi- and Many-Objective Evolutionary Algorithms.

A recent comparison of well-established multiobjective evolutionary algorithms (MOEAs) has helped better identify the current state-of-the-art by considering (i) parameter tuning through automatic configuration, (ii) a wide range of different setups, and (iii) various performance metrics. Here, we automatically devise MOEAs with verified state-of-the-art performance for multi- and many-objective continuous optimization. Our work is based on two main considerations. The first is that high-performing algorithms can be obtained from a configurable algorithmic framework in an automated way. The second is that multiple performance metrics may be required to guide this automatic design process. In the first part of this work, we extend our previously proposed algorithmic framework, increasing the number of MOEAs, underlying evolutionary algorithms, and search paradigms that it comprises. These components can be combined following a general MOEA template, and an automatic configuration method is used to instantiate high-performing MOEA designs that optimize a given performance metric and present state-of-the-art performance. In the second part, we propose a multiobjective formulation for the automatic MOEA design, which proves critical for the context of many-objective optimization due to the disagreement of established performance metrics. Our proposed formulation leads to an automatically designed MOEA that presents state-of-the-art performance according to a set of metrics, rather than a single one.

Sequence motif finder using memetic algorithm.

BACKGROUND: De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important role in understanding the mechanisms of gene regulation and helps to develop new drugs. RESULTS: We here present Memetic Framework for Motif Discovery (MFMD), an algorithm that uses semi-greedy constructive heuristics as a local optimizer. In addition, we used a hybridization of the classic genetic algorithm as a global optimizer to refine the solutions initially found. MFMD can find and classify overrepresented patterns in DNA sequences and predict their respective initial positions. MFMD performance was assessed using ChIP-seq data retrieved from the JASPAR site, promoter sequences extracted from the ABS site, and artificially generated synthetic data. The MFMD was evaluated and compared with well-known approaches in the literature, called MEME and Gibbs Motif Sampler, achieving a higher f-score in the most datasets used in this work. CONCLUSIONS: We have developed an approach for detecting motifs in biopolymers sequences. MFMD is a freely available software that can be promising as an alternative to the development of new tools for de novo motif discovery. Its open-source software can be downloaded at https://github.com/jadermcg/mfmd .

A Large-Scale Experimental Evaluation of High-Performing Multi- and Many-Objective Evolutionary Algorithms.

Research on multi-objective evolutionary algorithms (MOEAs) has produced over the past decades a large number of algorithms and a rich literature on performance assessment tools to evaluate and compare them. Yet, newly proposed MOEAs are typically compared against very few, often a decade older MOEAs. One reason for this apparent contradiction is the lack of a common baseline for comparison, with each subsequent study often devising its own experimental scenario, slightly different from other studies. As a result, the state of the art in MOEAs is a disputed topic. This article reports a systematic, comprehensive evaluation of a large number of MOEAs that covers a wide range of experimental scenarios. A novelty of this study is the separation between the higher-level algorithmic components related to multi-objective optimization (MO), which characterize each particular MOEA, and the underlying parameters-such as evolutionary operators, population size, etc.-whose configuration may be tuned for each scenario. Instead of relying on a common or "default" parameter configuration that may be low-performing for particular MOEAs or scenarios and unintentionally biased, we tune the parameters of each MOEA for each scenario using automatic algorithm configuration methods. Our results confirm some of the assumed knowledge in the field, while at the same time they provide new insights on the relative performance of MOEAs for many-objective problems. For example, under certain conditions, indicator-based MOEAs are more competitive for such problems than previously assumed. We also analyze problem-specific features affecting performance, the agreement between performance metrics, and the improvement of tuned configurations over the default configurations used in the literature. Finally, the data produced is made publicly available to motivate further analysis and a baseline for future comparisons.

Simulating the folding of HP-sequences with a minimalist model in an inhomogeneous medium.

The phenomenon of protein folding is a fundamental issue in the field of the computational molecular biology. The protein folding inside the cells is performed in a highly inhomogeneous, tortuous, and correlated environment. Therefore, it is important to include in the theoretical studies the medium where the protein folding is developed. In this work we present the combination of three models to mimic the protein folding inside of an inhomogeneous medium. The models used here are Hydrophobic-Polar (HP) in 2D square arrangement, Evolutionary Algorithms (EA), and the Dual Site Bond Model (DSBM). The DSBM model is used to simulate the environment where the HP beads are folded; in this case the medium is correlated and is fractal-like. The analysis of five benchmark HP sequences shows that the inhomogeneous space provided with a given correlation length and fractal dimension plays an important role for correct folding of these sequences, which does not occur in a homogeneous space.

Evolving Gaussian Mixture Models with Splitting and Merging Mutation Operators.

This paper describes the evolutionary split and merge for expectation maximization (ESM-EM) algorithm and eight of its variants, which are based on the use of split and merge operations to evolve Gaussian mixture models. Asymptotic time complexity analysis shows that the proposed algorithms are competitive with the state-of-the-art genetic-based expectation maximization (GA-EM) algorithm. Experiments performed in 35 data sets showed that ESM-EM can be computationally more efficient than the widely used multiple runs of EM (for different numbers of components and initializations). Moreover, a variant of ESM-EM free from critical parameters was shown to be able to provide competitive results with GA-EM, even when GA-EM parameters were fine-tuned a priori.