检索结果-内蒙古大学图书馆

arXiv 2023年

作者： Heming, Carolina A.M. Abdalla, Mohamed Mohanna, Shahram Ahluwalia, Monish Zhang, Linglin Trivedi, Hari Woo, MinJae Fine, Benjamin Gichoya, Judy Wawira Celi, Leo Anthony Seyyed-Kalantari, Laleh University of Iowa Iowa CityIA United States Institute for Better Health Trillium Health Partners 100 Queensway West 6th floor MississaugaONL5B 1B8 Canada Kingston Health Sciences Centre Queen's University 76 Stuart St. KingstonONK7L 2V7 Canada School of Data Science and Analytics Kennesaw State University 3391 Town Point Dr NW KennesawGA30144 United States Department of Radiology and Imaging Sciences Emory University 1364 E Clifton Rd NE AtlantaGA30322 United States Vector Institute of Artificial Intelligence 661 University Ave Suite 710 TorontoONM5G 1M1 Canada Massachusetts Institute of Technology 77 Massachusetts Avenue CambridgeMA02139 United States Harvard Medical School 25 Shattuck St BostonMA02115 United States Department of Electrical Engineering and Computer Science York University 4700 Keele St TorontoONM3J 1P3 Canada Department of Medicine University of Alberta Walter C Mackenzie Health Sciences Centre St. NW Edmonton Alberta 8440 112 Canada

The model facts labels are often used to communicate artificial intelligence (AI) model performance to the end users for proper deployment and often report the overall performance averaged across all populations. However, the overall performance is not generalizable to different subgroups of patients. In this paper, we highlight the importance of currently unforeseen aspects, essential for AI models in healthcare, that are not included in the model fact cards. We suggest including through bias and fairness analysis outcomes in model fact labels in the health care AI model including: (a) socio-demographic fairness factors (e.g., sexes, race, socioeconomic status, etc.) and (b) Technical, Environmental and Biological Bias Factors (e.g. disease-dependent, anatomical, or instrumental factors, etc.). The socio-demographic fairness factors have been explored in fairness analysis of AI models in healthcare but have not often been listed in model fact labels. Besides, the technical, environmental, and biological bias factors have not often been explored in the bias analysis of AI models in healthcare and have not been reported in model fact cards. Here, we demonstrate disparities with respect to both sets of factors. We suggest that clinical AI model reporting cards need to be expanded to communicate such a wider range of disparities to end users for precise patient care. Analysis and communication of such a wider range of biases identify potential drivers of bias, which pave the way to debiasing. As well, it highlights the model caveats and guides the end user and policymaker on how, when, and under what circumstances the model works or fails. Copyright © 2023, The Authors. All rights reserved.

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Small P values may not yield robust findings:an example using REST-meta-PD

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science Bulletin 2021年第21期66卷 2148-2152,M0003页

作者： Xi-Ze Jia Na Zhao Hao-Ming Dong Jia-Wei Sun Marek Barton Roxana Burciu Nicolas Carrière Antonio Cerasa Bo-Yu Chen Jun Chen Stephen Coombes Luc Defebvre Christine Delmaire Kathy Dujardin Fabrizio Esposito Guo-Guang Fan Federica Di Nardo Yi-Xuan Feng Brett W.Fling Saurabh Garg Moran Gilat Martin Gorges Shu-Leong Ho Fay BHorak Xiao Hu Xiao-Fei Hu Biao Huang Pei-Yu Huang Ze-Juan Jia Christina Jones Jan Kassubek Lenka Krajcovicova Ajay Kurani Jing Li Qing Li Ai-Ping Liu Bo Liu Hu Liu Wei-Guo Liu Renaud Lopes Yu-Ting Lou Wei Luo Tara Madhyastha Ni-Ni Mao Grainne McAlonan Martin J.McKeown Shirley Pang Andrea Quattrone Irena Rektorova Alessia Sarica Hui-Fang Shang James M.Shine Priyank Shukla Tomas Slavicek Xiao-Peng Song Gioacchino Tedeschi Alessandro Tessitore David Vaillancourt Jian Wang Jue Wang Z.Jane Wang Lu-Qing Wei Xia Wu Xiao-Jun Xu Lei Yan Jing Yang Wan-Qun Yang Nai-Lin Yao De-Long Zhang Jiu-Quan Zhang Min-Ming Zhang Yan-Ling Zhang Cai-Hong Zhou Chao-Gan Yan Xi-Nian Zuo Mark Hallett Tao Wu Yu-Feng Zang Center for Cognition and Brain Disorders the Affiliated HospitalHangzhou Normal UniversityHangzhou 310015China Zhejiang Key Laboratory for Research in Assessment of Cognitive Impairments Hangzhou 311121China National Basic Science Data Center Beijing 100190China State Key Laboratory of Cognitive Neuroscience and Learning&McGovern Institute for Brain Research Beijing Normal UniversityBeijing 100875China School of Information and Electronics Technology Jiamusi UniversityJiamusi 154007China Neuroscience Program Central European Institute of TechnologyCEITECMasaryk UniversityBrno 62500Czech Republic Department of Applied Physiology and Kinesiology University of FloridaGainesville FL 32611USA Univ.Lille InsermCHU LilleU1172-LilNCog-Lille Neuroscience&CognitionLille F-59000France The Institute for Biomedical Research and Innovation National Research CouncilMangone CS 87050Italy Department of Radiology The First Affiliated Hospital of China Medical UniversityShenyang 110001China Department of Radiology Guangdong Provincial Hospital of Chinese MedicineGuangzhou 510120China Department of Medicine Surgery and DentistryScuola Medica SalernitanaUniversity of SalernoFiscianoSA 132-84084Italy Department of Advanced Medical and Surgery Sciences University of Campania“Luigi Vanvitelli”Caserta 81100Italy Eye Center of the 2nd Affiliated Hospital Medical College of Zhejiang UniversityHangzhou 310020China Zhejiang Provincial Key Lab of Ophthalmology Hangzhou 310020China Department of Health and Exercise Science Colorado State UniversityFort Collins CO 80523USA Pacific Parkinson’s Research Centre University of British ColumbiaVancouver BC V6E 2M6Canada Department of Medicine(Neurology)University of British Columbia Vancouver BC V6T 1B7Canada Brain and Mind Center The University of SydneySydney NSW 2006Australia Department of Neurology Ulm UniversityUlm 89081Germany Division of Neurology Department of MedicineQueen Mary HospitalUniversity of Hong KongHong Kong 999077China Department of

Thousands of resting state functional magnetic resonance imaging(RS-f MRI)articles have been published on brain *** precise localization of abnormal brain activity,a voxel-level comparison is *** of the large number of voxels in the brain,multiple comparison correction(MCC)must be performed to reduce false positive rates,and a smaller P value(usually including either liberal or stringent MCC)is widely recommended[1].

关键词：帕金森病 precise correction

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An X Language-Driven Framework for Systematic Development of Digital Twin Healthcare Systems

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ACM Transactions on Multimedia computing, Communications, and Applications 1000年

作者： Kunyu Xie Lin Zhang Yuan Yang Xiaohe Li Ridha Khedri Zhen Chen M. Jamal Deen Simulation Technology Innovation Center Hangzhou International Innovation Institute of Beihang University Hangzhou 311115 Zhejiang China School of Automation Science and Electrical Engineering Beihang University Beijing 100191 China State Key Laboratory of Intelligent Manufacturing Systems Technology Beijing 100191 China School of Automation Science and Electrical Engineering Beihang University Beijing 100191 China Shenzhen Third People’s Hospital & Second Hospital Affiliated to Southern University of Science and Technology Shenzhen 518112 Guangdong China Dept. of Computing and Software McMaster University Hamilton Ontario Canada L8S 4K1 Department of Electrical and Computer Engineering McMaster University Hamilton ON L8S 4L8 Canada

The rapid advancements in big data and the Internet of Things (IoT) have significantly accelerated the digital transformation of medical institutions, leading to the widespread adoption of Digital Twin Healthcare (DTH). The Cloud DTH Platform (CDTH) serves as a cloud-based framework that integrates DTH models, healthcare resources, patient data, and medical services. By leveraging real-time data from medical devices, the CDTH platform enables intelligent healthcare services such as disease prediction and medical resource optimization. However, the platform functions as a system of systems (SoS), comprising interconnected yet independent healthcare services. This complexity is further compounded by the integration of both black-box AI models and domain-specific mechanistic models, which pose challenges in ensuring the interpretability and trustworthiness of DTH models. To address these challenges, we propose a Model-Based Systems engineering (MBSE)-driven DTH modeling methodology derived from systematic requirement and functional analyses. To implement this methodology effectively, we introduce a DTH model development approach using the X language, along with a comprehensive toolchain designed to streamline the development process. Together, this methodology and toolchain form a robust framework that enables engineers to efficiently develop interpretable and trustworthy DTH models for the CDTH platform. By integrating domain-specific mechanistic models with AI algorithms, the framework enhances model transparency and reliability. Finally, we validate our approach through a case study involving elderly patient care, demonstrating its effectiveness in supporting the development of DTH models that meet healthcare and interpretability requirements.

关键词： Digital Twin Model-based system engineering X Language Medical Cyber-Physical Systems Digital Twin Healthcare Design

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Vibration isolation system with a compact damping system for power recycling mirrors of KAGRA

arXiv

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arXiv 2019年

作者： Akiyama, Y. Akutsu, T. Ando, M. Arai, K. Arai, Y. Araki, S. Araya, A. Aritomi, N. Asada, H. Aso, Y. Bae, S. Baiotti, L. Barton, M.A. Cannon, K. Capocasa, E. Chen, C.-S. Chiu, T.-W. Cho, K. Chu, Y.-K. Craig, K. Dattilo, V. Doi, K. Enomoto, Y. Flaminio, R. Fujii, Y. Fujimoto, M.-K. Fukunaga, M. Fukushima, M. Furuhata, T. Haino, S. Hasegawa, K. Hashimoto, Y. Hashino, K. Hayama, K. Hirayama, T. Hirose, E. Hsieh, B.H. Huang, C.-Z. Ikenoue, B. Inoue, Y. Ioka, K. Itoh, Y. Izumi, K. Kaji, T. Kajita, T. Kakizaki, M. Kamiizumi, M. Kanbara, S. Kanda, N. Kanemura, S. Kang, G. Kasuya, J. Kawai, N. Kawasaki, T. Kim, C. Kim, W.S. Kim, J. Kim, J.C. Kimura, N. Kirii, S. Kitaoka, Y. Kitazawa, H. Kojima, Y. Kokeyama, K. Komori, K. Kong, A. Kotake, K. Kozu, R. Kumar, R. Kuo, H.-S. Kuroki, S. Kuroyanagi, S. Lee, H.K. Lee, H.M. Lee, H.W. Leonardi, M. Lin, C.-Y. Lin, F.-L. Liu, G.C. Marchio, M. Matsui, T. Michimura, Y. Mio, N. Miyakawa, O. Miyamoto, A. Miyoki, S. Morii, W. Morisaki, S. Moriwaki, Y. Musha, M. Nagano, S. Nagano, K. Nakamura, K. Nakamura, T. Nakano, H. Nakano, M. Narikawa, T. Quynh, L. Nguyen Ni, W.-T. Nishizawa, A. Obuchi, Y. Oh, J. Oh, S.H. Ohashi, M. Ohishi, N. Ohkawa, M. Okutomi, K. Ono, K. Oohara, K. Ooi, C.P. Pan, S.-S. Paoletti, F. Park, J. Passaquieti, R. Peña Arellano, F.E. Sago, N. Saito, S. Saito, Y. Sakai, K. Sakai, Y. Sasai, M. Sato, S. Sato, T. Sekiguchi, T. Sekiguchi, Y. Shibata, M. Shimoda, T. Shinkai, H. Shishido, T. Shoda, A. Someya, N. Somiya, K. Son, E.J. Suemasa, A. Suzuki, T. Suzuki, T. Tagoshi, H. Tahara, H. Takahashi, H. Takahashi, R. Takeda, H. Tanaka, H. Tanaka, K. Tanaka, T. Tanioka, S. San Martin, E.N. Tapia Tomaru, T. Tomura, T. Travasso, F. Tsubono, K. Tsuchida, S. Uchikata, N. Uchiyama, T. Uehara, T. Ueno, K. Uraguchi, F. Ushiba, T. van Putten, M.H.P.M. Vocca, H. Wakamatsu, T. Watanabe, Y. Xu, W.-R. Yamada, T. Yamamoto, K. Yamamoto, K. Yamamoto, S. Yamamoto, T. Yokogawa, K. Yokoyama, J. Yokozawa, T. Yoshioka, T. Yuzurihara, H. Zeidler, S. Zhu, Z.-H. Graduate School of Science and Engineering Hosei University TokyoKoganei184-8584 Japan National Astronomical Observatory of Japan TokyoMitaka181-8588 Japan Department of Physics University of Tokyo TokyoBunkyo113-0033 Japan University of Tokyo KashiwaChiba277-8582 Japan High Energy Accelerator Research Organization TsukubaIbaraki305-0801 Japan Earthquake Research Institute University of Tokyo TokyoBunkyo113-0032 Japan Department of Physics University of Tokyo TokyoBunkyo113-0033 Japan Department of Mathematics and Physics Hirosaki University AomoriHirosaki036-8561 Japan National Astronomical Observatory of Japan GifuHida506-1205 Japan Korea Institute of Science and Technology Information Yuseong Daejeon34141 Korea Republic of Department of Physics Osaka University ToyonakaOsaka560-0043 Japan University of Tokyo TokyoBunkyo113-0033 Japan Department of Physics National Taiwan Normal University Taipei116 Taiwan Department of Physics Sogang University Seoul121-742 Korea Republic of PisaCascinaI-56021 Italy Department of Physics University of Toyama ToyamaToyama930-8555 Japan Department of Astronomy University of Tokyo TokyoBunkyo113-0032 Japan Advanced Technology Center National Astronomical Observatory of Japan TokyoMitaka181-8588 Japan Institute of Physics Academia Sinica TaipeiNankang11529 Taiwan Department of Applied Physics Fukuoka University FukuokaJonan814-0180 Japan Yukawa Institute for Theoretical Physics Kyoto University KyotoSakyo606-8502 Japan Graduate School of Science Osaka City University OsakaSumiyosi558-8585 Japan Institute of Space and Astronautical Science Japan Aerospace Exploration Agency SagamiharaKanagawa252-5210 Japan University of Tokyo GifuHida506-1205 Japan Graduate Schoool of Science and Technology Tokyo Institute of Technology MeguroTokyo152-8551 Japan Department of Physics Ewha Womans University SeoulSeodaemun-gu03760 Korea Republic of National Institute for

A vibration isolation system called Type-Bp system used for power recycling mirrors has been developed for KAGRA, the interferometric gravitational-wave observatory in Japan. A suspension of the Type-Bp system passively isolates an optic from seismic vibration using three main pendulum stages equipped with two vertical vibration isolation systems. A compact reaction mass around each of the main stages allows for achieving sufficient damping performance with a simple feedback as well as vibration isolation ratio. Three Type-Bp systems were installed in KAGRA, and were proved to satisfy the requirements on the damping performance, and also on estimated residual displacement of the optics. Copyright © 2019, The Authors. All rights reserved.

关键词： Mirrors

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Whole-brain analysis of concurrent TMS-EEG-fMRI reveals brain-wide state-dependent TMS effects

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Brain Stimulation 2023年第1期16卷 405-405页

作者： He, Hengda Sun, Xiaoxiao Doose, Jayce Blankenship, Aidan Mclntosh, James Saber, Golbarg Faller, Josef Lin, Yida Teves, Joshua Huffman, Sarah Pantazatos, Spiro Goldman, Robin George, Mark Brown, Truman Sajda, Paul Department of Biomedical Engineering Columbia University USA Center for Biomedical Imaging Medical University of South Carolina USA Department of Radiology and Radiological Science Medical University of South Carolina USA Department of Orthopaedic Surgery Columbia University Irving Medical Center USA Department of Neurology University of Chicago USA Department of Computer Science Columbia University USA Department of Psychiatry and Behavioral Sciences Medical University of South Carolina USA Department of Psychiatry Columbia University Irving Medical Center USA Center for Healthy Minds University of Wisconsin-Madison USA Ralph H. Johnson VA Medical Center USA Department of Radiology Columbia University Irving Medical Center USA Department of Electrical Engineering Columbia University USA Data Science Institute Columbia University USA

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Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas Program

arXiv

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arXiv 2019年

作者： Snyder, Michael P. Lin, Shin Posgai, Amanda Atkinson, Mark Regev, Aviv Rood, Jennifer Rozenblatt-Rosen, Orit Gaffney, Leslie Hupalowska, Anna Satija, Rahul Gehlenborg, Nils Shendure, Jay Laskin, Julia Harbury, Pehr Nystrom, Nicholas A. Bar-Joseph, Ziv Zhang, Kun Börner, Katy Lin, Yiing Conroy, Richard Procaccini, Dena Roy, Ananda L. Pillai, Ajay Brown, Marishka Galis, Zorina S. Cai, Long Shendure, Jay Trapnell, Cole Lin, Shin Jackson, Dana Snyder, Michael P. Nolan, Garry Greenleaf, William James Lin, Yiing Plevritis, Sylvia Ahadi, Sara Lee, Hayan Nevins, Stephanie Esplin, Ed Horning, Aaron Bahmani, Amir Zhang, Kun Sun, Xin Jain, Sanjay Hagood, James Kharchenko, Peter Atkinson, Mark Bodenmiller, Bernd Brusko, Todd Clare-Salzler, Michael Nick, Harry Otto, Kevin Posgai, Amanda Wasserfall, Clive Maffioletti, Sergio Caprioli, Richard M. Spraggins, Jeffrey M. Gutierrez, Danielle Patterson, Nathan Heath Neumann, Elizabeth K. Harris, Raymond deCaestecker, Mark de Plas, Raf Van Lau, Ken Cai, Long Yuan, Guo-Cheng Zhu, Qian Dries, Ruben Yin, Peng Saka, Sinem K. Kishi, Jocelyn Y. Wang, Yu Goldaracena, Isabel Laskin, Julia Ye, DongHye Burnum-Johnson, Kristin E. Piehowski, Paul D. Ansong, Charles Zhu, Ying Harbury, Pehr Desai, Tushar Mulye, Jay Chou, Peter Nagendran, Monica Bar-Joseph, Ziv Teichmann, Sarah A. Paten, Benedict Murphy, Robert F. Ma, Jian Kiselev, Vladimir Yu Kingsford, Carl Ricarte, Allyson Ruffalo, Matthew Gehlenborg, Nils Kharchenko, Peter Vella, Margaret McCallum, Chuck Börner, Katy Cross, Leonard E. Friedman, Samuel H. Heiland, Randy Herr, Bruce Macklin, Paul Quardokus, Ellen M. Record, Lisel Sluka, James P. Weber, Griffin M. Nystrom, Nicholas A. Silverstein, Jonathan C. Blood, Philip D. Ropelewski, Alexander J. Shirey, William E. Mabee, Paula Lenhardt, W. Christopher Robasky, Kimberly Michailidis, Stavros Satija, Rahul Marioni, John Regev, Aviv Butler, Andrew Stuart, Tim Fisher, Eyal Ghazanfar, Shila Rood, Jennifer Gaffney, Leslie Ersalan, Gokcen Biancalani, Tommaso Conroy, Richard Procaccini, Dena Roy, Anan School of Medicine Stanford University 300 Pasteur Drive United States Department of Genetics Stanford School of Medicine StanfordCA94305 United States Department of Medicine University of Washington SeattleWA98195 United States Department of Pathology University of Florida Diabetes Institute GainesvilleFL32610 United States Klarman Cell Observatory Broad Institute of MIT and Harvard CambridgeMA02142 United States Howard Hughes Medical Institute Koch Institute of Integrative Cancer Research Department of Biology Massachusetts Institute of Technology CambridgeMA02140 United States New York Genome Center New York CityNY10013 United States New York University New YorkNY10012 United States Department of Biomedical Informatics Harvard Medical School BostonMA02115 United States Department of Genome Sciences University of Washington SeattleWA98105 United States Department of Chemistry Purdue University West LafayetteIN47907 United States Department of Biochemistry Stanford University School of Medicine StanfordCA94305 United States Pittsburgh Supercomputing Center Carnegie Mellon University PittsburghPA15213 United States Department of Computational Biology School of Computer Science Carnegie Mellon University PittsburghPA15213 United States Department of Bioengineering University of California San Diego La JollaCA92093 United States Department of Intelligent Systems Engineering School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States Department of Surgery Washington University School of Medicine St LouisMO63110 United States Division of Program Coordination Planning and Strategic Initiatives National Institutes of Health BethesdaMD20892 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Caltech-UW TMC Departmen

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings. Copyright © 2019, The Authors. All rights reserved.

关键词： Mapping

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Quantum Simulation for High-Energy Physics

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PRX Quantum 2023年第2期4卷 027001-027001页

作者： Christian W. Bauer Zohreh Davoudi A. Baha Balantekin Tanmoy Bhattacharya Marcela Carena Wibe A. de Jong Patrick Draper Aida El-Khadra Nate Gemelke Masanori Hanada Dmitri Kharzeev Henry Lamm Ying-Ying Li Junyu Liu Mikhail Lukin Yannick Meurice Christopher Monroe Benjamin Nachman Guido Pagano John Preskill Enrico Rinaldi Alessandro Roggero David I. Santiago Martin J. Savage Irfan Siddiqi George Siopsis David Van Zanten Nathan Wiebe Yukari Yamauchi Kübra Yeter-Aydeniz Silvia Zorzetti Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Department of Physics Maryland Center for Fundamental Physics and the NSF Institute for Robust Quantum Simulation University of Maryland College Park Maryland 20742 USA Department of Physics University of Wisconsin Madison Wisconsin 53706 USA T-2 Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Fermi National Accelerator Laboratory Batavia Illinois 60510 USA Enrico Fermi Institute University of Chicago Chicago Illinois 60637 USA Kavli Institute for Cosmological Physics University of Chicago Chicago Illinois 60637 USA Department of Physics University of Chicago Chicago Illinois 60637 USA Department of Physics and Illinois Center for the Advanced Study of the Universe and Illinois Quantum Information Science and Technology Center University of Illinois Urbana Illinois 61801 USA QuEra Computing Inc Boston Massachusetts 02135 USA Department of Mathematics University of Surrey Guildford Surrey GU2 7XH United Kingdom Center for Nuclear Theory Department of Physics and Astronomy Stony Brook University New York 11794-3800 USA Department of Physics Brookhaven National Laboratory Upton New York 11973 USA Peng Huanwu Center for Fundamental Theory Hefei Anhui 230026 China Interdisciplinary Center for Theoretical Study University of Science and Technology of China Hefei Anhui 230026 China Pritzker School of Molecular Engineering Chicago Quantum Exchange and Kadanoff Center for Theoretical Physics University of Chicago Illinois 60637 USA qBraid Co. Harper Court 5235 Chicago Illinois 60615 USA Department of Physics Harvard University Cambridge Massachusetts 02138 USA Department of Physics and Astronomy University of Iowa Iowa City Iowa 52242 USA Duke Quantum Center Duke University Durham North Carolina 27701 USA Department of Electrical and Computer Engineering Duke University Durham North Carolina 27708 USA Department of Physics Duke University

It is for the first time that quantum simulation for high-energy physics (HEP) is studied in the U.S. decadal particle-physics community planning, and in fact until recently, this was not considered a mainstream topic in the community. This fact speaks of a remarkable rate of growth of this subfield over the past few years, stimulated by the impressive advancements in quantum information sciences (QIS) and associated technologies over the past decade, and the significant investment in this area by the government and private sectors in the U.S. and other countries. High-energy physicists have quickly identified problems of importance to our understanding of nature at the most fundamental level, from tiniest distances to cosmological extents, that are intractable with classical computers but may benefit from quantum advantage. They have initiated, and continue to carry out, a vigorous program in theory, algorithm, and hardware co-design for simulations of relevance to the HEP mission. This Roadmap is an attempt to bring this exciting and yet challenging area of research to the spotlight, and to elaborate on what the promises, requirements, challenges, and potential solutions are over the next decade and beyond.

关键词： Quantum simulation

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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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A survey of classification methods for chest x-ray pathologies utilizing deep learning

引用

AIP Conference Proceedings 2023年第1期3015卷

作者： Israa Faisal Jassam Saleh Mesbah Elkaffas Adel A. El-Zoghabi Ayman Samir Beden Muhammad M. Saad Mohammed Tali Almalchy Registration and Students Affairs University Headquarter University of Anbar Anbar City 31001 Iraq. College of Computing and IT Arab Academy for Science Technology and Maritime Transport Alexandria Egypt. Institute of Graduate Studies and Research Alexandria University Alexandria Egypt. Department of Computer Technology Engineering Faculty of Information Technology Imam Ja’afar Al-Sadiq University Maysan 10011 Iraq. Lead Data Scientist Head of Nawah.ai Stuttgart Germany. Department of Computer Engineering Faculty of Information Technology Imam Ja’afar Al-Sadiq University Maysan 10011 Iraq.

Any urgent diagnosis of pneumonia can be affected by a chest x-ray (CXR henceforth), which is one of the most common types of radiography. Artificial intelligence (AI) has been employed by most researchers for the automatic detection of the complicated patterns in imaging data and to provide quantitative analysis of radiographic properties as well. In recent years, many advances have taken place, namely in the computer vision domain. As a consequence, these advances enable the researchers to provide in-depth analysis and investigation, especially with the existence of thousands of samples of CXR images. CXR samples and techniques provide a huge support for the radiologists in making crucial decisions while examining hundreds of images from different perspectives. Moreover, time consumption will be reduced because the most urgent cases will be correctly identified in a short period of time. The current study will analyze ten of the well-known deep learning (DL)techniques that tackled identifying CXR images in relation to their actual diagnosis. Each technique will be briefly addressed regarding data preparation, methodology, and model design. Furthermore, the accuracy measure generated by each model will be compared to the dataset used. It is hoped that the current study will be a reliable resource for DL to strategies in depicting CXR images in the medical domain.

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Identifying Reasons for Contraceptive Switching from Real-World data Using Large Language Models

arXiv

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arXiv 2024年

作者： Miao, Brenda Y. Williams, Christopher Y.K. Chinedu-Eneh, Ebenezer Zack, Travis Alsentzer, Emily Butte, Atul J. Chen, Irene Y. Bakar Computational Health Sciences Institute University of California San Francisco San FranciscoCA United States Department of Medicine University of California San Francisco San FranciscoCA United States Helen Diller Family Comprehensive Cancer Center University of California San Francisco San FranciscoCA United States Division of General Internal Medicine Brigham and Women's Hospital BostonMA United States Harvard Medical School BostonMA United States Center for Data-driven Insights and Innovation University of California Office of the President OaklandCA United States Computational Precision Health University of California Berkeley University of California San Francisco BerkeleyCA United States Electrical Engineering and Computer Science University of California Berkeley BerkeleyCA United States Berkeley AI Research University of California Berkeley BerkeleyCA United States

Background: Understanding why patients switch contraceptives is of significant interest but these factors are often only captured in unstructured clinical notes and can be difficult to extract. We evaluate the zero-shot abilities of a recently developed large language model, GPT-4, to identify reasons for switching between classes of contraceptives from clinical notes. Methods: Clinical notes associated with contraceptive switches, defined as a difference in prescribed contraceptive modality between consecutive encounters, were selected from the UCSF Information Commons dataset. GPT-4 (HIPAA-compliant Microsoft Azure API) was used to extract contraceptive class started, stopped, and reasons for switching from these clinical notes. We evaluated six prompts on a subset of human annotated notes, and extracted reasons for contraceptive switching from the full dataset using the best prompt based on microF1 scores. BERTopic topic modeling was used to identify key reasons for contraceptive switching and enrichment of topics was assessed in patient subgroups stratified by race and ethnicity. Results: We extracted 1,964 contraceptive switches from 1,515 patients. Younger patients and patients with self-reported race/ethnicities listed as "Black/African American" and "Latinx" had significantly higher rates of switching. GPT-4 demonstrated extraction of contraceptives started and stopped had MicroF1 scores of 0.849 and 0.881, respectively. Accuracy of GPT-4 extracted reasons for switching was 91.4% and 2.2% contained hallucinations. Key reasons for switching included patient preference, adverse events, and insurance. "Weight gain/mood change" and "insurance coverage" topics were enriched in patients self-reporting as being "Black or African American", "Latinx", or "Multi-Race/Ethnicity". Conclusion: We demonstrate that GPT-4 can accurately extract reasons for contraceptive switching and identify certain reasons that are disproportionately found in specific demographic populati

关键词： Extraction

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