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arXiv 2021年

作者： Lee, Benjamin D. Gitter, Anthony Greene, Casey S. Raschka, Sebastian Maguire, Finlay Titus, Alexander J. Kessler, Michael D. Lee, Alexandra J. Chevrette, Marc G. Stewart, Paul Allen Britto-Borges, Thiago Cofer, Evan M. Yu, Kun-Hsing Carmona, Juan Jose Fertig, Elana J. Kalinin, Alexandr A. Signal, Beth Lengerich, Benjamin J. Triche, Timothy J. Boca, Simina M. In-Q-Tel Labs School of Engineering and Applied Sciences Harvard University Department of Genetics Harvard Medical School United States Department of Biostatistics and Medical Informatics University of Wisconsin-Madison MadisonWI United States Morgridge Institute for Research MadisonWI United States Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine AuroraCO United States Center for Health AI University of Colorado School of Medicine AuroraCO United States Department of Statistics University of Wisconsin Madison United States Faculty of Computer Science Dalhousie University Canada University of New Hampshire Bioeconomy.XYZ United States Department of Oncology Johns Hopkins University United States Institute for Genome Sciences University of Maryland School of Medicine United States Genomics and Computational Biology Graduate Program University of Pennsylvania United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania United States Wisconsin Institute for Discovery Department of Plant Pathology University of Wisconsin-Madison United States Department of Biostatistics and Bioinformatics Moffitt Cancer Center TampaFL United States Section of Bioinformatics and Systems Cardiology Klaus Tschira Institute for Integrative Computational Cardiology University Hospital Heidelberg Germany University Hospital Heidelberg Germany Lewis-Sigler Institute for Integrative Genomics Princeton University PrincetonNJ United States Graduate Program in Quantitative and Computational Biology Princeton University PrincetonNJ United States Department of Biomedical Informatics Harvard Medical School United States Department of Pathology Brigham and Women's Hospital United States Philips Healthcare CambridgeMA United States Philips Research

Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others. © 2021, CC BY.

关键词： Learning algorithms

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Prediction of sleep quality scores using dynamic functional network connectivity of young adults: A reproducibility analysis

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Alzheimer's & Dementia 2023年第S3期19卷

作者： Mohammad S.E. Sendi Hossein Dini Elaheh Zendehrouh David H Salat Vince D Calhoun School of Electrical and Computer Engineering (ECE) at the Georgia Institute of Technology Atlanta GA USA Tri-Institutional Georgia State University/Georgia Institute of Technology/Emory University Center for Translational Research in Neuroimaging and Data Science Atlanta GA USA Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Tech Atlanta GA USA Aalborg University Copenhagen Denmark Georgia State University Atlanta GA USA Neuroimaging Research for Veterans Center VA Boston Healthcare System Jamaica Plain MA USA Massachusetts General Hospital Charlestown MA USA Harvard Medical School Boston MA USA Athinoula A. Martinos Center for Biomedical Imaging Charlestown MA USA

Background Dynamic functional network connectivity (dFNC) estimated from resting-state functional magnetic resonance imaging (rs-fMRI) is a potentially powerful approach to investigate human behavior and cognition. However, previous studies barely investigate the reproducibility of dFNC features links with cognition. This study aims to examine whether the data collected in four different sessions reproduce the same results using the sleep scores by applying a dFNC method to resting-state fMRI (rs-fMRI) data from the Human Connectome Project (HCP) Young Adult. Method We used the Pittsburgh Sleep Quality Index (PSQI) scores and four sessions of rs-fMRI (15 minutes each) from 833 young adults (age between 22 to 37yrs). We calculated the dFNC for each participant using a fully automated Neuromark independent component analysis and a sliding window technique to estimate dFNCs. A k-means clustering approach partitioned dFNCs into two group-level distinct states and subject-level state vectors. Next, we estimated dFNC features from each individual’s state vector and dFNCs. Finally, we trained a 10-fold support vector regression model to predict the sleep scores based on the dFNC features. We applied all the procedures mentioned above to all four sessions separately. Result We found dFNC features can successfully predict each participant’s night sleep time. The correlation between the actual score and the predicted one was R = 0.0853 (p = 0.0182) for session1, R = 0.0696 (p = 0.0485) for session2, R = 0.0764 (p = 0.0393) for session2, and r = 0.0788 (p = 0.0285) for session4. The dFNC features for none of four sessions could predict other sleep scores. Conclusion We showed that the dFNC feature could predict the amount of sleep during the night in the HCP Young Adult population. Additionally, we showed the prediction result replicates across all four rs-fMRI sessions. Future studies are needed to explore the reproducibility of the result within the age range of the HCP data

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Cadmium exposure induces histological damage and cytotoxicity in the cardiovascular system of mice

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Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association 2023年 175卷 113740页

作者： Shing-Hsien Chou Hung-Chen Lin Shao-Wei Chen Yu-Ting Tai Shih-Ming Jung Fu-Hsiang Ko Jong-Hwei Su Pang Pao-Hsien Chu Department of Cardiology Chang Gung Memorial Hospital Linkou Taoyuan Taiwan Graduate Institute of Clinical Medical Sciences College of Medicine Chang Gung University Taoyuan Taiwan. Department of Cardiology The University of Hong Kong-Shenzhen Hospital Shenzhen China. Division of Thoracic and Cardiovascular Surgery Chang Gung Memorial Hospital Linkou Taoyuan Taiwan Center for Big Data Analytics and Statistics Chang Gung Memorial Hospital Linkou Taoyuan Taiwan. Department of Materials Science and Engineering National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Pathology Chang Gung Memorial Hospital Chang Gung University College of Medicine Taoyuan Taiwan. College of Medicine Chang Gung University Taoyuan Taiwan Institute of Stem Cell and Translational Cancer Research Chang Gung Memorial Hospital Linkou Taiwan. Electronic address: pchu@cgmh.org.tw.

Epidemiological studies have reported an association between chronic cadmium (Cd) exposure and increased cardiovascular risk; however, their causal relationship remains unclear. The aim of this study is to explore the effects of Cd exposure on the cardiac and arterial systems in mice. According to the concentration of cadmium chloride in drinking water, male mice were randomly divided into control and low-dose and high-dose Cd exposure groups. The intervention duration was 12 weeks. In cardiac tissues, Cd exposure led to focal necrosis, myofibril disarray, perivascular and interstitial fibrosis, and disorganized sarcomere structures. Cd also induced the apoptosis of cardiomyocytes and increased the expression levels of matrix metalloproteinase (MMP)-2 and MMP-14 in cardiac tissues. In the arterial tissues, Cd exposure damaged the intimal and medial layers of the aorta. Cd further reduced the viability of aortic smooth muscle cells in vitro. This study provides evidence for the Cd-induced damage of the cardiovascular system, which may contribute to various cardiovascular diseases.

关键词： Cadmium Cardiovascular Matrix metalloproteinase (MMP) Mice Myocardium Smooth muscle cell

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Corrigendum to "Dissemination in time and space in presymptomatic granulin mutation carriers: A spatial chronnectome study" [Neurobiology of Aging Volume 108, December 2021, Pages 155-167]

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Neurobiology of aging 2022年 119卷 140-144页

作者： Enrico Premi Marcello Giunta Armin Iraji Srinivas Rachakonda VinceD Calhoun Stefano Gazzina Alberto Benussi Roberto Gasparotti Silvana Archetti Martina Bocchetta Dave Cash Emily Todd Georgia Peakman Rhian Convery John C van Swieten Lize Jiskoot Raquel Sanchez-Valle Fermin Moreno Robert Laforce Caroline Graff Matthis Synofzik Daniela Galimberti JamesB Rowe Mario Masellis Carmela Tartaglia Elizabeth Finger Rik Vandenberghe Alexandre de Mendonça Fabrizio Tagliavini Chris R Butler Isabel Santana Alexander Gerhard Isabelle Le Ber Florence Pasquier Simon Ducharme Johannes Levin Adrian Danek Sandro Sorbi Markus Otto Jonathan D Rohrer Barbara Borroni Stroke Unit Azienda Socio Sanitaria Territoriale Spedali Civili Brescia Brescia Italy. Centre for Neurodegenerative Disorders Department of Clinical and Experimental Sciences University of Brescia Brescia Italy. Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University Georgia Institute of Technology Emory University Atlanta GA USA. Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University Georgia Institute of Technology Emory University Atlanta GA USA Departments of Psychology and Computer Science Georgia State University Atlanta GA USA Department of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA USA. Neurophysiology Unit Azienda Socio Sanitaria Territoriale Spedali Civili Brescia Brescia Italy. Neuroradiology Unit University of Brescia Brescia Italy. Laboratory Unit Azienda Socio Sanitaria Territoriale Spedali Civili Brescia Brescia Italy. Department of Neurodegenerative Disease Dementia Research Centre UCL Institute of Neurology Queen Square London UK. Department of Neurology Erasmus Medical Centre Rotterdam the Netherlands. Alzheimer's disease and Other Cognitive Disorders Unit Neurology Service Hospital Clinic University of Barcelona Barcelona Spain. Cognitive Disorders Unit Department of Neurology Donostia University Hospital San Sebastian Gipuzkoa Spain. Clinique Interdisciplinaire de Memoire Department des Sciences Neurologiques CHU de Quebec and Faculte de Medecine Universite Laval Quebec Canada. Center for Alzheimer Research Division of Neurogeriatrics Department of Neurobiology Care Sciences and Society Bioclinicum Karolinska Institutet Solna Sweden. Department of Neurodegenerative Diseases Hertie-Institute for Clinical Brain Research and Center of Neurology University of Tubingen Tubingen Germany. Fondazione Ca' Granda IRCCS Ospedale Policlinico Milan Italy University of Milan

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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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Author Correction: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

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Nature methods 2025年第2期22卷 448页

作者： Marieke Vromman Jasper Anckaert Stefania Bortoluzzi Alessia Buratin Chia-Ying Chen Qinjie Chu Trees-Juen Chuang Roozbeh Dehghannasiri Christoph Dieterich Xin Dong Paul Flicek Enrico Gaffo Wanjun Gu Chunjiang He Steve Hoffmann Osagie Izuogu Michael S Jackson Tobias Jakobi Eric C Lai Justine Nuytens Julia Salzman Mauro Santibanez-Koref Peter Stadler Olivier Thas Eveline Vanden Eynde Kimberly Verniers Guoxia Wen Jakub Westholm Li Yang Chu-Yu Ye Nurten Yigit Guo-Hua Yuan Jinyang Zhang Fangqing Zhao Jo Vandesompele Pieter-Jan Volders OncoRNALab Cancer Research Institute Ghent (CRIG) Department of Biomolecular Medicine Ghent University Ghent Belgium. Department of Molecular Medicine University of Padova Padova Italy. Genomics Research Center Academia Sinica Taipei City Taiwan. Institute of Crop Science and Institute of Bioinformatics Zhejiang University Zhejiang China. Department of Biomedical Data Science and of Biochemistry Stanford University Stanford CA USA. Klaus Tschira Institute for Integrative Computational Cardiology Department of Internal Medicine III University Hospital Heidelberg German Center for Cardiovascular Research (DZHK) Heidelberg Germany. School of Basic Medical Science Department of Medical Genetics Wuhan University Wuhan China. EMBL-EBI Hinxton UK. Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine School of Artificial Intelligence and Information Technology Nanjing University of Chinese Medicine Nanjing China. Computational Biology Group Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Jena Germany. Biosciences Institute Faculty of Medical Sciences Newcastle University Newcastle UK. Translational Cardiovascular Research Center University of Arizona - College of Medicine Phoenix Phoenix AZ USA. Sloan Kettering Institute New York NY USA. Bioinformatics Group Department of Computer Science and Interdisciplinary Center for Bioinformatics Universität Leipzig Leipzig Germany. Data Science Institute I-Biostat Hasselt University Hasselt Belgium. State Key Laboratory of Bioelectronics School of Biological Sciences and Medical Engineering Southeast University Nanjing China. Department of Biochemistry and Biophysics National Bioinformatics Infrastructure Sweden Science for Life Laboratory Stockholm University Stockholm Sweden. Center for Molecular Medicine Children's Hospital Fudan University and Shanghai Key Laboratory of Medical Epigenetics International Laboratory of Medical Epigenetics and Metab

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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

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Genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)GmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been *** optimal performance,they require the fragment ion spectra of targeted peptides as prior *** this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue *** build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on *** then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer *** extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)***,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was *** a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control *** expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by *** data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker *** is freely accessible at https://***/page/***?id=IPX0001400000.

关键词： data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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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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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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