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The main objectives of this study were to 1) review the literature on the applications of soft computing concepts to the field of human factors and ergonomics (HFE) between 2013 and 2022 and 2) highlight future developments and trends. Multiple soft computing methods and techniques have been investigated for their ability to address various applications in HFE effectively. These techniques include fuzzy logic, artificial neural networks, genetic algorithms, and their combinations. Applications of these methods in HFE have been highlighted in one hundred and four articles selected from 406 papers. The results of this study help address the challenges of complexity, vagueness, and imprecision in human factors and ergonomics research through the application of soft computing methodologies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Background: Intervention planners use logic models to design evidence-based health behavior interventions. Logic models that capture the complexity of health behavior necessitate additional computational techniques to inform decisions with respect to the design of interventions., Objective: Using empirical data from a real intervention, the present paper demonstrates how machine learning can be used together with fuzzy cognitive maps to assist in designing health behavior change interventions., Methods: A modified Real Coded Genetic algorithm was applied on longitudinal data from a real intervention study. The dataset contained information about 15 determinants of fruit intake among 257 adults in the Netherlands. Fuzzy cognitive maps were used to analyze the effect of two hypothetical intervention scenarios designed by domain experts., Results: Simulations showed that the specified hypothetical interventions would have small impact on fruit intake. The results are consistent with the empirical evidence used in this paper., Conclusions: Machine learning together with fuzzy cognitive maps can assist in building health behavior interventions with complex logic models. The testing of hypothetical scenarios may help interventionists finetune the intervention components thus increasing their potential effectiveness., (© 2023. The Author(s).)

Introduction: Knacks of evolutionary computing paradigm-based heuristics has been exploited exhaustively for system modeling and parameter estimation of complex nonlinear systems due to their legacy of reliable convergence, accurate performance, simple conceptual design ease implementation ease and wider applicability., Objectives: The aim of the presented study is to investigate in evolutionary heuristics of weighted differential evolution (WDE) to estimate the parameters of Hammerstein-Wiener model (HWM) along with comparative evaluation from state-of-the-art counterparts. The objective function of the HWM for controlled autoregressive systems is efficaciously formulated by approximating error in mean square sense by computing difference between true and estimated parameters., Methods: The adjustable parameters of HWM are estimated through heuristics of WDE and genetic algorithms (GAs) for different degrees of freedom and noise levels for exhaustive, comprehensive, and robust analysis on multiple autonomous trials., Results: Comparison through sufficient large number of graphical and numerical illustrations of outcomes for single and multiple execution of WDE and GAs through different performance measuring metrics of precision, convergence and complexity proves the worth and value of the designed WDE algorithm. Statistical assessment studies further prove the efficacy of the proposed scheme., Conclusion: Extensive simulation based experimentations on measure of central tendency and variance authenticate the effectiveness of the designed methodology WDE as precise, efficient, stable, and robust computing platform for system identification of HWM for controlled autoregressive scenarios., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Production and hosting by Elsevier B.V.)

The harm of agricultural pests presents a remarkable effect on the quality and safety of edible farm products and the monitoring and identification of agricultural pests based on the Internet of Things (IoT) produce a large amount of data to be transmitted. To achieve efficient and real-time transmission of the sensors' data for pest monitoring, this paper selects 235 geographic coordinates of agricultural pest monitoring points and uses genetic algorithm (GA), particle swarm optimization (PSO), and simulated annealing (SA) to optimize the data transmission paths of sensors. The three intelligent algorithms are simulated by MATLAB software. The results show that the optimized path based on PSO can make the shortest time used for transmitting data, and its corresponding minimum time is 4.868012 s. This study can provide a reference for improving the transmission efficiency of agricultural pest monitoring data, provide a guarantee for developing real-time and effective pest control strategies, and further reduce the threat of pest damage to the safety of farm products.

We introduce a regret-based fitness assignment strategy for evolutionary algorithms to find Nash equilibria in noncooperative simultaneous combinatorial game theory problems where it is computationally intractable to enumerate all decision options of the players involved in the game. Applications of evolutionary algorithms to non-cooperative simultaneous games have been limited due to challenges in guiding the evolutionary search toward equilibria, which are usually inferior points in the objective space. We propose a regret-based approach to select candidate decision options of the players for the next generation in a multipopulation genetic algorithm called Regret-Based Nash Equilibrium Sorting Genetic Algorithm (RNESGA). We show that RNESGA can converge to multiple Nash equilibria in a single run using two- and three- player competitive knapsack games and other games from the literature. We also show that pure payoff-based fitness assignment strategies perform poorly in three-player games., (© 2022 Massachusetts Institute of Technology.)

Environmental variability often degrades the performance of algorithms designed to capture the global convergence of a given search space. Several approaches have been developed to challenge environmental uncertainty by incorporating biologically inspired notions, focusing on crossover, mutation, and selection. This study proposes a bio-inspired approach called NEAT-HD, which focuses on parent selection based on genetic similarity. The originality of the proposed approach rests on its use of a sigmoid function to accelerate species formation and contribute to population diversity. Experiments on two classic control tasks were performed to demonstrate the performance of the proposed method. The results show that NEAT-HD can dynamically adapt to its environment by forming hybrid individuals originating from genetically distinct parents. Additionally, an increase in diversity within the population was observed due to the formation of hybrids and novel individuals, which has never been observed before. Comparing two tasks, the characteristics of NEAT-HD were improved by appropriately setting the algorithm to include the distribution of genetic distance within the population. Our key finding is the inherent potential of newly formed individuals for robustness against dynamic environments., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The use of multidimensional forced-choice questionnaires has been proposed as a means of improving validity in the assessment of non-cognitive attributes in high-stakes scenarios. However, the reduced precision of trait estimates in this questionnaire format is an important drawback. Accordingly, this article presents an optimization procedure for assembling pairwise forced-choice questionnaires while maximizing posterior marginal reliabilities. This procedure is performed through the adaptation of a known genetic algorithm (GA) for combinatorial problems. In a simulation study, the efficiency of the proposed procedure was compared with a quasi-brute-force (BF) search. For this purpose, five-dimensional item pools were simulated to emulate the real problem of generating a forced-choice personality questionnaire under the five-factor model. Three factors were manipulated: (1) the length of the questionnaire, (2) the relative item pool size with respect to the questionnaire's length, and (3) the true correlations between traits. The recovery of the person parameters for each assembled questionnaire was evaluated through the squared correlation between estimated and true parameters, the root mean square error between the estimated and true parameters, the average difference between the estimated and true inter-trait correlations, and the average standard error for each trait level. The proposed GA offered more accurate trait estimates than the BF search within a reasonable computation time in every simulation condition. Such improvements were especially important when measuring correlated traits and when the relative item pool sizes were higher. A user-friendly online implementation of the algorithm was made available to the users., (© 2021. The Author(s).)

Intelligent Reflecting Surfaces (IRSs) are emerging as an effective technology capable of improving the spectral and energy efficiency of future wireless networks. The proposed scenario consists of a multi-antenna base station and a single-antenna user that is assisted by an IRS. The large number of reflecting elements at the IRS and its passive operation represent an important challenge in the acquisition of the instantaneous channel state information (I-CSI) of all links as it adds a very high overhead to the system and requires equipping the IRS with radio-frequency chains. To overcome this problem, a new approach is proposed in order to optimize beamforming at the BS and the phase shifts at the IRS without considering any knowledge of I-CSI but while only exploring the statistical channel state information (S-CSI). We aim at maximizing the user-achievable rate subject to a maximum transmit power constraint. To achieve this goal, we propose a new two-phase framework. In the first phase, both the beamforming at the BS and IRS are designed based only on S-CSI and, in the second phase, the previously designed beamforming pair is used as an initial solution, and beamforming at the BS and IRS is designed only by considering the feedback of the SNR at UE. Moreover, for each phase, we propose new methods based on Genetic Algorithms. Results show that the developed algorithms can approach beamforming with I-CSI but with significantly reduced channel estimation overhead.

Anaerobic digestion (AnD) is a process that allows the conversion of organic waste into a source of energy such as biogas, introducing sustainability and circular economy in waste treatment. AnD is an intricate process because of multiple parameters involved, and its complexity increases when the wastes are from different types of generators. In this case, a key point to achieve good performance is optimisation methods. Currently, many tools have been developed to optimise a single AnD plant. However, the study of a network of AnD plants and multiple waste generators, all in different locations, remains unexplored. This novel approach requires the use of optimisation methodologies with the capacity to deal with a highly complex combinatorial problem. This paper proposes and compares the use of three evolutionary algorithms: ant colony optimisation (ACO), genetic algorithm (GA) and particle swarm optimisation (PSO), which are especially suited for this type of application. The algorithms successfully solve the problem, using an objective function that includes terms related to quality and logistics. Their application to a real case study in Catalonia (Spain) shows their usefulness (ACO and GA to achieve maximum biogas production and PSO for safer operation conditions) for AnD facilities.

Experimental screening of large sets of compounds against macromolecular targets is a key strategy to identify novel bioactivities. However, large-scale screening requires substantial experimental resources and is time-consuming and challenging. Therefore, small to medium-sized compound libraries with a high chance of producing genuine hits on an arbitrary protein of interest would be of great value to fields related to early drug discovery, in particular biochemical and cell research. Here, we present a computational approach that incorporates drug-likeness, predicted bioactivities, biological space coverage, and target novelty, to generate optimized compound libraries with maximized chances of producing genuine hits for a wide range of proteins. The computational approach evaluates drug-likeness with a set of established rules, predicts bioactivities with a validated, similarity-based approach, and optimizes the composition of small sets of compounds towards maximum target coverage and novelty. We found that, in comparison to the random selection of compounds for a library, our approach generates substantially improved compound sets. Quantified as the "fitness" of compound libraries, the calculated improvements ranged from +60% (for a library of 15,000 compounds) to +184% (for a library of 1000 compounds). The best of the optimized compound libraries prepared in this work are available for download as a dataset bundle ("BonMOLière").

The study of power quality (PQ) has gained relevance over the years due to the increase in non-linear loads connected to the grid. Therefore, it is important to study the propagation of power quality disturbances (PQDs) to determine the propagation points in the grid, and their source of generation. Some papers in the state of the art perform the analysis of punctual measurements of a limited number of PQDs, some of them using high-cost commercial equipment. The proposed method is based upon a developed proprietary system, composed of a data logger FPGA with GPS, that allows the performance of synchronized measurements merged with the full parameterized PQD model, allowing the detection and tracking of disturbances propagating through the grid using wavelet transform (WT), fast Fourier transform (FFT), Hilbert-Huang transform (HHT), genetic algorithms (GAs), and particle swarm optimization (PSO). Measurements have been performed in an industrial installation, detecting the propagation of three PQDs: impulsive transients propagated at two locations in the grid, voltage fluctuation, and harmonic content propagated to all the locations. The results obtained show that the low-cost system and the developed methodology allow the detection of several PQDs, and track their propagation within a grid with 100% accuracy.

NeuroEvolution (NE) refers to a family of methods for optimizing Artificial Neural Networks (ANNs) using Evolutionary Computation (EC) algorithms. NeuroEvolution of Augmenting Topologies (NEAT) is considered one of the most influential algorithms in the field. Eighteen years after its invention, a plethora of methods have been proposed that extend NEAT in different aspects. In this article, we present a systematic literature review (SLR) to list and categorize the methods succeeding NEAT. Our review protocol identified 232 papers by merging the findings of two major electronic databases. Applying criteria that determine the paper's relevance and assess its quality, resulted in 61 methods that are presented in this article. Our review article proposes a new categorization scheme of NEAT's successors into three clusters. NEAT-based methods are categorized based on 1) whether they consider issues specific to the search space or the fitness landscape, 2) whether they combine principles from NE and another domain, or 3) the particular properties of the evolved ANNs. The clustering supports researchers 1) understanding the current state of the art that will enable them, 2) exploring new research directions or 3) benchmarking their proposed method to the state of the art, if they are interested in comparing, and 4) positioning themselves in the domain or 5) selecting a method that is most appropriate for their problem.

Brain-Computer Interface (BCI) systems establish a channel for direct communication between the brain and the outside world without having to use the peripheral nervous system. While most BCI systems use evoked potentials and motor imagery, in the present work we present a technique that employs visual imagery. Our technique uses neural networks to classify the signals produced in visual imagery. To this end, we have used densely connected neural and convolutional networks, together with a genetic algorithm to find the best parameters for these networks. The results we obtained are a 60% success rate in the classification of four imagined objects (a tree, a dog, an airplane and a house) plus a state of relaxation, thus outperforming the state of the art in visual imagery classification.

Evolution provides a creative fount of complex and subtle adaptations that often surprise the scientists who discover them. However, the creativity of evolution is not limited to the natural world: Artificial organisms evolving in computational environments have also elicited surprise and wonder from the researchers studying them. The process of evolution is an algorithmic process that transcends the substrate in which it occurs. Indeed, many researchers in the field of digital evolution can provide examples of how their evolving algorithms and organisms have creatively subverted their expectations or intentions, exposed unrecognized bugs in their code, produced unexpectedly adaptations, or engaged in behaviors and outcomes, uncannily convergent with ones found in nature. Such stories routinely reveal surprise and creativity by evolution in these digital worlds, but they rarely fit into the standard scientific narrative. Instead they are often treated as mere obstacles to be overcome, rather than results that warrant study in their own right. Bugs are fixed, experiments are refocused, and one-off surprises are collapsed into a single data point. The stories themselves are traded among researchers through oral tradition, but that mode of information transmission is inefficient and prone to error and outright loss. Moreover, the fact that these stories tend to be shared only among practitioners means that many natural scientists do not realize how interesting and lifelike digital organisms are and how natural their evolution can be. To our knowledge, no collection of such anecdotes has been published before. This article is the crowd-sourced product of researchers in the fields of artificial life and evolutionary computation who have provided first-hand accounts of such cases. It thus serves as a written, fact-checked collection of scientifically important and even entertaining stories. In doing so we also present here substantial evidence that the existence and importance of evolutionary surprises extends beyond the natural world, and may indeed be a universal property of all complex evolving systems.

Background: Feature selection is a crucial step in machine learning analysis. Currently, many feature selection approaches do not ensure satisfying results, in terms of accuracy and computational time, when the amount of data is huge, such as in 'Omics' datasets., Results: Here, we propose an innovative implementation of a genetic algorithm, called GARS, for fast and accurate identification of informative features in multi-class and high-dimensional datasets. In all simulations, GARS outperformed two standard filter-based and two 'wrapper' and one embedded' selection methods, showing high classification accuracies in a reasonable computational time., Conclusions: GARS proved to be a suitable tool for performing feature selection on high-dimensional data. Therefore, GARS could be adopted when standard feature selection approaches do not provide satisfactory results or when there is a huge amount of data to be analyzed.

Multi-linear gradients are a convenient solution to get separation of complex samples by modulating carefully the gradient slope, in order to accomplish the local selectivity needs for each particular solute cluster. These gradients can be designed by trial-and-error according to the chromatographer experience, but this strategy becomes quickly inappropriate for complex separations. More evolved solutions imply the sequential construction of multi-segmented gradients. However, this strategy discards part of the search space in each step of the construction and, again, cannot deal properly with very complex samples. When the complexity is too large, the only valid alternative for finding the best gradient is the use of global search methods, such as genetic algorithms (GAs). Recently, a new global approach where the level of detail is increased along the search has been proposed, namely Multi-scale optimisation (MSO). In this strategy, cubic splines are applied to build intermediate curves to define any arbitrary solvent variation function. Subdivision schemes are used to generate the cubic splines and control their level of detail. The search was subjected to a number of restrictions, such as avoiding long elution and favouring a balanced peak distribution. The aim of this work is evaluating and comparing the results of GAs and MSO. Both approaches were tested with a set of 14 diuretics and probenecid, eluted with acetonitrile-water mixtures using a C18 column. Satisfactory baseline resolution was obtained with an analysis time of 15-16 min. We found that GAs optimisation offered results equivalent to those provided by MSO, when the penalisation parameters were included in the cost function., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Objective: This paper presents a methodology to optimize, using Altman's Z-Score for private companies, the prediction of private companies of the Spanish health sector entering a situation of bankruptcy., Method: The proposed method consists of the application of genetic algorithms (GA) to find the coefficients of the formula of the chain of ratios proposed by Altman in the version of the score for private companies which optimize the prediction for Spanish private health companies, maximizing sensitivity and specificity, and thereby reducing type I and type II errors. For this purpose, a sample of 5,903 companies from the Spanish private health sector obtained from the database of the Iberian Balance Analysis System (SABI) between 2007 and 2015 was used., Results: The results show that the predictive model obtained with the AG presents greater accuracy, sensitivity and specificity than that proposed by Altman for private companies with both test data and all sample data., Conclusions: The most important finding of this study was to establish a methodology that can identify the optimized coefficients for the Altman Z-Score, which allows a more accurate prediction of bankruptcy in Spanish private healthcare companies., (Copyright © 2018 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.)

In this paper, the viscoelastic characterization of biosamples is addressed considering a measuring technique relying on the use of a MEMS techonology-based microgripper. A proper mechanical model is developed for the coupled nonlinear dynamics of the microsystem, composed of the measuring tool and the specimen to be analyzed. The Maxwell liquid drop model and the generalized Maxwell-Wiechert model are considered for the sample, and the identification of the viscoelastic parameters is performed by implementing a genetic algorithm., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Establishing the best layout configuration for software-generated interfaces and control panels is a complex problem when they include many controls and indicators. Several methods have been developed for arranging the interface elements; however, the results are usually conceptual designs that must be manually adjusted to obtain layouts valid for real situations. Based on these considerations, in this work we propose a new automatized procedure to obtain optimal layouts for software-based interfaces. Eye-tracking and mouse-tracking data collected during the use of the interface is used to obtain the best configuration for its elements. The solutions are generated using a slicing-trees based genetic algorithm. This algorithm is able to obtain really applicable configurations that respect the geometrical restrictions of elements in the interface. Results show that this procedure increases effectiveness, efficiency and satisfaction of the users when they interact with the obtained interfaces., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Sorting unsigned permutations by reversals is a difficult problem; indeed, it was proved to be NP -hard by Caprara ( 1997 ). Because of its high complexity, many approximation algorithms to compute the minimal reversal distance were proposed until reaching the nowadays best-known theoretical ratio of 1.375. In this article, two memetic algorithms to compute the reversal distance are proposed. The first one uses the technique of opposition-based learning leading to an opposition-based memetic algorithm; the second one improves the previous algorithm by applying the heuristic of two breakpoint elimination leading to a hybrid approach. Several experiments were performed with one-hundred randomly generated permutations, single benchmark permutations, and biological permutations. Results of the experiments showed that the proposed OBMA and Hybrid-OBMA algorithms achieve the best results for practical cases, that is, for permutations of length up to 120. Also, Hybrid-OBMA showed to improve the results of OBMA for permutations greater than or equal to 60. The applicability of our proposed algorithms was checked processing permutations based on biological data, in which case OBMA gave the best average results for all instances.

Background: In order to fully characterize the genome of an individual, the reconstruction of the two distinct copies of each chromosome, called haplotypes, is essential. The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the two chromosomes. Indeed, the knowledge of complete haplotypes is generally more informative than analyzing single SNPs and plays a fundamental role in many medical applications., Results: To reconstruct the two haplotypes, we addressed the weighted Minimum Error Correction (wMEC) problem, which is a successful approach for haplotype assembly. This NP-hard problem consists in computing the two haplotypes that partition the sequencing reads into two disjoint sub-sets, with the least number of corrections to the SNP values. To this aim, we propose here GenHap, a novel computational method for haplotype assembly based on Genetic Algorithms, yielding optimal solutions by means of a global search process. In order to evaluate the effectiveness of our approach, we run GenHap on two synthetic (yet realistic) datasets, based on the Roche/454 and PacBio RS II sequencing technologies. We compared the performance of GenHap against HapCol, an efficient state-of-the-art algorithm for haplotype phasing. Our results show that GenHap always obtains high accuracy solutions (in terms of haplotype error rate), and is up to 4× faster than HapCol in the case of Roche/454 instances and up to 20× faster when compared on the PacBio RS II dataset. Finally, we assessed the performance of GenHap on two different real datasets., Conclusions: Future-generation sequencing technologies, producing longer reads with higher coverage, can highly benefit from GenHap, thanks to its capability of efficiently solving large instances of the haplotype assembly problem. Moreover, the optimization approach proposed in GenHap can be extended to the study of allele-specific genomic features, such as expression, methylation and chromatin conformation, by exploiting multi-objective optimization techniques. The source code and the full documentation are available at the following GitHub repository: https://github.com/andrea-tango/GenHap .

Nuclear Magnetic Resonance Spectroscopy (most commonly known as NMR Spectroscopy) is used to generate approximate and partial distances between pairs of atoms of the native structure of a protein. To predict protein structure from these partial distances by solving the Euclidean distance geometry problem from the partial distances obtained from NMR Spectroscopy, we can predict three-dimensional (3D) structure of a protein. In this paper, a new genetic algorithm is proposed to efficiently address the Euclidean distance geometry problem towards building 3D structure of a given protein applying NMR's sparse data. Our genetic algorithm uses (i) a greedy mutation and crossover operator to intensify the search; (ii) a twin removal technique for diversification in the population; (iii) a random restart method to recover from stagnation; and (iv) a compaction factor to reduce the search space. Reducing the search space drastically, our approach improves the quality of the search. We tested our algorithms on a set of standard benchmarks. Experimentally, we show that our enhanced genetic algorithms significantly outperforms the traditional genetic algorithms and a previously proposed state-of-the-art method. Our method is capable of producing structures that are very close to the native structures and hence, the experimental biologists could adopt it to determine more accurate protein structures from NMR data., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Background: The Smad7 protein is negative regulator of the TGF-β signaling pathway, which is upregulated in patients with breast cancer. miRNAs regulate proteins expressions by arresting or degrading the mRNAs. The purpose of this work is to identify a miRNAs profile that regulates the expression of the mRNA coding for Smad7 in breast cancer using the data from patients with breast cancer obtained from the Cancer Genome Atlas Project., Methods: We develop an automatic search method based on genetic algorithms to find a predictive model based on deep neural networks (DNN) which fit the set of biological data and apply the Olden algorithm to identify the relative importance of each miRNAs., Results: A computational model of non-linear regression is shown, based on deep neural networks that predict the regulation given by the miRNA target transcripts mRNA coding for Smad7 protein in patients with breast cancer, with R 2 of 0.99 is shown and MSE of 0.00001. In addition, the model is validated with the results in vivo and in vitro experiments reported in the literature. The set of miRNAs hsa-mir-146a, hsa-mir-93, hsa-mir-375, hsa-mir-205, hsa-mir-15a, hsa-mir-21, hsa-mir-20a, hsa-mir-503, hsa-mir-29c, hsa-mir-497, hsa-mir-107, hsa-mir-125a, hsa-mir-200c, hsa-mir-212, hsa-mir-429, hsa-mir-34a, hsa-let-7c, hsa-mir-92b, hsa-mir-33a, hsa-mir-15b, hsa-mir-224, hsa-mir-185 and hsa-mir-10b integrate a profile that critically regulates the expression of the mRNA coding for Smad7 in breast cancer., Conclusions: We developed a genetic algorithm to select best features as DNN inputs (miRNAs). The genetic algorithm also builds the best DNN architecture by optimizing the parameters. Although the confirmation of the results by laboratory experiments has not occurred, the results allow suggesting that miRNAs profile could be used as biomarkers or targets in targeted therapies.

In this article, we consider a fitness-level model of a non-elitist mutation-only evolutionary algorithm (EA) with tournament selection. The model provides upper and lower bounds for the expected proportion of the individuals with fitness above given thresholds. In the case of so-called monotone mutation, the obtained bounds imply that increasing the tournament size improves the EA performance. As corollaries, we obtain an exponentially vanishing tail bound for the Randomized Local Search on unimodal functions and polynomial upper bounds on the runtime of EAs on the 2-SAT problem and on a family of Set Cover problems proposed by E. Balas.

Learning and exploiting problem structure is one of the key challenges in optimization. This is especially important for black-box optimization (BBO) where prior structural knowledge of a problem is not available. Existing model-based Evolutionary Algorithms (EAs) are very efficient at learning structure in both the discrete, and in the continuous domain. In this article, discrete and continuous model-building mechanisms are integrated for the Mixed-Integer (MI) domain, comprising discrete and continuous variables. We revisit a recently introduced model-based evolutionary algorithm for the MI domain, the Genetic Algorithm for Model-Based mixed-Integer opTimization (GAMBIT). We extend GAMBIT with a parameterless scheme that allows for practical use of the algorithm without the need to explicitly specify any parameters. We furthermore contrast GAMBIT with other model-based alternatives. The ultimate goal of processing mixed dependences explicitly in GAMBIT is also addressed by introducing a new mechanism for the explicit exploitation of mixed dependences. We find that processing mixed dependences with this novel mechanism allows for more efficient optimization. We further contrast the parameterless GAMBIT with Mixed-Integer Evolution Strategies (MIES) and other state-of-the-art MI optimization algorithms from the General Algebraic Modeling System (GAMS) commercial algorithm suite on problems with and without constraints, and show that GAMBIT is capable of solving problems where variable dependences prevent many algorithms from successfully optimizing them.

RGB-D sensors can collect postural data in an automatized way. However, the application of these devices in real work environments requires overcoming problems such as lack of accuracy or body parts' occlusion. This work presents the use of RGB-D sensors and genetic algorithms for the optimization of workstation layouts. RGB-D sensors are used to capture workers' movements when they reach objects on workbenches. Collected data are then used to optimize workstation layout by means of genetic algorithms considering multiple ergonomic criteria. Results show that typical drawbacks of using RGB-D sensors for body tracking are not a problem for this application, and that the combination with intelligent algorithms can automatize the layout design process. The procedure described can be used to automatically suggest new layouts when workers or processes of production change, to adapt layouts to specific workers based on their ways to do the tasks, or to obtain layouts simultaneously optimized for several production processes., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Intracellular protein folding (PF) is performed in a highly inhomogeneous, crowded, and correlated environment. Due to this inherent complexity, the study and understanding of PF phenomena is a fundamental issue in the field of computational systems biology. In particular, it is important to use a modeled medium that accurately reflects PF in natural systems. In the current study, we present a simulation wherein PF is carried out within an inhomogeneous modeled medium. Simulation resources included a two-dimensional hydrophobic-polar (HP) model, evolutionary algorithms, and the dual site-bond model. The dual site-bond model was used to develop an environment where HP beads could be folded. Our modeled medium included correlation lengths and fractal-like behavior, which were selected according to HP sequence lengths to induce folding in a crowded environment. Analysis of three benchmark HP sequences showed that the modeled inhomogeneous space played an important role in deeper energy folding and obtained better performance and convergence compared with homogeneous environments. Our computational approach also demonstrated that our correlated network provided a better space for PF. Thus, our approach represents a major advancement in PF simulations, not only for folding but also for understanding functional chemical structure and physicochemical properties of proteins in crowded molecular systems, which normally occur in nature.

In directed evolution (DE) the assessment of candidate enzymes and their modification is essential. In this study we have investigated genetic algorithms (GAs) in this context and conducted a systematic study of the behavior of GAs on 20 fitness landscapes (FLs) of varying complexity. This has allowed the tuning of the GAs to be explored. On the basis of this study, recommendations for the best GA settings to use for a GA-directed high-throughput experimental program (in which populations and the number of generations is necessarily low) are reported. The FLs were based upon simple linear models and were characterized by the behavior of the GA on the landscape as demonstrated by stall plots and the footprints and adhesion of candidate solutions, which highlighted local optima (LOs). In order to maximize progress of the GA and to reduce the chances of becoming stuck in a LO it was best to use: 1) a large number of generations, 2) high populations, 3) removal of duplicate sequences (clones), 4) double mutation, and 5) high selection pressure (the two best individuals go to the next generation), and 6) to consider using a designed sequence as the starting point of the GA run. We believe that these recommendations might be appropriate starting points for studies employing GAs within DE experiments., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

We reinvestigate a fundamental question: How effective is crossover in genetic algorithms in combining building blocks of good solutions? Although this has been discussed controversially for decades, we are still lacking a rigorous and intuitive answer. We provide such answers for royal road functions and OneMax, where every bit is a building block. For the latter, we show that using crossover makes every ([Formula: see text]+[Formula: see text]) genetic algorithm at least twice as fast as the fastest evolutionary algorithm using only standard bit mutation, up to small-order terms and for moderate [Formula: see text] and [Formula: see text]. Crossover is beneficial because it can capitalize on mutations that have both beneficial and disruptive effects on building blocks: crossover is able to repair the disruptive effects of mutation in later generations. Compared to mutation-based evolutionary algorithms, this makes multibit mutations more useful. Introducing crossover changes the optimal mutation rate on OneMax from [Formula: see text] to [Formula: see text]. This holds both for uniform crossover and k-point crossover. Experiments and statistical tests confirm that our findings apply to a broad class of building block functions.

The computer-aided diagnosis has become one of the major research topics in medical diagnostics. In this research paper, we focus on designing an automated computer diagnosis by combining two major methodologies, namely the fuzzy base systems and the evolutionary genetic algorithms and applying them to the Saudi Arabian breast cancer diagnosis database, to be employed for assisting physicians in the early detection of breast cancers, and hence obtaining an early-computerized diagnosis complementary to that by physicians. Our hybrid algorithm, the genetic-fuzzy algorithm, has produced optimized diagnosis systems that attain high classification performance, in fact, our best three rule system obtained a 97% accuracy, with simple and well interpretive rules, and with a good degree of confidence of 91%., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Evolutionary algorithms have previously been applied to the design of morphology and control of robots. The design space for such tasks can be very complex, which can prevent evolution from efficiently discovering fit solutions. In this article we introduce an evolutionary-developmental (evo-devo) experiment with real-world robots. It allows robots to grow their leg size to simulate ontogenetic morphological changes, and this is the first time that such an experiment has been performed in the physical world. To test diverse robot morphologies, robot legs of variable shapes were generated during the evolutionary process and autonomously built using additive fabrication. We present two cases with evo-devo experiments and one with evolution, and we hypothesize that the addition of a developmental stage can be used within robotics to improve performance. Moreover, our results show that a nonlinear system-environment interaction exists, which explains the nontrivial locomotion patterns observed. In the future, robots will be present in our daily lives, and this work introduces for the first time physical robots that evolve and grow while interacting with the environment.

Data mining methods in biomedical research might benefit by combining genetic algorithms with domain-specific knowledge. The objective of this research is to show how the evolution of treatment rules for autism might be guided. The semantic distance between two concepts in the taxonomy is measured by the number of relationships separating the concepts in the taxonomy. The hypothesis is that replacing a concept in a treatment rule will change the accuracy of the rule in direct proportion to the semantic distance between the concepts. The method uses a patient database and autism taxonomies. Treatment rules are developed with an algorithm that exploits the taxonomies. The results support the hypothesis. This research should both advance the understanding of autism data mining in particular and of knowledge-guided evolutionary search in biomedicine in general.

This paper presents an effective evolutionary hybrid for solving the permutation flowshop scheduling problem. Based on a memetic algorithm, the procedure uses a construction component that generates initial solutions through the use of a novel reblocking mechanism operating according to a biased random sampling technique. This component is aimed at forcing the operations having smaller processing times to appear on the critical path. The goal of the construction component is to fill an initial pool with high-quality solutions for a memetic algorithm that looks for even higher-quality solutions. In the memetic algorithm, whenever a crossover operator and possibly a mutation are performed, the offspring genome is fine-tuned by a combination of 2-exchange swap and insertion local searches. The same with the employed construction method; in these local searches, the critical path notion has been used to exploit the structure of the problem. The results of computational experiments on the benchmark instances indicate that these components have strong synergy, and their integration has created a robust and effective procedure that outperforms several state-of-the-art procedures on a number of the benchmark instances. By deactivating different components enhancing the evolutionary module of the procedure, the effects of these components have also been examined.

Biomimicry is a strategy that makes practical use of evolution to find efficient and sustainable ways to produce chemical compounds or engineer products. Exploring the natural machinery of enzymes for the production of desired compounds is a highly profitable investment, but the design of efficient biomimetic systems remains a considerable challenge. An ideal biomimetic system self-assembles in solution, binds a desired range of substrates and catalyzes reactions with turnover rates similar to the native system. To this end, tailoring catalytic functionality in engineered peptides generally requires site-directed mutagenesis or the insertion of additional amino acids, which entails an intensive search across chemical and sequence space. Here we discuss a novel strategy for the computational design of biomimetic compounds and processes that consists of a) characterization of the wild-type and biomimetic systems; b) identification of key descriptors for optimization; c) an efficient search through sequence and chemical space to tailor the catalytic capabilities of the biomimetic system. Through this proof-of-principle study, we are able to decisively understand and identify whether a given scaffold is useful, appropriate and tailorable for a given, desired task., (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Recent advances in macromolecular crystallography have made it practical to rapidly collect hundreds of sub-data sets consisting of small oscillations of incomplete data. This approach, generally referred to as serial crystallography, has many uses, including an increased effective dose per data set, the collection of data from crystals without harvesting (in situ data collection) and studies of dynamic events such as catalytic reactions. However, selecting which data sets from this type of experiment should be merged can be challenging and new methods are required. Here, it is shown that a genetic algorithm can be used for this purpose, and five case studies are presented in which the merging statistics are significantly improved compared with conventional merging of all data.

Bloodstain pattern analysis (BPA) is an approach to support forensic investigators in reconstructing the dynamics of bloody crimes. This forensic technique has been successfully applied in solving heinous and complex murder cases around the world and, recently, computer-based BPA approaches have been designed to better support investigators both in terms of speed and quality of analysis. However, despite its widespread use, current automatic techniques for BPA try to define some algorithmic steps to replicate a sequence of subjective investigators' tasks without relying on any mathematical formalism to compute an objective reconstruction of the crime. The lack of an objective mathematical foundation is a critical issue in a scenario where the quality of evidences can strongly affect a court trial and the life of people involved in that trial. This paper introduces the very first formal representation of BPA by means of an optimisation problem, on which to base the next generation of crime reconstruction techniques. As an example of the benefits provided by the proposed formal representation of BPA, a case study based on a genetic algorithm shows how the BPA optimisation problem can support investigators in performing a fast, precise, automatic and objective analysis., (Copyright © 2016. Published by Elsevier Ireland Ltd.)

Interactions among biological entities contain more information than purely the similarities between the entities. For example, interactions between genes, and gene products, can be more informative than the sequence similarities of the genes involved. However, the study of biological networks and their evolution in particular is still in its infancy. Simplified theoretical models of the development of biological networks from a starting state exist, but the problem of finding a distance between existing biological networks, with an unknown history, has seen less research. Metrics for network distance can also be used to measure the fit between theoretically derived networks and their real-world counterpart. In this article, we present a useful model of biological network distance and demonstrate an implementation using simulated gene regulatory networks. We compared our method with existing methods for network alignment and showed that we are much better able to identify evolutionary changes in biological networks. In particular, we can recover the evolutionary trees that describe the relationship between these networks.

This study focuses on improving the multi-objective memetic algorithm for protein-protein interaction (PPI) network alignment, Optimizing Network Aligner - OptNetAlign, via integration with other existing network alignment methods such as SPINAL, NETAL and HubAlign. The output of this algorithm is an elite set of aligned networks all of which are optimal with respect to multiple user-defined criteria. However, OptNetAlign is an unsupervised genetic algorithm that initiates its search with completely random solutions and it requires substantial running times to generate an elite set of solutions that have high scores with respect to the given criteria. In order to improve running time, the search space of the algorithm can be narrowed down by focusing on remarkably qualified alignments and trying to optimize the most desired criteria on a more limited set of solutions. The method presented in this study improves OptNetAlign in a supervised fashion by utilizing the alignment results of different network alignment algorithms with varying parameters that depend upon user preferences. Therefore, the user can prioritize certain objectives upon others and achieve better running time performance while optimizing the secondary objectives., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Background: Protein-protein interaction networks are receiving increased attention due to their importance in understanding life at the cellular level. A major challenge in systems biology is to understand the modular structure of such biological networks. Although clustering techniques have been proposed for clustering protein-protein interaction networks, those techniques suffer from some drawbacks. The application of earlier clustering techniques to protein-protein interaction networks in order to predict protein complexes within the networks does not yield good results due to the small-world and power-law properties of these networks., Results: In this paper, we construct a new clustering algorithm for predicting protein complexes through the use of genetic algorithms. We design an objective function for exclusive clustering and overlapping clustering. We assess the quality of our proposed clustering algorithm using two gold-standard data sets., Conclusions: Our algorithm can identify protein complexes that are significantly enriched in the gold-standard data sets. Furthermore, our method surpasses three competing methods: MCL, ClusterOne, and MCODE in terms of the quality of the predicted complexes. The source code and accompanying examples are freely available at http://faculty.kfupm.edu.sa/ics/eramadan/GACluster.zip .

Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more importantly, the use of effective sampling algorithms become crucial to address this problem. For protein structure modeling, an off-lattice model provides limited scopes to exercise and evaluate the algorithmic developments due to its astronomically large set of data-points. In contrast, an on-lattice model widens the scopes and permits studying the relatively larger proteins because of its finite set of data-points. In this work, we took the full advantage of an on-lattice model by using a face-centered-cube lattice that has the highest packing density with the maximum degree of freedom. We proposed a graded energy-strategically mixes the Miyazawa-Jernigan (MJ) energy with the hydrophobic-polar (HP) energy-based genetic algorithm (GA) for conformational search. In our application, we introduced a 2 × 2 HP energy guided macro-mutation operator within the GA to explore the best possible local changes exhaustively. Conversely, the 20 × 20 MJ energy model-the ultimate objective function of our GA that needs to be minimized-considers the impacts amongst the 20 different amino acids and allow searching the globally acceptable conformations. On a set of benchmark proteins, our proposed approach outperformed state-of-the-art approaches in terms of the free energy levels and the root-mean-square deviations., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

The parameter-less population pyramid (P3) is a recently introduced method for performing evolutionary optimization without requiring any user-specified parameters. P3's primary innovation is to replace the generational model with a pyramid of multiple populations that are iteratively created and expanded. In combination with local search and advanced crossover, P3 scales to problem difficulty, exploiting previously learned information before adding more diversity. Across seven problems, each tested using on average 18 problem sizes, P3 outperformed all five advanced comparison algorithms. This improvement includes requiring fewer evaluations to find the global optimum and better fitness when using the same number of evaluations. Using both algorithm analysis and comparison, we find P3's effectiveness is due to its ability to properly maintain, add, and exploit diversity. Unlike the best comparison algorithms, P3 was able to achieve this quality without any problem-specific tuning. Thus, unlike previous parameter-less methods, P3 does not sacrifice quality for applicability. Therefore we conclude that P3 is an efficient, general, parameter-less approach to black box optimization which is more effective than existing state-of-the-art techniques.

Biodiesel is a green (clean), renewable energy source and is an alternative for diesel fuel. Biodiesel can be produced from vegetable oil, animal fat and waste cooking oil or fat. Fats and oils react with alcohol to produce methyl ester, which is generally known as biodiesel. Because vegetable oil and animal fat wastes are cheaper, the tendency to produce biodiesel from these materials is increasing. In this research, the effect of some parameters such as the alcohol-to-oil molar ratio (4:1, 6:1, 8:1), the catalyst concentration (0.75%, 1% and 1.25% w/w) and the time for the transesterification reaction using ultrasonication on the rate of the fatty acids-to-methyl ester (biodiesel) conversion percentage have been studied (3, 6 and 9 min). In biodiesel production from chicken fat, when increasing the catalyst concentration up to 1%, the oil-to-biodiesel conversion percentage was first increased and then decreased. Upon increasing the molar ratio from 4:1 to 6:1 and then to 8:1, the oil-to-biodiesel conversion percentage increased by 21.9% and then 22.8%, respectively. The optimal point is determined by response surface methodology (RSM) and genetic algorithms (GAs). The biodiesel production from chicken fat by ultrasonic waves with a 1% w/w catalyst percentage, 7:1 alcohol-to-oil molar ratio and 9 min reaction time was equal to 94.8%. For biodiesel that was produced by ultrasonic waves under a similar conversion percentage condition compared to the conventional method, the reaction time was decreased by approximately 87.5%. The time reduction for the ultrasonic method compared to the conventional method makes the ultrasonic method superior., (Copyright © 2015. Published by Elsevier B.V.)

The aim of this article is to present a new face recognition system based on the fusion of visible and thermal features obtained from the most current local matching descriptors by maximizing face recognition rates through the use of genetic algorithms. The article considers a comparison of the performance of the proposed fusion methodology against five current face recognition methods and classic fusion techniques used commonly in the literature. These were selected by considering their performance in face recognition. The five local matching methods and the proposed fusion methodology are evaluated using the standard visible/thermal database, the Equinox database, along with a new database, the PUCV-VTF, designed for visible-thermal studies in face recognition and described for the first time in this work. The latter is created considering visible and thermal image sensors with different real-world conditions, such as variations in illumination, facial expression, pose, occlusion, etc. The main conclusions of this article are that two variants of the proposed fusion methodology surpass current face recognition methods and the classic fusion techniques reported in the literature, attaining recognition rates of over 97% and 99% for the Equinox and PUCV-VTF databases, respectively. The fusion methodology is very robust to illumination and expression changes, as it combines thermal and visible information efficiently by using genetic algorithms, thus allowing it to choose optimal face areas where one spectrum is more representative than the other.

This paper describes a hybrid level set approach for medical image segmentation. This new geometric deformable model combines region- and edge-based information with the prior shape knowledge introduced using deformable registration. Our proposal consists of two phases: training and test. The former implies the learning of the level set parameters by means of a Genetic Algorithm, while the latter is the proper segmentation, where another metaheuristic, in this case Scatter Search, derives the shape prior. In an experimental comparison, this approach has shown a better performance than a number of state-of-the-art methods when segmenting anatomical structures from different biomedical image modalities., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Artificial Neuron-Glia Networks (ANGNs) are a novel bio-inspired machine learning approach. They extend classical Artificial Neural Networks (ANNs) by incorporating recent findings and suppositions about the way information is processed by neural and astrocytic networks in the most evolved living organisms. Although ANGNs are not a consolidated method, their performance against the traditional approach, i.e. without artificial astrocytes, was already demonstrated on classification problems. However, the corresponding learning algorithms developed so far strongly depends on a set of glial parameters which are manually tuned for each specific problem. As a consequence, previous experimental tests have to be done in order to determine an adequate set of values, making such manual parameter configuration time-consuming, error-prone, biased and problem dependent. Thus, in this paper, we propose a novel learning approach for ANGNs that fully automates the learning process, and gives the possibility of testing any kind of reasonable parameter configuration for each specific problem. This new learning algorithm, based on coevolutionary genetic algorithms, is able to properly learn all the ANGNs parameters. Its performance is tested on five classification problems achieving significantly better results than ANGN and competitive results with ANN approaches.

In this paper we address the problem of picking a subset of bids in a general combinatorial auction so as to maximize the overall profit using the first-price model. This winner determination problem assumes that a single bidding round is held to determine both the winners and prices to be paid. We introduce six variants of biased random-key genetic algorithms for this problem. Three of them use a novel initialization technique that makes use of solutions of intermediate linear programming relaxations of an exact mixed integer linear programming model as initial chromosomes of the population. An experimental evaluation compares the effectiveness of the proposed algorithms with the standard mixed linear integer programming formulation, a specialized exact algorithm, and the best-performing heuristics proposed for this problem. The proposed algorithms are competitive and offer strong results, mainly for large-scale auctions.

Setting the control parameters of a genetic algorithm to obtain good results is a long-standing problem. We define an experiment design and analysis method to determine relative importance and effective settings for control parameters of any evolutionary algorithm, and we apply this method to a classic binary-encoded genetic algorithm (GA). Subsequently, as reported elsewhere, we applied the GA, with the control parameter settings determined here, to steer a population of cloud-computing simulators toward behaviors that reveal degraded performance and system collapse. GA-steered simulators could serve as a design tool, empowering system engineers to identify and mitigate low-probability, costly failure scenarios. In the existing GA literature, we uncovered conflicting opinions and evidence regarding key GA control parameters and effective settings to adopt. Consequently, we designed and executed an experiment to determine relative importance and effective settings for seven GA control parameters, when applied across a set of numerical optimization problems drawn from the literature. This paper describes our experiment design, analysis, and results. We found that crossover most significantly influenced GA success, followed by mutation rate and population size and then by rerandomization point and elite selection. Selection method and the precision used within the chromosome to represent numerical values had least influence. Our findings are robust over 60 numerical optimization problems.

Novelty search is a recent algorithm geared toward exploring search spaces without regard to objectives. When the presence of constraints divides a search space into feasible space and infeasible space, interesting implications arise regarding how novelty search explores such spaces. This paper elaborates on the problem of constrained novelty search and proposes two novelty search algorithms which search within both the feasible and the infeasible space. Inspired by the FI-2pop genetic algorithm, both algorithms maintain and evolve two separate populations, one with feasible and one with infeasible individuals, while each population can use its own selection method. The proposed algorithms are applied to the problem of generating diverse but playable game levels, which is representative of the larger problem of procedural game content generation. Results show that the two-population constrained novelty search methods can create, under certain conditions, larger and more diverse sets of feasible game levels than current methods of novelty search, whether constrained or unconstrained. However, the best algorithm is contingent on the particularities of the search space and the genetic operators used. Additionally, the proposed enhancement of offspring boosting is shown to enhance performance in all cases of two-population novelty search.

The use of combinations of organic additives to control crystallization, as occurs in biomineralization, is rarely investigated due to the vast potential reaction space. It is demonstrated here that combinatorial approaches led by genetic algorithm heuristics can enable identification of active additive combinations, and four key organic molecules are rapidly identified, which generate highly fluorescent CdS quantum dot superstructures., (© 2014 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In this study the problem of protein fold recognition, that is a classification task, is solved via a hybrid of evolutionary algorithms namely multi-gene Genetic Programming (GP) and Genetic Algorithm (GA). Our proposed method consists of two main stages and is performed on three datasets taken from the literature. Each dataset contains different feature groups and classes. In the first step, multi-gene GP is used for producing binary classifiers based on various feature groups for each class. Then, different classifiers obtained for each class are combined via weighted voting so that the weights are determined through GA. At the end of the first step, there is a separate binary classifier for each class. In the second stage, the obtained binary classifiers are combined via GA weighting in order to generate the overall classifier. The final obtained classifier is superior to the previous works found in the literature in terms of classification accuracy.