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PRIF: A Privacy-Preserving Interest-Based Forwarding Scheme for Social Internet of Vehicles Liehuang Zhu, Chuan Zhang, Chang Xu, Rixin Xu, Kashif Sharif are with

arXiv

引用

arXiv 2018年

作者： Zhu, Liehuang Zhang, Chuan Xu, Chang Du, Xiaojiang Xu, Rixin Sharif, Kashif Guizani, Mohsen Beijing Eng. Res. Center of Massive Language Information Processing and Cloud Computing Application Beijing Institute of Technology School of Computer Science and Technology Beijing China Department of Computer and Information Sciences Temple University Philadelphia United States Department of Electrical and Computer Engineering University of Idaho Moscow Idaho United States

Recent advances in Socially Aware Networks (SANs) have allowed its use in many domains, out of which social Internet of vehicles (SIOV) is of prime importance. SANs can provide a promising routing and forwarding paradigm for SIOV by using interest-based communication. Though able to improve the forwarding performance, existing interest-based schemes fail to consider the important issue of protecting users' interest information. In this paper, we propose a PRivacy-preserving Interest-based Forwarding scheme (PRIF) for SIOV, which not only protects the interest information, but also improves the forwarding performance. We propose a privacy-preserving authentication protocol to recognize communities among mobile nodes. During data routing and forwarding, a node can know others' interests only if they are affiliated with the same community. Moreover, to improve forwarding performance, a new metric community energy is introduced to indicate vehicular social proximity. Community energy is generated when two nodes encounter one another and information is shared among them. PRIF considers this energy metric to select forwarders towards the destination node or the destination community. Security analysis indicates PRIF can protect nodes' interest information. In addition, extensive simulations have been conducted to demonstrate that PRIF outperforms the existing algorithms including the BEEINFO, Epidemic, and PRoPHET. Copyright © 2018, The Authors. All rights reserved.

关键词： Vehicles

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PPLS: A privacy-preserving location-sharing scheme in vehicular social networks

arXiv

引用

arXiv 2018年

作者： Xu, Chang Xie, Xuan Zhu, Liehuang Sharif, Kashif Zhang, Chuan Du, Xiaojiang Guizani, Mohsen Beijing Eng. Res. Center of Massive Language Information Processing and Cloud Computing Application Beijing Institute of Technology School of Computer Science and Technology Beijing China Department of Computer and Information Sciences Temple University Philadelphia United States Department of Electrical and Computer Engineering University of Idaho MoscowID United States

The recent proliferation of mobile computing has given rise to vehicular so-cial networks (VSNs) which use the Internet of Vehicles and social networks as the main design elements. As one of the most critical components in VSNs, location sharing plays an important role in helping vehicles share information and strengthen their social bonds. This, however, may compromise vehicles' privacy, including location information and social relationship details. Some solutions have been proposed to address these challenges. However, none of them considers privacy of inter-user threshold distance, which e_ectively can be used to identify vehicles, their friends, and location information, by mali-cious or undesired elements of the system. In order to overcome this limitation, we propose a secure distance comparison protocol. Furthermore, we present a privacy-preserving location-sharing scheme in VSNs, namely PPLS, which al-lows vehicles to build more complex access control policies. The safety of our scheme is validated by the security analysis, and experimental results demon-strate the eficiency of PPLS scheme. Copyright © 2018, The Authors. All rights reserved.

关键词： Vehicles

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High-depth African genomes inform human migration and health (vol 586, pg 741, 2020)

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NATURE 2021年第7856期592卷 E26-E26页

作者： Choudhury, Ananyo Aron, Shaun Botigue, Laura R. Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Muzny, Donna Metcalf, Ginger Gibbs, Richard A. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Rotimi, Charles Ramsay, Michele Choudhury, Ananyo Choudhury, Ananyo Aron, Shaun Botigue, Laura Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Rotimi, Charles Ramsay, Michele Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Adebamowo, Clement Agongo, Godfred Boua, Romuald P. Oduro, Abraham Sorgho, Hermann Landoure, Guida Cisse, Lassana Diarra, Salimata Samassekou, Oumar Anabwani, Gabriel Matshaba, Mogomotsi Joloba, Moses Kekitiinwa, Adeodata Mardon, Graeme Mpoloka, Sununguko W. Kyobe, Samuel Mlotshwa, Busisiwe Mwesigwa, Savannah Retshabile, Gaone Williams, Lesedi Wonkam, Ambroise Moussa, Ahmed Adu, Dwomoa Ojo, Akinlolu Burke, David Salako, Babatunde O. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Awadalla, Philip Bruat, Vanessa Gbeha, Elias Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Sydney Brenner Institute for Molecular Bioscience Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa School of Electrical and Information Engineering University of the Witwatersrand Johannesburg South Africa Division of Human Genetics National Health Laboratory Service and School of Pathology Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa Navrongo Health Research Centre Navrongo Ghana Clinical Research Unit of Nanoro Institut de Recherche en Sciences de la Sante Bobo-Dioulasso Burkina Faso Center for Research in Agricultural Genomics (CRAG) Plant and Animal Genomics Program CSIC-IRTA-UAB-UB Barcelona Spain Computational Biology Division and H3ABioNet Department of Integrative Biomedical Sciences IDM University of Cape Town Cape Town South Africa System and Data Engineering Team Abdelmalek Essaadi University ENSA Tangier Morocco Centre for Proteomic and Genomic Research (CPGR) Cape Town South Africa South African National Bioinformatics Institute University of the Western Cape Bellville South Africa Africa Health Research Institute Durban South Africa Center for Research on Genomics and Global Health National Human Genome Research Institute National Institutes of Health Bethesda MD USA Department of Agriculture and Food Science Faculty of Agriculture University of Mauritius Reduit Mauritius Department of Digital Technologies Faculty of Information Communication & Digital Technologies University of Mauritius Reduit Mauritius Department of Public Health and Primary Care University of Cambridge Cambridge UK Institute of Human Virology Nigeria Abuja Nigeria Department of Epidemiology and Public Health University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA University of Maryland Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA Institute of Human Virology and Greeneba

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The Automatic Learning for the Rapid Classification of Events (ALeRCE) alert broker

arXiv

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arXiv 2020年

作者： Förster, Francisco Cabrera-Vives, G. Castillo-Navarrete, E. Estévez, P.A. Sánchez-Sáez, P. Arredondo, J. Bauer, F.E. Carrasco-Davis, R. Catelan, M. Elorrieta, F. Eyheramendy, S. Huijse, P. Pignata, G. Reyes, E. Reyes, I. Rodríguez-Mancini, D. Ruz-Mieres, D. Valenzuela, C. Álvarez-Maldonado, I. Astorga, N. Borissova, J. Clocchiatti, A. de Cicco, D. Donoso-Oliva, C. Graham, M.J. Kurtev, R. Mahabal, A. Maureira, J.C. Molina-Ferreiro, R. Moya, A. Palma, W. Prez-Carrasco, M. Protopapas, P. Romero, M. Sabatini-Gacitua, L. Snchez, A. San Martín, J. Sepúlveda-Cobo, C. Vera, E. Vergara, J.R. Center for Mathematical Modeling University of Chile AFB170001 Chile Millennium Institute of Astrophysics Nuncio Monseñor Sótero Sanz 100 Providencia Santiago Chile Departamento de Astronomía Universidad de Chile Casilla 36D Santiago Chile Department of Computer Science University of Concepcin Chile Department of Electrical Engineering Universidad de Chile Av. Tupper 2007 Santiago8320000 Chile Instituto de Astrofísica Facultad de Física Pontificia Universidad Católica de Chile Av. Vicuña Mackenna 4860 Macul Santiago7820436 Chile Department of Engineering and Science Universidad Adolfo Ibaez Av. Diagonal Las Torres 2700 Santiago Chile Centro de Astroingeniería Pontificia Universidad Católica de Chile Av. Vicuña Mackenna 4860 Macul Santiago7820436 Chile Space Science Institute 4750 Walnut Street Suite 205 BoulderCO80301 United States Department of Mathematics and Computer Science Universidad de Santiago de Chile Av. Libertador Bernardo OHiggins 3663 Estación Central Santiago Chile Instituto de Informática Universidad Austral de Chile General Lagos 2086 Valdivia Chile Departamento de Ciencias Físicas Universidad Andres Bello Avda. Republica 252 Santiago Chile Institute of Astronomy University of Cambridge Madingley Road CambridgeCB3 0HA United Kingdom Instituto de Física y Astronomía Universidad de Valparaíso Av. Gran Bretaña 1111 Playa Ancha Casilla5030 Chile Division of Physics Mathematics and Astronomy California Institute of Technology PasadenaCA91125 United States Center for Data Driven Discovery California Institute of Technology PasadenaCA91125 United States Institute for Applied Computational Science Harvard University CambridgeMA United States Departmento de Informática y Computación Universidad Tecnológica Metropolitana Santiago Chile

We introduce the Automatic Learning for the Rapid Classification of Events (ALeRCE) broker, an astronomical alert broker designed to provide a rapid and self–consistent classification of large etendue telescope alert streams, such as that provided by the Zwicky Transient Facility (ZTF) and, in the future, the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). ALeRCE is a Chilean–led broker run by an interdisciplinary team of astronomers and engineers, working to become intermediaries between survey and follow–up facilities. ALeRCE uses a pipeline which includes the real–time ingestion, aggregation, cross–matching, machine learning (ML) classification, and visualization of the ZTF alert stream. We use two classifiers: a stamp–based classifier, designed for rapid classification, and a light–curve–based classifier, which uses the multi–band flux evolution to achieve a more refined classification. We describe in detail our pipeline, data products, tools and services, which are made public for the community (see https://***). Since we began operating our real–time ML classification of the ZTF alert stream in early 2019, we have grown a large community of active users around the globe. We describe our results to date, including the real–time processing of 9.7×107 alerts, the stamp classification of 1.9 × 107 objects, the light curve classification of 8.5 × 105 objects, the report of 3088 supernova candidates, and different experiments using LSST-like alert streams. Finally, we discuss the challenges ahead to go from a single-stream of alerts such as ZTF to a multi–stream ecosystem dominated by LSST. Copyright © 2020, The Authors. All rights reserved.

关键词： Surveys

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Estimates, trends, and drivers of the global burden of type 2 diabetes attributable to PM_2·5 air pollution, 1990–2019: an analysis of data from the Global Burden of Disease Study 2019

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The Lancet Planetary Health 2022年第7期6卷 e586-e600页

作者： Burkart, Katrin Causey, Kate Cohen, Aaron J Wozniak, Sarah S Salvi, Devashri Digvijay Abbafati, Cristiana Adekanmbi, Victor Adsuar, Jose C Ahmadi, Keivan Alahdab, Fares Al-Aly, Ziyad Alipour, Vahid Alvis-Guzman, Nelson Amegah, Adeladza Kofi Andrei, Catalina Liliana Andrei, Tudorel Ansari, Fereshteh Arabloo, Jalal Aremu, Olatunde Aripov, Timur Babaee, Ebrahim Banach, MacIej Barnett, Anthony Bärnighausen, Till Winfried Bedi, Neeraj Behzadifar, Masoud Béjot, Yannick Bennett, Derrick A Bensenor, Isabela M Bernstein, Robert S Bhattacharyya, Krittika Bijani, Ali Biondi, Antonio Bohlouli, Somayeh Breitner, Susanne Brenner, Hermann Butt, Zahid A Cámera, Luis Alberto Cantu-Brito, Carlos Carvalho, Felix Cerin, Ester Chattu, Vijay Kumar Chauhan, Bal Govind Choi, Jee-Young Jasmine Chu, Dinh-Toi Dai, Xiaochen Dandona, Lalit Dandona, Rakhi Daryani, Ahmad Davletov, Kairat De Courten, Barbora Demeke, Feleke Mekonnen Denova-Gutiérrez, Edgar Dharmaratne, Samath Dhamminda Dhimal, Meghnath Diaz, Daniel Djalalinia, Shirin Duncan, Bruce B El Sayed Zaki, Maysaa Eskandarieh, Sharareh Fareed, Mohammad Farzadfar, Farshad Fattahi, Nazir Fazlzadeh, Mehdi Fernandes, Eduarda Filip, Irina Fischer, Florian Foigt, Nataliya A Freitas, Marisa Ghashghaee, Ahmad Gill, Paramjit Singh Ginawi, Ibrahim Abdelmageed Gopalani, Sameer Vali Guo, Yuming Gupta, Rajat Das Habtewold, Tesfa Dejenie Hamadeh, Randah R Hamidi, Samer Hankey, Graeme J Hasanpoor, Edris Hassen, Hamid Yimam Hay, Simon I Heibati, Behzad Hole, Michael K Hossain, Naznin Househ, Mowafa Irvani, Seyed Sina Naghibi Jaafari, Jalil Jakovljevic, Mihajlo Jha, Ravi Prakash Jonas, Jost B Jozwiak, Jacek Jerzy Kasaeian, Amir Kaydi, Neda Khader, Yousef Saleh Khafaie, Morteza Abdullatif Khan, Ejaz Ahmad Khan, Junaid Khan, Md Nuruzzaman Khatab, Khaled Khater, Amir M Kim, Yun Jin Kimokoti, Ruth W Kisa, Adnan Kivimäki, Mika Knibbs, Luke D Kosen, Soewarta Koul, Parvaiz A Koyanagi, Ai Defo, Barthelemy Kuate Kugbey, Nuworza Lauriola, Paolo Lee, Paul H Leili, Mostafa Lewycka, Sonia Li, Shanshan Lim, Lee-Ling Li Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Division of Plastic and Reconstructive Surgery University of Washington Seattle WA United States Research Insights and Innovation Seattle WA United States Health Effects Institute Boston MA United States School of Public Health Boston University Boston MA United States Department of Juridical and Economic Studies La Sapienza University Rome Italy Department of Population Medicine Cardiff University Cardiff United Kingdom Sport Science Department University of Extremadura Badajoz Spain School of Public Health Imperial College London London United Kingdom Department of Primary Care and Public Health Imperial College London London United Kingdom Mayo Evidence-based Practice Center Mayo Clinic Foundation for Medical Education and Research Rochester MN United States John T. Milliken Department of Internal Medicine Washington University in St. Louis St. Louis MO United States Clinical Epidemiology Center US Department of Veterans Affairs (VA) St Louis MO United States Health Management and Economics Research Center Iran University of Medical Sciences Tehran Iran Department of Health Economics Iran University of Medical Sciences Tehran Iran Preventive Medicine and Public Health Research Center Iran University of Medical Sciences Tehran Iran Pars Advanced and Minimally Invasive Medical Manners Research Center Iran University of Medical Sciences Tehran Iran Department of Community and Family Medicine Iran University of Medical Sciences Tehran Iran Research Group in Hospital Management and Health Policies Universidad de la Costa (University of the Coast) Barranquilla Colombia Research Group in Health Economics University of Cartagena Cartagena Colombia Department of Biomedical Science University of Cape Coast Cape Coast Ghana Cardiology Department Ca

Background: Experimental and epidemiological studies indicate an association between exposure to particulate matter (PM) air pollution and increased risk of type 2 diabetes. In view of the high and increasing prevalence of diabetes, we aimed to quantify the burden of type 2 diabetes attributable to PM_2·5 originating from ambient and household air pollution. Methods: We systematically compiled all relevant cohort and case-control studies assessing the effect of exposure to household and ambient fine particulate matter (PM_2·5) air pollution on type 2 diabetes incidence and mortality. We derived an exposure–response curve from the extracted relative risk estimates using the MR-BRT (meta-regression—Bayesian, regularised, trimmed) tool. The estimated curve was linked to ambient and household PM_2·5 exposures from the Global Burden of Diseases, Injuries, and Risk Factors Study 2019, and estimates of the attributable burden (population attributable fractions and rates per 100 000 population of deaths and disability-adjusted life-years) for 204 countries from 1990 to 2019 were calculated. We also assessed the role of changes in exposure, population size, age, and type 2 diabetes incidence in the observed trend in PM_2·5-attributable type 2 diabetes burden. All estimates are presented with 95% uncertainty intervals. Findings: In 2019, approximately a fifth of the global burden of type 2 diabetes was attributable to PM_2·5 exposure, with an estimated 3·78 (95% uncertainty interval 2·68–4·83) deaths per 100 000 population and 167 (117–223) disability-adjusted life-years (DALYs) per 100 000 population. Approximately 13·4% (9·49–17·5) of deaths and 13·6% (9·73–17·9) of DALYs due to type 2 diabetes were contributed by ambient PM2·5, and 6·50% (4·22–9·53) of deaths and 5·92% (3·81–8·64) of DALYs by household air pollution. High burdens, in terms of numbers as well as rates, were estimated in Asia, sub-Saharan Africa, and South Am

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AudioMNIST: Exploring Explainable Artificial Intelligence for Audio Analysis on a Simple Benchmark

arXiv

引用

arXiv 2018年

作者： Becker, Sören Vielhaben, Johanna Ackermann, Marcel Müller, Klaus-Robert Lapuschkin, Sebastian Samek, Wojciech Department of Artificial Intelligence Fraunhofer Heinrich-Hertz-Institute Berlin Germany Department of Electrical Engineering and Computer Science Technische Universität Berlin Berlin Germany Department of Brain and Cognitive Engineering Korea University Seoul Korea Republic of Max Planck Institute for Informatics Saarbrücken Germany BIFOLD Berlin Institute for the Foundations of Learning and Data Berlin Germany

Explainable Artificial Intelligence (XAI) is targeted at understanding how models perform feature selection and derive their classification decisions. This paper explores post-hoc explanations for deep neural networks in the audio domain. Notably, we present a novel Open Source audio dataset consisting of 30,000 audio samples of English spoken digits which we use for classification tasks on spoken digits and speakers’ biological sex. We use the popular XAI technique Layer-wise Relevance Propagation (LRP) to identify relevant features for two neural network architectures that process either waveform or spectrogram representations of the data. Based on the relevance scores obtained from LRP, hypotheses about the neural networks’ feature selection are derived and subsequently tested through systematic manipulations of the input data. Further, we take a step beyond visual explanations and introduce audible heatmaps. We demonstrate the superior interpretability of audible explanations over visual ones in a human user study. Copyright © 2018, The Authors. All rights reserved.

关键词： Speech recognition

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Dropping symmetry for fast symmetric nonnegative matrix factorization

arXiv

引用

arXiv 2018年

作者： Zhu, Zhihui Li, Xiao Liu, Kai Li, Qiuwei Mathematical Institute for Data Science Johns Hopkins University BaltimoreMD United States Department of Electronic Engineering Chinese University of Hong Kong ShatinNT Hong Kong Department of Computer Science Colorado School of Mines GoldenCO United States Department of Electrical Engineering Colorado School of Mines GoldenCO United States

Symmetric nonnegative matrix factorization (NMF)-a special but important class of the general NMF-is demonstrated to be useful for data analysis and in particular for various clustering tasks. Unfortunately, designing fast algorithms for Symmetric NMF is not as easy as for the nonsymmetric counterpart, the later admitting the splitting property that allows efficient alternating-type algorithms. To overcome this issue, we transfer the symmetric NMF to a nonsymmetric one, then we can adopt the idea from the state-of-the-art algorithms for nonsymmetric NMF to design fast algorithms solving symmetric NMF. We rigorously establish that solving nonsymmetric reformulation returns a solution for symmetric NMF and then apply fast alternating based algorithms for the corresponding reformulated problem. Furthermore, we show these fast algorithms admit strong convergence guarantee in the sense that the generated sequence is convergent at least at a sublinear rate and it converges globally to a critical point of the symmetric NMF. We conduct experiments on both synthetic data and image clustering to support our result.65K10, 90C26, 68Q25, 68W40, Copyright © 2018, The Authors. All rights reserved.

关键词： Matrix algebra

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A model for meme popularity growth in social networking systems based on biological principle and human interest dynamics

arXiv

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arXiv 2019年

作者： Wang, Le-Zhi Zhao, Zhi-Dan Jiang, Jun-Jie Guo, Bing-Hui Wang, Xiao Huang, Zi-Gang Lai, Ying-Cheng School of Electrical Computer and Energy Engineering Arizona State University TempeAZ85287 United States Web Sciences Center Big Data Research Center University of Electronic Science and Technology of China Chengdu610054 China School of Mathematics Beihang University Beijing100191 China School of Biological and Health Systems Engineering Arizona State University TempeAZ85287 United States School of Life Science and Technology Xi'An Jiaotong University Xi'an710049 China Institute of Computational Physics and Complex Systems Lanzhou University Lanzhou Gansu730000 China Department of Physics Arizona State University TempeAZ85287 United States

We analyze five big data sets from a variety of online social networking (OSN) systems and find that the growth dynamics of meme popularity exhibit characteristically different behaviors. For example, there is linear growth associated with online recommendation and sharing platforms, a plateaued (or an \S"-shape) type of growth behavior in a web service devoted to helping users to collect bookmarks, and an exponential increase on the largest and most popular microblogging website in China. Does a universal mechanism with a common set of dynamical rules exist, which can explain these empirically observed, distinct growth behaviors? We provide an affirmative answer in this paper. In particular, inspired by biomimicry to take advantage of cell population growth dynamics in microbial ecology, we construct a base growth model for meme popularity in OSNs. We then take into account human factors by incorporating a general model of human interest dynamics into the base model. The final hybrid model contains a small number of free parameters that can be estimated purely from data. We demonstrate that our model is universal in the sense that, with a few parameters estimated from data, it can successfully predict the distinct meme growth dynamics. Our study represents a successful effort to exploit principles in biology to understand online social behaviors by incorporating the traditional microbial growth model into meme popularity. Our model can be used to gain insights into critical issues such as classification, robustness, optimization, and control of OSN systems. Copyright © 2019, The Authors. All rights reserved.

关键词： Social networking (online)

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Author Correction: Federated learning enables big data for rare cancer boundary detection

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Nature communications 2023年第1期14卷 436页

作者： Sarthak Pati Ujjwal Baid Brandon Edwards Micah Sheller Shih-Han Wang G Anthony Reina Patrick Foley Alexey Gruzdev Deepthi Karkada Christos Davatzikos Chiharu Sako Satyam Ghodasara Michel Bilello Suyash Mohan Philipp Vollmuth Gianluca Brugnara Chandrakanth J Preetha Felix Sahm Klaus Maier-Hein Maximilian Zenk Martin Bendszus Wolfgang Wick Evan Calabrese Jeffrey Rudie Javier Villanueva-Meyer Soonmee Cha Madhura Ingalhalikar Manali Jadhav Umang Pandey Jitender Saini John Garrett Matthew Larson Robert Jeraj Stuart Currie Russell Frood Kavi Fatania Raymond Y Huang Ken Chang Carmen Balaña Jaume Capellades Josep Puig Johannes Trenkler Josef Pichler Georg Necker Andreas Haunschmidt Stephan Meckel Gaurav Shukla Spencer Liem Gregory S Alexander Joseph Lombardo Joshua D Palmer Adam E Flanders Adam P Dicker Haris I Sair Craig K Jones Archana Venkataraman Meirui Jiang Tiffany Y So Cheng Chen Pheng Ann Heng Qi Dou Michal Kozubek Filip Lux Jan Michálek Petr Matula Miloš Keřkovský Tereza Kopřivová Marek Dostál Václav Vybíhal Michael A Vogelbaum J Ross Mitchell Joaquim Farinhas Joseph A Maldjian Chandan Ganesh Bangalore Yogananda Marco C Pinho Divya Reddy James Holcomb Benjamin C Wagner Benjamin M Ellingson Timothy F Cloughesy Catalina Raymond Talia Oughourlian Akifumi Hagiwara Chencai Wang Minh-Son To Sargam Bhardwaj Chee Chong Marc Agzarian Alexandre Xavier Falcão Samuel B Martins Bernardo C A Teixeira Flávia Sprenger David Menotti Diego R Lucio Pamela LaMontagne Daniel Marcus Benedikt Wiestler Florian Kofler Ivan Ezhov Marie Metz Rajan Jain Matthew Lee Yvonne W Lui Richard McKinley Johannes Slotboom Piotr Radojewski Raphael Meier Roland Wiest Derrick Murcia Eric Fu Rourke Haas John Thompson David Ryan Ormond Chaitra Badve Andrew E Sloan Vachan Vadmal Kristin Waite Rivka R Colen Linmin Pei Murat Ak Ashok Srinivasan J Rajiv Bapuraj Arvind Rao Nicholas Wang Ota Yoshiaki Toshio Moritani Sevcan Turk Joonsang Lee Snehal Prabhudesai Fanny Morón Jacob Mandel Konstantinos Kamnitsas Ben Glocker Luke V M Dixon Matthew Williams Peter Zamp Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA. Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Informatics Technical University of Munich Munich Bavaria Germany. Intel Corporation Santa Clara CA USA. Department of Neuroradiology Heidelberg University Hospital Heidelberg Germany. Clinical Cooperation Unit Neuropathology German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) Heidelberg Germany. Department of Neuropathology Heidelberg University Hospital Heidelberg Germany. Division of Medical Image Computing German Cancer Research Center Heidelberg Germany. Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Heidelberg Germany. Neurology Clinic Heidelberg University Hospital Heidelberg Germany. Department of Radiology & Biomedical Imaging University of California San Francisco San Francisco CA USA. Symbiosis Center for Medical Image Analysis Symbiosis International University Pune Maharashtra India. Department of Neuroimaging and Interventional Radiology National Institute of Mental Health and Neurosciences Bangalore Karnataka India. Department of Radiology School of Medicine and Public Health University of Wisconsin Madison WI USA. Department of Medical Physics School of Medicine and Public Health University of Wisconsin Madison WI USA. Leeds Teaching Hospitals Trust Department of Radiology Leeds UK. Department of Radiology Brigham and Women's Hospital Harvard Medical School Boston MA USA. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA USA. Catalan Institute of Oncology Badalona Spain. Consorci MAR Parc de Salut de Barcelona Catalonia Spain. Department of Radiology (IDI

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Unsupervised extraction of phenotypes from cancer clinical notes for association studies

arXiv

引用

arXiv 2019年

作者： Stark, Stefan G. Hyland, Stephanie L. Pradier, Melanie F. Lehmann, Kjong-Van Wicki, Andreas Perez-Cruz, Fernando Vogt, Julia E. Rätsch, Gunnar Computational Biology Program Memorial Sloan Kettering Cancer Center New York United States Tri-Institutional Ph.D. Program in Computational Biology and Medicine Weill Cornell Medicine New York United States Department of Computer Science ETH Zürich Zürich Switzerland Medical Informatics Group University Hospital Zürich Zürich Switzerland Swiss Institute for Bioinformatics Zurich Switzerland Department of Biology ETH Zürich Zürich Switzerland Department of Signal Processing and Information Theory University Carlos III in Madrid Leganés Spain School of Engineering and Applied Sciences Harvard University CambridgeMA United States Department of Biomedicine University of Basel Basel Switzerland Tumorzentrum University Hospital Basel Basel Switzerland Swiss Data Science Center ETH Zürich and EPFL Lausanne Switzerland Department of Mathematics and Computer Science University of Basel Basel Switzerland

The recent adoption of Electronic Health Records (EHRs) by healthcare providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in combination with machine learning and statistical approaches, generate new opportunities for research and clinical care. However, many methods require the patient representations to be in structured formats, while the information in the EHR is often locked in unstructured text designed for human readability. In this work, we develop the methodology to automatically extract clinical features from clinical narratives from large EHR corpora without the need for prior knowledge. We consider medical terms and sentences appearing in clinical narratives as atomic information units. We propose an efficient clustering strategy suitable for the analysis of large text corpora and utilize the clusters to represent information about the patient compactly. Additionally, we define the sentences on ontologic and natural language vocabularies to automatically detect pertinent combinations of concepts present in the corpus, even when an ontology is not available. To demonstrate the utility of our approach, we perform an association study of clinical features with somatic mutation profiles from 4,007 cancer patients and their tumors. We apply the proposed algorithm to a dataset consisting of .65 thousand documents with a total of .3.2 million sentences. After correcting for cancer type and other confounding factors, we identify a total of 340 significant statistical associations between the presence of somatic mutations and clinical features. We annotated these associations according to their novelty and we report several known associations. We also propose 37 plausible, testable hypothesis for associations where the underlying biological mechanism does not appear to be known. These results illustrate that the automated discovery of clinical features

关键词： Diseases

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