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arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

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An Ontology Constructing Technology Oriented on Massive Social Security Policy Documents

引用

Journal of Physics: Conference Series 2019年第1期1325卷

作者： Liu Gang Zhang Hanmo Liu Wangyang Cheng xu Zhang Hanwen Harbin Engineering University College of Computer Science and Technology CETC big data research institute company limited China.

Because of the huge number of policy documents in the field of social security, there is a need to manage these information. In this paper, ontology is used to represent and store information in files. In order to ensure the accuracy of ontology structure, this paper first constructs ontology framework manually, and then extends ontology framework by the inclusion relationship between attribute set and object set. At the same time, this paper adopts the idea of statistics and rules in the field of natural language processing, extracts hierarchical and non-hierarchical concepts from the lexicon of social security field to construct ontology, and then puts forward the statistical models of concept phrase vector and high-frequency phrase vector. The experimental results show that the semi-automatic ontology construction process in the field of social security can effectively propose social security ontology from a large number of policy documents. The experimental results play a reference role for ontology construction in other fields.

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The SCIP optimization suite 8.0

arXiv

引用

arXiv 2021年

作者： Bestuzheva, Ksenia Besançon, Mathieu Chen, Wei-Kun Chmiela, Antonia Donkiewicz, Tim Van Doornmalen, Jasper Eifler, Leon Gaul, Oliver Gamrath, Gerald Gleixner, Ambros Gottwald, Leona Graczyk, Christoph Halbig, Katrin Hoen, Alexander Hojny, Christopher Van Der Hulst, Rolf Koch, Thorsten Lübbecke, Marco Maher, Stephen J. Matter, Frederic Mühmer, Erik Müller, Benjamin Pfetsch, Marc E. Rehfeldt, Daniel Schlein, Steffan Schlösser, Franziska Serrano, Felipe Shinano, Yuji Sofranac, Boro Turner, Mark Vigerske, Stefan Wegscheider, Fabian Wellner, Philipp Weninger, Dieter Witzig, Jakob Zuse Institute Berlin Department AIS2T Takustr. 7 Berlin14195 Germany School of Mathematics and Statistics Beijing Institute of Technology Beijing100081 China RWTH Aachen University Lehrstuhl für Operations Research Kackertstr. 7 Aachen52072 Germany Technische Universiteit Eindhoven Department of Mathematics and Computer Science P.O. Box 513 Eindhoven5600 MB Netherlands I2DAMO GmbH Englerallee 19 Berlin14195 Germany Friedrich-Alexander Universität Erlangen-Nürnberg Department of Data Science Cauerstr. 11 Erlangen91058 Germany University of Twente Department of Discrete Mathematics and Mathematical Programming P.O. Box 217 Enschede7500 AE Netherlands Technische Universität Berlin Software and Algorithms for Discrete Optimization Straße des 17. Juni 135 Berlin10623 Germany Zuse Institute Berlin Department A2IM Takustr. 7 Berlin14195 Germany University of Exeter College of Engineering Mathematics and Physical Sciences Exeter United Kingdom Technische Universität Darmstadt Fachbereich Mathematik Dolivostr. 15 Darmstadt64293 Germany Technische Universität Berlin Straße des 17. Juni 135 Berlin10623 Germany Software and Algorithms for Discrete Optimization Institute of Mathematics Technische Universität Berlin Straße des 17. Juni 135 Berlin10623 Germany GAMS Software GmbH C/o Zuse Institute Berlin Department AIS2T Takustr. 7 Berlin14195 Germany

The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 8.0 of the SCIP Optimization Suite. Major updates in SCIP include improvements in symmetry handling and decomposition algorithms, new cutting planes, a new plugin type for cut selection, and a complete rework of the way nonlinear constraints are handled. Additionally, SCIP 8.0 now supports interfaces for Julia as well as Matlab. Further, UG now includes a unified framework to parallelize all solvers, a utility to analyze computational experiments has been added to GCG, dual solutions can be postsolved by PaPILO, new heuristics and presolving methods were added to SCIP-SDP, and additional problem classes and major performance improvements are available in *** Codes 90C05, 90C10, 90C11, 90C30, 90C90, 65Y05 Copyright © 2021, The Authors. All rights reserved.

关键词： Integer programming

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GAN-based semi-supervised for imbalanced data classification

GAN-based semi-supervised for imbalanced data classification

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International Conference on Information Management (ICIM)

作者： Tingting Zhou Wei Liu Congyu Zhou Leiting Chen School of Computer Science and Engineering Dongguan Data Science software Technology Co. Ltd Dongguan China Chengdu Vocational and Technical College of Industry Dongguan Data Science software Technology Co. Ltd Dongguan China School of Computer Science and Engineering Institute of Electronic and Information Engineering UESTC in Guangdong Dongguan China

Most of the traditional classification algorithms are based on the premise that the datasets are uniformly distributed or roughly equivalent. Once the sample dataset is not balanced , the classification performance drops sharply. To efficiently deal with the imbalance of data, an improved generative adversarial network (GAN) algorithm is proposed in this work . Firstly, we construct artificial samples so that more minority-class's data can be obtained via optimizing GAN loss function. Secondly, we build a fully-connected network for structured data classification. Finally, experimental evaluations are conducted on two open structured-datasets and the results of the proposed algorithm demonstrate a good applicability for the classification of structured data.

关键词： Gallium nitride Generators Classification algorithms Training data models Feature extraction Radio frequency

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Cross-Project Change-Proneness Prediction

Cross-Project Change-Proneness Prediction

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IEEE Annual International computer software and Applications Conference (COMPSAC)

作者： Chao Liu Dan Yang Xin Xia Meng Yan Xiaohong Zhang School of Big Data & Software Engineering Chongqing University Chongqing China Faculty of Information Technology Monash University Melbourne Australia College of Computer Science and Technology Zhejiang University Hangzhou China

ISBN: (纸本)9781538626672

software change-proneness prediction (whether or not class files in a project will be changed in the next release) can help software developers to focus on preventive actions to reduce maintenance costs, and managers to allocate resources more effectively. Prior studies found that change-proneness prediction works well if there is sufficient amount of training data to build a model. However, it is not feasible for projects with limited historical data especially for new projects. To address this issue, cross-project change-proneness prediction, which builds a prediction model by using data in another project (i.e., source project), and predicts the change-proneness in a target project, is proposed. Considering there are a large number of source projects, one challenge for cross-project change-proneness prediction is that given a target project, how to automatically select a source project which could show good prediction accuracy on it. In this paper, we propose a selective cross-project (SCP) model for change-proneness prediction. SCP automatically finds the source project which has the similar data distribution with the target project by measuring distribution similarity between source and target projects. We evaluate SCP by conducting an empirical study on 14 open source projects. We compare it with 2 most related change-proneness models, including RCP (Random Cross-Project prediction) proposed by Malhotra and Bansal, and CLAMI+ developed by Yan et al. Experiment results show that SCP improves RCP and CLAMI+ by 25.34% and 4.30% in terms of AUC respectively; and by 171.42% and 172.31% in terms of cost-effectiveness, respectively.

关键词： Predictive models Measurement Complexity theory software data models Object oriented modeling Estimation

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

arXiv

引用

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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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

引用

Genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)GmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been *** optimal performance,they require the fragment ion spectra of targeted peptides as prior *** this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue *** build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on *** then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer *** extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)***,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was *** a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control *** expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by *** data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker *** is freely accessible at https://***/page/***?id=IPX0001400000.

关键词： data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

引用

database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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Feature extraction for hyperspectral imagery: The evolution from shallow to deep

arXiv

引用

arXiv 2020年

作者： Rasti, Behnood Hong, Danfeng Hang, Renlong Ghamisi, Pedram Kang, Xudong Chanussot, Jocelyn Benediktsson, Jon Atli Machine Learning Group Exploration Division Helmholtz Institute Freiberg for Resource Technology Helmholtz-Zentrum Dresden-Rossendorf Freiberg09599 Germany Univ. Grenoble Alpes CNRS Grenoble INP GIPSAlab Grenoble38000 France Jiangsu Key Laboratory of Big Data Analysis Technology School of Automation Nanjing University of Information Science and Technology Nanjing210044 China Machine Learning Group Exploration Division Helmholtz Institute Freiberg for Resource Technology Helmholtz-Zentrum Dresden-Rossendorf Freiberg09599 Germany College of Electrical and Information Engineering Hunan University Changsha410082 China Key Laboratory of Visual Perception and Artificial Intelligence of Hunan Province Changsha410082 China Univ. Grenoble Alpes Inria CNRS Grenoble INP LJK GrenobleF-38000 France Faculty of Electrical and Computer Engineering University of Iceland Reykjavik101 Iceland Faculty of Electrical and Computer Engineering University of Iceland Reykjavik107 Iceland

The final version of the paper can be found in IEEE Geoscience and Remote Sensing Magazine. Hyperspectral images provide detailed spectral information through hundreds of (narrow) spectral channels (also known as dimensionality or bands) with continuous spectral information that can accurately classify diverse materials of interest. The increased dimensionality of such data makes it possible to significantly improve data information content but provides a challenge to the conventional techniques (the so-called curse of dimensionality) for accurate analysis of hyperspectral images. Feature extraction, as a vibrant field of research in the hyperspectral community, evolved through decades of research to address this issue and extract informative features suitable for data representation and classification. The advances in feature extraction have been inspired by two fields of research, including the popularization of image and signal processing as well as machine (deep) learning, leading to two types of feature extraction approaches named shallow and deep techniques. This article outlines the advances in feature extraction approaches for hyperspectral imagery by providing a technical overview of the state-of-the-art techniques, providing useful entry points for researchers at different levels, including students, researchers, and senior researchers, willing to explore novel investigations on this challenging topic. In more detail, this paper provides a bird's eye view over shallow (both supervised and unsupervised) and deep feature extraction approaches specifically dedicated to the topic of hyperspectral feature extraction and its application on hyperspectral image classification. Additionally, this paper compares 15 advanced techniques with an emphasis on their methodological foundations in terms of classification accuracies. Furthermore, to push this vibrant field of research forward an impressive amount of codes and libraries is shared at: https://***/Behnoo

关键词： Feature extraction

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Adaptive neural output consensus control of stochastic nonlinear strict-feedback multi-agent systems

Adaptive neural output consensus control of stochastic nonli...

引用

2018 Australian and New Zealand Control Conference, ANZCC 2018

作者： Yang, Yang Miao, Songtao Xu, Chuang Yue, Dong Tan, Jie Tian, Yu-Chu College of Automation College of Artificial Intelligence Nanjing University of Posts and Telecommunications Nanjing210023 China Institute of Advanced Technology Nanjing University of Posts and Telecommunications Nanjing210023 China Jiangsu Engineering Laboratory of Big Data Analysis and Control for Active Distribution Network Nanjing University of Posts and Telecommunications Nanjing China School of Electrical Engineering and Computer Science Queensland University of Technology BrisbaneQLD4001 Australia

ISBN: (纸本)9781538666173

An adaptive neural output consensus control issue is considered for stochastic nonlinear strict-feedback multi-agent systems (MASs). The traditional backstepping framework is employed combing with the graph theory, as well as neural networks (NNs) technology. NNs are utilized for the approximation of unknown functions, and the Itô's lemma is used to deal with stochastic dynamics of the system. It is proved that all signals remain bounded in probability and that the tracking errors of all followers converge to a small neighborhood of the origin in the sense of mean quartic value by suitable choice of parameters. A simulation example is provided. © 2018 IEEE.

关键词： Multi agent systems

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