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arXiv 2024年

作者： Wang, Cheng Yuan, Zenghui Zhou, Pan Xu, Zichuan Li, Ruixuan Wu, Dapeng Oliver Hubei Engineering Research Center on Big Data Security Key Laboratory of Distributed System Security of Hubei Province School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan430074 China School of Software The Key Laboratory for Ubiquitous Network Service Software of Liaoning Province Dalian University of Technology Dalian116024 China Intelligent and Distributed Computing Laboratory School of Computer Science and Technology Huazhong University of Science and Technology Wuhan430074 China Department of Computer Science City University of Hong Kong Kowloon999077 Hong Kong

Mobile Edge computing (MEC) is a new computing paradigm that enables cloud computing and information technology (IT) services to be delivered at the network’s edge. By shifting the load of cloud computing to individual local servers, MEC helps meet the requirements of ultralow latency, localized data processing, and extends the potential of Internet of Things (IoT) for end-users. However, the crosscutting nature of MEC and the multidisciplinary components necessary for its deployment have presented additional security and privacy concerns. Fortunately, Artificial Intelligence (AI) algorithms can cope with excessively unpredictable and complex data, which offers a distinct advantage in dealing with sophisticated and developing adversaries in the security industry. Hence, in this paper we comprehensively provide a survey of security and privacy in MEC from the perspective of AI. On the one hand, we use European Telecommunications Standards Institute (ETSI) MEC reference architecture as our based framework while merging the Software Defined Network (SDN) and Network Function Virtualization (NFV) to better illustrate a serviceable platform of MEC. On the other hand, we focus on new security and privacy issues, as well as potential solutions from the viewpoints of AI. Finally, we comprehensively discuss the opportunities and challenges associated with applying AI to MEC security and privacy as possible future research directions. Copyright © 2024, The Authors. All rights reserved.

关键词： Network security

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Multi-Thread Concurrent Compression Algorithm for Genomic Big data

Multi-Thread Concurrent Compression Algorithm for Genomic Bi...

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IEEE International Conference on Parallel and Distributed computing, Applications and Technologies (PDCAT)

作者： Yimu Ji Shuai Chen Haichang Yao Houzhi Fang Kui Li Shangdong Liu Zhengyuan Xie Kairui Wang School of Computer Science Nanjing University of Posts and Telecommunications Institute of High Performance Computing and Big Data Nanjing University of Posts and Telecommunications Nanjing Center of HPC China Jiangsu HPC and Intelligent Processing Engineer Research Center Nanjing China School of Computer Science Nanjing University of Posts and Telecommunications Nanjing China School of Computer Science Nanjing University of Posts and Telecommunications School of Computer and Software Nanjing Institute of Industry Technology Nanjing China University of Toronto Toronto Canada BSc Mathematics with Finance University of Liverpool Liverpool United Kingdom

ISBN: (数字)9781728126166

ISBN: (纸本)9781728126173

At present, there are many excellent genome compression algorithms with high genome compression ratio. However, there is a lack of highly efficient compression algorithms for simultaneous compression of a large number of genomes. This manuscript presents an algorithm, which is called FastLNGC, for simultaneous compression of a large amount of genome data based on multi-thread concurrency. This algorithm is based on the LNGC (Large Number of Genomes Compressor) algorithm, and adopts multi-thread technology to achieve concurrent processing of genome data compression. A large number of experiments show that FastLNGC has better performance on compression of a large number of genes. The source code of FastLNGC is available at https://***/APandaThief/FastLNGC.

关键词： Bioinformatics Genomics Compression algorithms Instruction sets Telecommunications Computer science Concurrent computing

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Coordinate Attention Based 3D-CNN Using Ghost Multi-Scale for Diagnosing Alzheimer’s Disease

Coordinate Attention Based 3D-CNN Using Ghost Multi-Scale fo...

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International Joint Conference on Neural Networks (IJCNN)

作者： Xiaolu Lin Pinya Lu Jie Pan Hongqin Yang Xuemei Ding Fujian Provincial Engineering Research Center for Public Service Big Data Mining and Application Fujian Provincial University Engineering Research Center for Big Data Analysis and Application Fujian Normal University Fuzhou China Xiamen Jingyi Zhikang Technology Co. Ltd Xiamen China Fujian Provincial Key Laboratory for Photonics Technology Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education Fujian Normal University Fuzhou China School of Computing Engineering and Intelligent Systems Ulster University Derry-Londonderry NI UK

ISBN: (数字)9798350359312

ISBN: (纸本)9798350359329

Alzheimer's disease (AD) is a neurodegenerative disease and mild cognitive impairment (MCI) is the early stage of AD. Previous studies have predominantly focused on binary classification using 3 dimensional - convolutional neural network (3D-CNN) for AD diagnosis, with limited progress in multi-classification. Moreover, the current 3D-CNNs often adopt a single-scale architecture with massive parameters growth. Additionally, obtaining precise location information of brain imaging data is crucial for improving the classification accuracy with 3D-CNN. Hence, we propose a multi-scale 3D-CNN based on coordinate attention mechanism to marvelously capture and integrate 3D features with fewer parameters, improving the accuracy of AD diagnosis. A total of 447 cognitively normal (CN), 512 MCI, and 358 AD sMRI images from the Alzheimer's Disease Neuroimaging Initiative datasets are used for multi-class classification task, yielding a classification accuracy of 92.8%. The model merely involves 2.41 M parameters and achieves the best classification results with the least number of parameters when compared to other representative CNN architectures including ResNet 18, ResNet 34, ConvNeXt tiny, and VGG 11. Through the ablation experiment, the addition of attention mechanism and the multi-scale classification enhances the classification performance by 4.5% and 1.5%, respectively. Furthermore, our model outperforms the other six existing studies in terms of accuracy for classifying AD vs. MCI vs. CN. Overall, this study underscores the efficacy of our approach for AD diagnosis, showcasing its utility in diagnosing AD patients and providing novel insights for diagnosing other neurological disorder diseases.

关键词： Neuroimaging Accuracy Attention mechanisms Three-dimensional displays Resonance Convolutional neural networks Alzheimer's disease

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From FAIR to CURE: Guidelines for Computational Models of Biological Systems

arXiv

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arXiv 2025年

作者： Sauro, Herbert M. Agmon, Eran Blinov, Michael L. Gennari, John H. Hellerstein, Joe Heydarabadipour, Adel Hunter, Peter Jardine, Bartholomew E. May, Elebeoba Nickerson, David P. Smith, Lucian P. Bader, Gary D. Bergmann, Frank Boyle, Patrick M. Dräger, Andreas Faeder, James R. Feng, Song Freire, Juliana Fröhlich, Fabian Glazier, James A. Gorochowski, Thomas E. Helikar, Tomas Hoops, Stefan Imoukhuede, Princess Keating, Sarah M. Konig, Matthias Laubenbacher, Reinhard Loew, Leslie M. Lopez, Carlos F. Lytton, William W. McCulloch, Andrew Mendes, Pedro Myers, Chris J. Myers, Jerry G. Mulugeta, Lealem Niarakis, Anna van Niekerk, David D. Olivier, Brett G. Patrie, Alexander A. Quardokus, Ellen M. Radde, Nicole Rohwer, Johann M. Sahle, Sven Schaff, James C. Sego, T.J. Shin, Janis Snoep, Jacky L. Vadigepalli, Rajanikanth Wiley, H. Steve Waltemath, Dagmar Moraru, Ion Department of Bioengineering University of Washington SeattleWA98195-5061 United States Intelligent Systems Engineering and Biocomplexity Institute Indiana University Street BloomingtonIN47408 United States Center for Cardiovascular Biology University of Washington SeattleWA98195-5061 United States eScience Institute University of Washington SeattleWA98195-5061 United States Institute for Stem Cell and Regenerative Medicine University of Washington SeattleWA98195-5061 United States School of Biological Sciences University of Bristol 24 Tyndall Avenue BristolBS8 1TQ United Kingdom Departments of Physiology & Pharmacology Neurology Downstate Health Science University BrooklynNY11203 United States Department of Neurology Kings County Hospital BrooklynNY11203 United States NASA-John H. Glenn Research Center MS 110-3 21000 Brookpark Road ClevelandOH44135 United States Center for Cell Analysis and Modeling UConn Health 263 Farmington Avenue FarmingtonCT06030-6406 United States Amsterdam Institute for Life and Environment Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam1081 HZ Netherlands Department of Pathology and Genomic Medicine Thomas Jefferson University 1020 Locust St PhiladelphiaPA19107 United States Biological Sciences Division Pacific Northwest National Laboratory 902 Battelle Blvd RichlandWA99354 United States Auckland Bioengineering Institute University of Auckland Auckland1010 New Zealand Center of Integrative Biology University of Toulouse III-Paul Sabatier 165 Rue Marianne Grunberg-Manago Toulouse31400 France Lifeware Group Inria Building Alan Turing 1 Rue Honoré d’Estienne d’Orves Palaiseau91120 France Multiscale Modeling Group Altos Labs Redwood CityCA94065 United States partner site Tübingen Tübingen Germany Ottfried-Müller-Str. 37 Tübingen72076 Germany 06120 Germany Department of Computer Science Center for Data Science New York University New YorkNY11201 United States Department of Bi

Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data and models are key to progress. For this reason, and recognizing that such models are a very special type of "data", we argue that computational models, especially mechanistic models prevalent in medicine, physiology and systems biology, deserve a complementary set of guidelines. We propose the CURE principles, emphasizing that models should be Credible, Understandable, Reproducible, and Extensible. We delve into each principle, discussing verification, validation, and uncertainty quantification for model credibility;the clarity of model descriptions and annotations for understandability;adherence to standards and open science practices for reproducibility;and the use of open standards and modular code for extensibility and reuse. We outline recommended and baseline requirements for each aspect of CURE, aiming to enhance the impact and trustworthiness of computational models, particularly in biomedical applications where credibility is paramount. Our perspective underscores the need for a more disciplined approach to modeling, aligning with emerging trends such as Digital Twins and emphasizing the importance of data and modeling standards for interoperability and reuse. Finally, we emphasize that given the non-trivial effort required to implement the guidelines, the community moves to automate as many of the guidelines as possible. © 2025, CC BY.

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Deformable registration framework for glioma images with absent correspondence based on auxiliary-image-aided intensity-consistency constraint

Deformable registration framework for glioma images with abs...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Kun Tang Lihui Wang Menglong Yang Jingwen Xu Xinyu Cheng Jian Zhang Yuemin Zhu Hongjiang Wei Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province Engineering Research Center of Text Computing & Cognitive Intelligence Ministry of Education State Key Laboratory of Public Big Data College of Computer Science and Technology Guiyang China INSA Lyon CNRS Inserm Univ Lyon Lyon France School of Biomedical Engineering Shanghai Jiao Tong University Shanghai China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

Considering the tumor aggressive nature and the significant changes in anatomical structure, aligning the preoperative and follow up scans of glioma patients remains a challenge due to the presence of regions with absent correspondence. To address this challenge, this work proposed a novel bidirectional unsupervised deformable image registration framework for image pairs with missing correspondence based on an auxiliary-image-aided intensity-consistency constraint (ICC) strategy. Specifically, for any fixed and moving image pairs, we introduced an auxiliary image and warped it directly to fixed/moving image or warped it twice through a transition of moving/fixed image. By comparing the difference between these warped images, the weighting maps to identify and exclude regions with absent correspondence between fixed and moving image pairs can be generated. To verify the effectiveness of the proposed framework, we combined it with several deep learning-based registration models and tested it on BraTS-Reg challenge dataset, the results demonstrated that the proposed ICC strategy can improve the registration performance for all the models, with the improvement of average target registration error (TRE) and success rate (SR) being up to 44.9% and 66.7%, respectively. Comparing against the best existing forward-backward consistency strategy for dealing with missing correspondence registration, our auxiliary-image-aided ICC strategy can also decrease average TRE by 2.9%, demonstrating the superiority of the proposed framework. The present work is not limited to the glioma images, it can be used to address the registration problems for any image pairs with absent correspondence or inconsistent intensity.

关键词： Image registration Pathology Deformation Magnetic resonance imaging Anatomical structure Bioinformatics Tumors Biomedical imaging

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Tumor State-Space Network for High and Low Grade Glioma Classification

Tumor State-Space Network for High and Low Grade Glioma Clas...

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International Conference on Signal Processing Proceedings (ICSP)

作者： Qijian Chen Lihui Wang Zeyu Deng Li Wang Chen Ye YueMin Zhu Engineering Research Center of Text Computing Ministry of Education Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province State Key Laboratory of Public Big Data College of Computer Science and Technology Guizhou University Guiyang China INSA Lyon CNRS Inserm IRP Metislab CREATIS UMR5220 U1206 University Lyon Lyon France

ISBN: (数字)9798350387384

ISBN: (纸本)9798350387391

Accurately predicting the grade of gliomas is crucial for choosing right treatment plans. While current methods using radiomics and deep learning can predict glioma grades effectively using magnetic resonance imaging (MRI), they overlook dynamic changes in the tumor and its neighboring areas. To address this issue, we propose a tumor state-space network (TSSNet), which fully exploits changes in the tumor region and its surroundings through dynamical updating strategy. The experimental results demonstrated that TSSNet achieves 90.32% accuracy and 93.55% area under the curve (AUC) for the prediction of high-grade and low-grade gliomas, respectively, which are 2.4% and 2.5% higher than the best state-of-the-art deep learning models. Moreover, the proposed state-space module can effectively enhance prediction performance, which is advantageous for personalized glioma treatment.

关键词： Deep learning Accuracy Magnetic resonance imaging Signal processing Predictive models Tumors Radiomics

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Context-specific miRNA regulation network predicts cancer prognosis

Context-specific miRNA regulation network predicts cancer pr...

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IEEE International Conference on Systems Biology

作者： Xionghui Zhou Juan Liu Changning Liu Simon Rayner Fengji Liang Jingfang Ju Yinghui Li Shanguang Chen Jianghui Xiong School of Computer Science Wuhan University Wuhan China Bioinformatics Research Group Key Laboratory of Intelligent Information Processing Advanced Computing Research Laboratory Institute of Computing Technology Chinese Academy of Sciences (CAS) Beijing China Bioinformatics Group State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences (CAS) Wuhan China Bioinformatics Group and Data Coordination Center State Key Laboratory of Space Medicine Fundamentals and Application China Astronaut Research and Training Center Beijing China Department of Pathology Stony Brook University Medical Center New York USA

MicroRNAs can regulate hundreds of target genes and play a pivotal role in a broad range of biological process. However, relatively little is known about how these highly connected miRNAs-target networks are remodelled in the context of various diseases. Here we examine the dynamic alteration of context-specific miRNA regulation to determine whether modified microRNAs regulation on specific biological processes is a useful information source for predicting cancer prognosis. A new concept, Context-specific miRNA activity (CoMi activity) is introduced to describe the statistical difference between the expression level of a miRNA's target genes and non-targets genes within a given gene set (context).

关键词： Breast cancer Context Correlation Biological processes Metastasis Tumors

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SurgicalGaussian: Deformable 3D Gaussians for High-Fidelity Surgical Scene Reconstruction

arXiv

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arXiv 2024年

作者： Xie, Weixing Yao, Junfeng Cao, Xianpeng Lin, Qiqin Tang, Zerui Dong, Xiao Guo, Xiaohu Center for Digital Media Computing School of Film School of Informatics Xiamen University Xiamen China National Institute for Data Science in Health and Medicine Xiamen University China Key Laboratory of Digital Protection and Intelligent Processing of Intangible Cultural Heritage of Fujian and Taiwan Ministry of Culture and Tourism China Guangdong Provincial Key Laboratory IRADS Department of Computer Science BNU-HKBU United International College Zhuhai China Department of Computer Science The University of Texas at Dallas Dallas United States

Dynamic reconstruction of deformable tissues in endoscopic video is a key technology for robot-assisted surgery. Recent reconstruction methods based on neural radiance fields (NeRFs) have achieved remarkable results in the reconstruction of surgical scenes. However, based on implicit representation, NeRFs struggle to capture the intricate details of objects in the scene and cannot achieve real-time rendering. In addition, restricted single view perception and occluded instruments also propose special challenges in surgical scene reconstruction. To address these issues, we develop SurgicalGaussian, a deformable 3D Gaussian Splatting method to model dynamic surgical scenes. Our approach models the spatio-temporal features of soft tissues at each time stamp via a forward-mapping deformation MLP and regularization to constrain local 3D Gaussians to comply with consistent movement. With the depth initialization strategy and tool mask-guided training, our method can remove surgical instruments and reconstruct high-fidelity surgical scenes. Through experiments on various surgical videos, our network outperforms existing method on many aspects, including rendering quality, rendering speed and GPU usage. The project page can be found at https://***. © 2024, CC BY-SA.

关键词： Tissue

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Optimal Quantum State Tomography via Weak Value

arXiv

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arXiv 2024年

作者： Zhu, Xuanmin Zhang, Dezheng Gao, Runping Wei, Qun Liu, Lixia Luo, Zijiang Center for Quantum Information School of Information Guizhou University of Finance and Economics Guizhou Guiyang550025 China International Joint Research Center for Data Science and High-Performance Computing School of Information Guizhou University of Finance and Economics Guizhou Guiyang550025 China School of Physics and Optoelectronic Engineering Xidian University Xi’an710071 China School of Mathematics and Statistics Xidian University Xi’an710071 China Institute of Intelligent Manufacturing Shunde Polytechnic Guangdong Shunde 528300 China

To improve the efficiency of the state tomography strategy via weak value, we have searched the optimal coupling strength between the system and measuring device. For an arbitrary d-dimensional quantum system, the optimal strengths being used in measuring the real and imaginary parts of the density matrix are obtained. The optimal efficiency of the state tomography has also been studied by using mean square error. The minimal mean square errors in the reconstructed density matrices have been derived. The state tomography strategy studied in this article may be useful in the measurement of the unknown quantum states. Copyright © 2024, The Authors. All rights reserved.

关键词： Mean square error

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A deep learning system for predicting time to progression of diabetic retinopathy

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NATURE MEDICINE 2024年第2期30卷 358-359页

作者： [Anonymous] Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders Department of Computer Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Department of Endocrinology and Metabolism Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai Diabetes Institute Shanghai Clinical Center for Diabetes Shanghai China MOE Key Laboratory of AI School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai China Department of Ophthalmology Huadong Sanatorium Wuxi China Department of Ophthalmology Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai China Department of Ophthalmology and Visual Sciences The Chinese University of Hong Kong Hong Kong China Singapore Eye Research Institute Singapore National Eye Centre Singapore Singapore Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong China Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Hong Kong China State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat-sen University Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science Guangzhou China Department of Ophthalmology Peking Union Medical College Hospital Peking Union Medical College Chinese Academy of Medical Sciences Beijing China Medical Records and Statistics Office Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai China Department of Geriatrics Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Cluster and Grid Computing Lab School of Computer Science and Tech

We developed and validated a deep learning system (termed DeepDR Plus) in a diverse, multiethnic, multi-country dataset to predict personalized risk and time to progression of diabetic retinopathy. We show that DeepDR Plus can be integrated into the clinical workflow to promote individualized intervention strategies for the management of diabetic retinopathy.

关键词： Diabetes complications Machine learning Predictive markers

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