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Inferring microRNA-disease association by hybrid recommendation algorithm and unbalanced bi-random walk on heterogeneous network

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Scientific reports 2019年第1期9卷 2474页

作者： Dong-Ling Yu Yuan-Lin Ma Zu-Guo Yu Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 P.R. China. Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 P.R. China. yuzuguo@***. School of Electrical Engineering and Computer Science Queensland University of Technology Brisbane Q4001 Australia. yuzuguo@***.

More and more research works have indicated that microRNAs (miRNAs) play indispensable roles in exploring the pathogenesis of diseases. Detecting miRNA-disease associations by experimental techniques in biology is expensive and time-consuming. Hence, it is important to propose reliable and accurate computational methods to exploring potential miRNAs related diseases. In our work, we develop a novel method (BRWHNHA) to uncover potential miRNAs associated with diseases based on hybrid recommendation algorithm and unbalanced bi-random walk. We first integrate the Gaussian interaction profile kernel similarity into the miRNA functional similarity network and the disease semantic similarity network. Then we calculate the transition probability matrix of bipartite network by using hybrid recommendation algorithm. Finally, we adopt unbalanced bi-random walk on the heterogeneous network to infer undiscovered miRNA-disease relationships. We tested BRWHNHA on 22 diseases based on five-fold cross-validation and achieves reliable performance with average AUC of 0.857, which an area under the ROC curve ranging from 0.807 to 0.924. As a result, BRWHNHA significantly improves the performance of inferring potential miRNA-disease association compared with previous methods. Moreover, the case studies on lung neoplasms and prostate neoplasms also illustrate that BRWHNHA is superior to previous prediction methods and is more advantageous in exploring potential miRNAs related diseases. All source codes can be downloaded from https://***/myl446/BRWHNHA .

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Effects of RapidEye Imagery's Red-edge Band and Vegetation Indices on Land Cover Classification in an Arid Region

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Chinese Geographical Science 2017年第5期27卷 827-835页

作者： LI Xianju CHEN Gang LIU Jingyi CHEN Weitao CHENG Xinwen LIAO Yiwei College of Computer Science and Hubei Key Laboratory of Intelligent Geo-Information Processing China University of GeosciencesWuhan 430074China College of Marine Science and Technology China University of GeosciencesWuhan 430074China Laboratory of Geographic Information and Spatial Analysis Department of Geography and PlanningQueen's UniversityKingston ON K7L3N6Canada Faculty of Information Engineering China University of GeosciencesWuhan 430074China School of Electrical and Electronic Engineering Huazhong University of Science and TechnologyWuhan 430074China

Land cover classification(LCC) in arid regions is of great significance to the assessment, prediction, and management of land desertification. Some studies have shown that the red-edge band of RapidE ye images was effective for vegetation identification and could improve LCC accuracy. However, there has been no investigation of the effects of RapidE ye images' red-edge band and vegetation indices on LCC in arid regions where there are spectrally similar land covers mixed with very high or low vegetation coverage information and bare land. This study focused on a typical inland arid desert region located in Dunhuang Basin of northwestern China. First, five feature sets including or excluding the red-edge band and vegetation indices were constructed. Then, a land cover classification system involving plant communities was developed. Finally, random forest algorithm-based models with different feature sets were utilized for LCC. The conclusions drawn were as follows: 1) the red-edge band showed slight contribution to LCC accuracy; 2) vegetation indices had a significant positive effect on LCC; 3) simultaneous addition of the red-edge band and vegetation indices achieved a significant overall accuracy improvement(3.46% from 86.67%). In general, vegetation indices had larger effect than the red-edge band, and simultaneous addition of them significantly increased the accuracy of LCC in arid regions.

关键词： arid region land cover classification RapidEye red-edge band vegetation indices random forest Dunhuang Basin

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Breast Cancer Diagnosis Using an Unsupervised Feature Extraction Algorithm Based on Deep Learning

Breast Cancer Diagnosis Using an Unsupervised Feature Extrac...

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Chinese Control Conference

作者： Yawen Xiao Jun Wu Zongli Lin Xiaodong Zhao Department of Automation Key Laboratory of System Control and Information Processing of Ministry of Education Shanghai China The Center for Bioinformatics and Computational Biology East China Normal University Shanghai China Charles L. Brown Department of Electrical and Computer Engineering University of Virginia Charlottesville VA U.S.A School of Biomedical Engineering Shanghai Jiao Tong University Shanghai China

Breast cancer is the most often detected cancer in women. At the same time, it is one of the most curable types of cancer if diagnosed early. With the development of the detection technology, a growing amount of clinical data and high-dimensional features can be used for breast cancer diagnosis. The high-dimensional data contributes to advances in the diagnostic technology, but also incurs a large amount of computational redundancy. Thus, extracting important information and reducing the feature dimension is critical to effective prediction and an accurate treatment decision. However, the previous works for breast cancer diagnosis are mainly based on labeled data that is difficult to obtain. To address this issue, in this paper, we demonstrate a new scheme, which integrates a deep learning based unsupervised feature extraction algorithm, the stacked auto-encoders, with a support vector machine model (SAE-SVM), for breast cancer diagnosis. The stacked auto-encoders with the greedy layer-wise pre-training and an improved momentum update algorithm is applied to capture essential information and extract necessary features of the original data. Then, a support vector machine model is employed to classify the samples with new features into malignant or benign tumors. The proposed method was tested on the Wisconsin Diagnostic Breast Cancer data set. The performance is evaluated using various measures and compared with the previously published results. The comparison results show that the proposed SAE-SVM method improves the accuracy to 98.25% and outperforms the other methods. The deep learning based unsupervised feature extraction significantly improves the performance of classification and provides a promising approach to breast cancer diagnosis.

关键词： Breast cancer Feature extraction Machine learning Support vector machines Electronic mail Principal component analysis

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Comments on "Design of fractional-order variants of complex LMS and NLMS algorithms for adaptive channel equalization"

arXiv

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arXiv 2018年

作者： Khan, Shujaat Wahab, Abdul Naseem, Imran Moinuddin, Muhammad Bio-imaging and Signal Processing Laboratory Department of Bio and Brain Engineering Korea Advanced Institute of Science and Technology 291 Daehak-ro Daejeon Yuseong-gu34141 Korea Republic of Department of Mathematics University of Education Attock Campus43600 Pakistan School of Electrical Electronic and Computer Engineering University of Western Australia 35 Stirling Highway CrawleyWA6009 Australia College of Engineering Karachi Institute of Economics and Technology Korangi Creek Karachi75190 Pakistan King Abdulaziz University Jeddah Saudi Arabia Electrical and Computer Engineering Department King Abdulaziz University Jeddah Saudi Arabia

The purpose of this note is to highlight some critical flaws in recently proposed fractional-order variants of complex least mean square (CLMS) and normalized least mean square (NLMS) algorithms in "Design of Fractional-order Variants of Complex LMS and Normalized LMS Algorithms for Adaptive Channel Equalization" [Non-linear Dyn. 88(2), 839-858 (2017)]. It is substantiated that these algorithms do not always converge whereas they have no advantage over the CLMS and NLMS algorithms whenever they converge. Our claims are based on analytical reasoning supported by simulations. Copyright © 2018, The Authors. All rights reserved.

关键词： Equalizers

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Dense matter with eXTP

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Science China(Physics,Mechanics & Astronomy) 2019年第2期62卷 28-44页

作者： Anna L.Watts WenFei Yu Juri Poutanen Shu Zhang Sudip Bhattacharyya Slavko Bogdanov Long Ji Alessandro Patruno Thomas E.Riley Pavel Bakala Altan Baykal Federico Bernardini Ignazio Bombaci Edward Brown Yuri Cavecchi Deepto Chakrabarty Jér?me Chenevez Nathalie Degenaar Melania Del Santo Tiziana Di Salvo Victor Doroshenko Maurizio Falanga Robert D.Ferdman Marco Feroci Angelo F.Gambino MingYu Ge Svenja K.Greif Sebastien Guillot Can Gungor Dieter H.Hartmann Kai Hebeler Alexander Heger Jeroen Homan Rosario Iaria Jean in 't Zand Oleg Kargaltsev Aleksi KurkelaTheoretical Physics Department CERN XiaoYu Lai Ang Li XiangDong Li ZhaoSheng Li Manuel Linares FangJun Lu Simin Mahmoodifar Mariano Méndez M.Coleman Miller Sharon Morsink Joonas N?ttil? Andrea Possenti Chanda Prescod-Weinstein JinLu Qu Alessandro Riggio Tuomo Salmi Andrea Sanna Andrea Santangelo Hendrik Schatz Achim Schwenk LiMing Song Eva?rámková Benjamin Stappers Holger Stiele Tod Strohmayer Ingo Tews Laura Tolos Gabriel T?r?k David Tsang Martin Urbanec Andrea Vacchi RenXin Xu YuPeng Xu Silvia Zane GuoBao Zhang ShuangNan Zhang WenDa Zhang ShiJie Zheng Xia Zhou Anton Pannekoek Institute for Astronomy University of Amsterdam Shanghai Astronomical Observatory Tuorla Observatory Department of Physics and Astronomy University of Turku Nordita KTH Royal Institute of Technology and Stockholm University Institute of High Energy Physics Chinese Academy Sciences Tata Institute of Fundamental Research Columbia Astrophysics Laboratory Columbia University Institut für Astronomie und Astrophysik Tübingen Universit?t Tübingen Leiden Observatory Leiden University Research Center for Computational Physics and Data Processing Silesian University in Opava Physics Department Middle East Technical University INAF Osservatorio Astronomico di Roma New York University Abu Dhabi Dipartimento di Fisica Enrico Fermi University of Pisa INFN Italian National Institute for Nuclear Physics Department of Physics and Astronomy Michigan State University Department of Astrophysical Sciences Princeton University Mathematical Sciences and STAG Research Centre University of Southampton MIT Kavli Institute for Astrophysics and Space Research DTU Space Technical University of Denmark INAF/IASF Palermo via Ugo La Malfa 153 Universita degli Studi di Palermo Dipartimento di Fisica e Chimica International Space Science Institute (ISSI) Faculty of Science University of East Anglia INAF Istituto di Astrofisica e Planetologie Spaziali Institut für Kernphysik Technische Universit?t Darmstadt ExtreMe Matter Institute EMMI GSI Helmholtzzentrum für Schwerionenforschung GmbH Instituto de Astrof'?sica Pontificia Universidad Católica de Chile Department of Physics & Astronomy Kinard Lab of Physics Clemson University School of Physics and Astronomy Monash University SRON Netherlands Institute for Space Research Department of Physics The George Washington University Faculty of Science and Technology University of Stavanger School of Physics and Mechanical & Electrical Engineering Hubei University of Education Department of Astronomy Xiamen University (Haiyun Campus) School of Astronomy and Space

In this White Paper we present the potential of the Enhanced X-ray Timing and Polarimetry(eXTP) mission for determining the nature of dense matter; neutron star cores host an extreme density regime which cannot be replicated in a terrestrial laboratory. The tightest statistical constraints on the dense matter equation of state will come from pulse profile modelling of accretion-powered pulsars, burst oscillation sources, and rotation-powered pulsars. Additional constraints will derive from spin measurements, burst spectra, and properties of the accretion flows in the vicinity of the neutron star. Under development by an international Consortium led by the Institute of High Energy Physics of the Chinese Academy of Sciences, the eXTP mission is expected to be launched in the mid 2020 s.

关键词： neutron X-rays dense matter equation of state

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A Subpixel Target Detection Approach to Hyperspectral Image Classification

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IEEE Transactions on Geoscience and Remote Sensing 2017年第9期55卷 5093-5114页

作者： Xue, Bai Yu, Chunyan Wang, Yulei Song, Meiping Li, Sen Wang, Lin Chen, Hsian-Min Chang, Chein-I Center for Hyperspectral Imaging in Remote Sensing Information and Technology College Dalian Maritime University Dalian China Remote Sensing Signal and Image Processing Laboratory Department of Computer Science and Electrical Engineering University of Maryland Baltimore County BaltimoreMD21250 United States Key Laboratory of Spectral Imaging Technology Chinese Academy of Sciences Xi'an China State Key Laboratory of Integrated Services Networks Xi'an China School of Physics and Optoelectronic Engineering Xidian University Xi'an China Department of Medical Research Taichung Veterans General Hospital Taichung Taiwan Department of Computer Science and Information Management Providence University Taichung02912 Taiwan

Hyperspectral image classification faces various levels of difficulty due to the use of different types of hyperspectral image data. Recently, spectral-spatial approaches have been developed by jointly taking care of spectral and spatial information. This paper presents a completely different approach from a subpixel target detection view point. It implements four stage processes, a preprocessing stage, which uses band selection (BS) and nonlinear band expansion, referred to as BS-then-nonlinear expansion (BSNE), a detection stage, which implements constrained energy minimization (CEM) to produce subpixel target maps, and an iterative stage, which develops an iterative CEM (ICEM) by applying Gaussian filters to capture spatial information, and then feeding the Gaussian-filtered CEM-detection maps back to BSNE band images to reprocess CEM in an iterative manner. Finally, in the last stage Otsu's method is applied to converting ICEM-detected real-valued maps to discrete values for classification. The entire process is called BSNE-ICEM. Experimental results demonstrate BSNE-ICEM, which has advantages over support vector machine-based approaches in many aspects, such as easy implementation, fewer parameters to be used, and better false classification and precision rates. © 1980-2012 IEEE.

关键词： Support vector machines

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Multi-objective Learning and Mask-based Post-processing for Deep Neural Network based Speech Enhancement

arXiv

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arXiv 2017年

作者： Xu, Yong Du, Jun Huang, Zhen Dai, Li-Rong Lee, Chin-Hui National Engineering Laboratory for Speech and Language Information Processing University of Science and Technology of China China School of Electrical and Computer Engineering Georgia Institute of Technology United States

We propose a multi-objective framework to learn both secondary targets not directly related to the intended task of speech enhancement (SE) and the primary target of the clean log-power spectra (LPS) features to be used directly for constructing the enhanced speech signals. In deep neural network (DNN) based SE we introduce an auxiliary structure to learn secondary continuous features, such as mel-frequency cepstral coefficients (MFCCs), and categorical information, such as the ideal binary mask (IBM), and integrate it into the original DNN architecture for joint optimization of all the parameters. This joint estimation scheme imposes additional constraints not available in the direct prediction of LPS, and potentially improves the learning of the primary target. Furthermore, the learned secondary information as a byproduct can be used for other purposes, e.g., the IBM-based post-processing in this work. A series of experiments show that joint LPS and MFCC learning improves the SE performance, and IBM-based post-processing further enhances listening quality of the reconstructed speech. Copyright © 2017, The Authors. All rights reserved.

关键词： Mean square error

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Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing

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BMC genomics 2023年第1期24卷 388页

作者： Elena V Demidova Ilya G Serebriiskii Ramilia Vlasenkova Simon Kelow Mark D Andrake Tiffiney R Hartman Tatiana Kent James Virtucio Gail L Rosen Richard T Pomerantz Roland L Dunbrack Erica A Golemis Michael J Hall David Y T Chen Mary B Daly Sanjeevani Arora Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Kazan Federal University Kazan 420008 Russia. Program in Cancer Signaling and Microenvironment Fox Chase Cancer Center Philadelphia PA 19111 USA. Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA 19104 USA. Arcadia University Glenside PA USA. Department of Biochemistry & Molecular Biology Sidney Kimmel Cancer Center Thomas Jeferson University Philadelphia PA 19107 USA. Ecological and Evolutionary Signal-Processing and Informatics Laboratory Department of Electrical and Computer Engineering College of Engineering Drexel University Philadelphia PA 19104 USA. Department of Cancer and Cellular Biology Lewis Katz School of Medicine Philadelphia PA 19140 USA. Department of Clinical Genetics Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Department of Surgical Oncology Fox Chase Cancer Center Philadelphia PA 19111 USA. Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Mary.Daly@fccc.edu. Department of Clinical Genetics Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Mary.Daly@fccc.edu. Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Sanjeevani.Arora@fccc.edu. Department of Radiation Oncology Fox Chase Cancer Center Philadelphia PA 19111 USA. Sanjeevani.Arora@fccc.edu.

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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

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Energy-efficient resource allocation in noma heterogeneous networks

arXiv

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arXiv 2018年

作者： Zhang, Haijun Fang, Fang Cheng, Julian Long, Keping Wang, Wei Leung, Victor C.M. Engineering and Technology Research Center for Convergence Networks University of Science and Technology Beijing Beijing100083 China School of Engineering University of British Columbia KelownaBCV1X 1V7 Canada College of Information Science and Electronic Engineering Zhejiang University Hangzhou310027 China Zhejiang Provincial Key Laboratory of Information Processing Communication and Networking Hangzhou310027 China Department of Electrical and Computer Engineering University of British Columbia VancouverBCV6T 1Z4 Canada

Non-orthogonal multiple access (NOMA) has attracted much recent attention owing to its capability for improving the system spectral efficiency in wireless communications. Deploying NOMA in heterogeneous network can satisfy users' explosive data traffic requirements, and NOMA will likely play an important role in the fifth-generation (5G) mobile communication networks. However, NOMA brings new technical challenges on resource allocation due to the mutual cross-tier interference in heterogeneous networks. In this article, to study the tradeoff between data rate performance and energy consumption in NOMA, we examine the problem of energy-efficient user scheduling and power optimization in 5G NOMA heterogeneous networks. The energy-efficient user scheduling and power allocation schemes are introduced for the downlink 5G NOMA heterogeneous network for perfect and imperfect channel state information (CSI) respectively. Simulation results show that the resource allocation schemes can significantly increase the energy efficiency of 5G NOMA heterogeneous network for both cases of perfect CSI and imperfect CSI. Copyright © 2018, The Authors. All rights reserved.

关键词： Heterogeneous networks

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