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Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals

Cell 2025年第10期188卷 2794-2809.e21页

作者： Mi, Xuelong Chen, Alex Bo-Yuan Duarte, Daniela Carey, Erin Taylor, Charlotte R. Braaker, Philipp N. Bright, Mark Almeida, Rafael G. Lim, Jing-Xuan Ruetten, Virginia M.S. Wang, Yizhi Wang, Mengfan Zhang, Weizhan Zheng, Wei Reitman, Michael E. Huang, Yongkang Wang, Xiaoyu Li, Lei Deng, HanFei Shi, Song-Hai Poskanzer, Kira E. Lyons, David A. Nimmerjahn, Axel Ahrens, Misha B. Yu, Guoqiang Bradley Department of Electrical and Computer Engineering Virginia Polytechnic Institute and State University Arlington 22203 VA United States Janelia Research Campus Howard Hughes Medical Institute Ashburn 20147 VA United States Department of Molecular and Cellular Biology Harvard University Cambridge 02138 MA United States Graduate Program in Neuroscience Harvard Medical School Boston 02115 MA United States Waitt Advanced Biophotonics Center The Salk Institute for Biological Studies La Jolla 92037 CA United States Department of Biochemistry & Biophysics University of California San Francisco San Francisco CA United States Neuroscience Graduate Program University of California San Francisco San Francisco CA United States Centre for Discovery Brain Sciences University of Edinburgh Edinburgh BioQuarter Edinburgh EH16 4SB United Kingdom Gatsby Computational Neuroscience Unit UCL London W1T 4JG United Kingdom Kavli Institute for Fundamental Neuroscience San Francisco CA United States Department of Automation Tsinghua University Beijing 100084 China IDG/McGovern Institute for Brain Research Tsinghua University Beijing 100084 China New Cornerstone Science Laboratory Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Beijing 100084 China State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Institutes of Brain Science Fudan University Shanghai 200032 China Beijing National Research Center for Information Science and Technology Beijing 100084 China

Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce activity quantification and analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine-learning techniques. It decomposes complex live-imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, microscopy techniques, and imaging approaches. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, as well as distinct sensorimotor signal propagation patterns in the mouse spinal cord. © 2025 The Author(s)

关键词： AQuA2 astrocytes cell interaction analysis functional units glial cells image analysis machine learning molecular spatiotemporal signals neurons time-lapse imaging

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Ray-Based Characterization of the AMPLE Model from 0.85 to 5 GHz

arXiv

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arXiv 2025年

作者： Zhou, Lingyou Dong, Xin Qiu, Kehai Yu, Gang Zhang, Jie Zhang, Jiliang School of Electrical and Electronic Engineering The University of Sheffield SheffieldS10 2TN United Kingdom Ranplan Wireless Network Design Ltd. CambridgeCB23 3UY United Kingdom Department of Computer Science and Technology University of Cambridge CambridgeCB3 0FD United Kingdom College of Engineering Design and Physical Sciences Brunel University of London UxbridgeUB8 3PH United Kingdom 5G/6G Innovation Centre University of Surrey SurreyGU2 7XH United Kingdom State Key Laboratory of Synthetical Automation for Process Industries The College of Information Science and Engineering Northeastern University Shenyang110819 China National Mobile Communications Research Laboratory Southeast University Nanjing210096 China

In this paper, we characterize the adaptive multiple path loss exponent (AMPLE) radio propagation model under urban macrocell (UMa) and urban microcell (UMi) scenarios from 0.85-5 GHz using Ranplan Professional. We first enhance the original AMPLE model by introducing an additional frequency coefficient to support path loss prediction across multiple carrier frequencies. By using measurement-validated Ranplan Professional simulator, we simulate four cities and validate the simulations for further path loss model characterization. Specifically, we extract the close-in (CI) model parameters from the simulations and compare them with parameters extracted from measurements in other works. Under the ray-based model characterization, we compare the AMPLE model with the 3rd Generation Partnership Project (3GPP) path loss model, the CI model, the alpha-beta-gamma (ABG) model, and those with simulation calibrations. In addition to standard performance metrics, we introduce the prediction-measurement difference error (PMDE) to assess overall prediction alignment with measurement, and mean simulation time per data point to evaluate model complexity. The results show that the AMPLE model outperforms existing models while maintaining similar model complexity. Copyright © 2025, The Authors. All rights reserved.

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Simultaneous state and parameter estimation: The role of sensitivity analysis

arXiv

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arXiv 2020年

作者： Liu, Jianbang Gnanasekar, Aristarchus Zhang, Yi Bo, Song Liu, Jinfeng Hu, Jingtao Zou, Tao Key Laboratory of Networked Control Systems Shenyang Institute of Automation Chinese Academy of Sciences Shenyang110016 China Institute for Robotics & Intelligent Manufacturing Chinese Academy of Sciences Shenyang110016 China University of Chinese Academy of Sciences Beijing100049 China Department of Chemical & Materials Engineering University of Alberta EdmontonABT6G 1H9 Canada Key Laboratory of Energy Thermal Conversion & Control Southeast University Nanjing210096 China School of Mechanical and Electrical Engineering Guangzhou University Guangzhou510006 China

State and parameter estimation is essential for process monitoring and control. Observability plays an important role in both state and parameter estimation. In simultaneous state and parameter estimation, the parameters are often augmented as extra states of the original system. When the augmented system is observable, various existing state estimation approaches may be used to estimate the states and parameters simultaneously. However, when the augmented system is not observable, how we should proceed to maximally extract the information contained in the measured outputs is not clear. This paper concerns about simultaneous state and parameter estimation when the augmented system is not fully observable. Specifically, we first show how sensitivity analysis is related to observability of a dynamical system, and then illustrate how it may be used to select variables for simultaneous estimation. We also propose a moving horizon state estimation (MHE) design that can use the variable selection results in a natural way. Extensive simulations are carried out to show the efficiency of the proposed approach. Copyright © 2020, The Authors. All rights reserved.

关键词： Sensitivity analysis

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Deep learning for MIMO channel estimation: Interpretation, performance, and comparison

arXiv

引用

arXiv 2019年

作者： Hu, Qiang Gao, Feifei Zhang, Hao Jin, Shi Li, Geoffrey Ye Department of Electrical Engineering Tsinghua University Beijing100084 China Department of Automation Tsinghua University Beijing100084 China National Mobile Communications Research Laboratory Southeast University Nanjing210096 China School of Electrical and Computer Engineering Georgia Institute of Technology AtlantaGA United States

Deep learning (DL) has emerged as an effective tool for channel estimation in wireless communication systems, especially under some imperfect environments. However, even with such unprecedented success, DL methods still serve as black boxes and the lack of explanations on their internal mechanism severely limits further improvement and extension. In this paper, we present a preliminary theoretical analysis on DL based channel estimation for multiple-antenna systems to understand and interpret its internal mechanism. Deep neural network (DNN) with rectified linear unit (ReLU) activation function is mathematically equivalent to a set of local linear functions corresponding to different input regions. Hence, the DL estimator built on it can achieve universal approximation to a large family of functions by making efficient use of piecewise linearity. We demonstrate that DL based channel estimation does not restrict to any specific signal model and will approach to the minimum mean-squared error (MMSE) estimation in various scenarios without requiring any prior knowledge of channel statistics. Therefore, DL based channel estimation outperforms or is comparable with traditional channel estimation. Simulation results confirm the accuracy of the proposed interpretation and demonstrate the effectiveness of DL based channel estimation under both linear and nonlinear signal models. Copyright © 2019, The Authors. All rights reserved.

关键词： Channel estimation

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Overview of the recent experimental research on the J-TEXT tokamak

引用

Nuclear Fusion 2024年第11期64卷 112005-112005页

作者： Ding, Yonghua Wang, Nengchao Chen, Zhongyong Xia, Donghui Yang, Zhoujun Chen, Zhipeng Zheng, Wei Yan, Wei Li, Da Zhou, Song Xu, Xin Zhang, Xiaoyi Mao, Feiyue Fang, Jiangang Ren, Zhengkang Chen, Xixuan Zhang, Junli Zhang, Xiaobo He, Ying Zhang, Qi Li, You Bai, Wei Mou, Lingke Li, Feng Long, Ting Ke, Rui Gao, Li Shi, Peng Shen, Chengshuo Liu, Jiaxing Guo, Weixin Wang, Lu Li, Hanhui Jiang, Zhonghe Zhang, Xiaoqing Li, Jianchao Rao, Bo Cheng, Zhifeng Zhu, Ping Liu, Minghai Xu, Tao Ma, Shaoxiang Yang, Yong Li, Chuan Wang, Zhijiang Zhang, Ming Yu, Kexun Hu, Xiwei Liang, Y. Yu, Q. Gentle, K.W. Pan, Yuan Gentle, Kenneth William Yu, Qingquan Liang, Yunfeng Jiang, Wei Yi, Lin Zhang, Ya Hu, Qiming Li, Jianchao Huang, Mingxiang Li, Haolong Huang, Zhuo Huang, Jie Wang, Weijun He, Mei Zhao, Qing Xu, Jiayu Zhou, Gangyi Ba, Weigang Yang, Cheng Yao, Junjie Wang, Chuliang He, Bo Hu, Yongzhen Deng, Mingyang Fu, Jingwei Liang, Meiling Guan, Yehong Wu, Hongyan Zhuang, Ge Ding, Weixing Lan, Tao Zeng, Shiyong Hussain, Malik Sadam Lin, Zhifang Liu, Hai Sun, Youwen Zeng, Long Liu, Shaocheng Liao, Liang Zhong, Wulyu Shi, Zhongbing Jiang, Min Dong, Yunbo Xu, Min Wang, Aike Zhang, Xiaolong Liu, Linzi Tong, Ruihai Cheng, Jun Nie, Lin Li, Hui Xu, Jianqiang Yang, Zengchen Wen, Jie Liang, Anshu Zhang, Yipo Wu, Yifan Chen, Chengyuan Zhao, Kaijun Shi, Yuejiang Huang, He Austin, Max Lee, Sanggon Luhmann, Neville C. Domier, Calvin W. Zhu, Yilun Brower, David L. Chen, Jie Ida, K. Takemura, Y. Suzuki, Y. Nagasaki, K. Drews, P. Knieps, A. Han, Xiang Krämer-Flecken, A. Henkel, M. He, Jiyang Zhou, Yinan Jia, Ruo Peng, Yue Wang, Pengyu Li, Jiawei Yang, Jie Lu, Conghui Lu, Yiwei Wang, Rumeng Zhang, Hongqi Zeng, Yingqin Zhang, Guodong Ma, Fangyuan Bala, Abba Alhaji Li, Dingchen Hua, Jiankun Ai, Xinkun Tao, Qinlin Zhong, Yu Li, Yangbo He, Xiangrui Wan, Sui Huang, Shanni Ma, Yiming Qu, Zitong Yu, Shimin Huang, Zhangsheng Lei, Chi School of Electric and Electronic Engineering Huazhong University of Science and Technology Wuhan430074 China Southwestern Institute of Physics Chengdu China Institute of Plasma Physics Chinese Academy of Sciences Hefei China Guizhou University of Commerce Guiyang China Wuhan Institute of Technology Wuhan China ITER Organization Route de Vinon-sur-Verdon CS 90 046 Saint-Paul-lez-DuranceCedex 13067 France Forschungszentrum Jülich GmbH IEK-Plasmaphysik Jülich Germany Max-Planck-Institut für Plasmaphysik Garching Germany Institute of Fusion Studies University of Texas at Austin AustinTX United States University of Texas at Austin AustinTX78712 United States School of Physics Huazhong University of Science and Technology Wuhan430074 China Department of Physics Wuhan University of Technology Wuhan430070 China Princeton Plasma Physics Laboratory PO Box 451 PrincetonNJ08543 United States Hubei Key Laboratory of Optical Information and Pattern Recognition Wuhan Institute of Technology Wuhan430205 China College of Computer Science South-Central University for Nationalities Wuhan430074 China Shenzhen University Shenzhen518060 China University of Science and Technology of China Hefei230026 China School of Electrical Engineering & Automation Jiangsu Normal University Xuzhou221116 China Southwest Jiaotong University Chengdu China College of Nuclear Science and Engineer East China University of Technology PO Box Nanchang330013 China ENN Science and Technology Development Co. Ltd Hebei Key Laboratory of Compact Fusion Langfang065001 China National Fusion Research Institute Daejeon305-333 Korea Republic of University of California DavisCA95616 United States University of California Los Angeles Los AngelesCA90095 United States National Institute for Fusion Science Toki509-5292 Japan Graduate School of Advanced Science and Engineering Hiroshima University Hiroshima739-8527 Japan Institute of Advanced Energy Kyoto University Gokasho Ky

The J-TEXT capability is enhanced compared to two years ago with several upgrades of its diagnostics and the increase of electron cyclotron resonance heating (ECRH) power to 1 MW. With the application of electron cyclotron wave (ECW), the ECW assisted plasma startup is achieved;the tearing mode is suppressed;the toroidal injection of 300 kW ECW drives around 24 kA current;fast electrons are generated with toroidal injected ECW and the runaway current conversion efficiency increases with ECRH power. The mode coupling between 2/1 and 3/1 modes are extensively studied. The coupled 2/1 and 3/1 modes usually lead to major disruption. Their coupling can be either suppressed or avoided by external resonant magnetic perturbation fields and hence avoids the major disruption. It is also found that the 2/1 threshold of external field is significantly reduced by a pre-excited 3/1 mode, which can be either a locked island or an external kink mode. The disruption control is studied by developing prediction methods capable of cross tokamak application and by new mitigation methods, such as the biased electrode or electromagnetic pellet injector. The high-density operation and related disruptions are studied from various aspects. Approaching the density limit, the collapse of the edge shear layer is observed and such collapse can be prevented by applying edge biasing, leading to an increased density limit. The density limit is also observed to increase, if the plasma is operated in the poloidal divertor configuration or the plasma purity is increased by increasing the pre-filled gas pressure or ECRH power during the start-up phase. © 2024 The Author(s).

关键词： Tokamak devices

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Development of a Tetris playing robot controlled by KNR 15

Development of a Tetris playing robot controlled by KNR

引用

15th IEEE International Conference on Mechatronics and automation, ICMA 2018

作者： Wang, Ming Zhang, Yanlu Dong, Huifang Li, Xu Yu, Junzhi Department of Information and Electrical Engineering University of Shandong Jianzhu University Jinan250100 China Department of Intelligent Robotics State Key Laboratory of Management and Control for Complex Systems Institute of Automation Chinese Academy of Sciences Beijing100190 China

ISBN: (纸本)9781538660720

Robot plays an increasingly important role in daily life. This paper presents a vision-based wheeled robot for playing Tetris. How to control the robot is elaborated at length in this paper. The robot adopted a KNR controller as its core controller. With a CCD sensor, it identified colored blocks, lines and the destination. All algorithms are programed with LabVIEW. The experiments and the contest validated the effectiveness of the proposed vision-based wheeled robot system. © 2018 IEEE.

关键词： Controllers

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Delays in Model Reduction of Chemical Reaction Networks

引用

IFAC-PapersOnLine 2018年第14期51卷 100-105页

作者： Lipták, György Hangos, Katalin M. Process Control Research Group Systems and Control Laboratory Computer and Automation Research Institute Hungarian Academy of Sciences P.O. Box 63 BudapestH-1518 Hungary Department of Electrical Engineering and Information Systems University of Pannonia Veszprém Hungary

A novel engineering model reduction method is proposed in this paper that can be applied to a chemical reaction network (CRN) with chains of linear reactions. The reduced model is a delayed CRN with possibly different delays but with less state variables than the original model. As the first step of the model reduction, a decomposition method is also developed to transform chains with joint reactions into independent chains of linear reactions. The well known example of McKeithan's network is used as a case study to illustrate the basic concepts and the design method. © 2018

关键词： Reduction

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Enhancing sensitivity to ambient refractive index with tunable few-layer graphene/hBN nanoribbons

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Photonics Research 2019年第7期7卷 130-137页

作者： Huan Jiang Sajid Choudhury Zhaxylyk A.Kudyshev Di Wang Ludmila J.Prokopeva Peng Xiao Yongyuan Jiang Alexander V.Kildishev Institute of Modern Optics Department of PhysicsHarbin Institute of TechnologyHarbin 150001China School of Electrical and Computer Engineering and Birck Nanotechnology Center Purdue UniversityWest Lafayette Indiana 47907USA School of Electrical Engineering and Automation Harbin Institute of TechnologyHarbin 150001China Collaborative Innovation Center of Extreme Optics Shanxi UniversityTaiyuan 030006China Key Laboratory of Micro-Optics and Photonic Technology of Heilongjiang Province Harbin 150001China Key Laboratory of Micro-Nano Optoelectronic Information System of Ministry of Industry and Information Technology Harbin 150001China

Refractive index (RI) sensing helps to identify biomolecules and chemicals in the mid-infrared range for drug discovery, bioengineering, and environmental monitoring. In this paper, we numerically demonstrate an electrically tunable RI sensor with ultrahigh sensitivity using a three-layer graphene nanoribbon array separated by hexagonal boron nitride (hBN). Unlike the weak resonance in single-layer graphene nanoribbons, a much stronger plasmon resonance featuring a higher-quality factor can be excited in the graphene/hBN few-layer ribbon array. Simultaneously, the high purity of graphene on hBN results in an outstanding charge mobility above 4 ×10^4 cm^2 · V^-1·s^-1 at 300 K, which allows a larger modulation depth. The interaction between the locally enhanced field around graphene ribbons and its surrounding analyte leads to ultrahigh sensitivity (4.207μm/RIU), with the figure of merit reaching approximately ***, this ultrasensitive detector could selectively work in different wavebands by controlling gate voltages applied to *** merits of ultrahigh sensitivity and electrical tunability are major advances compared to previous RI sensors, paving a way toward ultrasensitive detection using graphene/hBN few-layer devices.

关键词： Enhancing sensitivity refractive index nanoribbons

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Permissioned blockchain for efficient and secure resource sharing in vehicular edge computing

arXiv

引用

arXiv 2019年

作者： Wang, Siming Huang, Xumin Yu, Rong Zhang, Yan Hossain, Ekram School of Automation Guangdong University of Technology University of Oslo Simula Research Laboratory Department of Electrical and Computer Engineering University of Manitoba WinnipegMBR3T2N2 Canada

With the fast expanding scale of vehicular networks, vehicular edge computing (VEC) has emerged and attracted growing attention from both industry and academia. Parked vehicles (PVs) have great potential to join vehicular networks for sharing their idle computing and networking resources. However, due to the underlying security and privacy threats, it is challenging to fairly motivate PVs for resource sharing in an efficient and secure way. In this paper, we propose a permissioned vehicular blockchain for secure and efficient resource sharing in VEC, namely Parkingchain. We first design smart contract to achieve secure resource sharing and efficient service provisioning between PVs and service requesters (SRs). A multi-weight subjective logic based delegated Byzantine Fault Tolerance (DBFT) consensus mechanism is presented to improve the consensus process in Parkingchain. Further, we design a contract theory-based incentive mechanism to model the interactions between SR and PVs under asymmetric information scenario. Finally, numerical results demonstrate that the proposed incentive mechanism is effective and efficient compared with existing schemes. Index Terms-Vehicular edge computing, vehicular blockchain, delegated Byzantine Fault Tolerance, contract theory. Copyright © 2019, The Authors. All rights reserved.

关键词： Edge computing

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Predictive Inverse Kinematics: optimizing Future Trajectory through Implicit Time Integration and Future Jacobian Estimation

Predictive Inverse Kinematics: optimizing Future Trajectory ...

引用

2019 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)

作者： Ko Ayusawa Wael Suleiman Eiichi Yoshida CNRS-AIST JRL (Joint Robotics Laboratory) UMI13218/RL Intelligent Systems Research Institute National Institute of Advanced Industrial Science and Technology (IS-AIST) Japan Electrical and Computer Engineering Department Faculty of Engineering University of Sherbrooke Canada

This paper presents an inverse kinematics (IK) method which can control future velocities and accelerations for multi-body systems. The proposed IK method is formulated as a quadratic programing (QP) that optimizes future joint trajectories. The features of the proposed IK are: (1) the evaluation of accelerations at future time instances, (2) the trajectory representation that can implicitly integrate the time integral formula into QP, (3) the computation of future Jacobian matrices based on the comprehensive theory of differential kinematics proposed in our previous work. Those features enable a stable and fast IK computation while evaluating the future accelerations. We also conducted thorough numerical studies to show the efficiency of the proposed method.

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