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Degeneration Directory:a multi-omics web resource for degenerative diseases

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Protein & Cell 2024年第5期15卷 385-392页

作者： Haoteng Yan Changfa Lu Chenyang Lan Si Wang Weiqi Zhang Zan He Jinghao Hu Jiaqi Ai Guang-Hui Liu Shuai Ma Yuanchun Zhou Jing Qu State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China Aging Translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China Computer Network Information Center Chinese Academy of SciencesBeijing 100190China The Fifth People’s Hospital of Chongqing Chongqing 400062China Aging Biomarker Consortium Beijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Sino-Danish College University of Chinese Academy of SciencesBeijing 101408China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China

Background of *** degeneration refers to the gradual decline in organ function and structure deterioration that occurs during aging,which represents the greatest risk factor for various degenerative diseases,including cardiovascular diseases,neurodegenerative diseases,and osteoarthritis,etc.(Aging Biomarker et al.,2023;Becker et al.,2018;Cai et al.,2022).

关键词： Directory web Becker

scCDCG: Efficient Deep Structural Clustering for single-cell RNA-seq via Deep Cut-informed Graph Embedding

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arXiv 2024年

作者： Xu, Ping Ning, Zhiyuan Xiao, Meng Feng, Guihai Li, Xin Zhou, Yuanchun Wang, Pengfei Computer Network Information Center Chinese Academy of Sciences China University of Chinese Academy of Sciences China Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences China State Key Laboratory of Stem Cell and Reproductive Biology Institute of Zoology Chinese Academy of Sciences China Institute for Stem Cell and Regenerative Medicine Chinese Academy of Science China Beijing Institute for Stem Cell and Regenerative Medicine Chinese Academy of Science China

Single-cell RNA sequencing (scRNA-seq) is essential for unraveling cellular heterogeneity and diversity, offering invaluable insights for bioinformatics advancements. Despite its potential, traditional clustering methods in scRNA-seq data analysis often neglect the structural information embedded in gene expression profiles, crucial for understanding cellular correlations and dependencies. Existing strategies, including graph neural networks, face challenges in handling the inefficiency due to scRNA-seq data’s intrinsic high-dimension and high-sparsity. Addressing these limitations, we introduce scCDCG (single-cell RNA-seq Clustering via Deep Cut-informed Graph), a novel framework designed for efficient and accurate clustering of scRNA-seq data that simultaneously utilizes intercellular high-order structural information. scCDCG comprises three main components: (i) A graph embedding module utilizing deep cut-informed techniques, which effectively captures intercellular high-order structural information, overcoming the over-smoothing and inefficiency issues prevalent in prior graph neural network methods. (ii) A self-supervised learning module guided by optimal transport, tailored to accommodate the unique complexities of scRNA-seq data, specifically its high-dimension and high-sparsity. (iii) An autoencoder-based feature learning module that simplifies model complexity through effective dimension reduction and feature extraction. Our extensive experiments on 6 datasets demonstrate scCDCG’s superior performance and efficiency compared to 7 established models, underscoring scCDCG’s potential as a transformative tool in scRNA-seq data analysis. Our code is available at: https://***/XPgogogo/scCDCG. © 2024, CC0.

关键词： RNA

Neural Gradient Regularizer

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arXiv 2023年

作者： Xu, Shuang Wang, Yifan Zhao, Zixiang Peng, Jiangjun Cao, Xiangyong Meng, Deyu Zhang, Yulun Timofte, Radu Van Gool, Luc School of Mathematics and Statistics Northwestern Polytechnical University Xi’an710021 China Research and Development Institute Northwestern Polytechnical University in Shenzhen Shenzhen518063 China School of Electronic and Information Engineering The Key Laboratory for Intelligent Networks and Network Security Ministry of Education Xi’an Jiaotong University Xi’an710049 China School of Mathematics and Statistics Xi’an Jiaotong University Xi’an710049 China Computer Vision Lab ETH Zurich Zürich8092 Switzerland

Owing to its significant success, the prior imposed on gradient maps has consistently been a subject of great interest in the field of image processing. Total variation (TV), one of the most representative regularizers, is known for its ability to capture the intrinsic sparsity prior underlying gradient maps. Nonetheless, TV and its variants often underestimate the gradient maps, leading to the weakening of edges and details whose gradients should not be zero in the original image (i.e., image structures is not describable by sparse priors of gradient maps). Recently, total deep variation (TDV) has been introduced, assuming the sparsity of feature maps, which provides a flexible regularization learned from large-scale datasets for a specific task. However, TDV requires to retrain the network with image/task variations, limiting its versatility. To alleviate this issue, in this paper, we propose a neural gradient regularizer (NGR) that expresses the gradient map as the output of a neural network. Unlike existing methods, NGR does not rely on any subjective sparsity or other prior assumptions on image gradient maps, thereby avoiding the underestimation of gradient maps. NGR is applicable to various image types and different image processing tasks, functioning in a zero-shot learning fashion, making it a versatile and plug-and-play regularizer. Extensive experimental results demonstrate the superior performance of NGR over state-of-the-art counterparts for a range of different tasks, further validating its effectiveness and versatility. © 2023, CC BY.

关键词： Large dataset

A Review of Multimodal Explainable Artificial Intelligence: Past, Present and Future

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arXiv 2024年

作者： Sun, Shilin An, Wenbin Tian, Feng Nan, Fang Liu, Qidong Liu, Jun Shah, Nazaraf Chen, Ping School of Computer Science and Technology Xi’an Jiaotong University Xi’an710049 China Ministry of Education Key Laboratory of Intelligent Networks and Network Security Xi’an Jiaotong University Xi’an710049 China Faculty of Electronic and Information Engineering Xi’an Jiaotong University Xi’an710049 China Shaanxi Province Key Laboratory of Big Data Knowledge Engineering Xi’an Jiaotong University Xi’an710049 China Institute for Future Transport and Cities Coventry University Priory Street CoventryCV1 5FB United Kingdom Department of Engineering University of Massachusetts Boston BostonMA02125 United States

Artificial intelligence (AI) has rapidly developed through advancements in computational power and the growth of massive datasets. However, this progress has also heightened challenges in interpreting the "black-box" nature of AI models. To address these concerns, eXplainable AI (XAI) has emerged with a focus on transparency and interpretability to enhance human understanding and trust in AI decision-making processes. In the context of multimodal data fusion and complex reasoning scenarios, the proposal of Multimodal eXplainable AI (MXAI) integrates multiple modalities for prediction and explanation tasks. Meanwhile, the advent of Large Language Models (LLMs) has led to remarkable breakthroughs in natural language processing, yet their complexity has further exacerbated the issue of MXAI. To gain key insights into the development of MXAI methods and provide crucial guidance for building more transparent, fair, and trustworthy AI systems, we review the MXAI methods from a historical perspective and categorize them across four eras: traditional machine learning, deep learning, discriminative foundation models, and generative LLMs. We also review evaluation metrics and datasets used in MXAI research, concluding with a discussion of future challenges and directions. A project related to this review has been created at https://***/ShilinSun/mxai_review. Copyright © 2024, The Authors. All rights reserved.

关键词： Data fusion

Low Complexity Detection of Spatial Modulation Aided OTFS in Doubly-Selective Channels

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arXiv 2023年

作者： Sui, Zeping Zhang, Hongming Xin, Yu Bao, Tong Yang, Lie-Liang Hanzo, Lajos The Institute of Acoustics Chinese Academy of Sciences Beijing100190 China The University of Chinese Academy of Sciences Beijing100049 China The School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing100876 China The State Key Laboratory of Mobile Network and Mobile Multimedia Technology ZTE Corporation Shenzhen518055 China The Department of Electronics and Computer Science University of Southampton SouthamptonSO17 1BJ United Kingdom

A spatial modulation-aided orthogonal time frequency space (SM-OTFS) scheme is proposed for high-Doppler scenarios, which relies on a low-complexity distance-based detection algorithm. We first derive the delay-Doppler (DD) domain input-output relationship of our SM-OTFS system by exploiting an SM mapper, followed by characterizing the doubly-selective channels considered. Then we propose a distance-based ordering subspace check detector (DOSCD) exploiting the a priori information of the transmit symbol vector. Moreover, we derive the discrete-input continuous-output memoryless channel (DCMC) capacity of the system. Finally, our simulation results demonstrate that the proposed SM-OTFS system outperforms the conventional single-input-multiple-output (SIMO)-OTFS system, and that the DOSCD conceived is capable of striking an attractive bit error ratio (BER) vs. complexity trade-off. Copyright © 2023, The Authors. All rights reserved.

关键词： Economic and social effects

Verifiable Privacy Preservation Scheme for Outsourcing Medi-cal Image to Cloud Through ROI Based Crypto-Watermarking

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Verifiable Privacy Preservation Scheme for Outsourcing Medi-...

IEEE/ACM Int'l Conference on & Int'l Conference on Cyber, Physical and Social Computing (CPSCom) Green Computing and Communications (GreenCom)

作者： Chuan Zhou Yi Zhou XingHan An Yan Liu Min Wang XiangZhi Liu Tianjin University Tianjin China Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center (National Supercomputer Center in Jinan) Qilu University of Technology (Shandong Academy of Sciences) Jinan China College of Environmental Science and Engineering Beijing Forestry University Beijing China Inspur Software Co. Ltd. Jinan China The Party School of cpc Jinan Municipal Committee Jinan China

A novel verifiable privacy preservation scheme for outsourcing medical image to cloud through ROI based crypto-watermarking is proposed in the paper. In the proposed scheme, data owner firstly carries out substitution of S-box for the region of interest (ROI) of medical image, and then separates the image into 4 most significant bits (MSBs) plane and 4 least significant bits (LSBs) plane images. Secondly, the hash value of ROI is embedded into the two separated bit plane images using reversible watermarking algorithm. Lastly, some selected hash values are transformed into the initial parameters of chaotic maps, and the two sharing secrets, which are produced through chaos based encryption algorithm, are finally outsourced to two different cloud servers. For authorized users, they can get shares from different cloud servers, and then can losslessly recover the original medical image through a series of decryption operations and extraction of watermarking. Furthermore, the users can verify whether the original image is completely reconstructed or not, they even can locate the tampered parts inside ROI if anyone of the sharing secrets is damaged. Some experiments analyses and comparisons are given to show the security and effectiveness of proposed scheme.

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GraphFederator: Federated Visual Analysis for Multi-party Graphs

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GraphFederator: Federated Visual Analysis for Multi-party Gr...

Pacific (formerly Asia-Pacific APVIS) Visualization Symposium

作者： Dongming Han Haiyang Zhu Wei Chen Rusheng Pan Yijing Liu Jiehui Zhou Haozhe Feng Tianye Zhang Xumeng Wang Minfeng Zhu Jianrong Tao Changjie Fan Xiaolong Luke Zhang State Key Lab of CAD&CG Zhejiang University China Hithink RoyalFlush Information Network Co. Ltd. China Wuchan Zhongda Digital Technology Co. Ltd. China Ministry of Education Laboratory of Art and Archaeology Image (Zhejiang University) China College of Computer Science Nankai University China Zhejiang University China Fuxi AI Lab Netease China Pennsylvania State University USA

ISBN: (数字)9798350393804

ISBN: (纸本)9798350393811

This paper presents GraphFederator, a novel approach to construct federated representations of multi-party graphs and supports privacy-preserving visual analysis of graphs. Inspired by the concept of federated learning, we reformulate the analysis of multi-party graphs into a decentralization process. The new federation framework consists of a shared module that is responsible for federated modeling and analysis, and a set of local modules that run on respective graph data. Specifically, we propose a Federated Graph Representation Model (FGRM) that is learned from encrypted characteristics of multi-party graphs in local modules. We also design multiple visualization tools for federated visualization, exploration, and analysis of multi-party graphs. Experimental results on two datasets demonstrate the effectiveness of our approach.

关键词： Visualization Analytical models Federated learning Data visualization Data models Encryption

SenseMag: Enabling low-cost traffic monitoring using non-invasive magnetic sensing

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arXiv 2021年

作者： Wang, Kafeng Xiong, Haoyi Zhang, Jie Chen, Hongyang Dou, Dejing Xu, Cheng-Zhong Shenzhen Institute of Advanced Technology Chinese Academy of Sciences University of Chinese Academy of Sciences Guangdong Shenzhen China Big Data Lab Baidu Inc. Haidian Beijing China Key Laboratory of High Confidence Software Technologies Peking University Haidian Beijing China Research Center for Intelligent Network Zhejiang Lab Zhejiang Hangzhou China State Key Laboratory of Internet of Things for Smart City Department of Computer and Information Science University of Macau Tapia Macau China Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China

The operation and management of intelligent transportation systems (ITS), such as traffic monitoring, relies on real-time data aggregation of vehicular traffic information, including vehicular types (e.g., cars, trucks, and buses), in the critical roads and highways. While traditional approaches based on vehicular-embedded GPS sensors or camera networks would either invade drivers’ privacy or require high deployment cost, this paper introduces a low-cost method, namely SenseMag, to recognize the vehicular type using a pair of non-invasive magnetic sensors deployed on the straight road section. SenseMag filters out noises and segments received magnetic signals by the exact time points that the vehicle arrives or departs from every sensor node. Further, SenseMag adopts a hierarchical recognition model to first estimate the speed/velocity, then identify the length of vehicle using the predicted speed, sampling cycles, and the distance between the sensor nodes. With the vehicle length identified and the temporal/spectral features extracted from the magnetic signals, SenseMag classify the types of vehicles accordingly. Some semi-automated learning techniques have been adopted for the design of filters, features, and the choice of hyper-parameters. Extensive experiment based on real-word field deployment (on the highways in Shenzhen, China) shows that SenseMag significantly outperforms the existing methods in both classification accuracy and the granularity of vehicle types (i.e., 7 types by SenseMag versus 4 types by the existing work in comparisons). To be specific, our field experiment results validate that SenseMag is with at least 90% vehicle type classification accuracy and less than 5% vehicle length classification error. Copyright © 2021, The Authors. All rights reserved.

关键词： Sensor nodes

Device Activity Detection in mMTC with Low-Resolution ADC: A New Protocol

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arXiv 2023年

作者： Wang, Zhaorui Liu, Ya-Feng Wang, Ziyue Liu, Liang Pan, Haoyuan Cui, Shuguang The Future Network of Intelligence Institute The School of Science and Engineering The Chinese University of Hong Kong Shenzhen518172 China The State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China The Department of Electronic and Information Engineering The Hong Kong Polytechnic University Hong Kong College of Computer Science and Software Engineering Shenzhen University Shenzhen China

This paper investigates the effect of low-resolution analog-to-digital converters (ADCs) on device activity detection in massive machine-type communications (mMTC). The low-resolution ADCs induce two challenges on the device activity detection compared with the traditional setup with the assumption of infinite ADC resolution. First, the codebook design for signal quantization by the low-resolution ADC is particularly important since a good design of the codebook can lead to small quantization error on the received signal, which in turn has significant influence on the activity detector performance. To this end, prior information about the received signal power is needed, which depends on the number of active devices K. This is sharply different from the activity detection problem in traditional setups, in which the knowledge of K is not required by the BS as a prerequisite. Second, the covariance-based approach achieves good activity detection performance in traditional setups while it is not clear if it can still achieve good performance in this paper. To solve the above challenges, we propose a communication protocol that consists of an estimator for K and a detector for active device identities: 1) For the estimator, the technical difficulty is that the design of the ADC quantizer and the estimation of K are closely intertwined and doing one needs the information/execution from the other. We propose a progressive estimator which iteratively performs the estimation of K and the design of the ADC quantizer;2) For the activity detector, we propose a custom-designed stochastic gradient descent algorithm to estimate the active device identities. Numerical results demonstrate the effectiveness of the communication protocol. © 2023, CC BY.

关键词： Stochastic systems