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arXiv 2020年

作者： Sekuboyina, Anjany Kumar Husseini, Malek E. Bayat, Amirhossein Löffler, Maximilian Liebl, Hans Li, Hongwei Tetteh, Giles Kukačka, Jan Payer, Christian Štern, Darko Urschler, Martin Chen, Maodong Cheng, Dalong Lessmann, Nikolas Hu, Yujin Wang, Tianfu Yang, Dong Xu, Daguang Ambellan, Felix Amiranashvili, Tamaz Ehlke, Moritz Lamecker, Hans Lehnert, Sebastian Lirio, Marilia de Olaguer, Nicolás Pérez Ramm, Heiko Sahu, Manish Tack, Alexander Zachow, Stefan Jiang, Tao Ma, Xinjun Angerman, Christoph Wang, Xin Brown, Kevin Kirszenberg, Alexandre Puybareau, Élodie Chen, Di Bai, Yiwei Rapazzo, Brandon H. Yeah, Timyoas Zhang, Amber Xu, Shangliang Hou, Feng He, Zhiqiang Zeng, Chan Xiangshang, Zheng Liming, Xu Netherton, Tucker J. Mumme, Raymond P. Court, Laurence E. Huang, Zixun He, Chenhang Wang, Li-Wen Ling, Sai Ho Huynh, Lê Duy Boutry, Nicolas Jakubicek, Roman Chmelik, Jiri Mulay, Supriti Sivaprakasam, Mohanasankar Paetzold, Johannes C. Shit, Suprosanna Ezhov, Ivan Wiestler, Benedikt Glocker, Ben Valentinitsch, Alexander Rempfler, Markus Menze, Björn H. Kirschke, Jan S. Department of Informatics Technical University of Munich Germany Munich School of BioEngineering Technical University of Munich Germany Department of Neuroradiology Klinikum Rechts der Isar Germany Department for Quantitative Biomedicine University of Zurich Switzerland Friedrich Miescher Institute for Biomedical Engineering Switzerland Institute of Biological and Medical Imaging Helmholtz Zentrum München Germany Department of Computing Imperial College London United Kingdom Institute of Computer Graphics and Vision Graz University of Technology Austria Gottfried Schatz Research Center: Biophysics Medical University of Graz Austria School of Computer Science The University of Auckland New Zealand Computer Vision Group iFLYTEK Research South China China Department of Radiology and Nuclear Medicine Radboud University Medical Center Nijmegen Netherlands Shenzhen Research Institute of Big Data China School of Biomedical Engineering Health Science Center Shenzhen University China NVIDIA Corporation United States Zuse Institute Berlin Germany 1000shapes GmbH Berlin Germany Damo Academy Alibaba Group China Department of Mathematics University of Innsbruck Austria Department of Electronic Engineering Fudan University China New York University United States France Deep Reasoning AI Inc United States Technical University of Munich Germany East China Normal University China Chinese Academy of Sciences China Lenovo Group China Ping An Technologies China College of Computer Science and Technology Zhejiang University China Real Doctor AI Research Centre Zhejiang University China The University of Texas MD Anderson Cancer Center United States Department of Electronic and Information Engineering The Hong Kong Polytechnic University China Department of Computing The Hong Kong Polytechnic University China The School of Biomedical Engineering University of Technology Sydney Australia Department of Biomedical Engineering Brno University of Technology Czech Republic India

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision support systems for diagnosis, surgery planning, and population-based analysis of spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms tackling the labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel level by a human-machine hybrid algorithm (https://***/nqjyw/, https://***/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the results of this evaluation and further investigate the performance variation at the vertebra level, scan level, and different fields of view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top-performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The VerSe content and code can be accessed at: https://***/anjany/verse. © 2020, CC BY-NC-ND.

关键词： computerized tomography

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FHEDN: A context modeling Feature Hierarchy Encoder-Decoder Network for face detection

FHEDN: A context modeling Feature Hierarchy Encoder-Decoder ...

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International Joint Conference on Neural Networks

作者： Zexun Zhou Zhongshi He Ziyu Chen Yuanyuan Jia Haiyan Wang Jinglong Du Dingding Chen Lulu Wang Jing Chen College of Computer Science Chongqing University Chongqing China College of Medical Informatics Chongqing Medical University Chongqing China Department of Art History Sichuan Fine Arts Institute Chongqing China School of Big Data and Software Engineering Chongqing University Chongqing China

Because of affected by weather conditions, camera pose and range, etc. objects are usually small, blurry, occluded and diverse pose in the images, which are gathered from outdoor surveillance cameras or access control system. It is challenging and important to detect faces precisely for face recognition system in the field of public security. In this paper, we design a context modeling network named Feature Hierarchy Encoder-Decoder Network for face detection (FHEDN), which can detect small, blurry and occluded faces hierarchy by hierarchy from the end to the beginning in a single stage. The proposed network consists of encoder and decoder subnetworks. The encoder subnetwork constructs a multi-scale feature hierarchy pyramid through VGG-16 as backbone network. The decoder subnetwork models context semantic information around face and fuses it into the feature hierarchy for face detection. In addition, we analyze the influence of distribution of training set, scale of feature hierarchy and receipt field size on the detection performance in implement stage. The experiments demonstrate that our network achieves the promising performance on AFW, PASCAL FACE, WIDER FACE and FDDB benchmarks.

关键词： Face Feature extraction Face detection Training Context modeling Decoding Semantics

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Research on Agricultural Environment Prediction Based on Deep Learning

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Procedia computer science 2018年 139卷 33-40页

作者： Shuchang Chen Bingchan Li Jie Cao Bo Mao College of Information Engineering Collaborative Innovation Center for Modern Grain Circulation and Safety Jiangsu Key Laboratory of Grain Big-data Mining Nanjing University of Finance & Economics Nanjing 210023 China School of Electrical and Automation Engineering Jiangsu Maritime Institute Nanjing 211170 China Computer Science and Technology Computer Science and Engineering College Nanjing University of Science and Technology Nanjing 210094 China

The environmental security of agriculture is closely related to human beings. Analytical training of agricultural environmental data, forecasting its development trend, has positive significance for the protection of the safety of agricultural products. This paper proposes an agricultural environment prediction model based on deep learning LSTM (Long Short-Term Memory). By analyzing the agricultural environment parameters of the current period, the environmental parameters of the next moment can be predicted to achieve the purpose of early warning. The experimental results show that the model’s prediction results have little deviation from the actual values; on this basis, the LSTM model is optimized to replace LSTM with GRU(Gated Recurrent Unit), and the model is more effective.

关键词： Deep learning Agricultural environment LSTM GRU

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Ten quick tips for deep learning in biology

arXiv

引用

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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Developing and validating multi-modal models for mortality prediction in COVID-19 patients: A multi-center retrospective study

arXiv

引用

arXiv 2021年

作者： Wu, Joy Tzung-Yu De La Hoz, Miguel Ángel Armengol Kuo, Po-Chih Paguio, Joseph Alexander Yao, Jasper Seth Dee, Edward Christopher Yeung, Wesley Jurado, Jerry Moulick, Achintya Milazzo, Carmelo Peinado, Paloma Villares, Paula Cubillo, Antonio Varona, José Felipe Lee, Hyung-Chul Estirado, Alberto Castellano, José Maria Celi, Leo Anthony Department of Radiology and Nuclear Medicine Stanford University Palo AltoCA United States Institute for Medical Engineering and Science Massachusetts Institute of Technology CambridgeMA United States Department of Anesthesia Critical Care and Pain Medicine Beth Israel Deaconess Medical Center BostonMA United States Big Data Department Fundacion Progreso y Salud Regional Ministry of Health of Andalucia Andalucia Spain Department of Computer Science National Tsing Hua University Hsinchu Taiwan Albert Einstein Medical Center PhiladelphiaPA United States Department of Radiation Oncology Memorial Sloan Kettering Cancer Center New YorkNY United States National University Heart Center National University Hospital Singapore Singapore Hoboken University Medical Center CarePoint Health HobokenNJ United States Centro Integral de Enfermedades Cardiovasculares Hospital Universitario Monteprincipe Grupo Hm Hospitales Madrid Spain Department of Anesthesiology and Pain Medicine Seoul National University College of Medicine Seoul Korea Republic of Centro Nacional de Investigaciones Cardiovasculares Instituto de Salud Carlos Iii Madrid Spain Department of Medicine Beth Israel Deaconess Medical Center BostonMA United States Department of Biostatistics Harvard T.H. Chan School of Public Health BostonMA United States

Background: The unprecedented global crisis brought about by the COVID-19 pandemic has sparked numerous efforts to create predictive models for the detection and prognostication of SARS-CoV-2 infections with the goal of helping health systems allocate resources. Machine learning models, in particular, hold promise for their ability to leverage patient clinical information and medical images for prediction. However, most of the published COVID-19 prediction models thus far have little clinical utility due to methodological flaws and lack of appropriate validation. Purpose: In this paper, we describe our methodology to develop and validate multi-modal models for COVID-19 mortality prediction using multi-center patient data. Materials and Methods: The models for COVID-19 mortality prediction were developed using retrospective data from Madrid, Spain (N=2547) and were externally validated in patient cohorts from a community hospital in New Jersey, USA (N=242) and an academic center in Seoul, Republic of Korea (N=336). The models we developed performed differently across various clinical settings, underscoring the need for a guided strategy when employing machine learning for clinical decision-making. Results: We demonstrated that using features from both the structured electronic health records and chest X-ray imaging data resulted in better 30-day-mortality prediction performance across all three datasets (areas under the receiver operating characteristic curves: 0.85 (95% confidence interval: 0.83-0.87), 0.76 (0.70-0.82), and 0.95 (0.92-0.98)). We discuss the rationale for the decisions made at every step in developing the models and have made our code available to the research community. Conclusion: We employed the best machine learning practices for clinical model development. Our goal is to create a toolkit that would assist investigators and organizations in building multi-modal models for prediction, classification and/or optimization. © 2021, CC BY.

关键词： Forecasting

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The SNM algorithm based on multiple edit distances and variable window 7

The SNM algorithm based on multiple edit distances and varia...

引用

7th International Conference on computer engineering and Networks, CENet 2017

作者： Yang, Qiaoqiao Guo, Zhenbo Wang, Kaixi Data Science and Software Engineering Institute of Qingdao University Qingdao266000 China College of Computer Science and Technology of Qingdao University Qingdao266000 China

In order to solve the drawback of SNM algorithm, which leads to inefficiency in detecting precision on approximately duplicate records when multiple sources need to be integrated, the improved SNM algorithm based on the variety of edit distance and the variable window is proposed in this paper. According to the record pattern of edit distance and the size of edit distance, the approximately duplicate records of data are deleted to reduce the number of comparisons. Then we put forward the mechanism of variable window to solve the problem. Empirical results show that this algorithm can effectively solve the problem that the window is too big or too small to leak. The experiment shows that the improved SNM algorithm can solve many problems in the integration of multi-source , and it has obvious advantages in ensuring precision and boosting efficiency. © Copyright owned by the author(s) under the terms of the Creative Commons.

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Crossbar-Net: A novel convolutional network for kidney tumor segmentation in CT images

arXiv

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arXiv 2018年

作者： Yu, Qian Shi, Yinghuan Sun, Jinquan Gao, Yang Zhu, Jianbing Dai, Yakang State Key Laboratory for Novel Software Technology National Research Institute for Big Data Science in Health and Medicine Collaborative Innovation Center of Novel Software Technology and Industrialization Nanjing University China School of Data and Computer Science Shandong Women’s University China Suzhou Science and Technology Town Hospital China Suzhou Institute of Biomedical Engineering and Technology Chinese Academy of Sciences China

Due to the unpredictable location, fuzzy texture and diverse shape, accurate segmentation of the kidney tumor in CT images is an important yet challenging task. To this end, we in this paper present a cascaded trainable segmentation model termed as Crossbar-Net. Our method combines two novel schemes: (1) we originally proposed the crossbar patches, which consists of two orthogonal non-squared patches (i.e., the vertical patch and horizontal patch). The crossbar patches are able to capture both the global and local appearance information of the kidney tumors from both the vertical and horizontal directions simultaneously. (2) With the obtained crossbar patches, we iteratively train two sub-models (i.e., horizontal sub-model and vertical sub-model) in a cascaded training manner. During the training, the trained sub-models are encouraged to become more focus on the difficult parts of the tumor automatically (i.e., mis-segmented regions). Specifically, the vertical (horizontal) sub-model is required to help segment the mis-segmented regions for the horizontal (vertical) sub-model. Thus, the two sub-models could complement each other to achieve the self-improvement until convergence. In the experiment, we evaluate our method on a real CT kidney tumor dataset which is collected from 94 different patients including 3,500 CT slices. Compared with the state-of-the-art segmentation methods, the results demonstrate the superior performance of our method on the Dice similarity coefficient, true positive fraction, centroid distance and Hausdorff distance. Moreover, to exploit the generalization to other segmentation tasks, we also extend our Crossbar-Net to two related segmentation tasks: (1) cardiac segmentation in MR images and (2) breast mass segmentation in X-ray images, showing the promising results for these two tasks. Our implementation is released at https: //***/Qianyu1226/*** Codes 68T45, 68T05 Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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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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big data analytics on Apache Spark

引用

International Journal of data science and Analytics 2016年第3-4期1卷 145-164页

作者： Salloum, Salman Dautov, Ruslan Chen, Xiaojun Peng, Patrick Xiaogang Huang, Joshua Zhexue Big Data Institute College of Computer Science and Software Engineering Shenzhen University ShenzhenGuangdong China

Apache Spark has emerged as the de facto framework for big data analytics with its advanced in-memory programming model and upper-level libraries for scalable machine learning, graph analysis, streaming and structured data processing. It is a general-purpose cluster computing framework with language-integrated APIs in Scala, Java, Python and R. As a rapidly evolving open source project, with an increasing number of contributors from both academia and industry, it is difficult for researchers to comprehend the full body of development and research behind Apache Spark, especially those who are beginners in this area. In this paper, we present a technical review on big data analytics using Apache Spark. This review focuses on the key components, abstractions and features of Apache Spark. More specifically, it shows what Apache Spark has for designing and implementing big data algorithms and pipelines for machine learning, graph analysis and stream processing. In addition, we highlight some research and development directions on Apache Spark for big data analytics. © 2016, Springer International Publishing Switzerland.

关键词： big 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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