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arXiv 2020年

作者： Giannakopoulos, Ilias I. Serrallés, José E.C. Daniel, Luca Sodickson, Daniel K. Polimeridis, Athanasios G. White, Jacob K. Lattanzi, Riccardo Skoltech Center for Computational Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow143026 Russia Research Laboratory of Electronics Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Department of Radiology New York University School of Medicine New YorkNY United States Q Bio CA94063 United States

Objective: Global Maxwell Tomography (GMT) is a recently introduced volumetric technique for noninvasive estimation of electrical properties (EP) from magnetic resonance measurements. Previous work evaluated GMT using ideal radiofrequency (RF) excitations. The aim of this simulation study was to assess GMT performance with a realistic RF coil. Methods: We designed a transmit-receive RF coil with 8 decoupled channels for 7T head imaging. We calculated the RF transmit field (B1+) inside heterogeneous head models for different RF shimming approaches, and used them as input for GMT to reconstruct EP for all voxels. Results: Coil tuning/decoupling remained relatively stable when the coil was loaded with different head models. Mean error in EP estimation changed from 7.5% to 9.5% and from 4.8% to 7.2% for relative permittivity and conductivity, respectively, when changing head model without re-tuning the coil. Results slightly improved when an SVD-based RF shimming algorithm was applied, in place of excitation with one coil at a time. Despite errors in EP, RF transmit field (B1+) and absorbed power could be predicted with less than 0.5% error over the entire head. GMT could accurately detect a numerically inserted tumor. Conclusion: This work demonstrates that GMT can reliably reconstruct EP in realistic simulated scenarios using a tailored 8-channel RF coil design at 7T. Future work will focus on construction of the coil and optimization of GMT's robustness to noise, to enable in-vivo GMT experiments. Significance: GMT could provide accurate estimations of tissue EP, which could be used as biomarkers and could enable patient-specific estimation of RF power deposition, which is an unsolved problem for ultrahigh-field magnetic resonance imaging. Copyright © 2020, The Authors. All rights reserved.

关键词： Integral equations

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Waterline mapping of inland great lake with subpixel accuracy from GF-3 SAR images 6

Waterline mapping of inland great lake with subpixel accurac...

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6th Asia-Pacific Conference on Synthetic Aperture Radar, APSAR 2019

作者： Li, Ning Niu, Shilin Wang, Robert Wu, Lin Guo, Zhengwei College of Computer and Information Engineering Henan University Kaifeng475004 China Henan Key Laboratory of Big Data Analysis and Processing Henan University Kaifeng475004 China Henan Engineering Research Center of Intelligent Technology and Application Kaifeng475004 China Department of Space Microwave Remote Sensing System Institute of Electronics Chinese Academy of Sciences Beijing100190 China

ISBN: (纸本)9781728129129

High-accuracy waterline mapping with Synthetic Aperture Radar (SAR) images is a challenging task because of the inhomogeneities of SAR imagery caused by the speckle noise and complex terrain. This paper presents a novel method for waterline mapping with subpixel accuracy. The proposed method mainly consists of three steps. Firstly, an improved Non-Local filter is adapted to suppress the speckle noise. Secondly, a Fuzzy C-Means (FCM) clustering algorithm is used to extract the pixel-level waterline. Thirdly, along the pixel-level waterline, a novel subpixel-scale waterline extraction method based on bicubic convolution and Geometric Active Contour (GAC) model is presented to further improve the accuracy of the waterline. Without loss of generality, the Danjiangkou reservoir (DJKR), which is the largest artificial freshwater lake in Asia, is selected as a study case. SAR images from Chinese GaoFen-3 (GF-3) satellite working on different modes are processed to demonstrate the effectiveness of the proposed method. © 2019 IEEE.

关键词： Synthetic aperture radar

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Hypertrophic cardiomyopathy diagnosis based on cardiovascular magnetic resonance using deep learning techniques

Research Square

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research Square 2021年

作者： Sharifrazi, Danial Alizadehsani, Roohallah Izadi, Navid Hoseini Roshanzamir, Mohamad Shoeibi, Afshin Khozeimeh, Fahime Sani, Fariba Alizadeh Sani, Zahra Alizadeh Hussain, Sadiq Harlapur, Chandrashekhar Gorriz, Juan M. Khosravi, Abbas Nahavandi, Saeid Sarrafzadegan, Nizal Islam, Sheikh Mohammed Shariful Department of Computer Engineering School of Technical and Engineering Shiraz Branch Islamic Azad University Shiraz Iran Deakin University Geelong Australia Department of Electrical and Computer Engineering Isfahan University of Technology Isfahan84156-83111 Iran Department of Computer Engineering Faculty of Engineering Fasa University Fasa74617-81189 Iran Computer Engineering Department Ferdowsi University of Mashhad Mashhad Iran Faculty of Electrical and Computer Engineering Biomedical Data Acquisition Lab K. N. Toosi University of Technology Tehran Iran Mashhad University of Medical science Mashhad Iran Department of Cardiac MRI Omid Hospital Tehran Iran Dibrugarh University Assam786004 India Emergency Department Epworth Hospital Geelong Australia Department of Signal Theory Networking and Communications Universidad de Granada Spain Department of Psychiatry University of Cambridge United Kingdom Faculty of Medicine SPPH University of British Columbia VancouverBC Canada Isfahan Cardiovascular Research Center Cardiovascular Research Institute Isfahan University of Medical Sciences Khorram Ave Isfahan Iran Institute for Physical Activity and Nutrition School of Exercise and Nutrition Sciences Deakin University GeelongVIC3220 Australia Cardiovascular Division The George Institute for Global Health Newtown Australia Sydney Medical School University of Sydney Camperdown Australia

Hypertrophic cardiomyopathy (HCM) can lead to serious cardiac problems. HCM is often diagnosed by an expert using cardiovascular magnetic resonance (CMR) images obtained from patients. In this research, we aimed to develop a deep learning technique to automate HCM diagnosis. CMR images of 37421 healthy and 21846 HCM patients were obtained during two years. Images obtained from female patients form 53% of the collected dataset. The mean and standard deviation of the dataset patients’ age are 48.2 and 19.5 years, respectively. Three experts inspected images and determined whether a case has HCM or not. New data augmentation was used to generate new images by employing color filtering on the existing ones. To classify the augmented images, we used a deep convolutional neural network (CNN). To the best of our knowledge, this is the first time CNN is used for HCM diagnosis. We designed our CNN from scratch to reach acceptable diagnosis accuracy. Comparing the designed algorithm output with the experts’ opinions, the method could achieve accuracy of 95.23%, recall of 97.90%, and specificity of 93.06% on the original dataset. The same performance metrics for the designed algorithm on the augmented dataset were 98.53%, 98.70%, and 95.21%, respectively. We have also experimented with different optimizers (e.g. Adadelta and Adagrad) and other data augmentation methods (e.g. height shift and rotation) to further evaluate the proposed method. Using our data augmentation method, accuracy of 98.53% were achieved which is higher than the best accuracy (95.83%) obtained by the other data augmentation methods which have been evaluated. The upper bound on difference between true error rate and empirical error rate of the proposed method has also been provided in order to present better performance analysis. The advantages of employing the proposed method are elimination of contrast agent and its complications, decreased CMR examination time, lower costs for patients and cardiac imagi

关键词： Diagnosis

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Computational Approaches to Explainable Artificial Intelligence: Advances Intheory, applications and Trends

SSRN

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SSRN 2023年

作者： Górriz, Juan Manuel Álvarez-Illán, I. Álvarez-Marquina, A. Arco, J.E. Atzmueller, M. Ballarini, F. Barakova, E. Bologna, G. Bonomini, P. Castellanos-Dominguez, G. Castillo-Barnes, D. Cho, S.B. Contreras, R. Cuadra, J.M. Domínguez, E. Domínguez-Mateos, F. Duro, R.J. Elizondo, D. Fernández-Caballero, A. Fernandez-Jover, E. Formoso, M.A. Gallego-Molina, N.J. Gamazo, J. García González, J. Garcia-Rodriguez, J. Garre, C. Garrigós, J. Gómez-Rodellar, A. Gómez-Vilda, P. Graña, M. Guerrero-Rodriguez, B. Hendrikse, S.C.F. Jimenez-Mesa, C. Jodra-Chuan, M. Julian, V. Kotz, G. Kutt, K. Leming, M. de Lope, J. Macas, B. Marrero-Aguiar, V. Martinez, J.J. Martinez-Murcia, F.J. Martínez-Tomás, R. Mekyska, J. Nalepa, G.J. Novais, P. Orellana, D. Ortiz, A. Palacios-Alonso, D. Palma, J. Pereira, A. Pinacho-Davidson, P. Pinninghoff, M.A. Ponticorvo, M. Psarrou, A. Ramírez, J. Rincón, M. Rodellar-Biarge, V. Rodríguez-Rodríguez, I. Roelofsma, P.H.M.P. Santos, J. Salas-Gonzalez, D. Salcedo-Lagos, P. Segovia, F. Shoeibi, A. Silva, M. Simic, D. Suckling, J. Treur, J. Tsanas, A. Varela, R. Wang, S.H. Wang, W. Zhang, Y.D. Zhu, H. Zhu, Z. Ferrández-Vicente, J.M. SiPBA at Data Science and Computational Intelligence Institute University of Granada Granada Spain University of Granada Granada Spain Dept. of Psychiatry University of Cambridge Cambridge United Kingdom Dept. of Communications Engineering University of Malaga Malaga Spain School of Computing and Mathematical Sciences University of Leicester Leicester United Kingdom Semantic Information Systems Group Osnabrück University Osnabrück Germany Osnabrück Germany Dept. of Electronics Computer Technology and Projects Universidad Politécnica de Cartagena Cartagena Spain Universitat Politècnica de València València Spain Institute of Applied Computer Science Jagiellonian University Kraków Poland Dept. of Information and Communication Engineering University of Murcia Murcia Spain Dept. of Computer Science and Information Technologies University of A Coruña A Coruña Spain Dept. of Computer Science University of Oviedo Oviedo Spain Buenos Aires Argentina Buenos Aires Argentina Eindhoven University of Technology Eindhoven5612 AZ Netherlands Dept. of Computer Science University of Malaga Malaga Spain De Montfort University Leicester United Kingdom Dept. of Computer Science Faculty of Engineering Universidad de Concepción Concepción Chile Neurocognition and Emotion Research Unit Albacete Research Institute of Informatics University of Castilla-La Mancha Albacete Spain Dept. of Educational Informatics Universidad de Concepción Concepción Chile Madrid Spain Dept. of Humanistic Studies University of Naples Federico II Napoli Italy Escuela Técnica Superior de Ingeniería Informática Universidad Rey Juan Carlos Campus de Móstoles Móstoles Madrid28933 Spain Neuromorphic Speech Processing Lab Center for Biomedical Technology Universidad Politécnica de Madrid Campus de Montegancedo Pozuelo de Alarcón Madrid28223 Spain Biomedical Research Networking Center in Mental Health Instituto de Salud Carlos III Madrid28016 Spain Usher Institute Faculty o

Groundbreaking advances in theoretical and applied Artificial Intelligence (ai). DL algorithms are groundedin non-linear and complex artificial neural systems that progressively extract higher-level features from *** is frequently compared with human-level performance in real-world tasks, such as clinical diagnostics. Itis also a turning point in solving otherwise intractable problems in the design of virtual agents or robotics;orin providing novel insight into disease progress in genomics and Neuroimaging (NI), understanding humanbrain function, the automation of industrial processes based on computer vision, and so on. In this paper, themost relevant advances from the last few years in ai and several applications to neuroscience, neuroimaging,computer vision, and robotics are presented, reviewed and discussed. In this way, we summarize the state-ofthe-art in ai methods, models and applications within a collection of works presented at the 9th InternationalConference on the Interplay between Natural and Artificial Computation (IWINAC). The works presentedin this paper are excellent examples of new scientific discoveries made in laboratories that are successfullytransferred to real-life applications. © 2023, The Authors. All rights reserved.

关键词： Neuroimaging

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A computational approach to measure the linguistic characteristics of psychotherapy timing, responsiveness, and consistency

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npj Mental Health research 2022年第1期1卷 19页

作者： Miner, Adam S. Fleming, Scott L. Haque, Albert Fries, Jason A. Althoff, Tim Wilfley, Denise E. Agras, W. Stewart Milstein, Arnold Hancock, Jeff Asch, Steven M. Stirman, Shannon Wiltsey Arnow, Bruce A. Shah, Nigam H. Department of Psychiatry and Behavioral Sciences Stanford University Stanford CA United States Center for Biomedical Informatics Research Stanford University Stanford CA United States Department of Biomedical Data Science Stanford University Stanford CA United States Department of Computer Science Stanford University Stanford CA United States Allen School of Computer Science & Engineering University of Washington Seattle WA United States Departments of Psychiatry Medicine Pediatrics and Psychological & Brain Sciences Washington University in St. Louis St. Louis MO United States Clinical Excellence Research Center Stanford University Stanford CA United States Department of Communication Stanford University Stanford CA United States VA Palo Alto Health Care System Palo Alto CA United States Division of Primary Care and Population Health Stanford University School of Medicine Stanford CA United States National Center for Posttraumatic Stress Disorders Dissemination and Training Division VA Palo Alto Healthcare System Menlo Park CA United States Technology and Digital Solutions Stanford Healthcare Stanford CA United States

Although individual psychotherapy is generally effective for a range of mental health conditions, little is known about the moment-to-moment language use of effective therapists. Increased access to computational power, coupled with a rise in computer-mediated communication (telehealth), makes feasible the large-scale analyses of language use during psychotherapy. Transparent methodological approaches are lacking, however. Here we present novel methods to increase the efficiency of efforts to examine language use in psychotherapy. We evaluate three important aspects of therapist language use - timing, responsiveness, and consistency - across five clinically relevant language domains: pronouns, time orientation, emotional polarity, therapist tactics, and paralinguistic style. We find therapist language is dynamic within sessions, responds to patient language, and relates to patient symptom diagnosis but not symptom severity. Our results demonstrate that analyzing therapist language at scale is feasible and may help answer longstanding questions about specific behaviors of effective therapists. © The Author(s) 2022.

关键词： Translational research Human behaviour

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A fundamental theorem for eco-environmental surface modelling and its applications

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science China Earth sciences 2020年第8期63卷 1092-1112页

作者： Tianxiang YUE Na ZHAO Yu LIU Yifu WANG Bin ZHANG Zhengping DU Zemeng FAN Wenjiao SHI Chuanfa CHEN Mingwei ZHAO Dunjiang SONG Shihai WANG Yinjun SONG Changqing YAN Qiquan LI Xiaofang SUN Lili ZHANG Yongzhong TIAN Wei WANG Ying’an WANG Shengnan MA Hongsheng HUANG Yimin LU Qing WANG Chenliang WANG Yuzhu WANG Ming LU Wei ZHOU Yi LIU Xiaozhe YIN Zong WANG Zhengyi BAO Miaomiao ZHAO Yapeng ZHAO Yimeng JIAO Ufra NASEER Bin FAN Saibo LI Yang YANG John PWILSON State Key L aboratory of Resources and Environment Information System Institute of Geographical Sciences and Natural Resources ResearchChinese Academy of SciencesBeijing 100101China College of Resources and Environment University of Chinese Academy of SciencesBeijing 100049China College of Land Resources and Environment Jiangxi Agricultural UniversityNanchang 330045China College of Geomatics Shandong University of Science and TechnologyQingdao 266590China College of Forestry Beijing Forestry UniversityBeijing 100083China School of Land and Resources China West Normal UniversityNanchong 637002China College of Geographical Information and Tourism Chuzhou UniversityChuzhou 239000China Institutes of Science and Development Chinese Academy of SciencesBeijing 100190China Department of Information Engineering Shandong University of Science and TechnologyTai'an 271019China College of Resources Sichuan Agricultural UniversityChengdu 611130China College of Geography and Tourism Qufu Normal UniversityRizhao 276828China Aerospace Information Research Institute Chinese Academy of SciencesBeijing 100101China School of Geographical Science Southwest UniversityChongqing 400715China National Disaster Reduction Center of China Ministry of Emergency ManagementBeijing 100721China Department for Population Data China Population and Development Research CenterBeijing 100081China Department for Industrial Standard China Standardization AdministrationBeijing 100088China The Academy of Digital China Fuzhou UniversityFuzhou 350002China National Institute of Environmental Health Chinese Center for Disease Control and PreventionBeijing 100021China School of Information Engineering China University of GeoscienceBeijing 100083China Qian Xuesen Laboratory of Space Technology Beijing 100094China College of Architecture and Urban Planning Chongqing Jiaotong UniversityChongqing 400074China Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application Nanjing

We propose a fundamental theorem for eco-environmental surface modelling(FTEEM) in order to apply it into the fields of ecology and environmental science more easily after the fundamental theorem for Earth’s surface system modeling(FTESM). The Beijing-Tianjin-Hebei(BTH) region is taken as a case area to conduct empirical studies of algorithms for spatial upscaling, spatial downscaling, spatial interpolation, data fusion and model-data assimilation, which are based on high accuracy surface modelling(HASM), corresponding with corollaries of FTEEM. The case studies demonstrate how eco-environmental surface modelling is substantially improved when both extrinsic and intrinsic information are used along with an appropriate method of HASM. Compared with classic algorithms, the HASM-based algorithm for spatial upscaling reduced the root-meansquare error of the BTH elevation surface by 9 m. The HASM-based algorithm for spatial downscaling reduced the relative error of future scenarios of annual mean temperature by 16%. The HASM-based algorithm for spatial interpolation reduced the relative error of change trend of annual mean precipitation by 0.2%. The HASM-based algorithm for data fusion reduced the relative error of change trend of annual mean temperature by 70%. The HASM-based algorithm for model-data assimilation reduced the relative error of carbon stocks by 40%. We propose five theoretical challenges and three application problems of HASM that need to be addressed to improve FTEEM.

关键词： HASM FTEEM Spatial upscaling Spatial downscaling Spatial interpolation data fusion Model-data assimilation Model coupling

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How do diseases spread at the critical state?

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Chaos, Solitons & Fractals 2025年 199卷

作者： Li-Feng Hou Shifu Wang Li Li Xin Lu Gui-Quan Sun Sino-Europe Complex Science Center School of Mathematics North University of China Shanxi Taiyuan 030051 China Complex Systems Research Center Shanxi University Taiyuan 030006 Shanxi China Department of Microbiology Laboratory Children’s Hospital Affiliated to Shandong University Jinan 250022 China School of Computer and Information Technology Shanxi University Taiyuan 030006 Shanxi China College of Systems Engineering National University of Defense Technology Changsha Hunan 410073 China Key Laboratory of Complex Systems and Data Science of Ministry of Education Taiyuan 030006 China

The transmission characteristics of infectious diseases near critical thresholds are essential for public health strategy formulation. This study employs reaction–diffusion SI with nonlinear and SIR models with saturated incidence rates, integrating optimal control theory to investigate epidemic propagation trends under critical conditions. The structural complexity of three epidemiological target states (extinction, quasi-uniform epidemic, and patterned epidemic) is quantitatively characterized using spatial entropy methods. A multi-indicator comparative analysis systematically reveals the evolutionary trends of epidemics in critical states from three dimensions: target attainability, average control intensity, and control complexity. The findings indicate that achieving a patterned epidemic state requires the lowest control intensity and spatial intervention complexity compared to extinction and quasi-uniform states, suggesting that epidemic systems in critical states are more inclined toward structured transmission patterns. The proposed framework for quantifying spatial structure and control complexity provides a theoretical basis and practical guidance for formulating spatial prevention and control strategies for infectious diseases in critical states.

关键词： Critical threshold Epidemic dynamics Optimal control Reaction–diffusion models Spatial entropy

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Author Correction: Mapping annual 10-m soybean cropland with spatiotemporal sample migration

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Scientific data 2024年第1期11卷 565页

作者： Hongchi Zhang Zihang Lou Dailiang Peng Bing Zhang Wang Luo Jianxi Huang Xiaoyang Zhang Le Yu Fumin Wang Linsheng Huang Guohua Liu Shuang Gao Jinkang Hu Songlin Yang Enhui Cheng Key Laboratory of Digital Earth Science Aerospace Information Research Institute Chinese Academy of Sciences Beijing 100094 China. International Research Center of Big Data for Sustainable Development Goals Beijing 100094 China. University of Chinese Academy of Sciences Beijing 100094 China. Key Laboratory of Digital Earth Science Aerospace Information Research Institute Chinese Academy of Sciences Beijing 100094 China. pengdl@***. International Research Center of Big Data for Sustainable Development Goals Beijing 100094 China. pengdl@***. Key Laboratory of Digital Earth Science Aerospace Information Research Institute Chinese Academy of Sciences Beijing 100094 China. zhangbing@***. University of Chinese Academy of Sciences Beijing 100094 China. zhangbing@***. Jiangxi Nuclearindustry Surveying and Mapping Institute Group Co. Ltd Nanchang 330038 China. College of Land Science and Technology China Agricultural University Beijing 100083 China. Geospatial Sciences Center of Excellence Department of Geography Geospatial Sciences South Dakota State University Brookings SD 57007 USA. Department of Earth System Science Tsinghua University Beijing 100084 China. Institute of Applied Remote Sensing & Information Technology Zhejiang University Hangzhou 310058 China. National Engineering Research Center for Agro-Ecological Big Data Analysis & Application Anhui University Hefei 230601 China. Innovation Academy for Microsatellites Chinese Academy of Sciences Shanghai 200120 China.

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The 2021 report of the Lancet Countdown on health and climate change: code red for a healthy future (vol 398, pg 1619, 2021)

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LANCET 2021年第10317期398卷 2148-2148页

作者： Romanello, M. McGushin, A. Di Napoli, C. [a]Institute for Global Health University College London London UK [b]Institute for Sustainable Resources University College London London UK [c]UCL Energy Institute University College London London UK [d]Institute for Environmental Design and Engineering University College London London UK [e]Department of Geography University College London London UK [f]The Bartlett School of Sustainable Construction University College London London UK [g]Centre for Human Health and Performance University College London London UK [h]School of Agriculture Policy and Development University of Reading Reading UK [i]Department of Meteorology University of Reading Reading UK [j]The Walker Institute University of Reading Reading UK [k]Department of Health Sciences University of York York UK [l]Institute for Environment and Human Security United Nations University Bonn Germany [m]Centre on Climate Change and Planetary Health London School of Hygiene & Tropical Medicine London UK [n]Centre for Mathematical Modelling of Infectious Diseases London School of Hygiene & Tropical Medicine London UK [o]Department of Public Health Environments and Society London School of Hygiene & Tropical Medicine London UK [p]Department of Earth System Science Tsinghua University Beijing China [q]Department of Environment Climate Change and Health World Health Organization Geneva Switzerland [r]Institute for Environmental Sciences World Health Organization Geneva Switzerland [s]Centre for Climate Change and Social Transformations School of Psychology Cardiff University Cardiff UK [t]Yale Center on Climate Change and Health Yale University New Haven CT USA [u]School of Government University of Birmingham Birmingham UK [v]Economic analysis of Climate Impacts and Policy Centro Euro-Mediterraneo sui Cambiamenti Climatici Venice Italy [w]Natural Resources Institute University of Greenwich London UK [x]Department of Global Health University of Washington Seattle WA USA [y]Centre for He

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An Open-Source Knowledge Graph Ecosystem for the Life sciences

arXiv

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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FaiR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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