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arXiv 2024年

作者： Zhang, Ruochi Wu, Haoran Liu, Chang Li, Huaping Wu, Yuqian Li, Kewei Wang, Yifan Deng, Yifan Chen, Jiahui Zhou, Fengfeng Gao, Xin Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Jilin Changchun130012 China School of Artificial Intelligence Jilin University Jilin Changchun130012 China Syneron Technology Guangzhou510700 China Beijing Life Science Academy Beijing102209 China School of Biomedical Sciences LKS Faculty of Medicine The University of Hong Kong Hong Kong Thuwal23955 Saudi Arabia Thuwal23955 Saudi Arabia College of Software Jilin University Jilin Changchun130012 China College of Computer Science and Technology Jilin University Jilin Changchun130012 China

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely unaddressed due to the difficulty in capturing the complex and sometimes unstable structures of peptides. This study introduces a novel multi-view contrastive learning framework PepHarmony for the sequence-based peptide encoding task. PepHarmony innovatively combines both sequence- and structure-level information into a sequence-level encoding module through contrastive learning. We carefully select datasets from the Protein Data Bank (PDB) and AlphaFold database to encompass a broad spectrum of peptide sequences and structures. The experimental data highlights PepHarmony's exceptional capability in capturing the intricate relationship between peptide sequences and structures compared with the baseline and fine-tuned models. The robustness of our model is confirmed through extensive ablation studies, which emphasize the crucial roles of contrastive loss and strategic data sorting in enhancing predictive performance. The proposed PepHarmony framework serves as a notable contribution to peptide representations, and offers valuable insights for future applications in peptide drug discovery and peptide engineering. We have made all the source code utilized in this study publicly accessible via GitHub at https://***/zhangruochi/PepHarmony or http://***/supp/. © 2024, CC BY-NC-ND.

关键词： Peptides

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Incorporating Surprisingly Popular Algorithm and Euclidean Distance-based Adaptive Topology into PSO

arXiv

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arXiv 2021年

作者： Wu, Xuan Han, Jizong Wang, Di Gao, Pengyue Cui, Quanlong Chen, Liang Liang, Yanchun Huang, Han Lee, Heow Pueh Miao, Chunyan Zhou, You Wu, Chunguo Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education College of Computer Science and Technology Jilin University Changchun130012 China Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly Nanyang Technological University 639798 Singapore State Key Laboratory of Superhard Materials International Center for Computational Method and Software College of Physics Jilin University Changchun130012 China Commercial Quality and Efficiency Department Baidu Inc Beijing100085 China Department of Computer Science Shantou University Shantou515063 China School of Computer Science Zhuhai College of Science and Technology Zhuhai519041 China School of Software Engineering The South China University of Technology Guangzhou510641 China Department of Mechanical Engineering National University of Singapore 117575 Singapore School of Computer Science and Engineering Nanyang Technological University 639798 Singapore College of Software Jilin University Changchun130012 China

While many Particle Swarm Optimization (PSO) algorithms only use fitness to assess the performance of particles, in this work, we adopt Surprisingly Popular Algorithm (SPA) as a complementary metric in addition to fitness. Consequently, particles that are not widely known also have the opportunity to be selected as the learning exemplars. In addition, we propose a Euclidean distance-based adaptive topology to cooperate with SPA, where each particle only connects to k number of particles with the shortest Euclidean distance during each iteration. We also introduce the adaptive topology into heterogeneous populations to better solve large-scale problems. Specifically, the exploration sub-population better preserves the diversity of the population while the exploitation sub-population achieves fast convergence. Therefore, large-scale problems can be solved in a collaborative manner to elevate the overall performance. To evaluate the performance of our method, we conduct extensive experiments on various optimization problems, including three benchmark suites and two real-world optimization problems. The results demonstrate that our Euclidean distance-based adaptive topology outperforms the other widely adopted topologies and further suggest that our method performs significantly better than state-of-the-art PSO variants on small, medium, and large-scale problems. Copyright © 2021, The Authors. All rights reserved.

关键词： Small-world networks

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An unmanned aerial vehicle pose estimation system based on SLAM

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IOP Conference Series: Materials Science and engineering 2019年第4期569卷

作者： Xinglei Dou Yuzhou Huo Yongchang Liu Xin Wang College of Software Engineering Jilin University Changchun Jilin 130012 China College of Computer Science and Technology Jilin University Changchun Jilin 130012 China Key Laboratory of Symbolic Computation and Knowledge Engineer of Ministry of Education Jilin University Changchun Jilin 130012 China

This paper presents an unmanned aerial vehicle (UAV) pose estimation system based on monocular simultaneous localization and mapping (SLAM) guided by the desired shot. The system enables UAV to automatically adjust the pose to achieve a shot close to the desired shot provided by the user. The SLAM module in the system includes ORB feature-based visual odometry and Levenberg-Marquardt method-based optimizer. To ensure the reliability of the camera pose estimation result, the bag of words model is used to select an image which has enough good matches with the desired shot. The experimental results prove that the system is valid and effective.

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Unraveling the Oxidation Behaviors of MXenes in Aqueous Systems by Active-Learning-Potential Molecular-Dynamics Simulation

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Angewandte Chemie 2023年第32期135卷

作者： Pengfei Hou Yumiao Tian Prof. Yu Xie Prof. Fei Du Prof. Gang Chen Dr. Aleksandra Vojvodic Prof. Jianzhong Wu Dr. Xing Meng Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education) College of Physics Jilin University 130012 Changchun P. R. China Department of Chemical and Biomolecular Engineering University of Pennsylvania PA 19104 Philadelphia USA Department of Chemical and Environmental Engineering University of California CA 92521 Riverside USA Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University 130012 Changchun P. R. China

MXenes are 2D materials with great potential in various applications. However, the degradation of MXenes in humid environments has become a main obstacle in their practical use. Here we combine deep neural networks and an active learning scheme to develop a neural network potential (NNP) for aqueous MXene systems with ab initio precision but low cost. The oxidation behaviors of super large aqueous MXene systems are investigated systematically at nanosecond timescales for the first time. The oxidation process of MXenes is clearly displayed at the atomic level. Free protons and oxides greatly inhibit subsequent oxidation reactions, leading to the degree of oxidation of MXenes to exponentially decay with time, which is consistent with the oxidation rate of MXenes measured experimentally. Importantly, this computational study represents the first exploration of the kinetic process of oxidation of super-sized aqueous MXene systems. It opens a promising avenue for the future development of effective protection strategies aimed at controlling the stability of MXenes.

关键词： MXenes Degradation Neural NetworksActive Learning Oxidation Protection

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Collaborative WSN-UAV Data Collection in Smart Agriculture: A Bi-objective Optimization Scheme

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ACM Transactions on Sensor Networks 1000年

作者： Geng Sun Xiaoya Zheng Jiahui Li Hui Kang Shuang Liang 1) College of Computer Science and Technology Jilin University 2) Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China College of Computer Science and Technology Jilin University China College of Information Science and Technology Northeast Normal University China

Smart agriculture which integrates the agriculture with Internet of Things (IoT) has attracted attention since it contributes to increase the productivity and quality of crops, reduce energy consumption and facilitate the farmers. Wireless sensor networks (WSNs) and unmanned aerial vehicles (UAVs) are two most commonly deployed devices that are used for enabling the smart agriculture. In this paper, we design a collaborative WSN-UAV system, wherein different clusters of sensor nodes form different sensor-based virtual antenna arrays (SVAAs) to transmit the collected data towards different receiver UAVs via adopting collaborative beamforming (CB), then the receiver UAVs will take the collected data back to the ground control station (GCS). We formulate a transmission rate and battery energy bi-objective optimization problem (TRBEBOP) to simultaneously maximize the total transmission rate of the sensor-based CB clusters and the total remaining battery energy of the selected sensor nodes, by selecting appropriate sensor nodes in each cluster that can form a predominant SVAA, determining suitable receiver UAVs and optimizing the excitation current weights of the selected sensor nodes. To handle the formulated TRBEBOP that is demonstrated to be non-convex and NP-hard, an enhanced non-dominated sorting genetic algorithm II (ENSGA-II) with several specific designs is presented. Simulation results validate the effectiveness of the proposed ENSGA-II for solving the formulated TRBEBOP. Moreover, compared with other benchmark algorithms, the superiority of the proposed ENSGA-II is demonstrated. In addition, the impacts of several fortuitous circumstances on the system are estimated, and the results illustrate the robustness of the proposed scheme. Finally, the discussion about several mechanisms to deal with the interference induced by the sidelobe levels and the impact of UAV movement on receiving rate are provided.

关键词： Smart agriculture wireless sensor networks unmanned aerial vehicles collaborative beamforming multi-objective optimization problem.

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Reinforcement Learning-based Non-Autoregressive Solver for Traveling Salesman Problems

arXiv

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arXiv 2023年

作者： Xiao, Yubin Wang, Di Li, Boyang Chen, Huanhuan Pang, Wei Wu, Xuan Li, Hao Xu, Dong Liang, Yanchun Zhou, You The Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education College of Computer Science and Technology Jilin University Changchun130012 China The Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly Nanyang Technological University 639798 Singapore The School of Computer Science and Engineering Nanyang Technological University 639798 Singapore The School of Computer Science University of Science & Technology of China Hefei230026 China The School of Mathematical and Computer Sciences Heriot-Watt University EdinburghEH14 4AS United Kingdom College of Computer National University of Defense Technology Hunan Changsha410073 China The Department of Electrical Engineering and Computer Science Bond Life Sciences Center University of Missouri Columbia United States The School of Computer Science Zhuhai College of Science and Technology Zhuhai519000 China

The Traveling Salesman Problem (TSP) is a well-known combinatorial optimization problem with broad real-world applications. Recently, neural networks have gained popularity in this research area because as shown in the literature, they provide strong heuristic solutions to TSPs. Compared to autoregressive neural approaches, non-autoregressive (NAR) networks exploit the inference parallelism to elevate inference speed but suffer from comparatively low solution quality. In this paper, we propose a novel NAR model named NAR4TSP, which incorporates a specially designed architecture and an enhanced reinforcement learning strategy. To the best of our knowledge, NAR4TSP is the first TSP solver that successfully combines RL and NAR networks. The key lies in the incorporation of NAR network output decoding into the training process. NAR4TSP efficiently represents TSP encoded information as rewards and seamlessly integrates it into reinforcement learning strategies, while maintaining consistent TSP sequence constraints during both training and testing phases. Experimental results on both synthetic and real-world TSPs demonstrate that NAR4TSP outperforms five state-of-the-art models in terms of solution quality, inference speed, and generalization to unseen scenarios. Copyright © 2023, The Authors. All rights reserved.

关键词： Traveling salesman problem

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The 2nd International Conference on Agricultural and Biological Sciences (ABS 2016)

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BMC Plant Biology 2016年第2期16卷 83-88页

作者： Lei Pei Zhenhua Wang Jinzhu Zhang Wenhao Li Adeline S. Y. Ting Yiing Y. Chow Sadequr Rahman Rongchang Wei Zhang Hu Sidong Li Chuyan Li Zijuan Li Guoxia Wang Yuzhen Yang Gang Chen Qing Luo Ruixia Liu Lipei Chen Zhiyang Lie Tongtong Zhou Weilong Huang Li Xue Jie Li Zhuomin Wang Ismail Bezirganoglu Pınar Uysal Shuihua Wang Zhihai Lu Jiquan Yang Yudong Zhang John Liu Ling Wei Shufang Chen Preetha Phillips Zhengchao Dong Hong Li Xutong Wang Fengliang Zhao Guisheng Yang Haijie Huang Weijian Huang Jinhui Wang Zhongrun Zhang Li Zhao Xiaojuan Li Ning Xu Guofu Zhou Ming Wan Fanyun Meng Jianxiu Li Qi Lin Yichang Chen Koayung Yu Chunpin Chang Zijuan Zhou Peixi Su Rui Shi Tingting Xie Xuelan Liu Yan Zhang Xiangfa Wei Chong Wu Yanlei Yin Lijuan Feng Xuemei Yang Fei Wang Hua Wang Huifa Zhuang Zihui Zhu Hui Wang College of Water & Architectural Engineering Shihezi University Shihezi City 832000 Xinjiang China Key Laboratory of Modern Water-Saving Irrigation Corp Shihezi University Shihezi City 832000 Xinjiang China School of Science Monash University Malaysia Jalan Lagoon Selatan 46150 Bandar Sunway Selangor Malaysia Guangxi Botanical Garden of Medicinal Plants Nanning Guangxi Province 530023 China Department of Chemistry College of Science Guangdong Ocean University Zhanjiang 524088 China School of Life Science Zhengzhou Normal University Zhengzhou 450044 China College of Forestry and Landscape Architecture South China Agricultural University Guangzhou 510642 China Deparment of Molecular Biology and Genetic Erzurum Technical University Erzurum 442 Turkey Ministry of Food Agriculture and Husbandry Eastern Anatolia Agriculture Research Institute Erzurum 442 Turkey Nanjing Normal University Nanjing Jiangsu 210023 China Key laboratory of symbolic computation and knowledge engineering of ministry of education Jilin University Changchun Jilin 130012 China Michigan State University East Lansing MI 48823 USA Shanghai Jiaotong University Shanghai 200030 China University of Electronic Science and Technology of China Chengdu Sichuan 611731 China Shepherd University Shepherdstown WV 25443 USA West Virginia University Morgantown WV 26505 USA New York State Psychiatric Institute New York NY 10032 USA Environment and Plant Protection Institute Chinese Academy of Tropical Agricultural Science Haikou Hainan 571101 China Tropical Crops Genetic Resources Institute CATAS Danzhou 571737 China College of Applied Science and Technology Hainan University Danzhou 571737 China Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine Beijing Normal University Beijing 100875 China State Key Laboratory Breeding Base of Dao-di Herbs National Resource Center for Chinese Materia Medica China Academy of Chinese Medical Science

01 The influence of soil salt content on the photosynthetic characteristics of spring wheat with trickle irrigationLei Pei, Zhenhua Wang, Jinzhu Zhang, Wenhao Li02 Comparing growth of fast-growing and slow-growing end... 详细信息

01 The influence of soil salt content on the photosynthetic characteristics of spring wheat with trickle irrigation

Lei Pei, Zhenhua Wang, Jinzhu Zhang, Wenhao Li

02 Comparing growth of fast-growing and slow-growing endophytes in plants via ergosterol quantification

Adeline SY Ting, Yiing Y Chow, Sadequr Rahman

03 Transcriptome and digital gene expression analysis identifies putative triterpene saponin-biosynthetic genes of Panax notoginseng

Rongchang Wei

04 Chitosan-assisted isolation and antioxidant evaluation of flavonoids from Sophora japonica L.

Zhang Hu, Sidong Li, Chuyan Li, Zijuan Li

05 Two kinds of new characteristics of the ektexine ornamentation of ginkgo pollen

Guoxia Wang, Yuzhen Yang, Gang Chen, Qing Luo

06 Analysis of nutrient and medicinal ingredients of Ginkgo pollen in different regions

Guoxia Wang, Ruixia Liu, Yuzhen Yang, Lipei Chen

07 Photosynthetic performance of greening seedlings of seven species to drought stress

Zhiyang Lie, Tongtong Zhou, Weilong Huang, Li Xue

08 Changes of fluorescence parameters of greening seedlings of seven species under drought stress

Jie Li, Zhuomin Wang, Li Xue

09 Mammalian sex hormone affects regeneration capacity and enzymes activity of Triticale L in vitro culture

Ismail Bezirganoglu, Pınar Uysal

10 Fractional Fourier entropy increases the recognition rate of fruit type detection

Shuihua Wang, Zhihai Lu, Jiquan Yang, Yudong Zhang, John Liu, Ling Wei, Shufang Chen, Preetha Phillips, Zhengchao Dong

11 Banana-peanut intercropping reduces Fusarium wilt disease in banana from enhancing soil bacterial microorganisms and leaf nutrition

Hong Li, Xutong Wang, Fengliang Zhao, Guisheng Yang

12 Manganese stress impairs stem ureide nitrogen fixation in yardlong-bean plants in the acidic environment

Hong Li

13 A new

关键词： Spring Wheat Vanilla Panax Notoginseng Soil Salt Content Digital Gene Expression Analysis

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Corrigendum to: Multi-Swarm Cuckoo Search Algorithm withQ-Learning Model

引用

The Computer Journal 2022年第7期65卷 1938-1938页

作者： Li, Juan Xiao, Dan-dan Zhang, Ting Liu, Chun Li, Yuan-xiang Wang, Gai-ge School of Artificial Intelligence Wuhan Technology and Business University Wuhan 430065 China School of Artificial Intelligence Wuchang University of Technology Wuhan 430223 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University No. 2699 Qianjin Street Gaoxin District Changchun Jilin China 130012 School of Computer Wuhan University No. 299 Bayi Street Wuchang District Wuhan Hubei China 430072 Department of Computer Science and Technology Ocean University of China No. 238 Songling Street Laoshan District Qingdao Shandong China 266100 Institute of Algorithm and Big Data Analysis Northeast Normal University No. 5268 Renmin Street Nanguan District Changchun Jilin China 130117

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Author Correction: Altered structural brain asymmetry in autism spectrum disorder in a study of 54 datasets

引用

Nature communications 2021年第1期12卷 7260页

作者： Merel C Postema Daan van Rooij Evdokia Anagnostou Celso Arango Guillaume Auzias Marlene Behrmann Geraldo Busatto Filho Sara Calderoni Rosa Calvo Eileen Daly Christine Deruelle Adriana Di Martino Ilan Dinstein Fabio Luis S Duran Sarah Durston Christine Ecker Stefan Ehrlich Damien Fair Jennifer Fedor Xin Feng Jackie Fitzgerald Dorothea L Floris Christine M Freitag Louise Gallagher David C Glahn Ilaria Gori Shlomi Haar Liesbeth Hoekstra Neda Jahanshad Maria Jalbrzikowski Joost Janssen Joseph A King Xiang Zhen Kong Luisa Lazaro Jason P Lerch Beatriz Luna Mauricio M Martinho Jane McGrath Sarah E Medland Filippo Muratori Clodagh M Murphy Declan G M Murphy Kirsten O'Hearn Bob Oranje Mara Parellada Olga Puig Alessandra Retico Pedro Rosa Katya Rubia Devon Shook Margot J Taylor Michela Tosetti Gregory L Wallace Fengfeng Zhou Paul M Thompson Simon E Fisher Jan K Buitelaar Clyde Francks Department of Language & Genetics Max Planck Institute for Psycholinguistics Nijmegen The Netherlands. Department of Cognitive Neuroscience Donders Institute for Brain Cognition and Behaviour Donders Centre for Cognitive Neuroimaging Radboud University Medical Centre Nijmegen The Netherlands. Bloorview Research Institute Holland Bloorview Kids Rehabilitation Hospital and Department of Pediatrics University of Toronto Toronto ON USA. Child and Adolescent Psychiatry Department Gregorio Marañón General University Hospital School of Medicine Universidad Complutense IiSGM CIBERSAM Madrid Spain. Institut de Neurosciences de la Timone UMR 7289 Aix Marseille Université CNRS Marseille France. Department of Psychology Carnegie Mellon University Pittsburgh PA USA. Laboratory of Psychiatric Neuroimaging (LIM-21) Departamento e Instituto de Psiquiatria Hospital das Clinicas HCFMUSP Faculdade de Medicina Universidade de Sao Paulo Sao Paulo SP Brazil. IRCCS Stella Maris Foundation viale del Tirreno 331 56128 Pisa Italy. Department of Clinical and Experimental Medicine University of Pisa Pisa Italy. Department of Child and Adolescent Psychiatry and Psychology Hospital Clinic Psychiatry Unit Department of Medicine 2017SGR881 University of Barcelona IDIBAPS CIBERSAM Barcelona Spain. Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry Psychology & Neuroscience King's College London London UK. Institute for Pediatric Neuroscience NYU Child Study Center New York NY USA. Department of Psychology Ben-Gurion University of the Negev Beer Sheva Israel. Brain Center Rudolf Magnus Department of Psychiatry University Medical Center Utrecht Utrecht The Netherlands. Department of Child and Adolescent Psychiatry Psychosomatics and Psychotherapy University Hospital Goethe University Frankfurt am Main Frankfurt Germany. Imaging Genetics Center Mark and Mary Stevens Neuroimaging and Informatics Institute Keck School of Medicine of USC University o

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