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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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Comparisons among Six Numerical Methods for Solving Repetitive Motion Planning of Redundant Robot Manipulators

Comparisons among Six Numerical Methods for Solving Repetiti...

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IEEE International Conference on Robotics and Biomimetics

作者： Zhijun Zhang Lingdong Kong Ziyi Yan Ke Chen Shuai Li Xilong Qu Ning Tan School of Automation Science & Engineering South China University of Technology Guangzhou China School of Electronic & Information Engineering South China University of Technology Guangzhou China Department of Computing Hong Kong Polytechnic University Hong Kong China School of Information Technology & Management Hunan University of Finance and Economics Changsha China School of Data & Computer Science Sun Yat-sen University Guangzhou China

ISBN: (纸本)9781728103785;9781728103778

To ensure that each joint of redundant robot manipulators can return to its initial state when completes a closed-path tracking task, a repetitive motion planning (RMP) scheme is presented. On the basis of a quadratic programming (QP) framework, this RMP can be equivalently converted into a linear-variational-inequality (LVI) problem, and then into a piecewise linear projection equation (PLPE). In this paper, three novel numerical methods (i.e., M3, M5 and M6) and three traditional numerical methods (i.e., 94LVI, E47 and M4) are exploited, analyzed, and compared to solve PLPE, as well as RMP. The convergence of M5 method is theoretically proved, and that of M3 and M6 methods is analyzed by simulations. Moreover, comparative simulations of two complex path tracking tasks performed on a PUMA560 robot manipulator further verify the feasibility and effectiveness of the proposed numerical methods.

关键词： Robot kinematics Motion planning Quadratic programming Complex path tracking

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Structured decomposition for reversible Boolean functions

arXiv

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arXiv 2018年

作者： Jiang, Jiaqing Sun, Xiaoming Sun, Yuan Wu, Kewen Xia, Zhiyu CAS Key Lab of Network Data Science and Technology Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineering and Computer Science Peking University Beijing China

Reversible Boolean function is a one-to-one function which maps n-bit input to n-bit output. Reversible logic synthesis has been widely studied due to its relationship with low-energy computation as well as quantum computation. In this work, we give a structured decomposition for even reversible Boolean functions (RBF). Specifically, for n ≥ 6, any even n-bit RBF can be decomposed to 7 blocks of (n − 1)-bit RBF, where 7 is a constant independent of n;and the positions of those blocks have large degree of freedom. Moreover, if the (n − 1)-bit RBFs are required to be even as well, we show for n ≥ 10, n-bit RBF can be decomposed to 10 even (n − 1)-bit RBFs. For simplicity, we say our decomposition has block depth 7 and even block depth 10. Our result improves Selinger’s work in block depth model, by reducing the constant from 9 to 7;and from 13 to 10 when the blocks are limited to be even. We emphasize that our setting is a bit different from Selinger’s. In Selinger’s constructive proof, each block is one of two specific positions and thus the decomposition has an alternating structure. We relax this restriction and allow each block to act on arbitrary (n − 1) bits. This relaxation keeps the block structure and provides more candidates when choosing positions of blocks. Copyright © 2018, The Authors. All rights reserved.

关键词： Logic gates

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Improved Cryptanalysis of an ISO Standard Lightweight Block Cipher with Refined MILP Modelling 13th

Improved Cryptanalysis of an ISO Standard Lightweight Block ...

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13th International Conference on Information Securityand Cryptology, Inscrypt 2017

作者： Yin, Jun Ma, Chuyan Lyu, Lijun Song, Jian Zeng, Guang Ma, Chuangui Wei, Fushan State Key Laboratory of Mathematical Engineering and Advanced Computing Zhengzhou450001 China State Key Laboratory of Cryptology P.O. Box 5159 Beijing100878 China Institute of Information Engineering Chinese Academy of Sciences Beijing100093 China Data Assurance and Communication Security Research Center Chinese Academy of Sciences Beijing100093 China School of Cyber Security University of Chinese Academy of Sciences Beijing100049 China National University of Defense Technology Changsha410073 China Army Aviation Institute Beijing101116 China

ISBN: (纸本)9783319751597

Differential and linear cryptanalysis are two of the most effective attacks on block ciphers. Searching for (near) optimal differential or linear trails is not only useful for the security evaluation of block ciphers against these attacks, but also indispensable to the cryptanalysts who want to attack a cipher with these techniques. In recent years, searching for trails automatically with Mixed-Integer Linear Programming (MILP) gets a lot of attention. At first, Mouha et al. translated the problem of counting the minimum number of differentially active S-boxes into an MILP problem for word-oriented block ciphers. Subsequently, in Asiacrypt 2014, Sun et al. extended Mouha et al.’s method, and presented a technique which can find actual differential or linear characteristics of a block cipher in both the single-key and related-key models. In this paper, we refine the constraints of the 2-XOR operation in order to reduce the overall number of variables and constraints. Experimental results show that MILP models with the refined constraints can be solved more efficiently. We apply our method to HIGHT (an ISO standard), and we find differential (covering 11 rounds) or linear trails (covering 10 rounds) with higher probability or correlation. Moreover, we find so far the longest differential and linear distinguishers of HIGHT. © Springer International Publishing AG, part of Springer Nature 2018.

关键词： ISO Standards

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Radio detection of an elusive millisecond pulsar in the Globular Cluster NGC 6397

arXiv

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arXiv 2022年

作者： Zhang, Lei Ridolfi, Alessandro Blumer, Harsha Freire, Paulo C.C. Manchester, Richard N. McLaughlin, Maura Kremer, Kyle Cameron, Andrew D. Zhang, Zhiyu Behrend, Jan Burgay, Marta Buchner, Sarah Champion, David J. Chen, Weiwei Dai, Shi Feng, Yi Fu, Xiaoting Guo, Meng Hobbs, George Keane, Evan F. Kramer, Michael Levin, Lina Li, Xiangdong Ni, Mengmeng Pan, Jingshan Padmanabh, Prajwal V. Possenti, Andrea Ransom, Scott M. Tsai, Chao-Wei Krishnan, Vivek Venkatraman Wang, Pei Zhang, Jie Zhi, Qijun Zhang, Yongkun Li, Di National Astronomical Observatories Chinese Academy of Sciences A20 Datun Road Chaoyang District Beijing100101 China Centre for Astrophysics and Supercomputing Swinburne University of Technology P.O. Box 218 HawthornVIC3122 Australia SelargiusI-09047 Italy Department of Physics and Astronomy West Virginia University MorgantownWV26506 United States Max-Planck Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany CSIRO Space and Astronomy Australia Telescope National Facility PO Box 76 EppingNSW1710 Australia TAPIR California Institute of Technology PasadenaCA91125 United States The Observatories of the Carnegie Institution for Science PasadenaCA91101 United States Swinburne University of Technology Mail H74 PO Box 218 VIC3122 Australia School of Astronomy and Space Science Nanjing University Nanjing210023 China Ministry of Education Nanjing210093 China South African Radio Astronomy Observatory Fir Street Black River Park Cape Town7925 South Africa School of Science Western Sydney University Locked Bag 1797 PenrithNSW2751 Australia Research Center for Intelligent Computing Platforms Zhejiang Laboratory Hangzhou311100 China Purple Mountain Observatory Chinese Academy of Sciences Nanjing210023 China National Supercomputing Center in Jinan Qilu University of Technology 28666 East Jingshi Road Licheng Distrist Jinan250103 China Jinan Institute of Supercomputing Technology 28666 East Jingshi Road Licheng Distrist Jinan250103 China School of Physics Trinity College Dublin College Green Dublin Ireland Jodrell Bank Centre for Astrophysics Department of Physics and Astronomy The University of Manchester ManchesterM13 9PL United Kingdom HannoverD-30167 Germany MonserratoI-09042 Italy NRAO 520 Edgemont Road CharlottesvilleVA22903 United States College of Physics and Electronic Engineering Qilu Normal University 2 Wenbo Road Zhangqiu District Jinan250200 China Guizhou Provincial Key Laboratory of Radio

We report the discovery of a new 5.78 ms-period millisecond pulsar (MSP), PSR J1740−5340B (NGC 6397B), in an eclipsing binary system discovered with the Parkes radio telescope (now also known as Murriyanga), Australia, and confirmed with the MeerKAT radio telescope in South Africa. The measured orbital period, 1.97 days, is the longest among all eclipsing binaries in globular clusters (GCs) and consistent with that of the coincident X-ray source U18, previously suggested to be a ‘hidden MSP’. Our XMM-Newton observations during NGC 6397B’s radio quiescent epochs detected no X-ray flares. NGC 6397B is either a transitional MSP or an eclipsing binary in its initial stage of mass transfer after the companion star left the main sequence. The discovery of NGC 6397B potentially reveals a subgroup of extremely faint and heavily obscured binary pulsars, thus providing a plausible explanation to the apparent dearth of binary neutron stars in core-collapsed GCs as well as a critical constraint on the evolution of GCs. Copyright © 2022, The Authors. All rights reserved.

关键词： Mass transfer

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An automatic biomedical ontology meta-matching technique

Journal of Network Intelligence

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Journal of Network Intelligence 2019年第3期4卷 109-113页

作者： Xue, Xingsi Yang, Haiyan Zhang, Jie Zhang, Jing Chen, Dongxu College of Information Science and Engineering Intelligent Information Processing Research Center Fujian Key Lab for Automotive Electronics and Electric Drive Fujian Provincial Key Laboratory of Big Data Mining and Applications Fujian University of Technology No.3 Xueyuan Road University Town Minhou Fuzhou CityFujian Province350118 China College of Information Science and Engineering Fujian University of Technology No.33 Xuefu South Road University Town Minhou Fuzhou CityFujian Province350118 China School of Computer Science and Engineering Yulin Normal University No.299 Education Middle Road Yulin CityGuanxi Province537000 China School of Computing Ulster University Jordanstown BT370QB United Kingdom Fujian Medical University Union Hospital No.29 Xinquan Road Gulou Fuzhou CityFujian Province350001 China

Biomedical ontology matching aims at determining the heterogeneous biomed-ical concepts, and bridging the semantic gap between heterogeneous biomedical ontologies. The foundation of a biomedical ontology matching technique is the Biomedical Concept Similarity Measure (BCSM), which calculates the similarity value between two biomed-ical concepts. Since various BCSMs have different advantages, usually several BCSMs are aggregated together to improve the result’s confidence. How to tune the aggregating weights to ensure the quality of the alignment is called biomedical ontology meta-matching problem, which is a challenge in the ontology matching domain. Currently, researchers mainly focus on how to tune the aggregating weights for various similarity measures to improve the quality of the ontology alignments. However, the ignorance of the effects brought about by different biomedical concept mapping’s preference on different similarity measures significantly reduces the alignment’s quality. To overcome this drawback, in this work, we formally define the biomedical ontology meta-matching problem, and then present an Ordered Weighted Average (OWA) based approach to automatically aggregate various biomedical concept similarity measures. In our method, the aggregating weights determined for each concept mapping is associated with the ordered position of the similarity value instead of a particular concept similarity measure. The experiment utilizes the large biomed track provided by Ontology Alignment Evaluation Initiative (OAEI) to test our proposal’s performance, and the experimental results show the effectiveness of our proposal. © 2019, Taiwan Ubiquitous Information. All rights reserved.

关键词： Semantics

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Dual encoding for zero-example video retrieval

arXiv

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arXiv 2018年

作者： Dong, Jianfeng Li, Xirong Xu, Chaoxi Ji, Shouling He, Yuan Yang, Gang Wang, Xun College of Computer and Information Engineering Zhejiang Gongshang University Key Lab of Data Engineering and Knowledge Engineering Renmin University of China AI & Media Computing Lab School of Information Renmin University of China College of Computer Science Zhejiang University Alibaba-Zhejiang University Joint Research Institute of Frontier Technologies Alibaba Group

This paper attacks the challenging problem of zero-example video retrieval. In such a retrieval paradigm, an end user searches for unlabeled videos by ad-hoc queries described in natural language text with no visual example provided. Given videos as sequences of frames and queries as sequences of words, an effective sequence-to-sequence cross-modal matching is required. The majority of existing methods are concept based, extracting relevant concepts from queries and videos and accordingly establishing associations between the two modalities. In contrast, this paper takes a concept-free approach, proposing a dual deep encoding network that encodes videos and queries into powerful dense representations of their own. Dual encoding is conceptually simple, practically effective and end-to-end. As experiments on three benchmarks, i.e. MSR-VTT, TRECVID 2016 and 2017 Ad-hoc Video Search show, the proposed solution establishes a new state-of-the-art for zero-example video retrieval. Copyright © 2018, The Authors. All rights reserved.

关键词： Signal encoding

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Creating bus timetables with maximal synchronization by a new algorithm based on the PSO 17

Creating bus timetables with maximal synchronization by a ne...

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17th COTA International Conference of Transportation Professionals: Transportation Reform and Change - Equity, Inclusiveness, Sharing, and Innovation, CICTP 2017

作者： Tian, Daxin Liu, Wenhao Guo, Peng Rong, Hui Wang, Wenyang Gong, Jinfeng Wang, Yunpeng Liu, He Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang Univ. Beijing100191 China Beijing Key Laboratory for Cooperative Vehicle Infrastructure Systems and Safety Control School of Transportation Science and Engineering Beihang Univ. Beijing100191 China Jiangsu Province Collaborative Innovation Center of Modern Urban Traffic Technologies Nanjing210096 China Quartermaster Equipment Institute of the General Logistics Dept. of CPLA Beijing100010 China

ISBN: (数字)9780784480915

ISBN: (纸本)9780784480915

This paper addresses the problem of receiving a timetable for a settled network with maximal synchronization. In this paper, a model has been developed to solve the problem which attaches importance to creating a timetable for maximizing their synchronization and enables the transfer of passengers from one route to another with least waiting times at transfer nodes. Next, this problem is formulated as a mixed integer linear programming problem, and a new algorithm based on the traditional particle swarm optimization (PSO) has been developed to solve the problem in a short time. Finally, the relationship of iterative time and the complexity of the given network is qualitatively established. © ASCE.

关键词： Synchronization

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A New Control Strategy Integrated into the Desired Safety Margin Car-Following Model Considering the Disturbance Level

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Transportation Research Record 2018年

作者： Zhang, Junjie Wang, Yunpeng Lu, Guangquan Beijing Advanced Innovation Center for Big Data and Brain Computing Beijing Key Laboratory for Cooperative Vehicle Infrastructure Systems and Safety Control Jiangsu Province Collaborative Innovation Center of Modern Urban Traffic Technologies School of Transportation Science and Engineering Beihang University Haidian District Beijing China China

A vehicular communication system can provide motion information based on various sensors. Thus, adaptive cruise control (ACC) systems based on a reliable communication system can relieve traffic congestion in a platoon. However, acquiring vehicle information entails uncertainties because the disturbance of traffic environment and vehicular communication systems influences vehicle control performance. In this study, the desired safety margin (DSM) model is employed to investigate the influence of uncertainty on car-following performance, such as starting, emergency braking, and car-following processes. Based on the DSM model, the disturbance level on perceived safety margin is introduced to characterize the uncertainty of vehicle information. The stability criterion of the DSM model with the disturbance level is derived via linear stability theory. Analytical results indicate that a negative value of disturbance level will enlarge the stable region. By contrast, a positive value is conducive for maintaining the consensus state and achieving the high acceleration and deceleration of following vehicles in the starting process. Findings show that disturbance in the vehicular system significantly influences car-following performance. To enhance the smoothness and stability of traffic flow evolution, a new control strategy is proposed in this study. Numerical experiments illustrate the effectiveness of the proposed control strategy in stabilizing traffic flow. This study highlights the need to resolve the stability of sensors and vehicular communication systems, and develop a vehicular controller to help ACC system improve vehicle control performance in the car-following process. © 2018, National Academy of Sciences: Transportation Research Board 2018.

关键词： Stability criteria

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Roadmap on Electronic Structure Codes in the Exascale Era

arXiv

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arXiv 2022年

作者： Gavini, Vikram Baroni, Stefano Blum, Volker Bowler, David R. Buccheri, Alexander Chelikowsky, James R. Das, Sambit Dawson, William Delugas, Pietro Dogan, Mehmet Draxl, Claudia Galli, Giulia Genovese, Luigi Giannozzi, Paolo Giantomassi, Matteo Gonze, Xavier Govoni, Marco Gulans, Andris Gygi, François Herbert, John M. Kokott, Sebastian Kühne, Thomas D. Liou, Kai-Hsin Miyazaki, Tsuyoshi Motamarri, Phani Nakata, Ayako Pask, John E. Plessl, Christian Ratcliff, Laura E. Richard, Ryan M. Rossi, Mariana Schade, Robert Scheffler, Matthias Schütt, Ole Suryanarayana, Phanish Torrent, Marc Truflandier, Lionel Windus, Theresa L. Xu, Qimen Yu, Victor W.-Z. Perez, Danny Department of Mechanical Engineering University of Michigan Ann ArborMI48109 United States SISSA ISAS Trieste Trieste34136 Italy IOM-CNR Trieste Trieste34136 Italy Duke University DurhamNC27708 United States London Centre for Nanotechnology LondonWC1H 0AH United Kingdom WPI-MANA National Institute for Materials Science Ibaraki305-0044 Japan Humboldt-Universität zu Berlin Berlin10117 Germany McKetta Department of Chemical Engineering University of Texas at Austin AustinTX78712 United States Center for Computational Materials Oden Institute University of Texas at Austin AustinTX78712 United States Department of Physics University of Texas at Austin AustinTX78712 United States RIKEN Center for Computational Science Hyogo Kobe650-0047 Japan Pritzker School of Molecular Engineering University of Chicago ChicagoIL60637 United States Materials Science Division Argonne National Laboratory LemontIL60439 United States Université Grenoble Alpes MEM L_Sim GrenobleF-38000 France University of Udine Udine33100 Italy IMCN Université catholique de Louvain Louvain-la-neuve Belgium University of Latvia RīgaLV-1586 Latvia University of California DavisCA95616 United States Department of Chemistry & Biochemistry The Ohio State University ColumbusOH43210 United States Berlin14195 Germany Dynamics of Condensed Matter Center for Sustainable Systems Design Chair of Theoretical Chemistry Paderborn University D-33098 Germany Paderborn Center for Parallel Computing Paderborn University D-33098 Germany Department of Computational and Data Sciences Indian Institute of Science Karnataka Bengaluru560012 India Lawrence Livermore National Laboratory LivermoreCA94550 United States Department of Computer Science Paderborn University D-33098 Germany Centre for Computational Chemistry School of Chemistry University of Bristol BristolBS8 1TS United Kingdom Ames National Laboratory AmesIA50011 United States Iowa State University AmesIA50

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing. Copyright © 2022, The Authors. All rights reserved.

关键词： Electronic structure

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