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arXiv 2020年

作者： Kavur, A. Emre Gezer, N. Sinem Barış, Mustafa Conze, Pierre-Henri Groza, Vladimir Pham, Duc Duy Chatterjee, Soumick Ernst, Philipp Özkan, Savaş Baydar, Bora Lachinov, Dmitry Han, Shuo Pauli, Josef Isensee, Fabian Perkonigg, Matthias Sathish, Rachana Rajan, Ronnie Aslan, Sinem Sheet, Debdoot Dovletov, Gurbandurdy Speck, Oliver Nürnberger, Andreas Maier-Hein, Klaus H. Akar, Gözde Bozdagı Ünal, Gözde Dicle, Oguz Selver, M. Alper Graduate School of Natural and Applied Sciences Dokuz Eylul University Izmir Turkey Department of Radiology Faculty Of Medicine Dokuz Eylul University Izmir Turkey Dept. of Ophthalmology and Optometry Medical Uni. of Vienna Austria Intelligent Systems Faculty of Engineering University of Duisburg-Essen Germany Division of Medical Image Computing German Cancer Research Center Heidelberg Germany CIR Lab Dept of Biomedical Imaging and Image-guided Therapy Medical Uni. of Vienna Austria IMT Atlantique LaTIM UMR 1101 Brest France Department of Electrical and Electronics Engineering Middle East Technical University Ankara Turkey Department of Electrical Engineering Indian Institute of Technology Kharagpur India School of Medical Science and Technology Indian Institute of Technology Kharagpur India Ca’ Foscari University of Venice ECLT DAIS Venice Italy Ege University International Computer Institute Izmir Turkey Johns Hopkins University Baltimore United States Data and Knowledge Engineering Group Otto von Guericke University Magdeburg Germany Magnetic Resonance Otto von Guericke University Magdeburg Germany Median Technologies Valbonne France Department of Computer Engineering Istanbul Technical University Istanbul Turkey Department of Electrical and Electronics Engineering Dokuz Eylul University Izmir Turkey

—Segmentation of abdominal organs has been a comprehensive, yet unresolved, research field for many years. In the last decade, intensive developments in deep learning (DL) have introduced new state-of-the-art segmentation systems. Despite outperforming the overall accuracy of existing systems, the effects of DL model properties and parameters on the performance is hard to interpret. This makes comparative analysis a necessary tool to achieve explainable studies and systems. Moreover, the performance of DL for emerging learning approaches such as cross-modality and multi-modal tasks have been rarely discussed. In order to expand the knowledge in these topics, CHAOS – Combined (CT-MR) Healthy Abdominal Organ Segmentation challenge has been organized in the IEEE International Symposium on Biomedical Imaging (ISBI), 2019, in Venice, Italy. Despite a large number of the previous abdomen related challenges, the majority of which are focused on tumor/lesion detection and/or classification with a single modality, CHAOS providesboth abdominal CT and MR data from healthy subjects. Five different and complementary tasks have been designed to analyze the capabilities of the current approaches from multiple perspectives. The results are investigated thoroughly, compared with manual annotations and interactive methods. The outcomes are reported in detail to reflect the latest advancements in the field. CHAOS challenge and data will be available online to provide a continuous benchmark resource for segmentation. Copyright © 2020, The Authors. All rights reserved.

关键词： Medical imaging

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s-LWSR: Super lightweight super-resolution network

arXiv

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arXiv 2019年

作者： Li, Biao Liu, Jiabin Wang, Bo Qi, Zhiquan Shi, Yong School of Economics and Management University of Chinese Academy of Sciences Beijing101408 China Research Center on Fictitious Economy and Data Science Chinese Academy of Sciences Beijing100190 China Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing100190 China School of Information Technology and Management University of International Business and Economics Beijing100029 China Department of Computer Science and Engineering Texas A&M University College StationTX77843 United States College of Information Science and Technology University of Nebraska OmahaNE68182 United States

Deep learning (DL) architectures for super-resolution (SR) normally contain tremendous parameters, which has been regarded as the crucial advantage for obtaining satisfying performance. However, with the widespread use of mobile phones for taking and retouching photos, this character greatly hampers the deployment of DL-SR models on the mobile devices. To address this problem, in this paper, we propose a super lightweight SR network: s-LWSR. There are mainly three contributions in our work. Firstly, in order to efficiently abstract features from the low resolution image, we build an information pool to mix multi-level information from the first half part of the pipeline. Accordingly, the information pool feeds the second half part with the combination of hierarchical features from the previous layers. Secondly, we employ a compression module to further decrease the size of parameters. Intensive analysis confirms its capacity of trade-off between model complexity and accuracy. Thirdly, by revealing the specific role of activation in deep models, we remove several activation layers in our SR model to retain more information for performance improvement. Extensive experiments show that our s-LWSR, with limited parameters and operations, can achieve similar performance to other cumbersome DL-SR methods. Copyright © 2019, The Authors. All rights reserved.

关键词： Chemical activation

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Mindestinformationsstandards in der Chemie: Ein Appell zum besseren Umgang mit Forschungsdaten

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Angewandte Chemie 2022年第51期134卷

作者： Prof. Dr. Sonja Herres-Pawlis Dr. Felix Bach Dr. Ian J. Bruno Dr. Stuart J. Chalk Dr. Nicole Jung Dr. Johannes C. Liermann Leah R. McEwen Dr. Steffen Neumann Prof. Dr. Christoph Steinbeck Matthias Razum Dr. Oliver Koepler Institut für Anorganische Chemie RWTH Aachen University Landoltweg 1A 52074 Aachen Deutschland E-Research FIZ Karlsruhe – Leibniz Institute for Information Infrastructure Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK Department of Chemistry University of North Florida 1 UNF Drive Jacksonville FL 32224 USA Institute of Biological and Chemical Systems (IBCS) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland Johannes Gutenberg University Mainz Department of Chemistry Duesbergweg 10–14 55128 Mainz Deutschland Cornell University Library 293 Clark Hall Ithaca NY 14853-2501 USA Bioinformatics and Scientific Data Leibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle Deutschland Institute for Inorganic and Analytical Chemistry Friedrich-Schiller-University Jena Lessingstr. 1 07743 Jena Deutschland Lab Linked Scientific Knowledge TIB – Leibniz Information Centre for Science and Technology Welfengarten 1B 30173 Hannover Deutschland

Forschungsdatenmanagement (FDM) ist erforderlich, um wissenschaftlichen Fortschritt und das Sammeln von Daten zu fördern. Viele Fördergeldgeber verlangen FDM, da Forschung oft durch Steuergelder finanziert wird und daraus resultierende Daten nachhaltig für kommende Generationen hinterlegt werden sollten. In heutigen Laboren sind Papier-Laborbücher allerdings noch immer gängige Praxis, und die Forschungsdaten werden oft in proprietären Dateiformaten ohne experimentellen Kontext gespeichert. Daten müssen über eine Rolle als bloßes Anhängsel von Publikationen hinauswachsen. Elektronische Laborbücher (ELN) und Laborinformationsmanagementsysteme (LIMS) ermöglichen es, Daten besser zu verwalten sowie Forschung und Veröffentlichung zu vereinfachen. Die in gutes FDM investierte Zeit zahlt sich später in vielerlei Hinsicht aus. Daher werden Mindestinformationsstandards (MI) für die Handhabung von Daten benötigt. Die Digitalisierung hält gerade Einzug in die Lehrpläne, sodass zukünftige Generationen von ChemikerInnen mit FDM und ELN-Nutzung vertraut sein werden.

关键词： Datenpublikation Elektronische Laborbücher Forschungsdatenmanagement Mindestinformation Repositorien

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SPA-SSD: Exploit Heterogeneity and Parallelism of 3D SLC-TLC Hybrid SSD to Improve Write Performance

SPA-SSD: Exploit Heterogeneity and Parallelism of 3D SLC-TLC...

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IEEE International Conference on Computer Design: VLSI in Computers and Processors, (ICCD)

作者： Wenhui Zhang Qiang Cao Hong Jiang Jie Yao Yuanyuan Dong Puyuan Yang Wuhan National Laboratory for Optoelectronics Key Laboratory of Information Storage System Engineering Research Center of Data Storage Systems and Technology Ministry of Education of China Huazhong University of Science and Technology Wuhan China Department of Computer Science and Engineering University of Texas at Arlington Arlington Texas School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China Alibaba Group. Hangzhou China

To address the write performance problem suffered by MLC/TLC flash, researchers have proposed hybrid SSD that aims to combine the strengths of SLC flash, used as the write-buffer zone for its superior write performance, and MLC/TLC flash, as the capacity zone for its high storage density. While leveraging SLC as a physical write-buffer zone is proven effective in traditional 2D hybrid SSDs, how to effectively incorporate SLC into a 3D-stacked TLC to form a hybrid SSD has not been studied to the best of our knowledge. Yet this is a timely and important performance issue for 3D-stacked TLC given its one-shot programming scheme that results in much worse write performance than the programming scheme in 2D TLC where pages are associated with different bits of a cell and programmed in sequence separately. We believe that naively adopting the two-physical-zone approach to 3D hybrid SSD will miss a great opportunity for performance optimization because it ignores the inherent four-level parallelism (channel/chip/die/plane) of the flash chip array. To this end, we propose in this paper an SLC and Parallelism Aware hybrid SSD (SPA-SSD) to take full advantages of SLC's superior write performance, the internal multi-level parallelism of SSD, and the high storage density of 3D-stacked TLC flash. Two novel techniques enable SPA-SSD to be highly effective: (1) Type-Parallelism Joint Page Allocation (TPJ-PA), which allocates pages for write transactions according to not only available SLC pages but also parallelism to maximize resource utilization within the hybrid SSD, and (2) Queue-length and Parallelism Constrained data Migration (QPC-DM), which triggers data migration without degrading user write performance by analyzing the device queue length and available flash resources. To evaluate performance of SPA-SSD, a hybrid SSD simulator, called HybridSim, is developed based on MQSim. Experimental results on HybridSim show that TPJ-PA improves write throughput by 60%, while QPC-DM

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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 2023年第6期20卷 824-835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

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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INTRODUCTION

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Bulletin of the American Meteorological Society 2024年第8期105卷 S1-S11页

作者： Boyer, T. Blunden, J. Dunn, R.J.H. NOAA/NESDIS National Centers for Environmental Information Silver Spring Maryland NOAA/NESDIS National Centers for Environmental Information Asheville North Carolina Met Office Hadley Centre Exeter United Kingdom European Centre for Medium-Range Weather Forecasts Reading United Kingdom University of Maryland College Park Maryland Scripps Institution of Oceanography University of California San Diego La Jolla California NOAA/NWS National Centers for Environmental Prediction Climate Prediction Center College Park Maryland Brandenburg University of Technology (BTU) Cottbus-Senftenberg Germany Servicio Meteorológico Nacional Buenos Aires Argentina NOAA/OAR Physical Sciences Laboratory Boulder Colorado European Centre for Medium-Range Weather Forecasts Bonn Germany Center for Geophysical Research and School of Physics University of Costa Rica San José Costa Rica Department of Meteorology and National Centre for Earth Observation University of Reading Reading United Kingdom Centro Nacional de Monitoramento e Alertas de Desastres Naturais CEMADEN São Paulo Brazil Université Grenoble Alpes Institut des Géosciences de l’Environnement IRD CNRS Grenoble INP Grenoble France Hampton University Hampton Virginia Seychelles Meteorological Authority Mahe Seychelles Section for Glaciers Ice and Snow Norwegian Water Resources and Energy Directorate Oslo Norway National Research Institute for Agriculture Food and Environment (INRAE) CARRTEL Université Savoie Mont Blanc Thonon les Bains France Graduate School of Agriculture Osaka Metropolitan University Sakai Japan Science Faculty Universidad Nacional de Colombia Bogotá Colombia University of Bremen Bremen Germany NOAA Global Monitoring Laboratory Boulder Colorado Servicio Nacional de Meteorología e Hidrología del Perú Lima Perú Centro de Investigaciones sobre Desertificación – Spanish National Research Council (CSIC-UV-GVA) Valencia Spain Hydro-Climate Extremes Lab (H-CEL) Ghent University Ghent Belgium Department o

In 2023, La Niña conditions that generally prevailed in the eastern Pacific Ocean from mid-2020 into early 2023 gave way to a strong El Niño by October. Atmospheric concentrations of Earth’s major greenhouse gases—carbon dioxide, methane, and nitrous oxide—all increased to record-high levels. The annual global average carbon dioxide concentration in the atmosphere rose to 419.3±0.1 ppm, which is 50% greater than the pre-industrial level. The growth from 2022 to 2023 was 2.8 ppm, the fourth highest in the record since the 1960s. The combined short-term effects of El Niño and the long-term effects of increasing levels of heat-trapping gases in the atmosphere contributed to new records for many essential climate variables reported here. The annual global temperature across land and oceans was the highest in records dating as far back as 1850, with the last seven months (June–December) having each been record warm. Over land, the globally averaged temperature was also record high. Dozens of countries reported record or near-record warmth for the year, including China and continental Europe as a whole (warmest on record), India and Russia (second warmest), and Canada (third warmest). Intense and widespread heatwaves were reported around the world. In Vietnam, an all-time national maximum temperature record of 44.2°C was observed at Tuong Duong on 7 May, surpassing the previous record of 43.4°C at Huong Khe on 20 April 2019. In Brazil, the air temperature reached 44.8°C in Araçuaí in Minas Gerais on 20 November, potentially a new national record and 12.8°C above normal. The effect of rising temperatures was apparent in the cryosphere, where snow cover extent by June 2023 was the smallest in the 56-year record for North America and seventh smallest for the Northern Hemisphere overall. Heatwaves contributed to the greatest average mass balance loss for Alpine glaciers around the world since the start of the record in 1970. Due to rapid volume loss beginning in 2021, St. A

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SEED: Entity oriented information search and exploration 22

SEED: Entity oriented information search and exploration

引用

22nd International Conference on Intelligent User Interfaces, IUI 2017

作者： Chen, Jun Jacucci, Giulio Chen, Yueguo Ruotsalo, Tuukka School of Information Renmin University of China China Key Laboratory of Data Engineering and Knowledge Engineering MOE China Helsinki Institute for Information Technology HIIT Department of Computer Science University of Helsinki Finland

ISBN: (纸本)9781450348935

Entity search and exploration can enrich search user interfaces by presenting relevant information instantly and offering relevant exploration pointers to users. Previous research has demonstrated that large knowledge Graphs allow exploitation and recommendation of explicit links between the entities and other information to improve information access and ranking. However, less attention has been devoted to user interfaces for effectively presenting results, recommending related entities and explaining relations between entities. We introduce a system called SEED which is designed to support entity search and exploration in large knowledge Graphs. We demonstrate SEED using a dataset of hundreds of thousands of movie related entities from the DBpedia knowledge Graph. The system utilizes a graph embedding model for ranking entities and their relations, recommending related entities, and explaining their interrelations. Copyright is held by the author/owner(s).

关键词： knowledge graph

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Publisher Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

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Nature genetics 2023年第1期55卷 166页

作者： Huipeng Li Elise T Courtois Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Paul Jongjoon Choi Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Paul Robson Shyam Prabhakar Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. Department of Computer Science and Engineering and Center for Computational Biology Indraprastha Institute of Information Technology Delhi India. Synthetic Biology Genome Institute of Singapore Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. Department of Pathology Singapore General Hospital Singapore Singapore. Department of Colorectal Surgery Singapore General Hospital Singapore Singapore. Data Analytics Department Institute for Infocomm Research Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. paul.robson@***. The Jackson Laboratory for Genomic Medicine Farmington Connecticut USA. paul.robson@***. Department of Genetics and Genome Sciences Institute for Systems Genomics University of Connecticut Farmington Connecticut USA. paul.robson@***. Department of Biological Sciences National University of Singapore Singapore Singapore. paul.robson@***. Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. prabhakars@gis.a-star.edu.sg.

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Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

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Nature communications 2023年第1期14卷 6540页

作者： Hitomi Takada Yohei Sasagawa Mika Yoshimura Kaori Tanaka Yoshimi Iwayama Tetsutaro Hayashi Ayako Isomura-Matoba Itoshi Nikaido Akira Kurisaki Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. itoshi.nikaido@riken.jp. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. itoshi.nikaido@riken.jp. Master's/Doctoral Program in Life Science Innovation (Bioinformatics) Degree Programs in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Tsukuba Ibaraki Japan. itoshi.nikaido@riken.jp. Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. akikuri@bs.naist.jp.

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A review of possible effects of cognitive biases on interpretation of rule-based machine learning models

arXiv

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arXiv 2018年

作者： Kliegr, Tomáš Bahník, Štěpán Fürnkranz, Johannes Department of Information and Knowledge Engineering Prague University of Economics and Business Czech Republic The Prague College of Psychosocial Studies Czech Republic Johannes Kepler University Computational Data Analytics Group Linz Austria

While the interpretability of machine learning models is often equated with their mere syntactic comprehensibility, we think that interpretability goes beyond that, and that human interpretability should also be investigated from the point of view of cognitive science. In particular, the goal of this paper is to discuss to what extent cognitive biases may affect human understanding of interpretable machine learning models, in particular of logical rules discovered from data. Twenty cognitive biases are covered, as are possible debiasing techniques that can be adopted by designers of machine learning algorithms and software. Our review transfers results obtained in cognitive psychology to the domain of machine learning, aiming to bridge the current gap between these two areas. It needs to be followed by empirical studies specifically focused on the machine learning domain. Copyright © 2018, The Authors. All rights reserved.

关键词： Machine learning

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