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IEEE International Conference on bioinformatics and Biomedicine (BIBM)

作者： Keliang Zhao Jovial Niyogisubizo Linxia Xiao Yi Pan Dongqing Wei Didi Rosiyadi Yanjie Wei Shenzhen Key Laboratory of Intelligent Bioinformatics and Center for High Performance Computing Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China College of Computer Science and Control Engineering Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai China Research Center for Artificial Intelligence and Cybersecurity National Research and Innovation Agency Bandung Indonesia

The precise segmentation and tracking of cells in microscopy image sequences play a pivotal role in biomedical research, facilitating the study of tissue, organ, and organism development. However, manual segmentation and tracking of cells is time-consuming and often require professional experiences. Besides, segmenting cells in the images with a low signal-to-noise ratio remains difficult. While deep learning (DL) has become a common method for cell segmentation, few DL- based methods address concurrent cell segmentation and tracking. In this paper, we propose a novel DL approach featuring graph-based tracking for cell segmentation and tracking in microscopy images. We combine Deeplabv3+ for semantic segmentation and ResNet50 for enhanced feature extraction, enabling comprehensive cell detection and instance segmentation. Post-processing, involving non-maxima suppression and outlier detection, refines predictions and produces final segmentation. The tracking method is based on the relative position of graph nodes to track segmented cells, encompassing cell division and apoptosis. We conduct our experiments on the induced pluripotent stem (iPS) cell datasets, and the results show that the segmentation and tracking performance of our method yields superior performance compared to the benchmark models. More specifically, our approach achieved DET values of 0.955 and 0.913, TRA values of 0.951 and 0.906, and SEG values of 0.690 and 0.665 on two iPS dataset videos, respectively. Additionally, the performance assessment encompasses four real microscopy datasets from the Cell Tracking Challenge (CTC). Our method greatly reduces the cost of manual labeling and labor-intensive costs.

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WaveFormer: A Wavelet Transformer for Parkinson Disease’s Retinal Layer Segmentation in OCT

WaveFormer: A Wavelet Transformer for Parkinson Disease’s R...

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International Joint Conference on Neural Networks (IJCNN)

作者： Yanlin Chen Xiaoqing Zhang Tianao Wang Chen Tang Haili Ye Jiang Liu Department of Computer Science and Engineering Research Institute of Trustworthy Autonomous Systems Southern University of Science and Technology Shenzhen China Shenzhen Institute of Advanced Technology Center for High Performance Computing and Shenzhen Key Laboratory of Intelligent Bioinformatics Chinese Academy of Sciences Shenzhen China School of Ophthalmology and Optometry Wenzhou Medical University Wenzhou China The Oujiang Laboratory The Affiliated Eye Hospital Wenzhou Medical University Wenzhou China

ISBN: (数字)9798350359312

ISBN: (纸本)9798350359329

Pathology symptoms of Parkinson disease (PD) are different from those of retinal diseases in the retinal layers, which are subtle. However, segmenting pathology information of PD from retinal layers automatically based on optical coherence tomography (OCT) images has not been studied before. Although existing Transformer-based segmentation methods have achieved good segmentation results, they have limitations in capturing local context information. Convolutional neural networks (CNNs) can construct local context dependencies among pixels, which is complementary to Transformers. Particularly, edge information extraction is significant for accurate retinal layer segmentation, which is ignored by both Transformers and CNNs but can be captured by frequency domain learning methods. To fully leverage the advantages of Transformers, CNNs, and frequency domain learning methods, we propose a Wavelet Transformer (WaveFormer) for retinal layer segmentation based on OCT images. In the WaveFormer, we design a Wavelet Spatial Attention block to exploit the potential of frequency information. Based on these advantages, WaveFormer can be data-efficient in limited OCT images of PD. The experimental results on the OCT-PD segmentation dataset show that our WaveFormer outperforms existing Transformers and CNNs. For example, WaveFormer outperforms Swin-UNet by 3.41% of IoU.

关键词： Learning systems Image segmentation Pathology Wavelet domain Image edge detection Frequency-domain analysis Transformers

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Medical Image Registration and Its Application in Retinal Images: A Review

arXiv

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arXiv 2024年

作者： Nie, Qiushi Zhang, Xiaoqing Hu, Yan Gong, Mingdao Liu, Jiang Research Institute of Trustworthy Autonomous Systems Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen518055 China Center for High Performance Computing Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen institute of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China Singapore Eye Research Institute 169856 Singapore State Key Laboratory of Ophthalmology Optometry and Visual Science Eye Hospital Wenzhou Medical University Wenzhou325027 China

Medical image registration is vital for disease diagnosis and treatment with its ability to merge diverse information of images, which may be captured under different times, angles, or modalities. Although several surveys have reviewed the development of medical image registration, these surveys have not systematically summarized methodologies of existing medical image registration methods. To this end, we provide a comprehensive review of these methods from traditional and deep learning-based directions, aiming to help audiences understand the development of medical image registration quickly. In particular, we review recent advances in retinal image registration at the end of each section, which has not attracted much attention. Additionally, we also discuss the current challenges of retinal image registration and provide insights and prospects for future research. © 2024, CC BY-NC-SA.

关键词： Deep learning

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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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Dual-View Pyramid Pooling in Deep Neural Networks for Improved Medical Image Classification and Confidence Calibration

arXiv

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arXiv 2024年

作者： Zhang, Xiaoqing Nie, Qiushi Xiao, Zunjie Zhao, Jilu Wu, Xiao Guo, Pengxin Li, Runzhi Liu, Jin Wei, Yanjie Pan, Yi Center for High Performance Computing Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Guangdong Shenzhen518055 China Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen518055 China Department of Statistics and Actuarial Science The University of Hong Kong 999077 Hong Kong Cooperative Innovation Center of Internet Healthcare Zhengzhou University Zhengzhou450001 China Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha410083 China Xinjiang Engineering Research Center of Big Data and Intelligent Software School of software Xinjiang University Wulumuqi830046 China Faculty of Computer Science and Control Engineering Shenzhen University of Advanced Technology Shenzhen China

Spatial pooling (SP) and cross-channel pooling (CCP) operators have been applied to aggregate spatial features and pixel-wise features from feature maps in deep neural networks (DNNs), respectively. Their main goal is to reduce computation and memory overhead without visibly weakening the performance of DNNs. However, SP often faces the problem of losing the subtle feature representations, while CCP has a high possibility of ignoring salient feature representations, which may lead to both miscalibration of confidence issues and suboptimal medical classification results. To address these problems, we propose a novel dual-view framework, the first to systematically investigate the relative roles of SP and CCP by analyzing the difference between spatial features and pixel-wise features. Based on this framework, we propose a new pooling method, termed dual-view pyramid pooling (DVPP), to aggregate multi-scale dual-view features. DVPP aims to boost both medical image classification and confidence calibration performance by fully leveraging the merits of SP and CCP operators from a dual-axis perspective. Additionally, we discuss how to fulfill DVPP with five parameter-free implementations. Extensive experiments on six 2D/3D medical image classification tasks show that our DVPP surpasses state-of-the-art pooling methods in terms of medical image classification results and confidence calibration across different DNNs. © 2024, CC BY.

关键词： Deep neural networks

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SEBF: A single-chain based extension model of blockchain for fintech 29

SEBF: A single-chain based extension model of blockchain for...

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29th International Joint Conference on Artificial Intelligence, IJCAI 2020

作者： Ji, Yimu Gu, Weiheng Chen, Fei Xiao, Xiaoying Sun, Jing Liu, Shangdong He, Jing Li, Yunyao Zhang, Kaixiang Mei, Fen Wu, Fei School of Computer Science Nanjing University of Posts and Telecommunications Nanjing China Jiangsu High Technology Research Key Laboratory for Wireless Sensor Networks Nanjing China Institue of High Performance Computing and Bigdata Nanjing University of Posts and Telecommunications Nanjing China Nanjing Center of HPC China Nanjing China Jiangsu HPC and Intelligent Processing Engineer Research Center Nanjing China Institute of Information Technology Nanjing University of Finance and Economics Nanjing China School of Software and Electrical Engineering Swinburne University of Technology Hawthorn Australia WeBank Co. Ltd. Shenzhen China College of Automation Nanjing University of Posts and Telecommunications Nanjing China

ISBN: (纸本)9780999241165

The traditional blockchain has the shortcoming that a single-chain can only deal with one or a few specific data types. The research question of how to make blockchain be able to deal with various data types has not been well studied. In this paper, we propose a single-chain based extension model of blockchain for fintech (SEBF). In the financial environment, we design a four-layer architecture for this model. By employing the external trusted oracle group and a financial regulator agency, a variety types of data can be effectively stored in the blockchain, such that the data type extension based on a single-chain is realized. The experimental results indicate that the proposed model can improve the efficiency of simplified payment verification. © 2020 Inst. Sci. inf., Univ. Defence in Belgrade. All rights reserved.

关键词： Blockchain

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Graph Confidence Intercalibration Network for Intracranial Aneurysm Lesion Instance Segmentation in Dsa

SSRN

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SSRN 2024年

作者： Ye, Haili Mo, Yancheng Tang, Chen Liao, Mingqian Zhang, Xiaoqing Dai, Limeng Li, Baihua Liu, Jiang Research Institute of Trustworthy Autonomous Systems Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen518055 China Department of Computer Science Loughborough University LoughboroughLE11 3TU United Kingdom School of Ophthalmology and Optometry Eye Hospital Wenzhou Medical University Wenzhou325027 China Center for High Performance Computing and Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China Shenzhen People’s Hospital Neurosurgery Department Shenzhen518020 China China

Intracranial aneurysm (IA) lesion segmentation is significant for its treatment and prognosis. Although exiting deep network-based instance methods have good IA lesion segmentation results based on digital subtraction angiography (DSA) images, they still face great challenges with instance confidence bias and imprecise boundary segmentation, which may negatively affect IA diagnosis. To tackle these problems, this paper proposes a novel graph confidence intercalibration network (GCINet) to automatically segment IA lesions from DSA images. To be specific, we design a graph confidence intercalibration (GCI) module to mitigate instance confidence bias by dynamically adjusting their confidence distributions. At the same time, we propose an edge space perception (ESP) module to correct ambiguous segmentation boundaries. Extensive experiments on a clinical IA-DSA and a publicly available LiTS dataset demonstrate that our GCINet outperforms state-of-the-art methods. Additionally, visual analysis and ablation studies are provided to verify the effectiveness of each module in GCINet. © 2024, The Authors. All rights reserved.

关键词： Image segmentation

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Accumulative time-based ranking method to reputation evaluation in information networks

arXiv

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arXiv 2019年

作者： Liao, Hao Liu, Qi-Xin Huang, Ze-Cheng Yeung, Chi Ho Zhang, Yi-Cheng National Engineering Laboratory on Big Data System Computing Technology Guangdong Province Engineering Center of China-made High Performance Data Computing System College of Computer Science and Software Engineering Shenzhen University Shenzhen518060 China Institute of Big Data Intelligent Management and Decision Shenzhen University Shenzhen518060 China Department of Science and Environmental Studies The Education University of Hong Kong Hong Kong Hong Kong Department of Physics University of Fribourg Fribourg Switzerland

With the rapid development of modern technology, the Web has become an important platform for users to make friends and acquire information. However, since information on the Web is over-abundant, information filtering becomes a key task for online users to obtain relevant suggestions. As most Websites can be ranked according to users’ rating and preferences, relevance to queries, and recency, how to extract the most relevant item from the over-abundant information is always a key topic for researchers in various fields. In this paper, we adopt tools used to analyze complex networks to evaluate user reputation and item quality. In our proposed accumulative time-based ranking (ATR) algorithm, we incorporate two behavioral weighting factors which are updated when users select or rate items, to reflect the evolution of user reputation and item quality over time. We showed that our algorithm outperforms state-of-the-art ranking algorithms in terms of precision and robustness on empirical datasets from various online retailers and the citation datasets among research publications. Copyright © 2019, The Authors. All rights reserved.

关键词： Information filtering

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Efficient Pyramid Channel Attention Network for Pathological Myopia Recognition

arXiv

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arXiv 2023年

作者： Zhang, Xiaoqing Zhao, Jilu Li, Yan Wu, Hao Zhou, Xiangtian Liu, Jiang Research Institute of Trustworthy Autonomous Systems Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen518055 China Center for High Performance Computing Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China National Clinical Research Center for Ocular Diseases Eye Hospital Wenzhou Medical University Wenzhou325027 China State Key Laboratory of Ophthalmology Optometry and Visual Science Eye Hospital Wenzhou Medical University Wenzhou325027 China Research Unit of Myopia Basic Research and Clinical Prevention and Control Chinese Academy of Medical Sciences Wenzhou325027 China Singapore Eye Research Institute 169856 Singapore

Pathological myopia (PM) is the leading ocular disease for impaired vision worldwide. Clinically, the characteristic of pathology distribution in PM is global-local on the fundus image, which plays a significant role in assisting clinicians in diagnosing PM. However, most existing deep neural networks focused on designing complex architectures but rarely explored the pathology distribution prior of PM. To tackle this issue, we propose an efficient pyramid channel attention (EPCA) module, which fully leverages the potential of the clinical pathology prior of PM with pyramid pooling and multi-scale context fusion. Then, we construct EPCA-Net for automatic PM recognition based on fundus images by stacking a sequence of EPCA modules. Moreover, motivated by the recent pretraining-and-finetuning paradigm, we attempt to adapt pre-trained natural image models for PM recognition by freezing them and treating the EPCA and other attention modules as adapters. In addition, we construct a PM recognition benchmark termed PM-fundus by collecting fundus images of PM from publicly available datasets. The comprehensive experiments demonstrate the superiority of EPCA-Net over state-of-the-art methods in the PM recognition task. For example, EPCA-Net achieves 97.56% accuracy and outperforms ViT by 2.85% accuracy on the PM-fundus dataset. The results also show that our method based on the pretraining-and-finetuning paradigm achieves competitive performance through comparisons to part of previous methods based on traditional fine-tuning paradigm with fewer tunable parameters, which has the potential to leverage more natural image foundation models to address the PM recognition task in limited medical data regime. Copyright © 2023, The Authors. All rights reserved.

关键词： Pathology

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A large-scale transcriptional study reveals inhibition of COVID-19 related cytokine storm by traditional Chinese medicines

引用

Science Bulletin 2021年第9期66卷 884-888,M0003页

作者： Yifei Dai Weijie Qiang Yu Gui Xue Tan Tianli Pei Kequan Lin Siwei Cai Liang Sun Guochen Ning Jianxun Wang Hongyan Guo Yimin Sun Jing Cheng Lan Xie Xun Lan Dong Wang State Key Laboratory of Southwestern Chinese Medicine Resources School of Basic Medical SciencesChengdu University of Traditional Chinese MedicineChengdu 611137China Department of Basic Medical Sciences School of MedicineTsinghua UniversityBeijing 100084China Institute of Medicinal Plant Development Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100193China School of Pharmacy Chengdu University of Traditional Chinese MedicineChengdu 611137China High Performance Computing Department National Supercomputing Center in ShenzhenShenzhen 518055China Department of Electronic and Computer Engineering College of EngineeringDrexel UniversityPhiladelphia 19104USA Dongli District Jinqiao Street Community Health Service Center Tianjin 300300China Department of Biomedical Engineering School of MedicineTsinghua UniversityBeijing 100084China School of Life Sciences Beijing University of Chinese MedicineBeijing 100029China National Engineering Research Center for Beijing Biochip Technology Beijing 102206China State Key Laboratory of Membrane Biology School of MedicineTsinghua UniversityBeijing 100084China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases Hangzhou 310003China Medical Systems Biology Research Center School of MedicineTsinghua UniversityBeijing 100084China

The application of traditional Chinese medicine(TCM)has made great contributions to the fight against the epidemic of coronavirus disease-2019(COVID-19).Despite the remarkable therapeutic effects of TCM,the molecular mechanisms of TCM formulae inhibiting COVID-19 are still not fully ***,we cφm-bined the automated high throughput sequencing-based high throughput screening(HTS^(2))assay with bioinformatics and computer-aided drug design(CADD)to investigate the molecular mechanisms of TCM-mediated therapeutic effects on COVID-19-related cytokine storm(Fig.1a).

关键词：细胞因子风暴六君子汤理中汤诊疗方案黄连解毒汤中药提取物肺炎分子机制

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