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Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization

National science Review 2023年第5期10卷 240-250页

作者： Sijie Zhou Yi Wu Yu Zhao Zhen Zhang Limin Jiang Lin Liu Yan Zhang Jijun Tang Ying-Jin Yuan Frontiers Science Center for Synthetic Biology (Ministry of Education) Tianjin University Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin University Institute for Systems Genetics NYU Langone Health School of Computer Science and Technology College of Intelligence and ComputingTianjin University Epigenetic Group Frasergen Bioinformatics Co.Ltd. Department of Computer Science University of South Carolina

Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary *** Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural ***,we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes(synⅡ,synⅢ,synⅤ,circular synⅥ,synⅨR and synⅩ).Remarkably,we find that the rearrangement events exhibit a specific landscape of *** further reveal that the landscape is shaped by the combined effects of chromatin accessibili and spatial contact *** rearrangements tend to occur in 3D spatially proximal and chromatin-accessible *** enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution,and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.

关键词： synthetic biology genome rearrangement hierarchical chromatin organization synthetic yeast genome SCRaMbLE Saccharomyces cerevisiae

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An Elite Archive-Assisted Multi-Objective evolutionary Algorithm for mRNA Design 13

An Elite Archive-Assisted Multi-Objective Evolutionary Algor...

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13th IEEE Congress on evolutionary Computation, CEC 2024

作者： Hong, Wenjing Chen, Cheng Zhu, Zexuan Tang, Ke Shenzhen University National Engineering Laboratory for Big Data System Computing Technology Shenzhen China Research Institute of Trustworthy Autonomous Systems Southern University of Science and Technology Shenzhen China Southern University of Science and Technology Department of Computer Science and Engineering Shenzhen China

ISBN: (纸本)9798350308365

Messenger RNA (mRNA) vaccines have emerged as highly effective strategies in the prophylaxis and treatment of diseases. mRNA design, a key to the success of mRNA vaccines, in-volves finding optimal codons and increasing secondary structure stability to lengthen mRNA half-life, ultimately enhancing protein expression. Despite receiving widespread attention, most methods primarily rely on manual design, which is time-consuming and labor-intensive. While optimization approaches can alleviate this issue, existing methods still exhibit critical limitations caused by conflicts between codon usage and mRNA structural stability, compounded by the vast design space of mRNA resulting from the presence of synonymous codons. In this paper, a novel multi-objective evolutionary optimization-based mRNA design method is proposed. We first formulate the mRNA design problem as a multi-objective optimization problem and then develop an Elite Archive-Assisted Multi-Objective evolutionary algorithm for mRNA Design, namely EAA-MOED, by incorporating a novel elite archive-assisted method into a weighted optimization framework to improve search efficiency. Experimental studies, involving two state-of-the-art mRNA design methods and five well-known MOEAs, show the competitiveness of the proposed EAA-MOED in mRNA design. © 2024 IEEE.

关键词： Vaccines

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Evolution of Web API Cooperation Network via Exploring Community Structure and Popularity

IEEE Transactions on Artificial Intelligence

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IEEE Transactions on Artificial Intelligence 2024年第12期5卷 6659-6671页

作者： Kang, Guosheng Wang, Yang Liu, Jianxun Cao, Buqing Xiao, Yong Xu, Yu Hunan University of Science and Technology Hunan Provincial Key Laboratory for Services Computing and Novel Software Technology School of Computer Science and Engineering Xiangtan411201 China University of Cambridge Cambridge Baker Systems Genomics Initiative British Heart Foundation Cardiovascular Epidemiology Unit Department of Public Health and Primary Care CambridgeCB1 8RN United Kingdom

With the growing popularity of the Internet, Web applications have become increasingly essential in our daily lives. Web application programming interfaces (Web APIs) play a crucial role in facilitating interaction between applications. However, most Web service platforms are suffering from the imbalance of Web services now, many services of good quality but low popularity are difficult to be invoked even once and do not create direct connections with the users. Some graph-based Web service recommendation methods also often present a long-tailed distribution of recommended Web services due to limited Mashup-API invocation relationships. To relieve this problem and promote service recommendation, in this article, we propose a community structure and popularity-based approach by constructing an evolving cooperation network for Web APIs. We leverage the Louvain algorithm in community detection to assign community structure to each Web API and consider both the popularity and community structure in constructing the network. By optimizing the Barabαsi-Albert (BA) evolving network model, we demonstrate that our approach outperforms the BA, Bianconi-Barabαsi (BB), and popularity-similarity optimization (PSO) models in Web service clustering. Based on our proposed evolutionary network model for the evolutionary extension of API cooperation network and used for downstream Web service recommendation tasks, the experimental results also show that our recommended approach outperforms some other baseline models for Web service recommendation. © 2020 IEEE.

关键词： Web services

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An Elite Archive-Assisted Multi-Objective evolutionary Algorithm for mRNA Design

An Elite Archive-Assisted Multi-Objective Evolutionary Algor...

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Congress on evolutionary Computation

作者： Wenjing Hong Cheng Chen Zexuan Zhu Ke Tang National Engineering Laboratory for Big Data System Computing Technology Shenzhen University Shenzhen China Research Institute of Trustworthy Autonomous Systems Southern University of Science and Technology Shenzhen China Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen China

ISBN: (数字)9798350308365

ISBN: (纸本)9798350308372

关键词： Measurement Design methodology evolutionary computation Search problems Linear programming Stability analysis Vaccines

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Fast Heterogeneous Multi-Problem Surrogates for Transfer evolutionary Multiobjective Optimization

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IEEE Transactions on evolutionary Computation 2024年 1-1页

作者： Li, Hao Xiong, Pu Gong, Maoguo Qin, A.K. Wu, Yue Xing, Lining Key Laboratory of Collaborative Intelligence Systems Ministry of Education School of Electronic Engineering Xidian University Xi’an China Department of Computing Technologies Swinburne University of Technology Hawthorn Victoria Australia School of Computer Science and Technology Xidian University Xi’an China

Transfer evolutionary multiobjective optimization leverages the relevant knowledge from other source problems (distinct but possibly related) to assist the optimization of the target problem of interest. Multi-problem surrogates stack multiple source surrogates to reduce the number of function evaluations of the target expensive problem. The current multi-problem surrogates only considers several source problems and the source and target problems are assumed to be homogeneous. In order to address the above issues, this paper proposes fast heterogeneous multi-problem surrogates for transfer evolutionary multiobjective optimization with a large number of surrogates. First, an iterative surrogate selection strategy is designed to select the highly relevant surrogates from the large-scale surrogate pool to avoid negative transfer. Second, heterogeneous multi-problem surrogates are established to align the features of the source and target models. Finally, an adaptive k-fold cross-validation method is proposed to obtain the predicted values of the target model with low computational costs. Experiments on the multiobjective optimization benchmark problems and multiobjective neural architecture search problems have demonstrated that the proposed method is able to avoid negative transfer in the large-scale scenarios and reduce the computational costs. IEEE

关键词： Multiobjective optimization

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Efficient Hybrid Multi-Population Genetic Algorithm for Multi-UAV Task Assignment in Consumer Electronics Applications

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IEEE Transactions on Consumer Electronics 2025年

作者： Bai, Xiaoshan Jiang, Haoyu Li, Chao Ullah, Inam Dabel, Maryam M. Al Bashir, Ali Kashif Wu, Zongze Sam, Shuzhi Shenzhen University College of Mechatronics and Control Engineering National Engineering Laboratory for Big Data System Computing Technology Shenzhen518060 China Shenzhen University College of Mechatronics and Control Engineering Shenzhen518060 China Shenzhen University Shenzhen City Joint Laboratory of Autonomous Unmanned Systems and Intelligent Manipulation Shenzhen518060 China Tashkent State University of Economics Department of Artificial Intelligence Tashkent100066 Uzbekistan University of Hafr Al Batin Department of Computer Science and Engineering College of Computer Science and Engineering Saudi Arabia Manchester Metropolitan University Manchester United Kingdom Shenzhen518060 China National University of Singapore Department of Electrical and Computer Engineering Singapore117576 Singapore

In recent years, as people’s living standards have improved and consumption concepts have been transformed, the demand for purchasing consumer electronics online has continued to grow, further stimulating the development of the logistics industry. Consequently, how to deliver consumer electronics to households at minimal cost has become a crucial factor that limits the development of the consumer technology industry. To tackle this problem, this paper studies the task assignment problem for multiple initially dispersed UAVs to deliver products to target locations while minimizing their total operation time. Each UAV can continuously provide delivery services to multiple target locations within its limited loading capacity and operation time. To solve this problem, we propose several hybrid multipopulation genetic algorithms. First, a novel crossover operator for the genetic algorithms is designed, through which a single parent chromosome can generate offspring individually. Second, two mutation mechanisms are performed to increase gene diversity. Third, multiple local search strategies are employed to enhance the populations’ fitness during each iteration of evolution. An improved 2-opt local search strategy is applied to optimize individual chromosomes when their similarity with the current best chromosome falls below a prescribed threshold. Alternatively, local search strategies are utilized for 1-opt, 2h-opt and interchange processes. Combining local search strategies, genetic operators, and the multi-population mechanism leads to several hybrid multi-population genetic algorithms. Numerical simulations and experimental tests demonstrate that the hybrid multi-population genetic algorithm, integrated with the improved 2-opt and 1-opt local search strategies, exhibits superior performance among the designed hybrid genetic algorithms, the minimum marginal cost algorithm (MMA), and the existing popular Co-evolutionary Multi-population Genetic Algorithm (CMGA). In exp

关键词： Genetic algorithms

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Many-Problem Surrogates for Transfer evolutionary Multiobjective Optimization With Sparse Transfer Stacking

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IEEE Transactions on evolutionary Computation 2025年

作者： Li, Hao Wan, Fanggao Gong, Maoguo Qin, A.K. Wu, Yue Xing, Lining Xidian University School of Electronic Engineering Key Laboratory of Collaborative Intelligence Systems Ministry of Education Shaanxi Province Xi'an710071 China Inner Mongolia Normal University School of Electronic Engineering Key Laboratory of Collaborative Intelligence Systems Ministry of Education Xidian University Xi'an China and Academy of Artificial Intelligence College of Mathematics Science Hohhot China Swinburne University of Technology Department of Computing Technologies HawthornVIC3122 Australia Xidian University School of Computer Science and Technology Xi'an710071 China

For expensive multiobjective optimization problems, there exists useful knowledge, e.g., the trained surrogate models, can be transferred to assist the optimization of a target optimization problem, which is termed as multi-problem surrogates. Stacking transfer is able to combine the pretrained source surrogate models and the preliminary target model with a meta-regression algorithm to transfer knowledge from source to target. However, when large-scale source models are involved in the many-problem scenarios, the less correlated sources may hurt the target performance, which is known as negative transfer. In this paper, sparse representation of the coefficients of meta-regression is considered to automatically select the most relevant source models for largely avoiding negative transfer. In the proposed many-problem surrogates, the coefficients of the source and target models are assumed to be sparse under the non-negativity and sum-to-one constraints. Then a sparse transfer stacking model is established with l1-norm of the coefficients. Next, the alternating direction method of multipliers is employed to solve the resulting constrained optimization problem by converting it into several much simpler problems. Most of the previous works assume that the costs for evaluation have no much difference and this assumption rarely holds in the real-world applications. In order to further reduce the total costs, an improved surrogate model with a cost-sensitive measure is designed to estimate the cost and select new solutions for real evaluation based on their estimated fitness, uncertainty and cost. Experimental results on synthetic and practical problems have demonstrated the superiority of the proposed many-problem surrogates. © 1997-2012 IEEE.

关键词： Multiobjective optimization sparse representation surrogate-assisted evolutionary algorithm transfer stacking

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Reliability-Aware Network Slicing based on Multi-Objective Optimization

Reliability-Aware Network Slicing based on Multi-Objective O...

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Congress on evolutionary Computation

作者： Qiqi Xia Jin Wang Chengqiang Huang Xin Yao Research Institute of Trustworthy Autonomous Systems (RITAS) Southern University of Science and Technology Shenzhen China Department of Computer Science and Engineering Guangdong Key Laboratory of Brain-inspired Intelligent Computation Southern University of Science and Technology Shenzhen China Reliability Technology Lab Huawei Technologies Co. Ltd. Shenzhen China Department of Computing and Decision Sciences Lingnan University Hong Kong SAR China

ISBN: (数字)9798350308365

ISBN: (纸本)9798350308372

Network slicing is an essential technology in 5G and the forthcoming 6G networks. It aims to embed multiple virtual networks, i.e., network slices, on top of a shared substrate network to meet diverse service requirements. While a considerable body of existing research strives to maximize overall profits by meeting the resource demands of the network slices, optimizing their reliability is frequently overlooked. In this paper, we formalize the network slicing problem as a multi-objective optimization problem that aims to maximize total profits and reliability of network slices. To tackle this problem, we propose a new multi-objective optimization approach that improves over the state-of-the-art algorithm, which can achieve good approximate Pareto front results balancing total profits and reliability of network slices. The performance of our proposed method is evaluated on both artificial and real-world network topologies. Experimental results demonstrate the superior performance of our proposed method compared to the baseline algorithm, outperforming the latter in 92% of instances in terms of the Hypervolume (HV) metric.

关键词： Measurement 6G mobile communication Costs Network topology Network slicing evolutionary computation Approximation algorithms

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Performance and energy-aware bi-objective tasks scheduling for cloud data centers 6

Performance and energy-aware bi-objective tasks scheduling f...

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6th Information systems International Conference, ISICO 2021

作者： Materwala, Huned Ismail, Leila Intelligent Distributed Computing and Systems Research Laboratory Department of Computer Science and Software Engineering College of Information Technology United Arab Emirates University Al Ain Abu Dhabi 15551 United Arab Emirates National Water and Energy Center United Arab Emirates University Al Ain Abu Dhabi United Arab Emirates

Cloud computing enables remote execution of users' tasks. The pervasive adoption of cloud computing in smart cities' services and applications requires timely execution of tasks adhering to Quality of Services (QoS). However, the increasing use of computing servers exacerbates the issues of high energy consumption, operating costs, and environmental pollution. Maximizing the performance and minimizing the energy in the cloud data center is challenging. In this paper, we propose a performance and energy optimization bi-objective algorithm to trade off the contradicting performance and energy objectives. An evolutionary algorithm-based multi-objective optimization is for the first time proposed using system performance counters. The performance of the proposed model is evaluated using a realistic cloud dataset in a cloud computing environment. Our experimental results achieve higher performance and lower energy consumption compared to a state-of-the-art algorithm. © 2021 The Authors. Published by Elsevier B.V.

关键词： Quality of service

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Performance and energy-aware bi-objective tasks scheduling for cloud data centers

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Procedia computer science 2022年 197卷 238-246页

作者： Huned Materwala Leila Ismail Intelligent Distributed Computing and Systems Research Laboratory Department of Computer Science and Software Engineering College of Information Technology United Arab Emirates University Al Ain Abu Dhabi 15551 United Arab Emirates National Water and Energy Center United Arab Emirates University Al Ain Abu Dhabi United Arab Emirates

Cloud computing enables remote execution of users’ tasks. The pervasive adoption of cloud computing in smart cities’ services and applications requires timely execution of tasks adhering to Quality of Services (QoS). However, the increasing use of computing servers exacerbates the issues of high energy consumption, operating costs, and environmental pollution. Maximizing the performance and minimizing the energy in the cloud data center is challenging. In this paper, we propose a performance and energy optimization bi-objective algorithm to trade off the contradicting performance and energy objectives. An evolutionary algorithm-based multi-objective optimization is for the first time proposed using system performance counters. The performance of the proposed model is evaluated using a realistic cloud dataset in a cloud computing environment. Our experimental results achieve higher performance and lower energy consumption compared to a state-of-the-art algorithm.

关键词： Autonomous agents cloud computing energy-efficiency evolutionary algorithm genetic algorithm quality of service multi-objective optimization performance

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