Protein structure prediction with energy minimization and deep learning approaches.

In this paper we discuss the advantages and problems of two alternatives for ab initio protein structure prediction. On one hand, recent approaches based on deep learning, which have significantly improved prediction results for a wide variety of proteins, are discussed. On the other hand, methods based on protein conformational energy minimization and with different search strategies are analyzed. In this latter case, our methods based on a memetic combination between differential evolution and the fragment replacement technique are included, incorporating also the possibility of niching in the evolutionary search. Different proteins have been used to analyze the pros and cons in both approaches, proposing possibilities of integration of both alternatives.

Speeding up Smartphone-Based Dew Computing: In Vivo Experiments Setup Via an Evolutionary Algorithm.

Dew computing aims to minimize the dependency on remote clouds by exploiting nearby nodes for solving non-trivial computational tasks, e.g., AI inferences. Nowadays, smartphones are good candidates for computing nodes; hence, smartphone clusters have been proposed to accomplish this task and load balancing is frequently a subject of research. Using the same real-i.e., in vivo-testbeds to evaluate different load balancing strategies based on energy utilization is challenging and time consuming. In principle, test repetition requires a platform to control battery charging periods between repetitions. Our Motrol hard-soft device has such a capability; however, it lacks a mechanism to assure and reduce the time in which all smartphone batteries reach the level required by the next test. We propose an evolutionary algorithm to execute smartphone battery (dis)charging plans to minimize test preparation time. Charging plans proposed by the algorithm include charging at different speeds, which is achieved by charging at maximum speed while exercising energy hungry components (the CPU and screen). To evaluate the algorithm, we use various charging/discharging battery traces of real smartphones and we compare the time-taken for our method to collectively prepare a set of smartphones versus that of individually (dis)charging all smartphones at maximum speed.

Plant and Salamander Inspired Network Attack Detection and Data Recovery Model.

The number of users of the Internet has been continuously rising, with an estimated 5.1 billion users in 2023, which comprises around 64.7% of the total world population. This indicates the rise of more connected devices to the network. On average, 30,000 websites are hacked daily, and nearly 64% of companies worldwide experience at least one type of cyberattack. As per IDC's 2022 Ransomware study, two-thirds of global organizations were hit by a ransomware attack that year. This creates the desire for a more robust and evolutionary attack detection and recovery model. One aspect of the study is the bio-inspiration models. This is because of the natural ability of living organisms to withstand various odd circumstances and overcome them with an optimization strategy. In contrast to the limitations of machine learning models with the need for quality datasets and computational availability, bio-inspired models can perform in low computational environments, and their performances are designed to evolve naturally with time. This study concentrates on exploring the evolutionary defence mechanism in plants and understanding how plants react to any known external attacks and how the response mechanism changes to unknown attacks. This study also explores how regenerative models, such as salamander limb regeneration, could build a network recovery system where services could be automatically activated after a network attack, and data could be recovered automatically by the network after a ransomware-like attack. The performance of the proposed model is compared to open-source IDS Snort and data recovery systems such as Burp and Casandra.

Inverse Generative Social Science: Backward to the Future.

The agent-based model is the principal scientific instrument of generative social science. Typically, we design completed agents-fully endowed with rules and parameters-to grow macroscopic target patterns from the bottom up. Inverse generative science (iGSS) stands this approach on its head: Rather than handcrafting completed agents to grow a target-the forward problem-we start with the macro-target and evolve micro-agents that generate it, stipulating only primitive agent-rule constituents and permissible combinators. Rather than specific agents as designed inputs, we are interested in agents-indeed, families of agents-as evolved outputs. This is the backward problem and tools from Evolutionary Computing can help us solve it. In this overarching essay of the current JASSS Special Section, Part 1 discusses the motivation for iGSS. Part 2 discusses its goals, as distinct from other approaches. Part 3 discusses how to do it concretely, previewing the five iGSS applications that follow. Part 4 discusses several foundational issues for agent-based modeling and economics. Part 5 proposes a central future application of iGSS: to evolve explicit formal alternatives to the Rational Actor, with Agent_Zero as one possible point of evolutionary departure. Conclusions and future research directions are offered in Part 6. Looking 'backward to the future,' I also include, as Appendices, a pair of 1992 memoranda to the then President of the Santa Fe Institute on the forward (growing artificial societies from the bottom up) and backward (iGSS) problems.

Placement of Optical Sensors in 3D Terrain Using a Bacterial Evolutionary Algorithm.

This paper proposes an optimization framework for terrain large scale optical sensor placement to improve border protection. Compared to the often used, maximal coverage of an area approach, this method minimizes the undetected passages in the monitored area. Border protection is one of the most critical areas for sensor placement. Unlike traditional border protection solutions, we do not optimize for 2D but for 3D to prevent transit. Additionally, we consider both natural and built environmental coverings. The applied environmental model creates a highly inhomogeneous sensing area for sensors instead of the previously used homogeneous one. The detection of each sensor was provided by a line-of-sight model supplemented with inhomogeneous probabilities. The optimization was performed using a bacterial evolutionary algorithm. In addition to maximizing detection, minimizing the number of the applied sensors played a crucial role in design. These two cost components are built on each other hierarchically. The developed simulation framework based on ray tracing provided an excellent opportunity to optimize large areas. The presented simulation results prove the efficiency of this method. The results were evaluated by testing on a large number of intruders. Using sensors with different quantities and layouts in the tested 1×1×1 km environment, we reduced the probability of undetected intrusion to below 0.1% and increased the probability of acceptable classification to 99%.

Design of a Low-Power Embedded System Based on a SoC-FPGA and the Honeybee Search Algorithm for Real-Time Video Tracking.

Video tracking involves detecting previously designated objects of interest within a sequence of image frames. It can be applied in robotics, unmanned vehicles, and automation, among other fields of interest. Video tracking is still regarded as an open problem due to a number of obstacles that still need to be overcome, including the need for high precision and real-time results, as well as portability and low-power demands. This work presents the design, implementation and assessment of a low-power embedded system based on an SoC-FPGA platform and the honeybee search algorithm (HSA) for real-time video tracking. HSA is a meta-heuristic that combines evolutionary computing and swarm intelligence techniques. Our findings demonstrated that the combination of SoC-FPGA and HSA reduced the consumption of computational resources, allowing real-time multiprocessing without a reduction in precision, and with the advantage of lower power consumption, which enabled portability. A starker difference was observed when measuring the power consumption. The proposed SoC-FPGA system consumed about 5 Watts, whereas the CPU-GPU system required more than 200 Watts. A general recommendation obtained from this research is to use SoC-FPGA over CPU-GPU to work with meta-heuristics in computer vision applications when an embedded solution is required.

Optimization of Deep Architectures for EEG Signal Classification: An AutoML Approach Using Evolutionary Algorithms.

Electroencephalography (EEG) signal classification is a challenging task due to the low signal-to-noise ratio and the usual presence of artifacts from different sources. Different classification techniques, which are usually based on a predefined set of features extracted from the EEG band power distribution profile, have been previously proposed. However, the classification of EEG still remains a challenge, depending on the experimental conditions and the responses to be captured. In this context, the use of deep neural networks offers new opportunities to improve the classification performance without the use of a predefined set of features. Nevertheless, Deep Learning architectures include a vast number of hyperparameters on which the performance of the model relies. In this paper, we propose a method for optimizing Deep Learning models, not only the hyperparameters, but also their structure, which is able to propose solutions that consist of different architectures due to different layer combinations. The experimental results corroborate that deep architectures optimized by our method outperform the baseline approaches and result in computationally efficient models. Moreover, we demonstrate that optimized architectures improve the energy efficiency with respect to the baseline models.

An optimal cascaded recurrent neural network for intelligent COVID-19 detection using Chest X-ray images.

In recent times, COVID-19, has a great impact on the healthcare sector and results in a wide range of respiratory illnesses. It is a type of Ribonucleic acid (RNA) virus, which affects humans as well as animals. Though several artificial intelligence-based COVID-19 diagnosis models have been presented in the literature, most of the works have not focused on the hyperparameter tuning process. Therefore, this paper proposes an intelligent COVID-19 diagnosis model using a barnacle mating optimization (BMO) algorithm with a cascaded recurrent neural network (CRNN) model, named BMO-CRNN. The proposed BMO-CRNN model aims to detect and classify the existence of COVID-19 from Chest X-ray images. Initially, pre-processing is applied to enhance the quality of the image. Next, the CRNN model is used for feature extraction, followed by hyperparameter tuning of CRNN via the BMO algorithm to improve the classification performance. The BMO algorithm determines the optimal values of the CRNN hyperparameters namely learning rate, batch size, activation function, and epoch count. The application of CRNN and hyperparameter tuning using the BMO algorithm shows the novelty of this work. A comprehensive simulation analysis is carried out to ensure the better performance of the BMO-CRNN model, and the experimental outcome is investigated using several performance metrics. The simulation results portrayed that the BMO-CRNN model has showcased optimal performance with an average sensitivity of 97.01%, specificity of 98.15%, accuracy of 97.31%, and F-measure of 97.73% compared to state-of-the-art methods.

Optimal Design of Switchable Wearable Antenna Array for Wireless Sensor Networks.

In the paper, we present a novel approach to the optimum design of wearable antenna arrays intended for off-body links of wireless body area networks. Specifically, we investigate a four-element array that has a switchable radiation pattern able to direct its higher gain towards a signal source and a lower gain towards an interference. The aim is to increase the signal to interference ratio. We apply a genetic algorithm to optimize both the spatial placement and the feed phasing of the elementary on-body antennas. We propose a simplified, computationally efficient model for the simulation of the array radiation pattern. The model is based on full-wave simulations obtained with a simplified cylindrical model of the human body. We also propose, implement, and evaluate four objective functions based on signal to interference ratio, i.e., min-max, nadir point distance maximization, utopia point distance minimization, and full Pareto-like. Our optimized design obtained with this approach exhibits a significant performance improvement in comparison to the initial heuristic design.

Many-Objective Automated Optimization of a Four-Band Antenna for Multiband Wireless Sensor Networks.

This paper describes a new design and an optimization framework for a four-band antenna to be used in wireless sensor networks. The antenna is designed to operate effectively in two open frequency bands (ISM-Industrial, Scientific, Medical), 2.4 GHz and 5.8 GHz, as well as in two bands allocated for the fifth-generation (5G) cellular networks, 0.7 GHz and 3.5 GHz. Our initial design was developed using the trial and error approach, modifying a circular disc monopole antenna widely used in ultra wideband (UWB) systems. This initial design covered the three upper bands, but impedance matching within the 700 MHz band was unsatisfactory. The antenna performance was then improved significantly using an optimization algorithm that applies a bi-objective fully-Paretian approach to its nine-parameter geometry. The optimization criteria were impedance matching and radiation efficiency. The final design exhibits good impedance matching in all four desired bands with the Voltage Standing Wave Ratio (VSWR) value below 2 and radiation efficiency of 88%. The simulated antenna performance was verified experimentally.

Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.

BACKGROUND: The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered. RESULTS: The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape. CONCLUSIONS: Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.

The ENCODE project and perspectives on pathways.

The recently completed ENCODE project is a new source of information on metabolic activity, unveiling knowledge about evolution and similarities among species, refuting the myth that most DNA is "junk" and has no actual function. With this expansive resource comes a challenge: integrating these new layers of information into our current knowledge of single-nucleotide polymorphisms and previously described metabolic pathways with the aim of discovering new genes and pathways related to human diseases and traits. Further, we must determine which computational methods will be most useful in this pursuit. In this paper, we speculate over the possible methods that will emerge in this new, challenging field.

Evolutionary strategy to develop learning-based decision systems. Application to breast cancer and liver fibrosis stadialization.

The purpose of this paper is twofold: first, to propose an evolutionary-based method for building a decision model and, second, to assess and validate the model's performance using five different real-world medical datasets (breast cancer and liver fibrosis) by comparing it with state-of-the-art machine learning techniques. The evolutionary-inspired approach has been used to develop the learning-based decision model in the following manner: the hybridization of algorithms has been considered as "crossover", while the development of new variants which can be thought of as "mutation". An appropriate hierarchy of the component algorithms was established based on a statistically built fitness measure. A synergetic decision-making process, based on a weighted voting system, involved the collaboration between the selected algorithms in making the final decision. Well-established statistical performance measures and comparison tests have been extensively used to design and implement the model. Finally, the proposed method has been tested on five medical datasets, out of which four publicly available, and contrasted with state-of-the-art techniques, showing its efficiency in supporting the medical decision-making process.

Image sequence sorting algorithm for commercial tasks.

Introduction: The sorting of sequences of images is crucial for augmenting user engagement in various virtual commercial platforms, particularly within the real estate sector. A coherent sequence of images respecting room type categorization significantly enhances the intuitiveness and seamless navigation of potential customers through listings. Methods: This study methodically formalizes the challenge of image sequence sorting and expands its applicability by framing it as an ordering problem. The complexity lies in devising a universally applicable solution due to computational demands and impracticality of exhaustive searches for optimal sequencing. To tackle this, our proposed algorithm employs a shortest path methodology grounded in semantic similarity between images. Tailored specifically for the real estate sector, it evaluates diverse similarity metrics to efficiently arrange images. Additionally, we introduce a genetic algorithm to optimize the selection of semantic features considered by the algorithm, further enhancing its effectiveness. Results: Empirical evidence from our dataset demonstrates the efficacy of the proposed methodology. It successfully organizes images in an optimal sequence across 85% of the listings, showcasing its effectiveness in enhancing user experience in virtual commercial platforms, particularly in real estate. Conclusion: This study presents a novel approach to sorting sequences of images in virtual commercial platforms, particularly beneficial for the real estate sector. The proposed algorithm effectively enhances user engagement by providing more intuitive and visually coherent image arrangements.

MEMINV: A hybrid efficient approximation method solving the multi skill-resource constrained project scheduling problem.

The Multi-Skill Resource-Constrained Project Scheduling Problem (MS-RCPSP) is an NP-Hard problem that involves scheduling activities while accounting for resource and technical constraints. This paper aims to present a novel hybrid algorithm called MEMINV, which combines the Memetic algorithm with the Inverse method to tackle the MS-RCPSP problem. The proposed algorithm utilizes the inverse method to identify local extremes and then relocates the population to explore new solution spaces for further evolution. The MEMINV algorithm is evaluated on the iMOPSE benchmark dataset, and the results demonstrate that it outperforms. The solution of the MS-RCPSP problem using the MEMINV algorithm is a schedule that can be used for intelligent production planning in various industrial production fields instead of manual planning.

Artificial selection methods from evolutionary computing show promise for directed evolution of microbes.

Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a general-purpose search engine for solutions to challenging computational problems. Despite their overlapping approaches, artificial selection methods from evolutionary computing are not commonly applied to living systems in the laboratory. In this work, we ask whether parent selection algorithms-procedures for choosing promising progenitors-from evolutionary computation might be useful for directing the evolution of microbial populations when selecting for multiple functional traits. To do so, we introduce an agent-based model of directed microbial evolution, which we used to evaluate how well three selection algorithms from evolutionary computing (tournament selection, lexicase selection, and non-dominated elite selection) performed relative to methods commonly used in the laboratory (elite and top 10% selection). We found that multiobjective selection techniques from evolutionary computing (lexicase and non-dominated elite) generally outperformed the commonly used directed evolution approaches when selecting for multiple traits of interest. Our results motivate ongoing work transferring these multiobjective selection procedures into the laboratory and a continued evaluation of more sophisticated artificial selection methods.

Humans have long known how to co-opt evolutionary processes for their own benefit. Carefully choosing which individuals to breed so that beneficial traits would take hold, they have domesticated dogs, wheat, cows and many other species to fulfil their needs. Biologists have recently refined these 'artificial selection' approaches to focus on microorganisms. The hope is to obtain microbes equipped with desirable features, such as the ability to degrade plastic or to produce valuable molecules. However, existing ways of using artificial selection on microbes are limited and sometimes not effective. Computer scientists have also harnessed evolutionary principles for their own purposes, developing highly effective artificial selection protocols that are used to find solutions to challenging computational problems. Yet because of limited communication between the two fields, sophisticated selection protocols honed over decades in evolutionary computing have yet to be evaluated for use in biological populations. In their work, Lalejini et al. compared popular artificial selection protocols developed for either evolutionary computing or work with microorganisms. Two computing selection methods showed promise for improving directed evolution in the laboratory. Crucially, these selection protocols differed from conventionally used methods by selecting for both diversity and performance, rather than performance alone. These promising approaches are now being tested in the laboratory, with potentially far-reaching benefits for medical, biotech, and agricultural applications. While evolutionary computing owes its origins to our understanding of biological processes, it has much to offer in return to help us harness those same mechanisms. The results by Lalejini et al. help to bridge the gap between computational and biological communities who could both benefit from increased collaboration.

Estimation of COVID-19 epidemic curves using genetic programming algorithm.

This paper investigates the possibility of the implementation of Genetic Programming (GP) algorithm on a publicly available COVID-19 data set, in order to obtain mathematical models which could be used for estimation of confirmed, deceased, and recovered cases and the estimation of epidemiology curve for specific countries, with a high number of cases, such as China, Italy, Spain, and USA and as well as on the global scale. The conducted investigation shows that the best mathematical models produced for estimating confirmed and deceased cases achieved R2 scores of 0.999, while the models developed for estimation of recovered cases achieved the R2 score of 0.998. The equations generated for confirmed, deceased, and recovered cases were combined in order to estimate the epidemiology curve of specific countries and on the global scale. The estimated epidemiology curve for each country obtained from these equations is almost identical to the real data contained within the data set.

COVID-19 Infection Detection from Chest X-Ray Images Using Hybrid Social Group Optimization and Support Vector Classifier.

A novel strain of Coronavirus, identified as the Severe Acute Respiratory Syndrome-2 (SARS-CoV-2), outbroke in December 2019 causing the novel Corona Virus Disease (COVID-19). Since its emergence, the virus has spread rapidly and has been declared a global pandemic. As of the end of January 2021, there are almost 100 million cases worldwide with over 2 million confirmed deaths. Widespread testing is essential to reduce further spread of the disease, but due to a shortage of testing kits and limited supply, alternative testing methods are being evaluated. Recently researchers have found that chest X-Ray (CXR) images provide salient information about COVID-19. An intelligent system can help the radiologists to detect COVID-19 from these CXR images which can come in handy at remote locations in many developing nations. In this work, we propose a pipeline that uses CXR images to detect COVID-19 infection. The features from the CXR images were extracted and the relevant features were then selected using Hybrid Social Group Optimization algorithm. The selected features were then used to classify the CXR images using a number of classifiers. The proposed pipeline achieves a classification accuracy of 99.65% using support vector classifier, which outperforms other state-of-the-art deep learning algorithms for binary and multi-class classification.

A comparative analysis of metaheuristics applied to adaptive curriculum sequencing.

The effective adoption of online learning depends on user satisfaction as distance education approaches suffer from a lack of commitment that may lead to failures and dropouts. The adaptive learning literature argues that an alternative to achieve student satisfaction is to treat them individually, delivering the educational content in a personalized manner. In addition, the sequencing of this content-called Adaptive Curriculum Sequencing (ACS)-is important to avoid cognitive overload and disorientation. The search for an optimal sequence from ever-growing databases is an NP-Hard combinatorial optimization problem. Although some approaches have been proposed, it is challenging to assess their contributions due to the lack of benchmark data available. This paper presents a procedure to create synthetic dataset to evaluate ACS approaches and, as a concept proof, analyzes metaheuristics usually used in ACS approaches: Genetic Algorithm, Particle Swarm Optimization (PSO) and Prey-Predator Algorithm using student's learning goals and their extrinsic and intrinsic information. We also propose an approach based on Differential Evolution (DE). The computational experiments include synthetic datasets with a varied amount of learning materials and real-world datasets for comparison. The results show that DE performed better than the other methods when less than 500 learning materials are used while PSO performed better for larger problems.

GeFeS: A generalized wrapper feature selection approach for optimizing classification performance.

In this paper, we propose a generalized wrapper-based feature selection, called GeFeS, which is based on a parallel new intelligent genetic algorithm (GA). The proposed GeFeS works properly under different numerical dataset dimensions and sizes, carefully tries to avoid overfitting and significantly enhances classification accuracy. To make the GA more accurate, robust and intelligent, we have proposed a new operator for features weighting, improved the mutation and crossover operators, and integrated nested cross-validation into the GA process to properly validate the learning model. The k-nearest neighbor (kNN) classifier is utilized to evaluate the goodness of selected features. We have evaluated the efficiency of GeFeS on various datasets selected from the UCI machine learning repository. The performance is compared with state-of-the-art classification and feature selection methods. The results demonstrate that GeFeS can significantly generalize the proposed multi-population intelligent genetic algorithm under different sizes of two-class and multi-class datasets. We have achieved the average classification accuracy of 95.83%, 97.62%, 99.02%, 98.51%, and 94.28% while reducing the number of features from 56 to 28, 34 to 18, 279 to 135, 30 to 16, and 19 to 9 under lung cancer, dermatology, arrhythmia, WDBC, and hepatitis, respectively.