Historical biogeography and evolutionary diversification of Lilium(Liliaceae): New insights from plastome phylogenomics

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium(14plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a timecalibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum(MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau(QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.

Evolutionary Optimization Methods for High-Dimensional Expensive Problems:A Survey

Evolutionary computation is a rapidly evolving field and the related algorithms have been successfully used to solve various real-world optimization problems.The past decade has also witnessed their fast progress to solve a class of challenging optimization problems called high-dimensional expensive problems(HEPs).The evaluation of their objective fitness requires expensive resource due to their use of time-consuming physical experiments or computer simulations.Moreover,it is hard to traverse the huge search space within reasonable resource as problem dimension increases.Traditional evolutionary algorithms(EAs)tend to fail to solve HEPs competently because they need to conduct many such expensive evaluations before achieving satisfactory results.To reduce such evaluations,many novel surrogate-assisted algorithms emerge to cope with HEPs in recent years.Yet there lacks a thorough review of the state of the art in this specific and important area.This paper provides a comprehensive survey of these evolutionary algorithms for HEPs.We start with a brief introduction to the research status and the basic concepts of HEPs.Then,we present surrogate-assisted evolutionary algorithms for HEPs from four main aspects.We also give comparative results of some representative algorithms and application examples.Finally,we indicate open challenges and several promising directions to advance the progress in evolutionary optimization algorithms for HEPs.

Integrating high-volume molecular and morphological data into the evolutionary studies of Allium

The genus Allium(Amaryllidaceae),which includes economically important plants such as onions,garlic,and leeks,is one of the most species-rich and diverse genera of monocotyledon plants in the Northern Hemisphere(Govaerts et al.,2021),with approximately 1000 species.The evolution of Allium is characterized by ecological diversification,with most species preferring open.

Evolutionary Multi/Many-Objective Optimisation via Bilevel

Decomposition of a complex multi-objective optimisation problem(MOP)to multiple simple subMOPs,known as M2M for short,is an effective approach to multi-objective optimisation.However,M2M facilitates little communication/collaboration between subMOPs,which limits its use in complex optimisation scenarios.This paper extends the M2M framework to develop a unified algorithm for both multi-objective and manyobjective optimisation.Through bilevel decomposition,an MOP is divided into multiple subMOPs at upper level,each of which is further divided into a number of single-objective subproblems at lower level.Neighbouring subMOPs are allowed to share some subproblems so that the knowledge gained from solving one subMOP can be transferred to another,and eventually to all the subMOPs.The bilevel decomposition is readily combined with some new mating selection and population update strategies,leading to a high-performance algorithm that competes effectively against a number of state-of-the-arts studied in this paper for both multiand many-objective optimisation.Parameter analysis and component analysis have been also carried out to further justify the proposed algorithm.

Evolutionary game dynamics of combining two different aspiration-driven update rules in structured populations

In evolutionary games,most studies on finite populations have focused on a single updating mechanism.However,given the differences in individual cognition,individuals may change their strategies according to different updating mechanisms.For this reason,we consider two different aspiration-driven updating mechanisms in structured populations:satisfied-stay unsatisfied shift(SSUS)and satisfied-cooperate unsatisfied defect(SCUD).To simulate the game player’s learning process,this paper improves the particle swarm optimization algorithm,which will be used to simulate the game player’s strategy selection,i.e.,population particle swarm optimization(PPSO)algorithms.We find that in the prisoner’s dilemma,the conditions that SSUS facilitates the evolution of cooperation do not enable cooperation to emerge.In contrast,SCUD conditions that promote the evolution of cooperation enable cooperation to emerge.In addition,the invasion of SCUD individuals helps promote cooperation among SSUS individuals.Simulated by the PPSO algorithm,the theoretical approximation results are found to be consistent with the trend of change in the simulation results.

On the evolutionary trail of MagRs

Magnetic sense,or termed magnetoreception,has evolved in a broad range of taxa within the animal kingdom to facilitate orientation and navigation.MagRs,highly conserved A-type iron-sulfur proteins,are widely distributed across all phyla and play essential roles in both magnetoreception and iron-sulfur cluster biogenesis.However,the evolutionary origins and functional diversification of MagRs from their prokaryotic ancestor remain unclear.In this study,MagR sequences from 131 species,ranging from bacteria to humans,were selected for analysis,with 23 representative sequences covering species from prokaryotes to Mollusca,Arthropoda,Osteichthyes,Reptilia,Aves,and mammals chosen for protein expression and purification.Biochemical studies revealed a gradual increase in total iron content in MagRs during evolution.Three types of MagRs were identified,each with distinct iron and/or iron-sulfur cluster binding capacity and protein stability,indicating continuous expansion of the functional roles of MagRs during speciation and evolution.This evolutionary biochemical study provides valuable insights into how evolution shapes the physical and chemical properties of biological molecules such as MagRs and how these properties influence the evolutionary trajectories of MagRs.

Optimizing Deep Learning for Computer-Aided Diagnosis of Lung Diseases: An Automated Method Combining Evolutionary Algorithm, Transfer Learning, and Model Compression

Recent developments in Computer Vision have presented novel opportunities to tackle complex healthcare issues,particularly in the field of lung disease diagnosis.One promising avenue involves the use of chest X-Rays,which are commonly utilized in radiology.To fully exploit their potential,researchers have suggested utilizing deep learning methods to construct computer-aided diagnostic systems.However,constructing and compressing these systems presents a significant challenge,as it relies heavily on the expertise of data scientists.To tackle this issue,we propose an automated approach that utilizes an evolutionary algorithm(EA)to optimize the design and compression of a convolutional neural network(CNN)for X-Ray image classification.Our approach accurately classifies radiography images and detects potential chest abnormalities and infections,including COVID-19.Furthermore,our approach incorporates transfer learning,where a pre-trainedCNNmodel on a vast dataset of chest X-Ray images is fine-tuned for the specific task of detecting COVID-19.This method can help reduce the amount of labeled data required for the task and enhance the overall performance of the model.We have validated our method via a series of experiments against state-of-the-art architectures.

Evolutionary Neural Architecture Search and Its Applications in Healthcare

Most of the neural network architectures are based on human experience,which requires a long and tedious trial-and-error process.Neural architecture search(NAS)attempts to detect effective architectures without human intervention.Evolutionary algorithms(EAs)for NAS can find better solutions than human-designed architectures by exploring a large search space for possible architectures.Using multiobjective EAs for NAS,optimal neural architectures that meet various performance criteria can be explored and discovered efficiently.Furthermore,hardware-accelerated NAS methods can improve the efficiency of the NAS.While existing reviews have mainly focused on different strategies to complete NAS,a few studies have explored the use of EAs for NAS.In this paper,we summarize and explore the use of EAs for NAS,as well as large-scale multiobjective optimization strategies and hardware-accelerated NAS methods.NAS performs well in healthcare applications,such as medical image analysis,classification of disease diagnosis,and health monitoring.EAs for NAS can automate the search process and optimize multiple objectives simultaneously in a given healthcare task.Deep neural network has been successfully used in healthcare,but it lacks interpretability.Medical data is highly sensitive,and privacy leaks are frequently reported in the healthcare industry.To solve these problems,in healthcare,we propose an interpretable neuroevolution framework based on federated learning to address search efficiency and privacy protection.Moreover,we also point out future research directions for evolutionary NAS.Overall,for researchers who want to use EAs to optimize NNs in healthcare,we analyze the advantages and disadvantages of doing so to provide detailed guidance,and propose an interpretable privacy-preserving framework for healthcare applications.

Constraints Separation Based Evolutionary Multitasking for Constrained Multi-Objective Optimization Problems

Constrained multi-objective optimization problems(CMOPs)generally contain multiple constraints,which not only form multiple discrete feasible regions but also reduce the size of optimal feasible regions,thus they propose serious challenges for solvers.Among all constraints,some constraints are highly correlated with optimal feasible regions;thus they can provide effective help to find feasible Pareto front.However,most of the existing constrained multi-objective evolutionary algorithms tackle constraints by regarding all constraints as a whole or directly ignoring all constraints,and do not consider judging the relations among constraints and do not utilize the information from promising single constraints.Therefore,this paper attempts to identify promising single constraints and utilize them to help solve CMOPs.To be specific,a CMOP is transformed into a multitasking optimization problem,where multiple auxiliary tasks are created to search for the Pareto fronts that only consider a single constraint respectively.Besides,an auxiliary task priority method is designed to identify and retain some high-related auxiliary tasks according to the information of relative positions and dominance relationships.Moreover,an improved tentative method is designed to find and transfer useful knowledge among tasks.Experimental results on three benchmark test suites and 11 realworld problems with different numbers of constraints show better or competitive performance of the proposed method when compared with eight state-of-the-art peer methods.

Enhancing Evolutionary Algorithms With Pattern Mining for Sparse Large-Scale Multi-Objective Optimization Problems

Sparse large-scale multi-objective optimization problems(SLMOPs)are common in science and engineering.However,the large-scale problem represents the high dimensionality of the decision space,requiring algorithms to traverse vast expanse with limited computational resources.Furthermore,in the context of sparse,most variables in Pareto optimal solutions are zero,making it difficult for algorithms to identify non-zero variables efficiently.This paper is dedicated to addressing the challenges posed by SLMOPs.To start,we introduce innovative objective functions customized to mine maximum and minimum candidate sets.This substantial enhancement dramatically improves the efficacy of frequent pattern mining.In this way,selecting candidate sets is no longer based on the quantity of nonzero variables they contain but on a higher proportion of nonzero variables within specific dimensions.Additionally,we unveil a novel approach to association rule mining,which delves into the intricate relationships between non-zero variables.This novel methodology aids in identifying sparse distributions that can potentially expedite reductions in the objective function value.We extensively tested our algorithm across eight benchmark problems and four real-world SLMOPs.The results demonstrate that our approach achieves competitive solutions across various challenges.

Hybrid Hierarchical Particle Swarm Optimization with Evolutionary Artificial Bee Colony Algorithm for Task Scheduling in Cloud Computing

Task scheduling plays a key role in effectively managing and allocating computing resources to meet various computing tasks in a cloud computing environment.Short execution time and low load imbalance may be the challenges for some algorithms in resource scheduling scenarios.In this work,the Hierarchical Particle Swarm Optimization-Evolutionary Artificial Bee Colony Algorithm(HPSO-EABC)has been proposed,which hybrids our presented Evolutionary Artificial Bee Colony(EABC),and Hierarchical Particle Swarm Optimization(HPSO)algorithm.The HPSO-EABC algorithm incorporates both the advantages of the HPSO and the EABC algorithm.Comprehensive testing including evaluations of algorithm convergence speed,resource execution time,load balancing,and operational costs has been done.The results indicate that the EABC algorithm exhibits greater parallelism compared to the Artificial Bee Colony algorithm.Compared with the Particle Swarm Optimization algorithm,the HPSO algorithmnot only improves the global search capability but also effectively mitigates getting stuck in local optima.As a result,the hybrid HPSO-EABC algorithm demonstrates significant improvements in terms of stability and convergence speed.Moreover,it exhibits enhanced resource scheduling performance in both homogeneous and heterogeneous environments,effectively reducing execution time and cost,which also is verified by the ablation experimental.

Enhancing Cancer Classification through a Hybrid Bio-Inspired Evolutionary Algorithm for Biomarker Gene Selection

In this study,our aim is to address the problem of gene selection by proposing a hybrid bio-inspired evolutionary algorithm that combines Grey Wolf Optimization(GWO)with Harris Hawks Optimization(HHO)for feature selection.Themotivation for utilizingGWOandHHOstems fromtheir bio-inspired nature and their demonstrated success in optimization problems.We aimto leverage the strengths of these algorithms to enhance the effectiveness of feature selection in microarray-based cancer classification.We selected leave-one-out cross-validation(LOOCV)to evaluate the performance of both two widely used classifiers,k-nearest neighbors(KNN)and support vector machine(SVM),on high-dimensional cancer microarray data.The proposed method is extensively tested on six publicly available cancer microarray datasets,and a comprehensive comparison with recently published methods is conducted.Our hybrid algorithm demonstrates its effectiveness in improving classification performance,Surpassing alternative approaches in terms of precision.The outcomes confirm the capability of our method to substantially improve both the precision and efficiency of cancer classification,thereby advancing the development ofmore efficient treatment strategies.The proposed hybridmethod offers a promising solution to the gene selection problem in microarray-based cancer classification.It improves the accuracy and efficiency of cancer diagnosis and treatment,and its superior performance compared to other methods highlights its potential applicability in realworld cancer classification tasks.By harnessing the complementary search mechanisms of GWO and HHO,we leverage their bio-inspired behavior to identify informative genes relevant to cancer diagnosis and treatment.

Nonlinear Relationship and Its Evolutionary Trace between Node Degree and Average Path Length of China Aviation Network Based on Complex Network

In order to reveal the complex network characteristics and evolution principle of China aviation network,the relationship between the node degree and the average path length of China aviation network in 1988,1994,2001,2008 and 2015 was studied.According to the theory and method of complex network,the network system was constructed with the city where the airport was located as the network node and the airline as the edge of the network.On the basis of the statistical data,the node average path length of China aviation network in 1988,1994,2001,2008 and 2015 was calculated.Through regression analysis,it was found that the node degree had a logarithmic relationship with the average length of node path,and the two parameters of the logarithmic relationship had linear evolutionary trace.Key word:China aviation network,complex network,node degree,average length of node path,logarithmic relationship,evolutionary trace.

A Fast Clustering Based Evolutionary Algorithm for Super-Large-Scale Sparse Multi-Objective Optimization

During the last three decades,evolutionary algorithms(EAs)have shown superiority in solving complex optimization problems,especially those with multiple objectives and non-differentiable landscapes.However,due to the stochastic search strategies,the performance of most EAs deteriorates drastically when handling a large number of decision variables.To tackle the curse of dimensionality,this work proposes an efficient EA for solving super-large-scale multi-objective optimization problems with sparse optimal solutions.The proposed algorithm estimates the sparse distribution of optimal solutions by optimizing a binary vector for each solution,and provides a fast clustering method to highly reduce the dimensionality of the search space.More importantly,all the operations related to the decision variables only contain several matrix calculations,which can be directly accelerated by GPUs.While existing EAs are capable of handling fewer than 10000 real variables,the proposed algorithm is verified to be effective in handling 1000000 real variables.Furthermore,since the proposed algorithm handles the large number of variables via accelerated matrix calculations,its runtime can be reduced to less than 10%of the runtime of existing EAs.

Evolutionary privacy-preserving learning strategies for edge-based IoT data sharing schemes

The fast proliferation of edge devices for the Internet of Things(IoT)has led to massive volumes of data explosion.The generated data is collected and shared using edge-based IoT structures at a considerably high frequency.Thus,the data-sharing privacy exposure issue is increasingly intimidating when IoT devices make malicious requests for filching sensitive information from a cloud storage system through edge nodes.To address the identified issue,we present evolutionary privacy preservation learning strategies for an edge computing-based IoT data sharing scheme.In particular,we introduce evolutionary game theory and construct a payoff matrix to symbolize intercommunication between IoT devices and edge nodes,where IoT devices and edge nodes are two parties of the game.IoT devices may make malicious requests to achieve their goals of stealing privacy.Accordingly,edge nodes should deny malicious IoT device requests to prevent IoT data from being disclosed.They dynamically adjust their own strategies according to the opponent's strategy and finally maximize the payoffs.Built upon a developed application framework to illustrate the concrete data sharing architecture,a novel algorithm is proposed that can derive the optimal evolutionary learning strategy.Furthermore,we numerically simulate evolutionarily stable strategies,and the final results experimentally verify the correctness of the IoT data sharing privacy preservation scheme.Therefore,the proposed model can effectively defeat malicious invasion and protect sensitive information from leaking when IoT data is shared.

Integrating genomic and morphological data into bamboo taxonomicand evolutionary studies

The Bambusoideae (bamboos),with over 1700 described species,is the third largest subfamily of the Poaceae (grasses),native to all continents except Antarctica and Europe (Clark et al.,2015;Soreng et al.,2022).Within the Bambusoideae,three tribes representing the three major lineages are recognized.The Olyreae comprise the ca.130 species of herbaceous bamboos,which are smaller and much less lignified than their woody cousins.

Dose reconstruction with Compton camera during proton therapy via subset-driven origin ensemble and double evolutionary algorithm

Compton camera-based prompt gamma(PG) imaging has been proposed for range verification during proton therapy. However, a deviation between the PG and dose distributions, as well as the difference between the reconstructed PG and exact values, limit the effectiveness of the approach in accurate range monitoring during clinical applications. The aim of the study was to realize a PG-based dose reconstruction with a Compton camera, thereby further improving the prediction accuracy of in vivo range verification and providing a novel method for beam monitoring during proton therapy. In this paper, we present an approach based on a subset-driven origin ensemble with resolution recovery and a double evolutionary algorithm to reconstruct the dose depth profile(DDP) from the gamma events obtained by a cadmium-zinc-telluride Compton camera with limited position and energy resolution. Simulations of proton pencil beams with clinical particle rate irradiating phantoms made of different materials and the CT-based thoracic phantom were used to evaluate the feasibility of the proposed method. The results show that for the monoenergetic proton pencil beam irradiating homogeneous-material box phantom,the accuracy of the reconstructed DDP was within 0.3 mm for range prediction and within 5.2% for dose prediction. In particular, for 1.6-Gy irradiation in the therapy simulation of thoracic tumors, the range deviation of the reconstructed spreadout Bragg peak was within 0.8 mm, and the relative dose deviation in the peak area was less than 7% compared to the exact values. The results demonstrate the potential and feasibility of the proposed method in future Compton-based accurate dose reconstruction and range verification during proton therapy.

Design and optimization of diffraction-limited storage ring lattices based on many-objective evolutionary algorithms

Multi-objective evolutionary algorithms(MOEAs) are typically used to optimize two or three objectives in the accelerator field and perform well. However, the performance of these algorithms may severely deteriorate when the optimization objectives for an accelerator are equal to or greater than four. Recently, many-objective evolutionary algorithms(MaOEAs)that can solve problems with four or more optimization objectives have received extensive attention. In this study, two diffraction-limited storage ring(DLSR) lattices of the Extremely Brilliant Source(ESRF-EBS) type with different energies were designed and optimized using three MaOEAs and a widely used MOEA. The initial population was found to have a significant impact on the performance of the algorithms and was carefully studied. The performances of the four algorithms were compared, and the results demonstrated that the grid-based evolutionary algorithm(GrEA) had the best performance.Ma OEAs were applied in many-objective optimization of DLSR lattices for the first time, and lattices with natural emittances of 116 and 23 pm·rad were obtained at energies of 2 and 6 GeV, respectively, both with reasonable dynamic aperture and local momentum aperture(LMA). This work provides a valuable reference for future many-objective optimization of DLSRs.

Dynamic Evolutionary Game-based Modeling,Analysis and Performance Enhancement of Blockchain Channels

The recent development of channel technology has promised to reduce the transaction verification time in blockchain operations.When transactions are transmitted through the channels created by nodes,the nodes need to cooperate with each other.If one party refuses to do so,the channel is unstable.A stable channel is thus required.Because nodes may show uncooperative behavior,they may have a negative impact on the stability of such channels.In order to address this issue,this work proposes a dynamic evolutionary game model based on node behavior.This model considers various defense strategies'cost and attack success ratio under them.Nodes can dynamically adjust their strategies according to the behavior of attackers to achieve their effective defense.The equilibrium stability of the proposed model can be achieved.The proposed model can be applied to general channel networks.It is compared with two state-of-the-art blockchain channels:Lightning network and Spirit channels.The experimental results show that the proposed model can be used to improve a channel's stability and keep it in a good cooperative stable state.Thus its use enables a blockchain to enjoy higher transaction success ratio and lower transaction transmission delay than the use of its two peers.

Tourism Route Recommendation Based on A Multi-Objective Evolutionary Algorithm Using Two-Stage Decomposition and Pareto Layering

Tourism route planning is widely applied in the smart tourism field.The Pareto-optimal front obtained by the traditional multi-objective evolutionary algorithm exhibits long tails,sharp peaks and disconnected regions problems,which leads to uneven distribution and weak diversity of optimization solutions of tourism routes.Inspired by these limitations,we propose a multi-objective evolutionary algorithm for tourism route recommendation(MOTRR)with two-stage and Pareto layering based on decomposition.The method decomposes the multiobjective problem into several subproblems,and improves the distribution of solutions through a two-stage method.The crowding degree mechanism between extreme and intermediate populations is used in the two-stage method.The neighborhood is determined according to the weight of the subproblem for crossover mutation.Finally,Pareto layering is used to improve the updating efficiency and population diversity of the solution.The two-stage method is combined with the Pareto layering structure,which not only maintains the distribution and diversity of the algorithm,but also avoids the same solutions.Compared with several classical benchmark algorithms,the experimental results demonstrate competitive advantages on five test functions,hypervolume(HV)and inverted generational distance(IGD)metrics.Using the experimental results of real scenic spot datasets from two famous tourism social networking sites with vast amounts of users and large-scale online comments in Beijing,our proposed algorithm shows better distribution.It proves that the tourism routes recommended by our proposed algorithm have better distribution and diversity,so that the recommended routes can better meet the personalized needs of tourists.