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DeePMD-kit v2: A software package for Deep Potential models

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

A threshold effect of coupling delays on intra-layer synchronization in duplex networks

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Science China(Technological Sciences) 2018年第12期61卷 1907-1914页

作者： TANG LongKun LU JunAn Lü JinHu Fujian Province University Key Laboratory of Computation Science School of Mathematical Sciences Huaqiao University Department of Mathematics & Statistics Georgia State University School of Mathematics and Statistics Wuhan University School of Automation Science and Electrical Engineering State Key Laboratory of Software Development Environment and Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University

This paper investigates the impact of inter-layer coupling functions and intra-layer coupling delays on intra-layer synchronization regions and sychronizability. It is found that the inter-layer coupling functions have great influence on intra-layer synchronization regions, as well as on the intra-layer synchronizability. In particular, there exists an inter-layer coupling function such that the inter-layer coupling strength neither improves nor weakens the intra-layer synchronizability. Furthermore, no matter which one of three inter-layer coupling functions is chosen, a small intra-layer delay always keeps the intra-layer synchronized regions almost unchanged, implying that the small delay neither enhances nor suppresses the intra-layer synchronizability. At the same time the delay greatly frustrates the synchronizability in each layer when it is greater than some threshold. Our results may have potential applications for interconnected technological networks where communication delays are inevitably present.

关键词： multiplex network master stability function intra-layer synchronization synchronized region time delay

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Ball k-means

arXiv 2020年

作者： Xia, Shuyin Peng, Daowan Meng, Deyu Zhang, Changqing Wang, Guoyin Chen, Zizhong Wei, Wei Department of Chongqing Key Laboratory of Computational Intelligence Chongqing University of Posts and Telecommunications Chongqing400065 China National Engineering Laboratory for Algorithm and Analysis Technologiy on Big Data Xian Jiaotong University Xi'an710049 China College of Intelligence and Computing Tianjin University 300072 China Department of Computer Science and Engineering University of California Riverside 900 University Avenue RiversideCA92521 United States School of Computer Science and Engineering Xi'an University of Technology Xi'an710048 China

This paper presents a novel accelerated exact k-means algorithm called the Ball k-means algorithm, which uses a ball to describe a cluster, focusing on reducing the point-centroid distance computation. The Ball k-means can accurately find the neighbor clusters for each cluster resulting distance computations only between a point and its neighbor clusters centroids instead of all centroids. Moreover, each cluster can be divided into a stable area and an active area, and the later one can be further divided into annulus areas. The assigned cluster of the points in the stable area is not changed in the current iteration while the points in the annulus area will be adjusted within a few neighbor clusters in the current iteration. Also, there are no upper or lower bounds in the proposed Ball k-means. Furthermore, reducing centroid-centroid distance computation between iterations makes it efficient for large k clustering. The fast speed, no extra parameters and simple design of the Ball k-means make it an all-around replacement of the naive k-means algorithm. Copyright © 2020, The Authors. All rights reserved.

关键词： K-means clustering

Wireless Large AI Model: Shaping the AI-Native Future of 6G and Beyond

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arXiv 2025年

作者： Zhu, Fenghao Wang, Xinquan Li, Xinyi Zhang, Maojun Chen, Yixuan Huang, Chongwen Yang, Zhaohui Chen, Xiaoming Zhang, Zhaoyang Jin, Richeng Huang, Yongming Feng, Wei Yang, Tingting Bai, Baoming Gao, Feifei Yang, Kun Liu, Yuanwen Muhaidat, Sami Yuen, Chau Huang, Kaibin Wong, Kai-Kit Niyato, Dusit Debbah, Mérouane College of Information Science and Electronic Engineering Zhejiang University Hangzhou310027 China School of Automation Southeast University Nanjing210096 China Tsinghua University Beijing100084 China Pengcheng Laboratory Shenzhen518066 China State Key Laboratory of Integrated Service Networks Xidian University Xi’an710071 China State Key Laboratory of Novel Software Technology Nanjing University Nanjing210008 China Suzhou215163 China The University of Hong Kong Hong Kong KU 6G Research Center Computer and Communication Engineering Khalifa University Abu Dhabi127788 United Arab Emirates School of Electrical and Electronic Engineering Nanyang Technological University Singapore Singapore Department of Electronic and Electrical Engineering University College London LondonWC1E 7JE United Kingdom College of Computing and Data Science Nanyang Technological University Singapore639798 Singapore KU 6G Research Center Department of Computer and Information Engineering Khalifa University Abu Dhabi127788 United Arab Emirates

The emergence of sixth-generation and beyond communication systems is expected to fundamentally transform digital experiences through introducing unparalleled levels of intelligence, efficiency, and connectivity. A promising technology poised to enable this revolutionary vision is the wireless large AI model (WLAM), characterized by its exceptional capabilities in data processing, inference, and decision-making. In light of these remarkable capabilities, this paper provides a comprehensive survey of WLAM, elucidating its fundamental principles, diverse applications, critical challenges, and future research opportunities. We begin by introducing the background of WLAM and analyzing the key synergies with wireless networks, emphasizing the mutual benefits. Subsequently, we explore the foundational characteristics of WLAM, delving into their unique relevance in wireless environments. Then, the role of WLAM in optimizing wireless communication systems across various use cases and the reciprocal benefits are systematically investigated. Furthermore, we discuss the integration of WLAM with emerging technologies, highlighting their potential to enable transformative capabilities and breakthroughs in wireless communication. Finally, we thoroughly examine the high-level challenges hindering the practical implementation of WLAM and discuss pivotal future research directions. Copyright © 2025, The Authors. All rights reserved.

关键词： Sorting

A Localization Method of High Energy Transients for All-Sky Gamma-Ray Monitor

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arXiv 2022年

作者： Zhao, Yi Xue, Wangchen Xiong, Shaolin Luo, Qi Wang, Yuanhao Liu, Jiacong Yu, Heng Zhao, Xiaoyun Huang, Yue Liao, Jinyuan Sun, Jianchao Li, Xiaobo Yi, Qibin Cai, Ce Xiao, Shuo Xie, Shenglun Zheng, Chao Zhang, Yanqiu Wang, Chenwei Tan, Wenjun Guo, Zhiwei Li, Chaoyang An, Zhenghua Chen, Gang Du, Yanqi Gao, Min Gong, Ke Guo, Dongya He, Jiang He, Jianjian Li, Bing Li, Gang Li, Xinqiao Liang, Jing Liang, Xiaohua Liu, Yaqing Ma, Xiang Qiao, Rui Song, Liming Song, Xinying Sun, Xilei Wang, Jin Wang, Ping Wen, Xiangyang Wu, Hong Xu, Yanbing Yang, Sheng Zhang, Dali Zhang, Fan Zhang, Hongmei Zhang, Peng Zhang, Shu Zhang, Zhen Zheng, Shijie Zhang, Keke Han, Xingbo Wu, Haiyan Hu, Tai Geng, Hao Lu, Gaopeng Xu, Wei Lyu, Fanchao Zhang, Hongbo Lu, Fangjun Zhang, Shuangnan Department of Astronomy Beijing Normal University Beijing100875 China Key Laboratory of Particle Astrophysics Institute of High Energy Physics Chinese Academy of Sciences Beijing100049 China University of Chinese Academy of Sciences Beijing100049 China School of Physics and Optoelectronics Xiangtan University Hunan Xiangtan411105 China College of Physics Hebei Normal University Shijiazhuang050024 China Guizhou Provincial Key Laboratory of Radio Astronomy and Data Processing Guizhou Normal University Guiyang550001 China School of Physics and Electronic Science Guizhou Normal University Guiyang550001 China Institute of Astrophysics Central China Normal University Wuhan430079 China College of physics Sciences Technology Hebei University Baoding071002 China Physics and Space Science College China West Normal University Nanchong637002 China School of Computing and Artificial Intelligence Southwest Jiaotong University Chengdu611756 China College of Electronic and information Engineering Tongji University Shanghai201804 China Innovation Academy for Microsatellites of Chinese Academy of Sciences Shanghai201304 China National Space Science Center Chinese Academy of Sciences Beijing100190 China School of Earth and Space Sciences University of Science and Technology of China Hefei230026 China Electronic Information School Wuhan University Hubei Wuhan430072 China Key Laboratory of Transportation Meteorology of China Meteorological Administration Nanjing Joint China Key Laboratory of Middle Atmosphere and Global Environment Observation Institute of Atmospheric Physics Chinese Academy of Sciences Beijing100029 China

Fast and reliable localization of high-energy transients is crucial for characterizing the burst properties and guiding the follow-up observations. Localization based on the relative counts of different detectors has been widely used for all-sky gamma-ray monitors. There are two major methods for this counts distribution localization: χ2 minimization method and the Bayesian method. Here we propose a modified Bayesian method that could take advantage of both the accuracy of the Bayesian method and the simplicity of the χ2 method. With comprehensive simulations, we find that our Bayesian method with Poisson likelihood is generally more applicable for various bursts than χ2 method, especially for weak bursts. We further proposed a location-spectrum iteration approach based on the Bayesian inference, which could alleviate the problems caused by the spectral difference between the burst and location templates. Our method is very suitable for scenarios with limited computation resources or time-sensitive applications, such as in-flight localization software, and low-latency localization for rapid follow-up observations. Copyright © 2022, The Authors. All rights reserved.

关键词： Gamma rays

NERank+: a graph-based approach for entity ranking in document collections

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计算机科学前沿 2018年第3期12卷 504-517页

作者： Chengyu WANG Guomin ZHOU Xiaofeng HE Aoying ZHOU Shanghai Key Laboratory of Trustworthy Computing School of Computer Science and Software EngineeringEast China Normal University Shanghai 200062 China Department of Computer and Information Technology Zhejiang Police College Hangzhou 310053 China School of Data Science and Engineering East China Normal University Shanghai 200062 China

Most entity ranking research aims to retrieve a ranked list of entities from a Web corpus given a user *** rank order of entities is determined by the relevance between the query and contexts of ***,entities can be ranked directly based on their relative importance in a document collection,independent of any *** this paper,we introduce an entity ranking algorithm named NERank+.Given a document collection,NERank+ first constructs a graph model called Topical Tripartite Graph,consisting of document,topic and entity *** design separate ranking functions to compute the prior ranks of entities and topics,respectively.A meta-path constrained random walk algorithm is proposed to propagate prior entity and topic ranks based on the graph *** evaluate NERank+ over real-life datasets and compare it with *** results illustrate the effectiveness of our approach.

关键词： entity ranking Topical Tripartite Graph prior rank estimation meta-path constrained random walk

A personalized privacy protection data uploading scheme for mobile crowdsensing 2

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A personalized privacy protection data uploading scheme for ...

2nd IEEE International Conference on Industrial Internet Cloud, ICII 2019

作者： Ma, Rong Chen, Lei Xiong, Jinbo Tian, Youliang Li, Qi Liu, Ximeng Fujian Provincial Key Laboratory of Network Security and Cryptology College of Mathematics and Informatics Fujian Normal University Fuzhou350117 China College of Engineering and Computing Georgia Southern University GA30458 United States Guizhou Provincial Key Laboratory of Public Big Data Guizhou University Guiyang550025 China School of Computer Science Nanjing University of Posts and Telecommunications Nanjing210023 China Fujian Provincial Key Laboratory of Information Security of Network Systems College of Mathematics and Computer Science Fuzhou University Fuzhou350108 China

ISBN: (纸本)9781728129778

Mobile crowdsensing is a typical application of the Industrial Internet of hings and brings a promising opportunity to construct powerful industrial systems and services. The existing privacy protection schemes usually adopt a unified privacy protection policy for all sensing data due to lack of effective privacy metrics, thereby resulting in excessive or insufficient protection of privacy information and low accuracy of sensing data. To tackle these issues, in this paper, we propose a personalized privacy protection data uploading (PPDU) scheme based on game theory and sensing user's historical spatio-temporal data. In PPDU, a personalized privacy measurement algorithm is designed to obtain the personalized privacy degree of user sensing data. Based on the privacy degree, a user uploading behavior game is designed by employing an incomplete information game, and a game-based spatio-temporal sensing data uploading method is proposed for user privacy protection. Simulation experiments with real trajectory data show that the PPDU scheme makes a reasonable balance between retaining high quality of crowdsensing service and protecting user's privacy. © 2019 IEEE.

关键词： Game theory

Micro-supervised disturbance learning: A perspective of representation probability distribution

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arXiv 2020年

作者： Chu, Jielei Liu, Jing Wang, Hongjun Meng, Hua Gong, Zhiguo Li, Tianrui The School of Computing and Artificial Intelligence Southwest Jiaotong University Chengdu611756 China National Engineering Laboratory of Integrated Transportation Big Data Application Technology Southwest Jiaotong University Chengdu611756 China The School of Business Sichuan University Sichuan Chengdu610065 China The State Key Laboratory of Internet of Things for Smart City Department of Computer and Information Science University of Macau China

The instability is shown in the existing methods of representation learning based on Euclidean distance under a broad set of conditions. Furthermore, the scarcity and high cost of labels prompt us to explore more expressive representation learning methods which depends on the labels as few as possible. To address these issues, the small-perturbation ideology is firstly introduced on the representation learning model based on the representation probability distribution. The positive small-perturbation information (SPI) which only depend on two labels of each cluster is used to stimulate the representation probability distribution and then two variant models are proposed to fine-tune the expected representation distribution of RBM, namely, Micro-supervised Disturbance GRBM (Micro-DGRBM) and Micro-supervised Disturbance RBM (Micro-DRBM) models. The Kullback-Leibler (KL) divergence of SPI is minimized in the same cluster to promote the representation probability distributions to become more similar in Contrastive Divergence (CD) learning. In contrast, the KL divergence of SPI is maximized in the different clusters to enforce the representation probability distributions to become more dissimilar in CD learning. To explore the representation learning capability under the continuous stimulation of the SPI, we present a deep Micro-supervised Disturbance Learning (Micro-DL) framework based on the Micro-DGRBM and Micro-DRBM models and compare it with a similar deep structure which has not any external stimulation. Experimental results demonstrate that the proposed deep Micro-DL architecture shows better performance in comparison to the baseline method, the most related shallow models and deep frameworks for clustering. © 2020, CC0.

关键词： Probability distributions

CMR×Recon: An open cardiac MRI dataset for the competition of accelerated image reconstruction

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arXiv 2023年

作者： Wang, Chengyan Lyu, Jun Wang, Shuo Qin, Chen Guo, Kunyuan Zhang, Xinyu Yu, Xiaotong Li, Yan Wang, Fanwen Jin, Jianhua Shi, Zhang Xu, Ziqiang Tian, Yapeng Hua, Sha Chen, Zhensen Liu, Meng Sun, Mengting Kuang, Xutong Wang, Kang Wang, Haoran Li, Hao Chu, Yinghua Yang, Guang Bai, Wenjia Zhuang, Xiahai Wang, He Qin, Jing Qu, Xiaobo Human Phenome Institute Fudan University Shanghai China School of Nursing The Hong Kong Polytechnic University Hong Kong Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Department of Electrical and Electronic Engineering & I-X Imperial College London United Kingdom Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Institute of Artificial Intelligence Xiamen University Xiamen China Department of Radiology Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Department of Bioengineering/˜Imperial-X Imperial College London United Kingdom School of Data Science Fudan University Shanghai China Department of Radiology Zhongshan Hospital Fudan University Shanghai China School of Health Science and Engineering University of Shanghai for Science and Technology Shanghai China Department of Computer Science The University of Texas Dallas United States Department of Cardiovascular Medicine Ruijin Hospital Lu Wan Branch Shanghai Jiao Tong University School of Medicine Shanghai China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai200433 China Simens Healthineers Ltd. China Department of Brain Sciences Imperial College London London United Kingdom Department of Computing Imperial College London London United Kingdom

Cardiac magnetic resonance imaging (CMR) has emerged as a valuable diagnostic tool for cardiac diseases. However, a limitation of CMR is its slow imaging speed, which causes patient discomfort and introduces artifacts in the images. There has been growing interest in deep learning-based CMR imaging algorithms that can reconstruct high-quality images from highly under-sampled k-space data. However, the development of deep learning methods requires large training datasets, which have not been publicly available for CMR. To address this gap, we released a dataset that includes multi-contrast, multi-view, multi-slice and multi-coil CMR imaging data from 300 subjects. Imaging studies include cardiac cine and mapping sequences. Manual segmentations of the myocardium and chambers of all the subjects are also provided within the dataset. Scripts of state-of-the-art reconstruction algorithms were also provided as a point of reference. Our aim is to facilitate the advancement of state-of-the-art CMR image reconstruction by introducing standardized evaluation criteria and making the dataset freely accessible to the research community. Researchers can access the dataset at https://***/#!Synapse:syn51471091/wiki/. Copyright © 2023, The Authors. All rights reserved.

关键词： Image reconstruction