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Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3 — Ex vivo imaging: data processing, comparisons with microscopy, and tractography

arXiv

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arXiv 2024年

作者： Schilling, Kurt G. Howard, Amy F.D. Grussu, Francesco Ianus, Andrada Hansen, Brian Barrett, Rachel L.C. Aggarwal, Manisha Michielse, Stijn Nasrallah, Fatima Syeda, Warda Wang, Nian Veraart, Jelle Roebroeck, Alard Bagdasarian, Andrew F. Eichner, Cornelius Sepehrband, Farshid Zimmermann, Jan Soustelle, Lucas Bowman, Christien Tendler, Benjamin C. Hertanu, Andreea Jeurissen, Ben Verhoye, Marleen Frydman, Lucio van de Looij, Yohan Hike, David Dunn, Jeff F. Miller, Karla Landman, Bennett A. Shemesh, Noam Anderson, Adam McKinnon, Emilie Farquharson, Shawna Dell' Acqua, Flavio Pierpaoli, Carlo Drobnjak, Ivana Leemans, Alexander Harkins, Kevin D. Descoteaux, Maxime Xu, Duan Huang, Hao Santin, Mathieu D. Grant, Samuel C. Obenaus, Andre Kim, Gene S. Wu, Dan Le Bihan, Denis Blackband, Stephen J. Ciobanu, Luisa Fieremans, Els Bai, Ruiliang Leergaard, Trygve B. Zhang, Jiangyang Dyrby, Tim B. Johnson, G. Allan Cohen-Adad, Julien Budde, Matthew D. Jelescu, Ileana O. Radiology and Radiological Sciences Vanderbilt University Medical Center NashvilleTN United States Vanderbilt University Institute of Imaging Science Vanderbilt University NashvilleTN United States Department of Bioengineering Imperial College London London United Kingdom FMRIB Centre Wellcome Centre for Integrative Neuroimaging Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom Radiomics Group Vall d’Hebron Institute of Oncology Vall d’Hebron Barcelona Hospital Campus Barcelona Spain Queen Square MS Centre Queen Square Institute of Neurology Faculty of Brain Sciences University College London London United Kingdom Champalimaud Research Champalimaud Foundation Lisbon Portugal Center of Functionally Integrative Neuroscience Aarhus University Aarhus Denmark Department of Neuroimaging Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom NatBrainLab Department of Forensics and Neurodevelopmental Sciences Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom Russell H. Morgan Department of Radiology and Radiological Science Johns Hopkins University School of Medicine BaltimoreMD United States Maastricht University Medical Center Maastricht Netherlands The Queensland Brain Institute The University of Queensland Queensland Australia Melbourne Neuropsychiatry Centre The University of Melbourne ParkvilleVIC Australia Department of Radiology and Imaging Sciences Indiana University IN United States Stark Neurosciences Research Institute Indiana University School of Medicine IN United States Center for Biomedical Imaging NYU Grossman School of Medicine New YorkNY United States Faculty of psychology and Neuroscience Maastricht University Maastricht Netherlands Department of Chemical & Biomedical Engineering FAMU-FSU College of Engineering Florida State University TallahasseeFL United States Center for Interdisciplinary Magnetic Res

Preclinical diffusion MRI (dMRI) has proven value in methods development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages that facilitate high spatial resolution and high signal-to-noise ratio (SNR) images, cutting-edge diffusion contrasts, and direct comparison with histological data as a methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work concludes a 3-part series of recommendations and considerations for preclinical dMRI. Herein, we describe best practices for dMRI of ex vivo tissue, with a focus on image pre-processing, data processing and model fitting, and tractography. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. We end by providing guidelines on code sharing and data sharing, and point towards open-source software and databases specific to small animal and ex vivo imaging. © 2024, CC BY.

关键词： Data Sharing

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The medical segmentation decathlon

arXiv

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arXiv 2021年

作者： Antonelli, Michela Reinke, Annika Bakas, Spyridon Farahani, keyvan Kopp-Schneider, Annette Landman, Bennett A. Litjens, Geert Menze, Bjoern Ronneberger, Olaf Summers, Ronald M. van Ginneken, Bram Bilello, Michel Bilic, Patrick Christ, Patrick F. Do, Richard K.G. Gollub, Marc J. Heckers, Stephan H. Huisman, Henkjan Jarnagin, William R. McHugo, Maureen K. Napel, Sandy Golia Pernicka, Jennifer S. Rhode, Kawal Tobon-Gomez, Catalina Vorontsov, Eugene Hulsmon, Hankan Meakin, James A. Ourselin, Sebastien Wiesenfarth, Manuel Arbeláez, Pablo Bae, Byeonguk Chen, Sihong Daza, Laura Feng, Jianjiang He, Baochun Isensee, Fabian Ji, Yuanfeng Jia, Fucang Kim, Namkug Kim, Ildoo Merhof, Dorit Pai, Akshay Park, Beomhee Perslev, Mathias Rezaiifar, Ramin Rippel, Oliver Sarasua, Ignacio Shen, Wei Son, Jaemin Wachinger, Christian Wang, Liansheng Wang, Yan Xia, Yingda Xu, Daguang Xu, Zhanwei Zheng, Yefeng Simpson, Amber L. Maier-Hein, Lena Cardoso, M. Jorge School of Biomedical Engineering & Imaging Sciences King’s College London London United Kingdom Heidelberg Germany Heidelberg Germany Faculty of Mathematics and Computer Science University of Heidelberg Heidelberg Germany University of Pennsylvania PhiladelphiaPA United States BethesdaMD United States Heidelberg Germany Electrical Engineering and Computer Science Vanderbilt University NashvilleTN United States Radboud University Medical Center Radboud Institute for Health Sciences Nijmegen Netherlands Quantitative Biomedicine University of Zurich Zurich Switzerland DeepMind London United Kingdom School of Computing Department of Biomedical and Molecular Sciences Queen’s University KingstonON Canada Department of Surgery Memorial Sloan Kettering Cancer Center New YorkNY United States BethesdaMD United States Department of Informatics Technische Universität München Germany Department of Radiology Memorial Sloan Kettering Cancer Center New YorkNY United States Department of Psychiatry & Behavioral Sciences Vanderbilt University Medical Center NashvilleTN United States Department of Radiology Stanford University StanfordCA United States Department of Computer Science and Software Engineering École Polytechnique de Montréal Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Medical Faculty University of Heidelberg Heidelberg Germany VUNO Inc. Seoul Korea Republic of Universidad de los Andes Colombia Department of Automation Tsinghua University Beijing China Heidelberg Germany Department of Computer Science Xiamen University Xiamen361005 China Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Kakao Brain Korea Republic of Institute of Imaging & Computer Vision RWTH Aachen University Aachen Germany Cere

International challenges have become the de facto standard for comparative assessment of image analysis algorithms given a specific task. Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem. We hypothesized that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. To investigate the hypothesis, we organized the Medical Segmentation Decathlon (MSD)—a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities. The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data and small objects. The MSD challenge confirmed that algorithms with a consistent good performance on a set of tasks preserved their good average performance on a different set of previously unseen tasks. Moreover, by monitoring the MSD winner for two years, we found that this algorithm continued generalizing well to a wide range of other clinical problems, further confirming our hypothesis. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms are mature, accurate, and generalize well when retrained on unseen tasks;(2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability;(3) the training of accurate AI segmentation models is now commoditized to non AI *** Codes 68T07. © 2021, CC BY-NC-SA.

关键词： Image segmentation

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JETSCAPE framework: p+p results

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Physical Review C 2020年第5期102卷 054906-054906页

作者： A. Kumar Y. Tachibana D. Pablos C. Sirimanna R. J. Fries A. Majumder A. Angerami S. A. Bass S. Cao Y. Chen J. Coleman L. Cunqueiro T. Dai L. Du H. Elfner D. Everett W. Fan C. Gale Y. He U. Heinz B. V. Jacak P. M. Jacobs S. Jeon K. Kauder E. Khalaj W. Ke M. Kordell, II T. Luo M. McNelis J. Mulligan C. Nattrass D. Oliinychenko L.-G. Pang C. Park J.-F. Paquet J. H. Putschke G. Roland B. Schenke L. Schwiebert C. Shen R. A. Soltz G. Vujanovic X.-N. Wang R. L. Wolpert Y. Xu Z. Yang Department of Physics and Astronomy Wayne State University Detroit Michigan 48201 USA Department of Physics and Astronomy McGill University Montréal Quebec Canada H3A 2T8 Cyclotron Institute Texas A&M University College Station Texas 77843 USA Department of Physics and Astronomy Texas A&M University College Station Texas 77843 USA Lawrence Livermore National Laboratory Livermore California 94550 USA Department of Physics Duke University Durham North Carolina 27708 USA Laboratory for Nuclear Science Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Department of Statistical Science Duke University Durham North Carolina 27708 USA Department of Physics and Astronomy University of Tennessee Knoxville Tennessee 37996 USA Department of Physics The Ohio State University Columbus Ohio 43210 USA GSI Helmholtzzentrum für Schwerionenforschung 64291 Darmstadt Germany Institute for Theoretical Physics Goethe University 60438 Frankfurt am Main Germany Frankfurt Institute for Advanced Studies 60438 Frankfurt am Main Germany Key Laboratory of Quark and Lepton Physics (MOE) and Institute of Particle Physics Central China Normal University Wuhan 430079 China Department of Physics University of California Berkeley California 94270 USA Nuclear Science Division Lawrence Berkeley National Laboratory Berkeley California 94270 USA Physics Department Brookhaven National Laboratory Upton New York 11973 USA Department of Computer Science Wayne State University Detroit Michigan 48202 USA Department of Physics Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA

The JETSCAPE framework is a modular and versatile Monte Carlo software package for the simulation of high energy nuclear collisions. In this work we present a new tune of JETSCAPE, called PP19, and validate it by comparison to jet-based measurements in p+p collisions, including inclusive single jet cross sections, jet shape observables, fragmentation functions, charged hadron cross sections, and dijet mass cross sections. These observables in p+p collisions provide the baseline for their counterparts in nuclear collisions. Quantifying the level of agreement of JETSCAPE results with p+p data is thus necessary for meaningful applications of JETSCAPE to A+A collisions. The calculations use the JETSCAPE PP19 tune, defined in this paper, based on version 1.0 of the JETSCAPE framework. For the observables discussed in this work calculations using JETSCAPE PP19 agree with data over a wide range of collision energies at a level comparable to standard Monte Carlo codes. These results demonstrate the physics capabilities of the JETSCAPE framework and provide benchmarks for JETSCAPE users.

关键词： Fragmentation into hadrons Jets & heavy flavor physics Particle & resonance production Relativistic heavy-ion collisions

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The LHCb Upgrade I

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Journal of Instrumentation 2024年第5期19卷 P05065-P05065页

作者： Ayres Rocha, D. Baptista de Souza Leite, J. Bediaga, I.B. Cruz Torres, M. De Freitas Carneiro Da Graca, U. De Miranda, J.M. dos Reis, A.C. Falcao, L.N. Gomes, A. Massafferri, A. Torres Machado, D. Amato, S. De Paula, L. Ferreira Rodrigues, F. Gandelman, M. Hicheur, A. Lopes, J.H. Meyer Garcia, L. Nasteva, I. Otalora Goicochea, J.M. Polycarpo, E. Rangel, M.S. Souza De Almeida, F.L. Souza De Paula, B. Dong, C. Gan, Y. Gong, G. Gu, C. Hu, X. Kang, Y. Li, A. Luo, Y. Mu, H. Qi, H.R. Qin, N. Qu, S. Ren, Z. Tan, Y. Tou, D.Y. Wang, J. Wang, Z. Xu, L. Yang, D. Zeng, M. Zhang, L. Zhu, X. Batsukh, B. Chen, S. Jiang, X. Li, T. Li, Y. Liu, S. Lu, Y. Miao, D. Sheng, S. Tobin, M. Zou, Q. Dai, X. Gao, Y. Hu, W. Shang, Y. Shen, Z. Tong, X. Wan, G. Wei, Y. Xu, A. Yang, X. Yang, Z. Zhang, C. Zhang, S. Zhang, Y. Zhou, T. Ao, D. Campoverde Quezada, A.F. Fan, Y. Fu, J. Hao, L. He, J. Huang, W. Jiang, Y. Lin, C. Liu, H. Liu, Q. Lyu, X.-R. Ma, R. Piandani, R. Popov, D. Qian, W. Shi, B. Su, Y.S. Tuci, G. Xiang, Z. Xu, J. Xu, Q. Xu, Z. Yang, S. Yang, Y. Zheng, Y. Zhou, X. Zhou, Y. Zhu, Z. Han, Q. Hou, R. Li, K. Li, S. Wang, G. Wang, Y. Wu, J. Xie, Y. Yin, H. Zhang, D. Bachiller Perea, I.B. Brunetti, L. Chefdeville, M. Decamp, D. Downes, A.G. Hou, Y. Lieunard, B. Marchand, J.F. Rio de Janeiro Brazil Rio de Janeiro Brazil Center for High Energy Physics Tsinghua University Beijing China Beijing China School of Physics State Key Laboratory of Nuclear Physics and Technology Peking University Beijing China University of Chinese Academy of Sciences Beijing China Institute of Particle Physics Central China Normal University Hubei Wuhan China Université Savoie Mont Blanc CNRS IN2P3-LAPP Annecy France Université Clermont Auvergne CNRS/IN2P3 LPC Clermont-Ferrand France Aix Marseille Univ CNRS/IN2P3 CPPM Marseille France Université Paris-Saclay CNRS/IN2P3 IJCLab Orsay France Laboratoire Leprince-Ringuet CNRS/IN2P3 Ecole Polytechnique Institut Polytechnique de Paris Palaiseau France LPNHE Sorbonne Université Paris Diderot Sorbonne Paris Cité CNRS/IN2P3 Paris France I. Physikalisches Institut RWTH Aachen University Aachen Germany Fakultät Physik Technische Universität Dortmund Dortmund Germany Heidelberg Germany Physikalisches Institut Ruprecht-Karls-Universität Heidelberg Heidelberg Germany School of Physics University College Dublin Dublin Ireland INFN Sezione di Bari Bari Italy INFN Sezione di Bologna Bologna Italy INFN Sezione di Ferrara Ferrara Italy INFN Sezione di Firenze Firenze Italy INFN Laboratori Nazionali di Frascati Frascati Italy INFN Sezione di Genova Genova Italy INFN Sezione di Milano Milano Italy INFN Sezione di Milano-Bicocca Milano Italy INFN Sezione di Cagliari Monserrato Italy Università degli Studi di Padova Università e INFN Padova Padova Italy INFN Sezione di Pisa Pisa Italy INFN Sezione di Roma La Sapienza Roma Italy INFN Sezione di Roma Tor Vergata Roma Italy Nikhef National Institute for Subatomic Physics Amsterdam Netherlands Nikhef National Institute for Subatomic Physics and VU University Amsterdam Amsterdam Netherlands AGH - University of Science and Technology Faculty of Physics and Applied Computer Science Kraków Poland Henryk Niewodniczanski Institute of Nuclear Physic

The LHCb upgrade represents a major change of the experiment. The detectors have been almost completely renewed to allow running at an instantaneous luminosity five times larger than that of the previous running periods. Readout of all detectors into an all-software trigger is central to the new design, facilitating the reconstruction of events at the maximum LHC interaction rate, and their selection in real time. The experiment's tracking system has been completely upgraded with a new pixel vertex detector, a silicon tracker upstream of the dipole magnet and three scintillating fibre tracking stations downstream of the magnet. The whole photon detection system of the RICH detectors has been renewed and the readout electronics of the calorimeter and muon systems have been fully overhauled. The first stage of the all-software trigger is implemented on a GPU farm. The output of the trigger provides a combination of totally reconstructed physics objects, such as tracks and vertices, ready for final analysis, and of entire events which need further offline reprocessing. This scheme required a complete revision of the computing model and rewriting of the experiment's software. © 2024 CERN for the benefit of the LHCb collaboration.

关键词： Data acquisition

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Reinforcement learning meets minority game: Toward optimal resource allocation

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Physical Review E 2019年第3期99卷 032302-032302页

作者： Si-Ping Zhang Jia-Qi Dong Li Liu Zi-Gang Huang Liang Huang Ying-Cheng Lai The Key Laboratory of Biomedical Information Engineering of Ministry of Education The Key Laboratory of Neuro-informatics & Rehabilitation Engineering of Ministry of Civil Affairs and Institute of Health and Rehabilitation Science School of Life Science and Technology Xi'an Jiaotong University Xi'an 710049 China Institute of Computational Physics and Complex Systems Lanzhou University Lanzhou 730000 China Institute of Theoretical Physics Key Laboratory of Theoretical Physics Chinese Academy of Sciences P.O. Box 2735 Beijing 100190 China School of Software Engineering Chongqing University Chongqing 400044 People's Republic of China School of Electrical Computer and Energy Engineering Department of Physics Arizona State University Tempe Arizona 85287 USA

The main point of this paper is to provide an affirmative answer through exploiting reinforcement learning (RL) in artificial intelligence (AI) for eliminating herding without any external control in complex resource allocation systems. In particular, we demonstrate that when agents are empowered with RL (e.g., the popular Q-learning algorithm in AI) in that they get familiar with the unknown game environment gradually and attempt to deliver the optimal actions to maximize the payoff, herding can effectively be eliminated. Furthermore, computations reveal the striking phenomenon that, regardless of the initial state, the system evolves persistently and relentlessly toward the optimal state in which all resources are used efficiently. However, the evolution process is not without interruptions: there are large fluctuations that occur but only intermittently in time. The statistical distribution of the time between two successive fluctuating events is found to depend on the parity of the evolution, i.e., whether the number of time steps in between is odd or even. We develop a physical analysis and derive mean-field equations to gain an understanding of these phenomena. Since AI is becoming increasingly widespread, we expect our RL empowered minority game system to have broad applications.

关键词： Collective dynamics Competition Self-organized systems Mean field theory

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Application-centric SSD cache allocation for hadoop applications 17

Application-centric SSD cache allocation for hadoop applicat...

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9th Asia-Pacific Symposium on Internetware, Internetware 2017

作者： Tang, Zhen Wang, Wei Huang, Yu Wu, Heng Wei, Jun Huang, Tao State Key Laboratory of Computer Science Institute of Software Chinese Academy of Sciences University of Chinese Academy of Sciences China State Key Laboratory for Novel Software Technology Department of Computer Science and Technology Nanjing University China

ISBN: (纸本)1595930361

Flash-based Solid state Drive (SSD) is widely used in the virtualization environment, usually as the cache of the hard disk drive-based Virtual Machine (VM) storage, to improve the IO performance. Existing SSD caching schemes are mainly driven by VM-centric metrics. They treat the VMs as independent units and focus on critical low-level performance metrics of individual VMs, such as the working set, the IO latency, or the throughput. However, for elastic Hadoop applications consisting of multiple VMs, the workload is rapidly changing, and the importance of differnet VMs may be different even if they have the same low-level IO pattern. In this situation, the VM-centric SSD caching schemes may not lead to the best performance, i.e., the shortest job completion time. Considering the importance of VMs and relationships among VMs inside the application may potentially better improve the performance, which we regard as the application-centric metrics. We propose the Application-Centric SSD caching for Hadoop applications (ACSSD), which reduces the job completion time from the application level. AC-SSD uses the genetic algorithm based approach to calculate the nearly optimal weights of virtual machines for allocating SSD cache space and controlling the I/O Operations Per Second (IOPS) based on the importance of the VMs. Moreover, AC-SSD introduces the closed-loop adaptation to face the rapidly changing workload. The evaluation shows that AC-SSD reduces the job completion time by up to 39% for IO sensitive workloads, and up to 29% for rapidly changing workloads. © 2017 Association for Computing Machinery.

关键词： Virtualization

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MedShapeNet - A Large-Scale Dataset of 3D Medical Shapes for computer Vision

arXiv

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arXiv 2023年

作者： Li, Jianning Zhou, Zongwei Yang, Jiancheng Pepe, Antonio Gsaxner, Christina Luijten, Gijs Qu, Chongyu Zhang, Tiezheng Chen, Xiaoxi Li, Wenxuan Wodzinski, Marek Friedrich, Paul Xie, Kangxian Jin, Yuan Ambigapathy, Narmada Nasca, Enrico Solak, Naida Melito, Gian Marco Vu, Viet Duc Memon, Afaque R. Schlachta, Christopher De Ribaupierre, Sandrine Patel, Rajnikant Eagleson, Roy Chen, Xiaojun Mächler, Heinrich Kirschke, Jan Stefan de la Rosa, Ezequiel Christ, Patrick Ferdinand Li, Hongwei Bran Ellis, David G. Aizenberg, Michele R. Gatidis, Sergios Küstner, Thomas Shusharina, Nadya Heller, Nicholas Andrearczyk, Vincent Depeursinge, Adrien Hatt, Mathieu Sekuboyina, Anjany Löffler, Maximilian Liebl, Hans Dorent, Reuben Vercauteren, Tom Shapey, Jonathan Kujawa, Aaron Cornelissen, Stefan Langenhuizen, Patrick Ben-Hamadou, Achraf Rekik, Ahmed Pujades, Sergi Boyer, Edmond Bolelli, Federico Grana, Costantino Lumetti, Luca Salehi, Hamidreza Ma, Jun Zhang, Yao Gharleghi, Ramtin Beier, Susann Sowmya, Arcot Garza-Villarreal, Eduardo A. Balducci, Thania Angeles-Valdez, Diego Souza, Roberto Rittner, Leticia Frayne, Richard Ji, Yuanfeng Ferrari, Vincenzo Chatterjee, Soumick Dubost, Florian Schreiber, Stefanie Mattern, Hendrik Speck, Oliver Haehn, Daniel John, Christoph Nürnberger, Andreas Pedrosa, João Ferreira, Carlos Aresta, Guilherme Cunha, António Campilho, Aurélio Suter, Yannick Garcia, Jose Lalande, Alain Vandenbossche, Vicky Van Oevelen, Aline Duquesne, Kate Mekhzoum, Hamza Vandemeulebroucke, Jef Audenaert, Emmanuel Krebs, Claudia van Leeuwen, Timo Vereecke, Evie Heidemeyer, Hauke Röhrig, Rainer Hölzle, Frank Badeli, Vahid Krieger, Kathrin Gunzer, Matthias Chen, Jianxu van Meegdenburg, Timo Dada, Amin Balzer, Miriam Fragemann, Jana Jonske, Frederic Rempe, Moritz Malorodov, Stanislav Bahnsen, Fin H. Seibold, Constantin Jaus, Alexander Marinov, Zdravko Jaeger, Paul F. Stiefelhagen, Rainer Santos, Ana Sofia Lindo, Mariana Ferreira, André Alves, Victor Kamp, Michael Abourayya, Amr Nensa, Felix Hörst, Fabian Brehmer, Alexander Hein Girardetstraße 2 Essen45131 Germany Graz University of Technology Inffeldgasse 16c Graz8010 Austria Graz Austria The Department of Computer Science Johns Hopkins University Malone Hall 3400 N Charles St BaltimoreMD21218 United States Rte Cantonale Lausanne1015 Switzerland The Department of Measurement and Electronics AGH University of Science and Technology Krakow Poland Sierre Switzerland Department of Biomedical Engineering University of Basel Hegenheimermattweg Allschwil167C CH-4123 Switzerland The Boston College 140 Commonwealth Ave Chestnut HillMA02467 United States University Hospital B7-200 339 Windermere Road LondonN6A 5A5 Canada The Department of Radiology Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai200240 China The Research Center for Connected Healthcare Big Data ZhejiangLab Zhejiang Hangzhou311121 China The Faculty of Statistics Technical University Dortmund August-Schmidt-Straße 1 Dortmund44227 Germany The Institute of Mechanics Graz University of Technology Kopernikusgasse 24/IV Graz8010 Austria The Institute of Biomedical Manufacturing and Life Quality Engineering State Key Laboratory of Mechanical System and Vibration School of Mechanical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai200240 China The Department of Cardiac Surgery Medical University Graz Auenbruggerplatz 29 Graz8036 Austria The Department of Diagnostic and Interventional Radiology University Hospital Giessen Justus-Liebig-University Giessen Klinikstraße 33 Giessen35392 Germany The Department of Mechanical Engineering Mehran University of Engineering and Technology Jamshoro Sindh76062 Pakistan The Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China The Geschäftsführender Oberarzt Abteilung für Interventionelle und Diagnostische Neuroradiologie Universitätsklinikum der Technischen Universität München Ismaningerstr. 22 München81675 Germany icometrix Kolonel Be

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 datasets with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://***/ and https://***/Jianningli/*** Codes 68T01 © 2023, CC BY.

关键词： Large dataset

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Enhancing Security of FPGA-Based Embedded Systems with Combinational Logic Binding

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Journal of computer science & technology 2017年第2期32卷 329-339页

作者： Ji-Liang Zhang Wei-Zheng Wang Xing-Wei Wang Zhi-Hua Xia Software College Northeastern University Shenyang 110169 China Key Laboratory of Computer Network and Information Integration (Southeast University) Ministry of Education Nanjing 210096 China Department of Computer and Communication Engineering Changsha University of Science and Technology Changsha 410014 China School of Computer and Software Nanjing University of Information Science and Technology Nanjing 210044 China

With the increasing use of field-programmable gate arrays （FPGAs） in embedded systems and many embedded applications, the failure to protect FPGA-based embedded systems from cloning attacks has brought serious losses to system developers. This paper proposes a novel combinational logic binding technique to specially protect FPGA-based embedded systems from cloning attacks and provides a pay-per-device licensing model for the FPGA market. Security analysis shows that the proposed binding scheme is robust against various types of malicious attacks. Experimental evaluations demonstrate the low overhead of the proposed technique.

关键词： cloning attack reverse engineering FPGA （field-programmable gate array） security hardware security

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Equivalence Checking of Sequential Quantum Circuits

arXiv

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arXiv 2018年

作者： Wang, Qisheng Li, Riling Ying, Mingsheng The Department of Computer Science and Technology Tsinghua University Beijing100084 China The State Key Laboratory of Computer Science Institute of Software Chinese Academy of Sciences Beijing100190 China

We define a formal framework for equivalence checking of sequential quantum circuits. The model we adopt is a quantum state machine, which is a natural quantum generalisation of Mealy machines. A major difficulty in checking quantum circuits (but not present in checking classical circuits) is that the state spaces of quantum circuits are continuums. This difficulty is resolved by our main theorem showing that equivalence checking of two quantum Mealy machines can be done with input sequences that are taken from some chosen basis (which are finite) and have a length quadratic in the dimensions of the state Hilbert spaces of the machines. Based on this theoretical result, we develop an (and to the best of our knowledge, the first) algorithm for checking equivalence of sequential quantum circuits with running time O(23m+5l(23m + 23l)), where m and l denote the numbers of input and internal qubits, respectively. The complexity of our algorithm is comparable with that of the known algorithms for checking classical sequential circuits in the sense that both are exponential in the number of (qu)bits. Several case studies and experiments are presented. Copyright © 2018, The Authors. All rights reserved.

关键词： Timing circuits

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Dynamic network embedding via incremental skip-gram with negative sampling

arXiv

引用

arXiv 2019年

作者： Peng, Hao Li, Jianxin Yan, Hao Gong, Qiran Wang, Senzhang Liu, Lin Wang, Lihong Ren, Xiang Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University Beijing China State Key Laboratory of Software Development Environment Beihang University Beijing China Collage of Computer Science and Technology Nanjing University of Aeronautics and Astronautics Nanjing China National Computer Network Emergency Response Technical Team Coordination Center of China Beijing China Department of Computer Science University of Southern California Los Angeles United States

Network representation learning, as an approach to learn low dimensional representations of vertices, has attracted considerable research attention recently. It has been proven extremely useful in many machine learning tasks over large graph. Most existing methods focus on learning the structural representations of vertices in a static network, but cannot guarantee an accurate and efficient embedding in a dynamic network scenario. The fundamental problem of continuously capturing the dynamic properties in an efficient way for a dynamic network remains unsolved. To address this issue, we present an efficient incremental skip-gram algorithm with negative sampling for dynamic network embedding, and provide a set of theoretical analyses to characterize the performance guarantee. Specifically, we first partition a dynamic network into the updated, including addition/deletion of links and vertices, and the retained networks over time. Then we factorize the objective function of network embedding into the added, vanished and retained parts of the network. Next we provide a new stochastic gradient-based method, guided by the partitions of the network, to update the nodes and the parameter vectors. The proposed algorithm is proven to yield an objective function value with a bounded difference to that of the original objective function. The first order moment of the objective difference converges in order of O( 1/n2 ), and the second order moment of the objective difference can be stabilized in order of O(1). Experimental results show that our proposal can significantly reduce the training time while preserving the comparable performance. We also demonstrate the correctness of the theoretical analysis and the practical usefulness of the dynamic network embedding. We perform extensive experiments on multiple real-world large network datasets over multi-label classification and link prediction tasks to evaluate the effectiveness and efficiency of the proposed framework, and up

关键词： Classification (of information)

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