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Correction: Machine learning-based prediction of COVID-19 mortality using immunological and metabolic biomarkers

BMC Digital Health 2023年第1期1卷 1-1页

作者： Thomas Wetere Tulu Ching Long Chan Chun Hei Wu Kei Hang Katie Chan Tsz Kin Wan Peter Yat Ming Woo Cee Zhung Steven Tseng Asmir Vodencarevic Cristina Menni Department of Biomedical Sciences City University of Hong Kong Hong Kong SAR China Computational Data Science Program Addis Ababa University Addis Ababa Ethiopia Department of Electrical Engineering City University of Hong Kong Hong Kong SAR China Department of Epidemiology and Center for Global Cardiometabolic Health School of Public Health Brown University Providence RI USA Department of Neurosurgery Kwong Wah Hospital Hong Kong SAR China Department of Medicine and Geriatrics Kwong Wah Hospital Hong Kong SAR China Innovative Medicines Novartis Pharma GmbH 90429 Nuremberg Germany Department of Twin Research King’s College London London UK

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Roadmap on Electronic Structure Codes in the Exascale Era

arXiv

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arXiv 2022年

作者： Gavini, Vikram Baroni, Stefano Blum, Volker Bowler, David R. Buccheri, Alexander Chelikowsky, James R. Das, Sambit Dawson, William Delugas, Pietro Dogan, Mehmet Draxl, Claudia Galli, Giulia Genovese, Luigi Giannozzi, Paolo Giantomassi, Matteo Gonze, Xavier Govoni, Marco Gulans, Andris Gygi, François Herbert, John M. Kokott, Sebastian Kühne, Thomas D. Liou, Kai-Hsin Miyazaki, Tsuyoshi Motamarri, Phani Nakata, Ayako Pask, John E. Plessl, Christian Ratcliff, Laura E. Richard, Ryan M. Rossi, Mariana Schade, Robert Scheffler, Matthias Schütt, Ole Suryanarayana, Phanish Torrent, Marc Truflandier, Lionel Windus, Theresa L. Xu, Qimen Yu, Victor W.-Z. Perez, Danny Department of Mechanical Engineering University of Michigan Ann ArborMI48109 United States SISSA ISAS Trieste Trieste34136 Italy IOM-CNR Trieste Trieste34136 Italy Duke University DurhamNC27708 United States London Centre for Nanotechnology LondonWC1H 0AH United Kingdom WPI-MANA National Institute for Materials Science Ibaraki305-0044 Japan Humboldt-Universität zu Berlin Berlin10117 Germany McKetta Department of Chemical Engineering University of Texas at Austin AustinTX78712 United States Center for Computational Materials Oden Institute University of Texas at Austin AustinTX78712 United States Department of Physics University of Texas at Austin AustinTX78712 United States RIKEN Center for Computational Science Hyogo Kobe650-0047 Japan Pritzker School of Molecular Engineering University of Chicago ChicagoIL60637 United States Materials Science Division Argonne National Laboratory LemontIL60439 United States Université Grenoble Alpes MEM L_Sim GrenobleF-38000 France University of Udine Udine33100 Italy IMCN Université catholique de Louvain Louvain-la-neuve Belgium University of Latvia RīgaLV-1586 Latvia University of California DavisCA95616 United States Department of Chemistry & Biochemistry The Ohio State University ColumbusOH43210 United States Berlin14195 Germany Dynamics of Condensed Matter Center for Sustainable Systems Design Chair of Theoretical Chemistry Paderborn University D-33098 Germany Paderborn Center for Parallel Computing Paderborn University D-33098 Germany Department of Computational and Data Sciences Indian Institute of Science Karnataka Bengaluru560012 India Lawrence Livermore National Laboratory LivermoreCA94550 United States Department of Computer Science Paderborn University D-33098 Germany Centre for Computational Chemistry School of Chemistry University of Bristol BristolBS8 1TS United Kingdom Ames National Laboratory AmesIA50011 United States Iowa State University AmesIA50

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing. Copyright © 2022, The Authors. All rights reserved.

关键词： Electronic structure

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Decoding of visual-related information from the human EEG using an end-to-end deep learning approach

arXiv

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arXiv 2019年

作者： Yang, Lingling Chan, Leanne Lai Hang Lu, Yao University of Minnesota Department of Electrical Engineering City University of Hong Kong HKSAR China School of Data and Computer Science and Guangdong Province Key Laboratory of Computational Science Sun Yat-Sen University Guangzhou China

There is increasing interest in using deep learning approach for EEG analysis as there are still rooms for the improvement of EEG analysis in its accuracy. Convolutional long short-term (CNNLSTM) has been successfully applied in time series data with spatial structure through end-to-end learning. Here, we proposed a CNNLSTM based neural network architecture termed EEG-CNNLSTMNet for the classification of EEG signals in response to grating stimuli with different spatial frequencies. EEG-CNNLSTMNet comprises two convolutional layers and one bidirectional long short-term memory (LSTM) layer. The convolutional layers capture local temporal characteristics of the EEG signal at each channel as well as global spatial characteristics across channels, while the LSTM layer extracts long-term temporal dependency of EEG signals. Our experiment showed that EEG-CNNLSTMNet performed much better at EEG classification than a traditional machine learning approach, i.e. a support vector machine (SVM) with features. Additionally, EEG-CNNLSTMNet outperformed EEGNet, a state-of-art neural network architecture for the intra-subject case. We infer that the underperformance when using an LSTM layer in the inter-subject case is due to long-term dependency characteristics in the EEG signal that vary greatly across subjects. Moreover, the inter-subject fine-tuned classification model using very little data of the new subject achieved much higher accuracy than that trained only on the data from the other subjects. Our study suggests that the fine-tuned inter-subject model can be a potential end-to-end EEG analysis method considering both the accuracy and the required training data of the new subject. Copyright © 2019, The Authors. All rights reserved.

关键词： Convolution

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Genome assembly and transcriptome analysis provide insights into the antischistosome mechanism of Microtus fortis

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Journal of Genetics and Genomics 2020年第12期47卷 743-755页

作者： Hong Li Zhen Wang Shumei Chai Xiong Bai Guohui Ding Yuanyuan Li Junyi Li Qingyu Xiao Benpeng Miao Weili Lin Jie Feng Mingyue Huang Cheng Gao Bin Li Wei Hu Jiaojiao Lin Zhiqiang Fu Jianyun Xie Yixue Li Bio-Med Big Data Center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesKey Laboratory of Animal ParasitologyMinistry of AgricultureShanghai 200241China Shanghai Laboratory Animal Research Center Shanghai 201203China Institute for Digital Health International Human Phenome Institutes(Shanghai)Shanghai 200433China Shanghai Center for Bioinformation Technology Shanghai Academy of Science and TechnologyShanghai 201203China School of Computer Science and Technology Harbin Institute of Technology(Shenzhen)ShenzhenGuangdong 518055China Shanghai Institute of Immunology Department of Immunology and MicrobiologyShanghai JiaoTong University School of MedicineShanghai 200025China State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Contemporary AnthropologyCollaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan UniversityShanghai 200438China Hangzhou Institute for Advanced Study University of Chinese Academy of SciencesHangzhouZhejiang 330106China

Microtus fortis is the only mammalian host that exhibits intrinsic resistance against Schistosoma japonicum ***,the underlying molecular mechanisms of this resistance are not yet ***,we perform the first de novo genome assembly of ***,comprehensive gene annotation analysis,and evolution ***,we compare the recovery rate of schistosomes,pathological changes,and liver transcriptomes between *** and mice at different time points after *** observe that the time and type of immune response in *** are different from those in *** activates immune and inflammatory responses on the 10th day post infection,such as leukocyte extravasation,antibody activation,Fc-gamma receptor-mediated phagocytosis,and the interferon signaling cascade,which play important roles in preventing the development of *** contrast,an intense immune response occurrs in mice at the late stages of infection and could not eliminate *** mice suffer severe pathological injury and continuous decreases in cell cycle,lipid metabolism,and other *** findings offer new insights into the intrinsic resistance mechanism of *** against schistosome *** genome sequence also provides the basis for future studies of other important traits in ***.

关键词： Genome assembly Microtus fortis Schistosome Immune Transcriptome

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Correction to: Path-based estimation for link prediction

引用

International Journal of Machine Learning and Cybernetics 2021年第9期12卷 2459-2459页

作者： Ma, Guoshuai Yan, Hongren Qian, Yuhua Wang, Lingfeng Dang, Chuangyin Zhao, Zhongying Institute of Big Data Science and Industry Shanxi University Taiyuan China School of Computer and Information Technology Shanxi University Taiyuan China Key Laboratory of Computational Intelligence and Chinese Information Processing of Ministry of Education Shanxi University Taiyuan China Department of Electrical Engineering and Computer Science University of Wisconsin-Milwaukee Milwaukee USA Department of Manufacture Engineering and Engineering Management City University of Hong Kong Kowloon Tong Hong Kong The School of Computer Science and Engineering Shandong University of Science and Technology Qingdao China

A correction to this paper has been published: https://***/10.1007/s13042-021-01350-4

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UNCOVER: Illuminating the Early Universe — JWST/NIRSpec Confirmation of z > 12 Galaxies

arXiv

引用

arXiv 2023年

作者： Wang, Bingjie Fujimoto, Seiji Labbé, Ivo Furtak, Lukas J. Miller, Tim B. Setton, David J. Zitrin, Adi Atek, Hakim Bezanson, Rachel Brammer, Gabriel Leja, Joel Oesch, Pascal A. Price, Sedona H. Chemerynska, Iryna Cutler, Sam E. Dayal, Pratika van Dokkum, Pieter Goulding, Andy D. Greene, Jenny E. Fudamoto, Y. Khullar, Gourav Kokorev, Vasily Marchesini, Danilo Pan, Richard Weaver, John R. Whitaker, Katherine E. Williams, Christina C. Department of Astronomy & Astrophysics The Pennsylvania State University University ParkPA16802 United States Institute for Computational & Data Sciences The Pennsylvania State University University ParkPA16802 United States Institute for Gravitation and the Cosmos The Pennsylvania State University University ParkPA16802 United States Department of Astronomy The University of Texas at Austin AustinTX78712 United States Centre for Astrophysics and Supercomputing Swinburne University of Technology MelbourneVIC3122 Australia Department of Physics Ben-Gurion University of the Negev P.O. Box 653 Be’er-Sheva84105 Israel Department of Astronomy Yale University New HavenCT06511 United States Department of Physics & Astronomy Northwestern University IL60201 United States Department of Physics & Astronomy and PITT PACC University of Pittsburgh PittsburghPA15260 United States Institut d’Astrophysique de Paris CNRS Sorbonne Université 98bis Boulevard Arago ParisF-75014 France Niels Bohr Institute University of Copenhagen Jagtvej 128 København NDK-2200 Denmark Department of Astronomy University of Geneva Chemin Pegasi 51 Versoix1290 Switzerland Institut d’Astrophysique de Paris CNRS Sorbonne Université 98bis Boulevard Arago Paris75014 France Department of Astronomy University of Massachusetts AmherstMA01003 United States Kapteyn Astronomical Institute University of Groningen Groningen9700 AV Netherlands Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Waseda Research Institute for Science and Engineering Faculty of Science and Engineering Waseda University 3-4-1 Okubo Shinjuku Tokyo169-8555 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo Japan Department of Physics & Astronomy Tufts University MA02155 United States NSF’s National Optical-Infrared Astronomy Research Laboratory TucsonAZ85719 United States Steward Observatory University of Arizona TucsonAZ8

Observations of high-redshift galaxies provide a critical direct test to the theories of early galaxy formation, yet to date, only three have been spectroscopically confirmed at z > 12. Due to strong gravitational lensing over a wide area, the galaxy cluster field A2744 is ideal for searching for the earliest galaxies. Here we present JWST/NIRSpec observations of two galaxies: a robust detection at (formula presented), and a plausible candidate at (formula presented). The galaxies are discovered in JWST/NIRCam imaging and their distances are inferred with JWST/NIRSpec spectroscopy, all from the JWST Cycle 1 UNCOVER Treasury survey. Detailed stellar population modeling using JWST NIRCam and NIRSpec data corroborates the primeval characteristics of these galaxies: low mass (∼ 108 M☉), young, rapidly-assembling, metal-poor, and star-forming. Interestingly, both galaxies are spatially resolved, having lensing-corrected rest-UV effective radii on the order of 300–400 pc, which are notably larger than other spectroscopically confirmed systems at similar redshifts. The observed dynamic range of z 10 sizes spans over 1 order of magnitude, implying a significant scatter in the size–mass relation at early times. Deep into the epoch of reionization, these discoveries elucidate the emergence of the first galaxies. Copyright © 2023, The Authors. All rights reserved.

关键词： Galaxies

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

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

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

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

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Preface

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2022年 13469 LNAI卷 v-vi页

作者： Bringas, Pablo García García, Hilde Pérez de Pisón, Francisco Javier Martínez Flecha, José Ramón Villar Lora, Alicia Troncoso de la Cal, Enrique A. Herrero, Álvaro Álvarez, Francisco Martínez Psaila, Giuseppe Quintián, Héctor Corchado, Emilio University of Deusto Bilbao Spain University of León León Spain University of La Rioja La Rioja Logroño Spain University of Oviedo Oviedo Spain Data Science and Big Data Analytics Lab Pablo de Olavide University Sevilla Spain Department of Computer Science University of Oviedo Oviedo Spain Applied Computational Intelligence University of Burgos Burgos Burgos Spain Universidad Pablo de Olavide Seville Spain DIGIP University of Bergamo Dalmine Bergamo Italy Department of Industrial Engineering University of A Coruña Ferrol Spain University of Salamanca Salamanca Spain

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Estimating international trade status of countries from global liner shipping networks

arXiv

引用

arXiv 2020年

作者： Xu, Mengqiao Pan, Qian Xia, Haoxiang Masuda, Naoki School of Economics and Management Dalian University of Technology No. 2 Linggong Road Ganjingzi District Dalian City Liaoning Province116024 China Department of Mathematics University at Buffalo BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York BuffaloNY14260-5030 United States

Maritime shipping is a backbone of international trade and thus the world economy. Vessels travel from a port of one country to another on networks of ports to carry cargos, which contribute to countries’ international trade values. We hypothesize that ports that involve transshipment activities serve as a third-party middleman to mediate trade between two foreign countries and contribute to the corresponding country's status in international trade. We test this hypothesis using a port-level data set of global liner shipping services. We propose two indices that quantify the importance of countries in the global liner shipping network and show that they explain a large amount of variation in the international trade value and related measures of individual countries. These results support a long-standing view in maritime economics, which has yet been directly tested, that countries that are strongly integrated into the global maritime transportation network have enhanced access to global markets and trade opportunities. Copyright © 2020, The Authors. All rights reserved.

关键词： International trade

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SI-spreading-based network embedding in static and temporal networks

arXiv

引用

arXiv 2020年

作者： Zhan, Xiu-Xiu Li, Ziyu Masuda, Naoki Holme, Petter Wang, Huijuan Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology Mekelweg 4 Delft2628 CD Netherlands Department of Mathematics University at Buffalo State University of New York Buffalo New YorkNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York Buffalo New YorkNY14260-2900 United States Institute of Innovative Research Tokyo Institute of Technology Yokohama226-8503 Japan

Link prediction can be used to extract missing information, identify spurious interactions as well as forecast network evolution. Network embedding is a methodology to assign coordinates to nodes in a low-dimensional vector space. By embedding nodes into vectors, the link prediction problem can be converted into a similarity comparison task. Nodes with similar embedding vectors are more likely to be connected. Classic network embedding algorithms are random-walk-based. They sample trajectory paths via random walks and generate node pairs from the trajectory paths. The node pair set is further used as the input for a Skip-Gram model, a representative language model that embeds nodes (which are regarded as words) into vectors. In the present study, we propose to replace random walk processes by a spreading process, namely the susceptible-infected (SI) model, to sample paths. Specifically, we propose two SI-spreading-based algorithms, SINE and TSINE, to embed static and temporal networks, respectively. The performance of our algorithms is evaluated by the missing link prediction task in comparison with state-of-the-art static and temporal network embedding algorithms. Results show that SINE and TSINE outperform the baselines across all six empirical datasets. We further find that the performance of SINE is mostly better than TSINE, suggesting that temporal information does not necessarily improve the embedding for missing link prediction. Moreover, we study the effect of the sampling size, quantified as the total length of the trajectory paths, on the performance of the embedding algorithms. The better performance of SINE and TSINE requires a smaller sampling size in comparison with the baseline algorithms. Hence, SI-spreading-based embedding tends to be more applicable to large-scale networks. Copyright © 2020, The Authors. All rights reserved.

关键词： Network embeddings

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