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OpenHI2 - Open source histopathological image platform

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OpenHI2 - Open source histopathological image platform

IEEE International Conference on Bioinformatics and Biomedicine

作者： Pargorn Puttapirat Haichuan Zhang Jingyi Deng Yuxin Dong Jiangbo Shi Hongyu He Zeyu Gao Chunbao Wang Xiangrong Zhang Chen Li National Engineering Lab for Big Data Analytics Xi'an Jiao tong University Shaanxi Province Key Laboratory of Satellite and Terrestrial Network Tech. R&D Xi'an Jiaotong University Department of Power System and Automation School of Electrical Engineering Xi'an Jiaotong University Department of Pathology the First Affiliated Hospital of Xi'an Jiaotong University Institute of Intelligent Information Processing Xidian University

ISBN: (纸本)9781728118680

Transition from conventional to digital pathology requires a new category of biomedical informatic infrastructure which could facilitate delicate pathological routine. Pathological diagnoses are sensitive to many external factors and is known to be subjective. Only systems that can meet strict requirements in pathology would be able to run along pathological routines and eventually digitized the area, and the developed platform should comply with existing pathological routines and international standards. Currently, there are a number of available software tools which can perform histopathological tasks including virtual slide viewing, annotating, and basic image analysis, however, none of them can serve as a digital platform for pathology. Here we describe OpenHI2, an enhanced version Open Histopathological Image platform which is capable of supporting all basic pathological tasks and file formats;ready to be deployed in medical institutions on a standard server environment or cloud computing infrastructure. In this paper, we also describe the development decisions for the platform and propose solutions to overcome technical challenges including responsive region retrieval and viewing, virtual slide magnification, recording of diagnostic areas. These factors would promote OpenHI2 be used as a platform for histopathological images in real-world clinical settings. Furthermore, in research, OpenHI2 inherited the annotation functionality from the previous version, thus acquired annotations can be directly utilized by the newly added machine learning module which include popular machine learning models to perform tasks such as histology image classification and segmentation in the same environment. Addition can be made to the platform since each component is modularized and fully documented. OpenHI2 is free, open-source, and available at .

关键词： OpenHI digital pathology histopathological image analysis open source software open source software pathology Platform Software Tools open source Religious Missions External factors images

Corrigendum to "Generation of a local lung respiratory motion model using a weighted sparse algorithm and motion prior-based registration" [Comput. Biol. Med. 123 (2020) 103913]

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Computers in biology and medicine 2021年 140卷 104271页

作者： Dong Chen Hongzhi Xie Lixu Gu Jing Liu Liang Tian College of Computer and Cyber Security Hebei Normal University Shijiazhuang China Hebei Provincial Engineering Research Center for Supply Chain Big Data Analytics and Data Security Hebei Normal University Shijiazhuang China Key Laboratory of Augmented Reality College of Mathematics and Information Science Hebei Normal University Shijiazhuang China. Department of Cardiothoracic Surgery Peking Union Medical College Hospital Beijing China. School of Biomedical Engineering Shanghai Jiao Tong University Shanghai China. Key Laboratory of Augmented Reality College of Mathematics and Information Science Hebei Normal University Shijiazhuang China. Electronic address: liujing01@***. Key Laboratory of Augmented Reality College of Mathematics and Information Science Hebei Normal University Shijiazhuang China. Electronic address: tianliang@***.

Impact of Prior Knowledge and data Correlation on Privacy Leakage: A Unified Analysis

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arXiv 2019年

作者： Li, Yanan Ren, Xuebin Yang, Shusen Yang, Xinyu National Engineering Laboratory for Big Data Analytics [NEL-BDA Xi’an Jiaotong University Xi’an Shaanxi710049 China School of Mathematics and Statistics Xi’an Jiaotong University Xi’an Shaanxi710049 China School of Electronic and Information Engineering Xi’an Jiaotong University Xi’an Shaanxi710049 China Ministry of Education Key Lab for Intelligent Networks and Network Security [MOE KLINNS Lab Xi’an Jiaotong University Xi’an Shaanxi710049 China

It has been widely understood that differential privacy (DP) can guarantee rigorous privacy against adversaries with arbitrary prior knowledge. However, recent studies demonstrate that this may not be true for correlated data, and indicate that three factors could influence privacy leakage: the data correlation pattern, prior knowledge of adversaries, and sensitivity of the query function. This poses a fundamental problem: what is the mathematical relationship between the three factors and privacy leakage? In this paper, we present a unified analysis of this problem. A new privacy definition, named prior differential privacy (PDP), is proposed to evaluate privacy leakage considering the exact prior knowledge possessed by the adversary. We use two models, the weighted hierarchical graph (WHG) and the multivariate Gaussian model to analyze discrete and continuous data, respectively. We demonstrate that positive, negative, and hybrid correlations have distinct impacts on privacy leakage. Considering general correlations, a closed-form expression of privacy leakage is derived for continuous data, and a chain rule is presented for discrete data. Our results are valid for general linear queries, including count, sum, mean, and histogram. Numerical experiments are presented to verify our theoretical analysis. Copyright © 2019, The Authors. All rights reserved.

关键词： Machine learning

IRTED-TL: An Inter-Region Tax Evasion Detection Method Based on Transfer Learning

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IRTED-TL: An Inter-Region Tax Evasion Detection Method Based...

IEEE International Conference on Trust, Security and Privacy in Computing and Communications (TrustCom)

作者： Xulyu Zhu Zheng Yan Jianfei Ruan Qinghua Zheng Bo Dong School of Electronic and Information Engineering Xi'an Jiaotong University China State Key Laboratory on Integrated Services Networks Xidian University China National Engineering Lab for Big Data Analytics Xi'an Jiaotong University China

Tax evasion detection plays a crucial role in addressing tax revenue loss. Many efforts have been made to develop tax evasion detection models by leveraging machine learning techniques, but they have not constructed a uniform model for different geographical regions because an ample supply of training examples is a fundamental prerequisite for an effective detection model. When sufficient tax data are not readily available, the development of a representative detection model is more difficult due to unequal feature distributions in different regions. Existing methods face a challenge in explaining and tracing derived results. To overcome these challenges, we propose an Inter-Region Tax Evasion Detection method based on Transfer Learning (IRTED-TL), which is optimized to simultaneously augment training data and induce interpretability into the detection model. We exploit evasion-related knowledge in one region and leverage transfer learning techniques to reinforce the tax evasion detection tasks of other regions in which training examples are lacking. We provide a unified framework that takes advantage of auxiliary data using a transfer learning mechanism and builds an interpretable classifier for inter-region tax evasion detection. Experimental tests based on real-world tax data demonstrate that the IRTED-TL can detect tax evaders with higher accuracy and better interpretability than existing methods.

关键词： Finance Feature extraction Biological system modeling data models Learning systems Training Training data

Dual flow immunochromatographic assay for rapid and simultaneous quantitative detection of ochratoxin A and zearalenone in corn, wheat, and feed samples

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2018年第11期19卷 871-883页

作者： Xian ZHANG Ke HE Yun FANG Tong CAO Narayan PAUDYAL Xiao-feng ZHANG Hou-hui SONG Xiao-liang LI Wei-huan FANG China-Australian Joint Laboratory for Animal Health Big Data Analytics Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet TechnologyCollege of Animal Science and TechnologyZhejiang A&F UniversityLin'an 311300China Zhejiang University Institute of Preventive Veterinary Medicine Zhejiang Provincial Key Laboratory of Preventive Veterinary MedicineHangzhou 310058China Zhejiang Academy of Science and Technology for Inspection and Quarantine Hangzhou 310012China

A one-step dual flow immunochromatographic assay （DICGA）, based on a competitive format, was de- veloped for simultaneous quantification of ochratoxin A （OTA） and zearalenone （ZEN） in corn, wheat, and feed sam- ples. The limit of detection for OTA was 0.32 ng/ml with a detection range of 0.53-12.16 ng/ml, while for ZEN it was 0.58 ng/ml with a detection range of 1.06-39.72 ng/ml. The recovery rates in corn, wheat, and feed samples ranged from 77.3% to 106.3% with the coefficient of variation lower than 15%. Naturally contaminated corn, wheat, and feed samples were analyzed using both DICGA and liquid chromatography-tandem mass spectrometry （LC-MS/MS） and the correlation between the two methods was evaluated using a regression analysis. The DICGA method shows great potential for simple, rapid, sensitive, and cost-effective quantitative detection of OTA and ZEN in food safety control.

关键词： Immunochromatographic assay Gold nanoparticles Ochratoxin A Zearalenone Quantification

$\rho$ -Dominant Skyline Computation on data Stream

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IEEE Access 2018年 6卷 53201-53213页

作者： Zhiqiong Wang Junchang Xin Linlin Ding Jianmin Ba Xiaosong Gao Neusoft Institute of Intelligent Healthcare Technology Co. Ltd. Key Laboratory of Big Data Management and Analytics Shenyang China School of Information Liaoning University Shenyang China School of Computer Science and Engineering Northeastern University Shenyang China Sino-Dutch Biomedical and Information Engineering School Northeastern University Shenyang China

Skyline query is widely used in multi-standard decision making process. As the extension to skyline query, p-dominant skyline query controls the base of the result set by adjusting data proportion, which is suitable for the application on fast deciding data stream. However, skyline query on data stream cannot satisfy the need for skyline query of corresponding value ratio, and the traditional p-dominant skyline query cannot provide skyline query with frequent data update. As a result, a data stream-based algorithm that can achieve the goal of p-dominant skyline query is proposed. First, the definitions of full-dominant relationship and p-dominance are given, after which the definitions of p-dominant skyline and p-dominant skyline based on data stream are proposed. Second, by analyzing the characters of data stream-based p-dominant skyline, a new data filtering method is established. Based on the method, p-Dominant Skyline Query on data stream over Sliding Window (DSSW) is proposed in order to improve the efficiency of p-dominant skyline query. After that, we expend the p-dominant skyline query of data stream into n-of-N p-dominant skyline query and the (n1, n 2 )-of-Np-dominant skyline query in data stream. Finally, we prove that DSSW has obvious advantages in responding time and storage skyline space by comparing with the traditional p-dominant skyline query algorithms through abundant experiments.

关键词： IEEE merchandise Microsoft Windows Indexes Decision making Heuristic algorithms Computer science

Title-guided encoding for keyphrase generation

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arXiv 2018年

作者： Chen, Wang Gao, Yifan Zhang, Jiani King, Irwin Lyu, Michael R. Department of Computer Science and Engineering Chinese University of Hong Kong Shatin N.T. Hong Kong Shenzhen Key Laboratory of Rich Media Big Data Analytics and Application Shenzhen Research Institute Chinese University of Hong Kong Shenzhen China

Keyphrase generation (KG) aims to generate a set of keyphrases given a document, which is a fundamental task in natural language processing (NLP). Most previous methods solve this problem in an extractive manner, while recently, several attempts are made under the generative setting using deep neural networks. However, the state-of-the-art generative methods simply treat the document title and the document main body equally, ignoring the leading role of the title to the overall document. To solve this problem, we introduce a new model called Title-Guided Network (TG-Net) for automatic keyphrase generation task based on the encoderdecoder architecture with two new features: (i) the title is additionally employed as a query-like input, and (ii) a titleguided encoder gathers the relevant information from the title to each word in the document. Experiments on a range of KG datasets demonstrate that our model outperforms the state-of-the-art models with a large margin, especially for documents with either very low or very high title length ratios. Copyright © 2018, The Authors. All rights reserved.

关键词： Deep neural networks

IoT Stream Processing and analytics in The Fog

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arXiv 2017年

作者： Yang, Shusen National Engineering Laboratory for Big Data Algorithms and Analytics Technology Xi’an Jiaotong University China

The emerging Fog paradigm has been attracting increasing interests from both academia and industry, due to the low-latency, resilient, and cost-effective services it can provide. Many Fog applications such as video mining and event monitoring, rely on data stream processing and analytics, which are very popular in the Cloud, but have not been comprehensively investigated in the context of Fog architecture. In this article, we present the general models and architecture of Fog data streaming, by analyzing the common properties of several typical applications. We also analyze the design space of Fog streaming with the consideration of four essential dimensions (system, data, human, and optimization), where both new design challenges and the issues arise from leveraging existing techniques are investigated, such as Cloud stream processing, computer networks, and mobile computing. Copyright © 2017, The Authors. All rights reserved.

关键词： Fog

Top-N-Rank: A Scalable List-wise Ranking Method for Recommender Systems

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arXiv 2018年

作者： Liang, Junjie Hu, Jinlong Dong, Shoubin Honavar, Vasant Artificial Intelligence Research Laboratory Center for Big Data Analytics and Discovery Informatics College of Information Sciences and Technology Pennsylvania State University University ParkPA16802 United States Guangdong Key Laboratory of Communication & Computer Network School of Computer Science and Engineering South China University of Technology Guangzhou510006 China

We propose Top-N-Rank, a novel family of list wise Learning-to-Rank models for reliably recommending the N top-ranked items. The proposed models optimize a variant of the widely used discounted cumulative gain (DCG) objective function which differs from DCG in two important aspects: (i) It limits the evaluation of DCG only on the top N items in the ranked lists, thereby eliminating the impact of low-ranked items on the learned ranking function;and (ii) it incorporates weights that allow the model to leverage multiple types of implicit feedback with differing levels of reliability or trustworthiness. Because the resulting objective function is non-smooth and hence challenging to optimize, we consider two smooth approximations of the objective function, using the traditional sigmoid function and the rectified linear unit (ReLU). We propose a family of learning-to-rank algorithms (Top-N-Rank) that work with any smooth objective function. Then, a more efficient variant, ***, is introduced, which effectively exploits the properties of ReLU function to reduce the computational complexity of Top-N-Rank from quadratic to linear in the average number of items rated by users. The results of our experiments using two widely used benchmarks, namely, the MovieLens data set and the Amazon Video Games data set demonstrate that: (i) The "top-N truncation" of the objective function substantially improves the ranking quality of the top N recommendations;(ii) using the ReLU for smoothing the objective function yields significant improvement in both ranking quality as well as runtime as compared to using the sigmoid;and (iii) *** substantially outperforms the well-performing list-wise ranking methods in terms of ranking quality. Copyright © 2018, The Authors. All rights reserved.

关键词： Benchmarking