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The Journal of Machine Learning Research 2020年第1期21卷 8590-8628页

作者： Fanghui Liu Xiaolin Huang Chen Gong Jie Yang Li Li Department of Electrical Engineering ESAT-STADIUS KU Leuven Belgium Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China PCA Lab Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education School of Computer Science and Engineering Nanjing University of Science and Technology China and Department of Computing Hong Kong Polytechnic University Hong Kong SAR China Department of Automation BNRist Tsinghua University China

In this paper, we propose a data-adaptive non-parametric kernel learning framework in margin based kernel methods. In model formulation, given an initial kernel matrix, a data-adaptive matrix with two constraints is imposed in an entry-wise scheme. Learning this data-adaptive matrix in a formulation-free strategy enlarges the margin between classes and thus improves the model flexibility. The introduced two constraints are imposed either exactly (on small data sets) or approximately (on large data sets) in our model, which provides a controllable trade-off between model flexibility and complexity with theoretical demonstration. In algorithm optimization, the objective function of our learning framework is proven to be gradient-Lipschitz continuous. Thereby, kernel and classifier/regressor learning can be efficiently optimized in a unified framework via Nesterov's acceleration. For the scalability issue, we study a decomposition-based approach to our model in the large sample case. The effectiveness of this approximation is illustrated by both empirical studies and theoretical guarantees. Experimental results on various classification and regression benchmark data sets demonstrate that our non-parametric kernel learning framework achieves good performance when compared with other representative kernel learning based algorithms.

关键词： support vector machines non-parametric kernel learning gradient-Lipschitz continuous

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An Early Stage Researcher's Primer on systems Medicine Terminology

Network and Systems Medicine

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Network and systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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Achieving Data Truthfulness and Privacy Preservation in Data Markets

arXiv

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arXiv 2018年

作者： Niu, Chaoyue Zheng, Zhenzhe Wu, Fan Gao, Xiaofeng Chen, Guihai IEEE IEEE IEEE Shanghai Key Laboratory of Scalable Computing and Systems Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai200000 China

As a significant business paradigm, many online information platforms have emerged to satisfy society’s needs for person-specific data, where a service provider collects raw data from data contributors, and then offers value-added data services to data consumers. However, in the data trading layer, the data consumers face a pressing problem, i.e., how to verify whether the service provider has truthfully collected and processed data? Furthermore, the data contributors are usually unwilling to reveal their sensitive personal data and real identities to the data consumers. In this paper, we propose TPDM, which efficiently integrates data Truthfulness and Privacy preservation in Data Markets. TPDM is structured internally in an Encrypt-then-Sign fashion, using partially homomorphic encryption and identity-based signature. It simultaneously facilitates batch verification, data processing, and outcome verification, while maintaining identity preservation and data confidentiality. We also instantiate TPDM with a profile matching service and a distribution fitting service, and extensively evaluate their performances on Yahoo! Music ratings dataset and 2009 RECS dataset, respectively. Our analysis and evaluation results reveal that TPDM achieves several desirable properties, while incurring low computation and communication overheads when supporting large-scale data markets. Copyright © 2018, The Authors. All rights reserved.

关键词： Cryptography

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Fine-Grained User Profiling for Personalized Task Matching in Mobile Crowdsensing

arXiv

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arXiv 2018年

作者： Yang, Shuo Zheng, Zhenzhe Tang, Shaojie Wu, Fan Chen, Guihai Shanghai Key Laboratory of Scalable Computing and Systems Department of Computer Science and Engineering Shanghai Jiao Tong University China Department of Information Systems University of Texas Dallas United States

In mobile crowdsensing, finding the best match between tasks and users is crucial to ensure both the quality and effectiveness of a crowdsensing system. Existing works usually assume a centralized task assignment by the crowdsensing platform, without addressing the need of fine-grained personalized task matching. In this paper, we argue that it is essential to match tasks to users based on a careful characterization of both the users’ preference and reliability. To that end, we propose a personalized task recommender system for mobile crowdsensing, which recommends tasks to users based on a recommendation score that jointly takes each user’s preference and reliability into consideration. We first present a hybrid preference metric to characterize users’ preference by exploiting their implicit feedback. Then, to profile users’ reliability levels, we formalize the problem as a semi-supervised learning model, and propose an efficient block coordinate descent algorithm to solve the problem. For some tasks that lack users’ historical information, we further propose a matrix factorization method to infer the users’ reliability levels on those tasks. We conduct extensive experiments to evaluate the performance of our system, and the evaluation results demonstrate that our system can achieve superior performance to the benchmarks in both user profiling and personalized task recommendation. Copyright © 2018, The Authors. All rights reserved.

关键词： Recommender systems

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FDRC: Flow-driven rule caching optimization in software defined networking

arXiv

引用

arXiv 2018年

作者： Li, He Guo, Song Wu, Chentao Li, Jie University of Aizu Aizuwakamatsu Fukushima Japan Shanghai Key Laboratory of Scalable Computing and Systems Department of Computer Science & Engineering Shanghai Jiao Tong University Shanghai200240 China

With the sharp growth of cloud services and their possible combinations, the scale of data center network traffic has an inevitable explosive increasing in recent years. Software defined network (SDN) provides a scalable and flexible structure to simplify network traffic management. It has been shown that Ternary Content Addressable Memory (TCAM) management plays an important role on the performance of SDN. However, previous literatures, in point of view on rule placement strategies, are still insufficient to provide high scalability for processing large flow sets with a limited TCAM size. So caching is a brand new method for TCAM management which can provide better performance than rule placement. In this paper, we propose FDRC, an efficient flow-driven rule caching algorithm to optimize the cache replacement in SDN-based networks. Different from the previous packet-driven caching algorithm, FDRC is characterized by trying to deal with the challenges of limited cache size constraint and unpredictable flows. In particular, we design a caching algorithm with low-complexity to achieve high cache hit ratio by prefetching and special replacement strategy for predictable and unpredictable flows, respectively. By conducting extensive simulations, we demonstrate that our proposed caching algorithm significantly outperforms FIFO and least recently used (LRU) algorithms under various network settings. Copyright © 2018, The Authors. All rights reserved.

关键词： Software defined networking

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Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

arXiv

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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

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Publisher Correction: SODB facilitates comprehensive exploration of spatial omics data

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Nature methods 2023年第4期20卷 623页

作者： Zhiyuan Yuan Wentao Pan Xuan Zhao Fangyuan Zhao Zhimeng Xu Xiu Li Yi Zhao Michael Q Zhang Jianhua Yao Institute of Science and Technology for Brain-Inspired Intelligence MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence MOE Frontiers Center for Brain Science Fudan University Shanghai China. zhiyuan@***. Tencent AI Lab Shenzhen China. zhiyuan@***. Tencent AI Lab Shenzhen China. Shenzhen International Graduate School Tsinghua University Shenzen China. Institute of Computing Technology Chinese Academy of Sciences Beijing China. University of Chinese Academy of Sciences Beijing China. Department of Biological Sciences Center for Systems Biology The University of Texas Richardson TX USA. michael.zhang@utdallas.edu. Tencent AI Lab Shenzhen China. jianhuayao@***.

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REFUGE2 CHALLENGE: A TREASURE TROVE FOR MULTI-DIMENSION ANALYSIS AND EVALUATION IN GLAUCOMA SCREENING

arXiv

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arXiv 2022年

作者： Fang, Huihui Li, Fei Wu, Junde Fu, Huazhu Sun, Xu Son, Jaemin Yu, Shuang Zhang, Menglu Yuan, Chenglang Bian, Cheng Lei, Baiying Zhao, Benjian Xu, Xinxing Li, Shaohua Fumero, Francisco Sigut, José Almubarak, Haidar Bazi, Yakoub Guo, Yuanhao Zhou, Yating Baid, Ujjwal Innani, Shubham Guo, Tianjiao Yang, Jie Orlando, José Ignacio Bogunović, Hrvoje Zhang, Xiulan Xu, Yanwu The REFUGE2 Challenge Australia State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat-Sen University Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science Guangzhou China Intelligent Healthcare Unit Baidu Inc. Beijing China The Institute of High Performance Computing Agency for Science Technology and Research Singapore Yatiris Group PLADEMA Institute CONICET UNICEN Tandil Argentina Christian Doppler Lab for Artificial Intelligence in Retina Department of Ophthalmology and Optometry Medical University of Vienna Vienna Austria VUNO Inc Seoul Korea Republic of Tencent HealthCare Tencent Shenzhen China Computer Vision Institute College of Computer Science and Software Engineering of Shenzhen University Shenzhen China School of Biomedical Engineering Health Science Center Shenzhen University China Xiaohe Healthcare ByteDance Guangdong Guangzhou510000 China School of Biomedical Engineering Shenzhen University China College of Computer Science & Software Engineering Shenzhen University China Department of Computer Science and Systems Engineering Universidad de La Laguna Spain Saudi Electronic University Saudi Arabia King Saud University Saudi Arabia Institute of Automation Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China SGGS Institute of Engineering and Technology India Institute of Medical Robotics Shanghai Jiao Tong University China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University China

With the rapid development of artificial intelligence (AI) in medical image processing, deep learning in color fundus photography (CFP) analysis is also evolving. Although there are some open-source, labeled datasets of CFPs in the ophthalmology community, large-scale datasets for screening only have labels of disease categories, and datasets with annotations of fundus structures are usually small in size. In addition, labeling standards are not uniform across datasets, and there is no clear information on the acquisition device. Here we release a multi-annotation, multi-quality, and multi-device color fundus image dataset for glaucoma analysis on an original challenge-Retinal Fundus Glaucoma Challenge 2nd Edition (REFUGE2). The REFUGE2 dataset contains 2000 color fundus images with annotations of glaucoma classification, optic disc/cup segmentation, as well as fovea localization. Meanwhile, the REFUGE2 challenge sets three sub-tasks of automatic glaucoma diagnosis and fundus structure analysis and provides an online evaluation framework. Based on the characteristics of multi-device and multi-quality data, some methods with strong generalizations are provided in the challenge to make the predictions more robust. This shows that REFUGE2 brings attention to the characteristics of real-world multi-domain data, bridging the gap between scientific research and clinical application. © 2022, CC BY-NC-ND.

关键词： Color

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Optimizations for High Performance Network Virtualization

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Journal of Computer Science & Technology 2016年第1期31卷 107-116页

作者： Fan-Fu Zhou Ru-Hui Ma Jian Li Li-Xia Chen Wei-Dong Qiu Hai-Bing Guan Shanghai Key Laboratory of Scalable Computing and Systems Shanghai Jiao Tong University Shanghai 200240 China

The increasing requirements of intensive interoperaterbility among the distributed nodes desiderate the high performance network connections, owing to the substantial growth of cloud computing and datacenters. Network I/O virtualization aggregates the network resource and separates it into manageable parts for particular servers or devices, which provides effective consolidation and elastic management with high agility, flexibility and scalability as well as reduced cost and cabling. However, both network I/O virtualization aggregation and the increasing network speed incur higher traffic density, which generates a heavy system stress for I/O data moving and I/O event processing. Consequently, many researchers have dedicated to enhancing the system performance and alleviating the system overhead for high performance networking virtualizatiou. This paper first elaborates the mainstreaming I/O virtualization methodologies, including device emulation, split-driver model and hardware assisted model. Then, the paper discusses and compares their specific advantages in addition to performance bottlenecks in practical utilities. This paper mainly focuses on the comprehensive survey of state- of-the-art approaches for performance optimizations and improvements as well as the portability management for network I/O virtualization. The approaches include various novel data delivery schemes, overhead mitigations for interrupt processing and adequate resource allocations for dynamic network states. Finally, we highlight the diversity of I/O virtualization besides the performance improvements in network virtualization infrastructure.

关键词： network virtualization single root I/O virtualization （SR-IOV） virtual machine monitor （VMM）

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Reverse Furthest Neighbors Query in Road Networks

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Journal of Computer Science & Technology 2017年第1期32卷 155-167页

作者： Xiao-Jun Xu Jin-Song Bao Bin Yao Jing-Yu Zhou Fei-Long Tang Min-Yi Guo Jian-Qiu Xu School of Software Beijing Institute of Technology Beijing 100081 China First Research Institute of Ministry of Public Security Beijing 100048 China College of Mechanical Engineering Donghua University Shanghai 200051 China Shanghai Key Laboratory of Scalable Computing and Systems Shanghai Jiao Tong University Shanghai 200240 China Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai 200240 China College of Computer Science and Technology Nanjing University of Aeronautics and Astronautics Nanjing 210016 China

Given a road network G = （V, E）, where V（E） denotes the set of vertices（edges） in G, a set of points of interest P and a query point q residing in G, the reverse furthest neighbors （RFNR） query in road networks fetches a set of points p ∈ P that take q as their furthest neighbor compared with all points in P ∪ {q}. This is the monochromatic RFNR （MRFNR） query. Another interesting version of RFNR query is the bichromatic reverse furthest neighbor （BRFNR） query. Given two sets of points P and Q, and a query point q ∈ Q, a BRFNR query fetches a set of points p ∈ P that take q as their furthest neighbor compared with all points in Q. This paper presents efficient algorithms for both MRFNR and BRFNR queries, which utilize landmarks and partitioning-based techniques. Experiments on real datasets confirm the efficiency and scalability of proposed algorithms.

关键词： reverse furthest neighbor road network landmark hierarchical partition

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