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arXiv 2020年

作者： Shoeibi, Afshin Khodatars, Marjane Jafari, Mahboobeh Ghassemi, Navid Sadeghi, Delaram Moridian, Parisa Khadem, Ali Alizadehsani, Roohallah Hussain, Sadiq Zare, Assef Sani, Zahra Alizadeh Khozeimeh, Fahime Nahavandi, Saeid Rajendra Acharya, U. Gorriz, Juan M. The Data Science and Computational Intelligence Institute University of Granada Spain The Computer Engineering Department Ferdowsi University of Mashhad Mashhad Iran Deakin University VIC3217 Australia The Faculty of Electrical Engineering K. N. Toosi University of Technology Tehran Iran System Administrator at Dibrugarh University Assam786004 India Faculty of Electrical Engineering Gonabad Branch Islamic Azad University Gonabad Iran Rajaie Cardiovascular Medical and Research Center Iran University of Medical Sciences Tehran Iran The School of Mathematics Physics and Computing University of Southern Queensland Springfield Australia Dept. of Psychiatry University of Cambridge United Kingdom

Coronavirus, or COVID-19, is a hazardous disease that has endangered the health of many people around the world by directly affecting the lungs. COVID-19 is a medium-sized, coated virus with a single-stranded RNA, and also has one of the largest RNA genomes and is approximately 120 nm. The X-Ray and computed tomography (CT) imaging modalities are widely used to obtain a fast and accurate medical diagnosis. Identifying COVID-19 from these medical images is extremely challenging as it is time-consuming and prone to human errors. Hence, artificial intelligence (AI) methodologies can be used to obtain consistent high performance. Among the AI methods, deep learning (DL) networks have gained popularity recently compared to conventional machine learning (ML). Unlike ML, all stages of feature extraction, feature selection, and classification are accomplished automatically in DL models. In this paper, a complete survey of studies on the application of DL techniques for COVID-19 diagnostic and segmentation of lungs is discussed, concentrating on works that used X-Ray and CT images. Additionally, a review of papers on the forecasting of coronavirus prevalence in different parts of the world with DL is presented. Lastly, the challenges faced in the detection of COVID-19 using DL techniques and directions for future research are discussed. © 2020, CC BY-NC-ND.

关键词： COVID-19

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Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

arXiv

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arXiv 2023年

作者： Yang, Kaiyuan Musio, Fabio Ma, Yihui Juchler, Norman Paetzold, Johannes C. Al-Maskari, Rami Höher, Luciano Li, Hongwei Bran Hamamci, Ibrahim Ethem Sekuboyina, Anjany Shit, Suprosanna Huang, Houjing Prabhakar, Chinmay de la Rosa, Ezequiel Waldmannstetter, Diana Kofler, Florian Navarro, Fernando Menten, Martin Ezhov, Ivan Rueckert, Daniel Vos, Iris Ruigrok, Ynte Velthuis, Birgitta Kuijf, Hugo Hämmerli, Julien Wurster, Catherine Bijlenga, Philippe Westphal, Laura Bisschop, Jeroen Colombo, Elisa Baazaoui, Hakim Makmur, Andrew Hallinan, James Wiestler, Bene Kirschke, Jan S. Wiest, Roland Montagnon, Emmanuel Letourneau-Guillon, Laurent Galdran, Adrian Galati, Francesco Falcetta, Daniele Zuluaga, Maria A. Lin, Chaolong Zhao, Haoran Zhang, Zehan Ra, Sinyoung Hwang, Jongyun Park, Hyunjin Chen, Junqiang Wodzinski, Marek Müller, Henning Shi, Pengcheng Liu, Wei Ma, Ting Yalçin, Cansu Hamadache, Rachika E. Salvi, Joaquim Llado, Xavier Estrada, Uma Maria Lal-Trehan Abramova, Valeriia Giancardo, Luca Oliver, Arnau Liu, Jialu Huang, Haibin Cui, Yue Lin, Zehang Liu, Yusheng Zhu, Shunzhi Patel, Tatsat R. Tutino, Vincent M. Orouskhani, Maysam Wang, Huayu Mossa-Basha, Mahmud Zhu, Chengcheng Rokuss, Maximilian R. Kirchhoff, Yannick Disch, Nico Holzschuh, Julius Isensee, Fabian Maier-Hein, Klaus Sato, Yuki Hirsch, Sven Wegener, Susanne Menze, Bjoern Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Center for Computational Health Zurich University of Applied Sciences Zurich Switzerland Department of Neuroradiology University Hospital of Zurich Zurich Switzerland Department of Neurosurgery Zhongnan Hospital of Wuhan University Wuhan China Department of Computing Imperial College London London United Kingdom Helmholtz Center Munich Germany Athinoula A. Martinos Center for Biomedical Imaging Harvard Medical School Boston United States School of Medicine Technical University of Munich Munich Germany Department of Informatics Technical University of Munich Munich Germany Helmholtz AI Helmholtz Munich Munich Germany Image Sciences Institute UMC Utrecht Utrecht Netherlands Department of Neurology UMC Utrecht Utrecht Netherlands Department of Radiology UMC Utrecht Utrecht Netherlands Department of Clinical Neurosciences Division of Neurosurgery Geneva University Hospitals Geneva Switzerland Department of Neurology University Hospital of Zurich Zurich Switzerland Department of Physiology University of Toronto Toronto Canada Department of Neurosurgery University Hospital of Zurich Zurich Switzerland Department of Diagnostic Imaging National University Hospital Singapore Department of Diagnostic and Interventional Neuroradiology University Hospital Berne University of Berne Berne Switzerland Montreal Canada Universitat Pompeu Fabra Barcelona Spain EURECOM Biot France Institute of Medical Technology Peking University Health Science Center Beijing China Hangzhou Genlight Medtech Co. Ltd. Hangzhou China Department of Artificial Intelligence Sungkyunkwan University Seoul Korea Republic of Department of Electrical and Computer Engineering Sungkyunkwan University Seoul Korea Republic of Shanghai MediWorks Precision Instruments Co. Ltd. Shanghai China Institute of Informatics HES-SO Valais-Wallis Switzerland Department of Measurement and Electronics AGH University

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited public datasets with annotations on CoW anatomy, especially for CTA. Therefore we organized the TopCoW Challenge in 2023 with the release of an annotated CoW dataset. The TopCoW dataset was the first public dataset with voxel-level annotations for thirteen possible CoW vessel components, enabled by virtual-reality (VR) technology. It was also the first large dataset with paired MRA and CTA from the same patients. TopCoW challenge formalized the CoW characterization problem as a multiclass anatomical segmentation task with an emphasis on topological metrics. We invited submissions worldwide for the CoW segmentation task, which attracted over 140 registered participants from four continents. The top performing teams managed to segment many CoW components to Dice scores around 90%, but with lower scores for communicating arteries and rare variants. There were also topological mistakes for predictions with high Dice scores. Additional topological analysis revealed further areas for improvement in detecting certain CoW components and matching CoW variant topology accurately. TopCoW represented a first attempt at benchmarking the CoW anatomical segmentation task for MRA and CTA, both morphologically and topologically. © 2023, CC BY-NC-ND.

关键词： Large datasets

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Assessing the Potential of GPT-4 to Annotate Medical Notes Across Different Languages and Countries: A Model Evaluation Study

SSRN

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SSRN 2024年

作者： Saad Menezes, Maria Clara Hoffman, Alexander F. Tan, Amelia L.M. Nalbandyan, Mariné Omenn, Gilbert S. Mazzotti, Diego R. Hernández-Arango, Alejandro Visweswaran, Shyam Venkatesh, Shruthi Mandl, Kenneth D. Bourgeois, Florence T. Lee, James W.K. Makmur, Andrew Hanauer, David A. Semanik, Michael G. Kerivan, Lauren T. Hill, Terra Forero, Julian Restrepo Castro, Carlos Andrés C.R. Vigna, Matteo Ceriana, Piero Abu-El-rub, Noor Avillach, Paul Bellazzi, Riccardo Callaci, Thomas Gutiérrez-Sacristán, Alba Malovini, Alberto Mathew, Jomol P. Morris, Michele Murthy, Venkatesh Parimbelli, Enea Patel, Lav P. Sáez, Carlos Samayamuthu, Malarkodi Jebathilagam Thompson, Jeffrey A. Tibollo, Valentina Xia, Zongqi Kohane, Isaac S. Harvard Medical School Department of Biomedical Informatics 10 Shattuck Street BostonMA02115 United States School of Medicine and Public Health University of Wisconsin-Madison Office of Informatics and Information Technology 750 Highland Ave MadisonWI53705 United States University of Michigan Department of Computational Medicine & Bioinformatics Internal Medicine Human Genetics Environmental Health 100 Washtenaw Avenue Ann ArborMI48109 United States University of Kansas Medical Center Division of Medical Informatics Division of Pulmonary Critical Care and Sleep Medicine Department of Internal Medicine 3901 Rainbow Blvd Kansas CityKS66160 United States University of Antioquia Hospital Alma Máter de Antioquia Department of Internal Medicine Calle 64 N°51 D - 154 Medellín Colombia University of Pittsburgh Department of Biomedical Informatics 5607 Baum Blvd PittsburghPA15206 United States University of Pittsburgh Department of Neurology 3501 5th Avenue PittsburghPA15206 United States Boston Children's Hospital Computational Health Informatics Program 300 Longwood Avenue BostonMA02115 United States Boston Children's Hospital Department of Pediatrics 300 Longwood Avenue BostonMA02115 United States National University Health System Department of Surgery 1E Kent Ridge Rd Singapore119228 Singapore National University Health System Department of Diagnostic Imaging 1E Kent Ridge Rd Singapore119228 Singapore University of Michigan Department of Learning Health Sciences NCRC 100 2800 Plymouth Road Ann ArborMI48109 United States University of Kansas Medical Center Department of Surgery 3901 Rainbow Blvd Kansas CityKS66160 United States Istituti Clinici Scientifici Maugeri IRCCS Respiratory rehabilitation unit Via Maugeri 10 Pavia27100 Italy University of Kansas Medical Center 3901 Rainbow Blvd Kansas CityKS66160 United States University of Pavia Department of Electrical Computer and Biomedical Engineering via Ferrata 5 Pavia2710

Background: Physicians invest hours creating patient notes, which are rich in information but difficult for computers to analyze due to their unstructured format. GPT-4 reshaped our ability to process text, yet it is unknown how well this model can handle medical notes. This project aims to compare GPT-4’s ability to annotate medical notes against experienced physicians across three different languages at multiple institutions and countries. Methods: This study included eight sites from four countries - the United States, Colombia, Singapore, and Italy. Each site contributed seven de-identified notes (admission, progress, or consult) from hospitalized patients. GPT-4 assessed each note by answering 14 questions, including demographic information, clinical judgments, data quality, and patients’ eligibility for a hypothetical study enrollment. For validation, two physicians from each site independently evaluated GPT-4's responses. Findings: Overall, 56 medical notes, written in English, Italian, and Spanish, were analyzed. A total of 784 responses from GPT-4 were generated. Both physicians agreed with GPT-4’s response 79% of the time (622/784, 95%CI 76-82%). Only one of the two physicians agreed with GPT-4’s response 10% of the time (82/784, 95%CI 8-13%). Neither physician agreed with GPT-4’s response 10% of the time (80/784, 95%CI 8-13%). Both physicians agreed with GPT-4 more often in notes written in Spanish and Italian than in English, with agreement rates of 88% (86/98, 95%CI 79-93%), 84% (82/98, 95%CI 75-90%), and 77% (454/588, 95%CI 74-80%), respectively. Hallucinations were rare (10/784, 95%CI 0-2%). GPT-4 correctly selected patients for a hypothetical study enrollment based on three criteria 90% of the time (95%CI 81-98%). Interpretation: The findings indicate that GPT-4 annotations demonstrated a high agreement rate with physicians across all languages. We also demonstrate GPT-4's potential to assist in patient selection for studies. Funding: None. Declarati

关键词： Medical computing

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HIV and COVID-19 co-infection: A mathematical model and optimal control

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Informatics in Medicine Unlocked 2022年 31卷 100978页

作者： Ringa, N. Diagne, M.L. Rwezaura, H. Omame, A. Tchoumi, S.Y. Tchuenche, J.M. Data and Analytic Services British Columbia Centre for Disease Control 655 W 12th Ave Vancouver BC V5Z 4R4 Canada School of Population and Public Health University of British Columbia 2329 West Mall Vancouver BC V6T 1Z4 Canada Département de Mathématiques UFR des Sciences et Technologies Université de Thiès Thiès BP 967 Senegal Mathematics Department University of Dar es Salaam P.O. Box 35062 Dar es Salaam Tanzania Department of Mathematics Federal University of Technology Owerri Nigeria Abdus Salam School of Mathematical Sciences Government College University Lahore Pakistan Department of Mathematics and Computer Sciences ENSAI University of Ngaoundéré P.O. Box 455 Ngaoundéré Cameroon School of Computer Science and Applied Mathematics University of the Witwatersrand Private Bag 3 Wits 2050 Johannesburg South Africa School of Computational and Communication Sciences and Engineering Nelson Mandela African Institution of Science and Technology P.O. Box 447 Arusha Tanzania

A new mathematical model for COVID-19 and HIV/AIDS is considered to assess the impact of COVID-19 on HIV dynamics and vice-versa. Investigating the epidemiologic synergy between COVID-19 and HIV is important. The dynamics of the full model is driven by that of its sub-models;therefore, basic analysis of the two sub-models;HIV-only and COVID-19 only is carried out. The basic reproduction number is computed and used to prove local and global asymptotic stability of the sub-models’ disease-free and endemic equilibria. Using the fmincon function in the Optimization Toolbox of MATLAB, the model is fitted to real COVID-19 data set from South Africa. The impact of intervention measures, namely, COVID-19 and HIV prevention interventions and COVID-19 treatment are incorporated into the model using time-dependent controls. It is observed that HIV prevention measures can significantly reduce the burden of co-infections with COVID-19, while effective treatment of COVID-19 could reduce co-infections with opportunistic infections such as HIV/AIDS. In particular, the COVID-19 only prevention strategy averted about 10,500 new co-infection cases, with similar number also averted by the HIV-only prevention control. © 2022 The Author(s)

关键词： Basic reproduction number Co-infection COVID-19 HIV Optimal control

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Small inter-event times govern epidemic spreading on temporal networks

arXiv

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arXiv 2019年

作者： Masuda, Naoki Holme, Petter Department of Mathematics University at Buffalo State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York BuffaloNY14260-5030 United States Institute of Innovative Research Tokyo Institute of Technology Yokohama226-8503 Japan

Just like the degrees of human and animal interaction networks, the distribution of the times between interactions is known to often be right-skewed and fat-tailed. Both these distributions affect epidemic dynamics strongly, but, as we show in this Letter, for very different reasons. Whereas the high degrees of the tail are critical for facilitating epidemics, it is the small interevent times that control the dynamics of epidemics. We investigate this effect both analytically and numerically for different versions of the Susceptible-Infected-Recovered model on different types of networks. Copyright © 2019, The Authors. All rights reserved.

关键词： Epidemiology

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Modeling state-transition dynamics in resting-state brain signals by the hidden Markov and Gaussian mixture models

arXiv

引用

arXiv 2020年

作者： Ezaki, Takahiro Himeno, Yu Watanabe, Takamitsu Masuda, Naoki Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba Meguro-ku Tokyo153-8904 Japan PRESTO JST 4-1-8 Honcho Kawaguchi Saitama332-0012 Japan Department of Aeronautics and Astronautics The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo113-8656 Japan Laboratory for Cognition Circuit Dynamics RIKEN Centre for Brain Science Saitama351-0198 Japan International Research Center for Neurointelligence The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo113-0033 Japan Department of Mathematics State University of New York at Buffalo BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States

Recent studies have proposed that one can summarize brain activity into dynamics among a relatively small number of hidden states and that such an approach is a promising tool for revealing brain function. Hidden Markov models (HMMs) are a prevalent approach to inferring such neural dynamics among discrete brain states. However, the impact of assuming Markovian structure in neural time series data has not been sufficiently examined. Here, to address this situation and examine the performance of the HMM, we compare the model with the Gaussian mixture model (GMM), which is with no temporal regularization and thus a statistically simpler model than the HMM, by applying both models to synthetic time series generated from empirical resting-state functional magnetic resonance imaging (fMRI) data. We compared the GMM and HMM for various sampling frequencies, lengths of recording per participant, numbers of participants, and numbers of independent component signals. We find that the HMM attains a better accuracy of estimating the hidden state than the GMM in a majority of cases. However, we also find that the accuracy of the GMM is comparable to that of the HMM under the condition that the sampling frequency is reasonably low (e.g., TR = 2.88 or 3.60 s) or the data is relatively short. These results suggest that the GMM can be a viable alternative to the HMM for investigating hidden-state dynamics under this condition. Copyright © 2020, The Authors. All rights reserved.

关键词： Hidden Markov models

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Study and Trend Prediction of Covid-19 cases in India using Deep Learning Techniques

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Journal of Physics: Conference Series 2021年第1期1950卷

作者： V K Shrivastava Ajay Kumar A Shrivastava A Tiwari K Thiru R Batra Department of Big Data Analytics Adani Institute of Digital Technology Management Gandhinagar Gujrat 382423 India. Department of Mechanical Engineering SGT University Gurugram Haryana 122505 India. Department of Electronics and Tele Communication Engineering IIIT Bhubaneswar Odisha 751003 India. Department of Information Technology Madhav Institute of Technology and Science Gwalior 474005 India. United World School of Computational Intelligence Karnavati University Gandhinagar Gujrat 383422 India. Reenu Batra Department of Computer Science and Engineering SGT University Gurugram Haryana 122505 India.

The novel coronavirus or officially known as SARS-CoV 2 (Severe Acute Respiratory Syndrome Coronavirus 2) has caused a severe pandemic over the world affecting not only the economy of the countries but also the lifestyle of the people worldwide. As on 31.12.2020, Covid-19 (coronavirus disease) has infecting more than 10266674 people and causing about 148738 deaths in India. It has been seen through various statistics of various countries that the number of Covid-19 cases grows exponentially as the number of test increases then after some period, the rate of new cases decreases. In this research paper, researchers have created deep learning-based model to predict the curve of the new Covid-19 cases vs the total number of tests conducted in India. There is still lockdown in some part of the country while some states have partially relaxed the rules and some states totally lifted the lockdown. Predicting the number of new cases and their trend can help in deciding what is the optimal time to release the lockdown. It will also help in determining when the coronavirus will loosen its grip from India.

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Big-data clustering: K-Means or k-indicators?

arXiv

引用

arXiv 2019年

作者： Chen, Feiyu Yang, Yuchen Xu, Liwei Zhang, Taiping Zhang, Yin School of Big Data and Software Engineering Chongqing University Chongqing China Department of Computational and Applied Mathematics Rice University HoustonTX United States School of Mathematical Sciences University of Electronic Science and Technology of China Chengdu Sichuan China College of Computer Science Chongqing University Chongqing China Institute for Data and Decision Analytics Chinese University of Hong Kong Shenzhen China

The K-means algorithm is arguably the most popular data clustering method, commonly applied to processed datasets in some "feature spaces", as is in spectral clustering. Highly sensitive to initializations, however, K-means encounters a scalability bottleneck with respect to the number of clusters K as this number grows in big data applications. In this work, we promote a closely related model called K-indicators model and construct an efficient, semi-convex-relaxation algorithm that requires no randomized initializations. We present extensive empirical results to show advantages of the new algorithm when K is large. In particular, using the new algorithm to start the K-means algorithm, without any replication, can significantly outperform the standard K-means with a large number of currently state-ofthe-A rt random replications. Copyright © 2019, The Authors. All rights reserved.

关键词： K-means clustering

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Synergy of Binary Substitutions for Improving the Cycle Performance in LiNiO2 Revealed by Ab Initio Materials Informatics

arXiv

引用

arXiv 2020年

作者： Yoshida, Tomohiro Maezono, Ryo Hongo, Kenta Department of Computer-Aided Engineering and Development Sumitomo Metal Mining Co. Ltd. 3-5 Sobiraki-cho NiihamaEhime792-0001 Japan School of Information Science JAIST Asahidai 1-1 IshikawaNomi923-1292 Japan Computational Engineering Applications Unit RIKEN 2-1 Hirosawa SaitamaWako351-0198 Japan Research Center for Advanced Computing Infrastructure JAIST Asahidai 1-1 NomiIshikawa923-1292 Japan Center for Materials Research by Information Integration Research and Services Division of Materials Data and Integrated System National Institute for Materials Science 1-2-1 Sengen TsukubaIbaraki305-0047 Japan PRESTO Japan Science and Technology Agency 4-1-8 Honcho SaitamaKawaguchi-shi322-0012 Japan

We explore LiNiO2-based cathode materials with two-element substitutions by an ab initio simulation based materials informatics (AIMI) approach. According to our previous study, a higher cycle performance strongly correlates with less structural change during charge–discharge cycles;the latter can be used for evaluating the former. However, if we target the full substitution space, full simulations are infeasible even for all binary combinations. To circumvent such an exhaustive search, we rely on Bayesian optimization. Actually, by searching only 4% of all the combinations, our AIMI approach discovered two promising combinations, Cr-Mg and Cr-Re, whereas each atom itself never improved the performance. We conclude that the synergy never emerges from a common strategy restricted to combinations of "good" elements that individually improve the performance. In addition, we propose a guideline for the binary substitutions by elucidating the mechanism of crystal structure change. Copyright © 2020, The Authors. All rights reserved.

关键词： Binary alloys

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A scalable weakly-synchronous algorithm for solving partial differential equations

arXiv

引用

arXiv 2019年

作者： Aditya, Konduri Gysi, Tobias Kwasniewski, Grzegorz Hoefler, Torsten Donzis, Diego A. Chen, Jacqueline H. Combustion Research Facility Sandia National Laboratories LivermoreCA94550 United States Department of Computer Science ETH Zurich Zuirch8092 Switzerland Department of Aerospace Engineering Texas A&M University College StationTX77843 United States Department of Computational and Data Sciences Indian Institute of Science Bangalore India

Synchronization overheads pose a major challenge as applications advance towards extreme scales. In current large-scale algorithms, synchronization as well as data communication delay the parallel computations at each time step in a time-dependent partial differential equation (PDE) solver. This creates a new scaling wall when moving towards exascale. We present a weakly-synchronous algorithm based on novel asynchrony-tolerant (AT) finite-difference schemes that relax synchronization at a mathematical level. We utilize remote memory access programming schemes that have been shown to provide significant speedup on modern supercomputers, to efficiently implement communications suitable for AT schemes, and compare to two-sided communications that are state-of-practice. We present results from simulations of Burgers' equation as a model of multi-scale strongly non-linear dynamical systems. Our algorithm demonstrate excellent scalability of the new AT schemes for large-scale computing, with a speedup of up to 3.3x in communication time and 2.19x in total runtime. We expect that such schemes can form the basis for exascale PDE algorithms. Copyright © 2019, The Authors. All rights reserved.

关键词： Synchronization

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