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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

Insights into end-to-end learning scheme for language identification

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arXiv 2018年

作者： Cai, Weicheng Cai, Zexin Liu, Wenbo Wang, Xiaoqi Li, Ming School of Electronics and Information Technology Sun Yat-sen University Guangzhou China Data Science Research Center Duke Kunshan University Kunshan China Department of Electrical and Computer Engineering Carnegie Mellon University Pittsburgh United States Jiangsu Jinling Science and Technology Group Limited

A novel interpretable end-to-end learning scheme for language identification is proposed. It is in line with the classical GMM i-vector methods both theoretically and practically. In the end-to-end pipeline, a general encoding layer is employed on top of the front-end CNN, so that it can encode the variable-length input sequence into an utterance level vector automatically. After comparing with the state-of-the-art GMM i-vector methods, we give insights into CNN, and reveal its role and effect in the whole pipeline. We further introduce a general encoding layer, illustrating the reason why they might be appropriate for language identification. We elaborate on several typical encoding layers, including a temporal average pooling layer, a recurrent encoding layer and a novel learnable dictionary encoding layer. We conducted experiment on NIST LRE07 closed-set task, and the results show that our proposed end-to-end systems achieve state-of-the-art performance. Copyright © 2018, The Authors. All rights reserved.

关键词： Signal encoding

Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2024年第10期21卷 1959页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

Publisher Correction: Reporting guideline for the early-stage clinical evaluation of decision support systems driven by artificial intelligence: DECIDE-AI

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Nature medicine 2022年第10期28卷 2218页

作者： Baptiste Vasey Myura Nagendran Bruce Campbell David A Clifton Gary S Collins Spiros Denaxas Alastair K Denniston Livia Faes Bart Geerts Mudathir Ibrahim Xiaoxuan Liu Bilal A Mateen Piyush Mathur Melissa D McCradden Lauren Morgan Johan Ordish Campbell Rogers Suchi Saria Daniel S W Ting Peter Watkinson Wim Weber Peter Wheatstone Peter McCulloch Nuffield Department of Surgical Sciences University of Oxford Oxford UK. baptiste.vasey@***. Institute of Biomedical Engineering Department of Engineering Science University of Oxford Oxford UK. baptiste.vasey@***. Critical Care Research Group Nuffield Department of Clinical Neurosciences University of Oxford Oxford UK. baptiste.vasey@***. UKRI Centre for Doctoral Training in AI for Healthcare Imperial College London London UK. University of Exeter Medical School Exeter UK. Royal Devon and Exeter Hospital Exeter UK. Institute of Biomedical Engineering Department of Engineering Science University of Oxford Oxford UK. Centre for Statistics in Medicine Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences University of Oxford Oxford UK. Institute of Health Informatics University College London London UK. British Heart Foundation Data Science Centre London UK. Health Data Research UK London UK. UCL Hospitals Biomedical Research Centre London UK. University Hospitals Birmingham NHS Foundation Trust Birmingham UK. Academic Unit of Ophthalmology Institute of Inflammation and Ageing College of Medical and Dental Sciences University of Birmingham Birmingham UK. Moorfields Eye Hospital NHS Foundation Trust London UK. Healthplus.ai-R&D BV Amsterdam The Netherlands. Nuffield Department of Surgical Sciences University of Oxford Oxford UK. Department of Surgery Maimonides Medical Center Brooklyn NY USA. The Wellcome Trust London UK. The Alan Turing Institute London UK. Department of General Anesthesiology Anesthesiology Institute Cleveland Clinic Cleveland OH USA. The Hospital for Sick Children Toronto ON Canada. Dalla Lana School of Public Health University of Toronto Toronto ON Canada. Morgan Human Systems Ltd Shrewsbury UK. Medicines and Healthcare products Regulatory Agency London UK. HeartFlow Inc. Redwood City CA USA. Departments of Computer Science Statistics and Health Policy and Division of Informatics Johns Hopkins Un

Alert classification for the alerce broker system: The real-time stamp classifier

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arXiv 2020年

作者： Carrasco-Davis, Rodrigo Reyes, E. Valenzuela, C. Förster, F. Estévez, P.A. Pignata, G. Bauer, F.E. Reyes, I. Sánchez-Sáez, P. Cabrera-Vives, G. Eyheramendy, S. Catelan, M. Arredondo, J. Castillo-Navarrete, E. Rodríguez-Mancini, D. Ruz-Mieres, D. Moya, A. Sabatini-Gacitúa, L. Sepúlveda-Cobo, C. Mahabal, A.A. Silva-Farfán, J. Camacho-Iñiguez, E. Galbany, L. Nuncio Monseñor Sótero Sanz 100 Providencia Santiago Chile Department of Electrical Engineering Universidad de Chile Av. Tupper 2007 Santiago8320000 Chile Center for Mathematical Modeling Universidad de Chile Beauchef 851 North building 7th floor Santiago8320000 Chile Faculty of Engineering and Sciences Universidad Adolfo Ibañez Diagonal Las Torres 2700 Peñalolén Santiago Chile Data Observatory Santiago Chile Departamento de Astronomía Universidad de Chile Casilla 36D Santiago Chile Departamento de Ciencias Físicas Universidad Andres Bello Av. Republica 230 Santiago8370146 Chile Instituto de Astrofísica and Centro de Astroingeniería Facultad de Física Pontificia Universidad Católica de Chile Casilla 306 Santiago 22 Chile Space Science Institute 4750 Walnut Street Suite 205 BoulderCO80301 United States Inria Chile Research Center Av. Apoquindo 2827 Las Condes Chile Department of Computer Science Universidad de Concepción Edmundo Larenas 219 Concepción Chile Institute of Astronomy University of Cambridge Madingley Road CambridgeCB3 0HA United Kingdom Cahill Center for Astrophysics California Institute of Technology 1200 E. California Boulevard PasadenaCA91125 United States Center for Data Driven Discovery California Institute of Technology PasadenaCA91125 United States Departamento de Física Teórica y del Cosmos Universidad de Granada GranadaE-18071 Spain

We present a real-time stamp classifier of astronomical events for the ALeRCE (Automatic Learning for the Rapid Classification of Events) broker. The classifier is based on a convolutional neural network, trained on alerts ingested from the Zwicky Transient Facility (ZTF). Using only the science, reference and difference images of the first detection as inputs, along with the metadata of the alert as features, the classifier is able to correctly classify alerts from active galactic nuclei, supernovae (SNe), variable stars, asteroids and bogus classes, with high accuracy (∼94%) in a balanced test set. In order to find and analyze SN candidates selected by our classifier from the ZTF alert stream, we designed and deployed a visualization tool called SN Hunter, where relevant information about each possible SN is displayed for the experts to choose among candidates to report to the Transient Name Server database. From June 26th 2019 to February 28th 2021, we have reported 6846 SN candidates to date (11.8 candidates per day on average), of which 971 have been confirmed spectroscopically. Our ability to report objects using only a single detection means that 70% of the reported SNe occurred within one day after the first detection. ALeRCE has only reported candidates not otherwise detected or selected by other groups, therefore adding new early transients to the bulk of objects available for early follow-up. Our work represents an important milestone toward rapid alert classifications with the next generation of large etendue telescopes, such as the Vera C. Rubin Observatory. Copyright © 2020, The Authors. All rights reserved.

关键词： Supernovae

Author Correction: Inferring structural variant cancer cell fraction

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Nature communications 2022年第1期13卷 7568页

作者： Marek Cmero Ke Yuan Cheng Soon Ong Jan Schröder Niall M Corcoran Tony Papenfuss Christopher M Hovens Florian Markowetz Geoff Macintyre Department of Surgery Division of Urology Royal Melbourne Hospital and University of Melbourne Parkville VIC 3050 Australia. cmerom@unimelb.edu.au. The Epworth Prostate Centre Epworth Hospital Richmond VIC 3121 Australia. cmerom@unimelb.edu.au. Department of Computing and Information Systems University of Melbourne Parkville VIC 3010 Australia. cmerom@unimelb.edu.au. Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia. cmerom@unimelb.edu.au. Murdoch Children's Research Institute Parkville VIC 3052 Australia. cmerom@unimelb.edu.au. School of Computing Science University of Glasgow Sir Alwyn Williams Building Glasgow G12 8RZ UK. Cancer Research UK Cambridge Institute University of Cambridge Cambridge CB2 0RE UK. Electrical and Electronic Engineering University of Melbourne Parkville VIC 3010 Australia. Machine Learning Research Group Data61 Canberra ACT 2601 Australia. Research School of Computer Science Australian National University Canberra ACT 2601 Australia. Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia. Department of Surgery Division of Urology Royal Melbourne Hospital and University of Melbourne Parkville VIC 3050 Australia. The Epworth Prostate Centre Epworth Hospital Richmond VIC 3121 Australia. Department of Computing and Information Systems University of Melbourne Parkville VIC 3010 Australia. geoff.macintyre@cruk.cam.ac.uk. Cancer Research UK Cambridge Institute University of Cambridge Cambridge CB2 0RE UK. geoff.macintyre@cruk.cam.ac.uk.

Layerwise perturbation-based adversarial training for hard drive health degree prediction

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arXiv 2018年

作者： Zhang, Jianguo Wang, Ji He, Lifang Li, Zhao Yu, Philip S. Department of Computer Science University of Illinois at Chicago ChicagoIL United States College of Systems Engineering National University of Defense Technology Changsha Hunan China Weill Cornell Department of Healthcare Policy & Research Cornell University NY United States Alibaba Group Hangzhou Zhejiang China Shanghai Institute for Advanced Communication and Data Science Shanghai Key Laboratory of Data Science Fudan University Shanghai China

With the development of cloud computing and big data, the reliability of data storage systems becomes increasingly important. Previous researchers have shown that machine learning algorithms based on SMART attributes are effective methods to predict hard drive failures. In this paper, we use SMART attributes to predict hard drive health degrees which are helpful for taking different fault tolerant actions in advance. Given the highly imbalanced SMART datasets, it is a nontrivial work to predict the health degree precisely. The proposed model would encounter overfitting and biased fitting problems if it is trained by the traditional methods. In order to resolve this problem, we propose two strategies to better utilize imbalanced data and improve performance. Firstly, we design a layerwise perturbation-based adversarial training method which can add perturbations to any layers of a neural network to improve the generalization of the network. Secondly, we extend the training method to the semi-supervised settings. Then, it is possible to utilize unlabeled data that have a potential of failure to further improve the performance of the model. Our extensive experiments on two real-world hard drive datasets demonstrate the superiority of the proposed schemes for both supervised and semi-supervised classification. The model trained by the proposed method can correctly predict the hard drive health status 5 and 15 days in advance. Finally, we verify the generality of the proposed training method in other similar anomaly detection tasks where the dataset is imbalanced. The results argue that the proposed methods are applicable to other domains. Copyright © 2018, The Authors. All rights reserved.

关键词： Forecasting

Case study: Approximations of the bessel function

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arXiv 2017年

作者： Karachalios, D.S. Gosea, I.V. Zhang, Q. Antoulas, A.C. Data-Driven System Reduction and Identification Group Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg Germany Department of Electrical and Computer Engineering Rice University Houston United States

The purpose of this note is to compare various approximation methods as applied to the inverse of the Bessel function of the first kind J01(s), in a given domain of the complex plane.30E10, 03C40, 65E99 Copyright ... 详细信息

关键词： Bessel functions

Scholarly Influence of the Conference and Labs of the Evaluation Forum eHealth Initiative: Review and Bibliometric Study of the 2012 to 2017 Outcomes

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JMIR research Protocols 2018年第7期7卷 e10961页

作者： Suominen, Hanna Kelly, Liadh Goeuriot, Lorraine Research School of Computer Science College of Engineering and Computer Science The Australian National University Canberra ACT Australia Machine Learning Research Group Data61 Commonwealth Scientific and Industrial Research Organisation Canberra ACT Australia Faculty of Science and Technology University of Canberra Canberra ACT Australia Department of Future Technologies Faculty of Science and Engineering University of Turku Turku Finland Department of Computer Science Maynooth University Maynooth Co Kildare Ireland Grenoble Informatics Laboratory Université Grenoble Alpes Grenoble France

Background: The eHealth initiative of the Conference and Labs of the Evaluation Forum (CLEF) has aimed since 2012 to provide researchers working on health text analytics with annual workshops, shared development challenges and tasks, benchmark datasets, and software for processing and evaluation. In 2012, it ran as a scientific workshop with the aim of establishing an evaluation lab, and since 2013, this annual workshop has been supplemented with 3 or more preceding labs each year. An evaluation lab is an activity where the participating individuals or teams’ goal is to solve the same problem, typically using the same dataset in a given time frame. The overall purpose of this initiative is to support patients, their next of kin, clinical staff, health scientists, and health care policy makers in accessing, understanding, using, and authoring health information in a multilingual setting. In the CLEF eHealth 2013 to 2017 installations, the aim was to address patient-centric text processing. From 2015, the scope was also extended to aid both patients’ understanding and clinicians’ authoring of various types of medical content. CLEF eHealth 2017 introduced a new pilot task on technology-assisted reviews (TARs) in empirical medicine in order to support health scientists and health care policymakers’ information access. Objectives: This original research paper reports on the outcomes of the first 6 installations of CLEF eHealth from 2012 to 2017. The focus is on measuring and analyzing the scholarly influence by reviewing CLEF eHealth papers and their citations. Methods: A review and bibliometric study of the CLEF eHealth proceedings, working notes, and author-declared paper extensions were conducted. Citation content analysis was used for the publications and their citations collected from Google Scholar. Results: As many as 718 teams registered their interest in the tasks, leading to 130 teams submitting to the 15 tasks. A total of 184 papers using CLEF eHealth data gen

关键词： Evaluation studies as topic Health records Information extraction Information storage and retrieval Information visualization Patient education as topic Speech recognition Systematic reviews Test-set generation Text classification