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arXiv 2025年

作者： Li, Heng Li, Haojin Ou, Mingyang Yu, Xiangyang Zhang, Xiaoqing Niu, Ke Fu, Huazhu Liu, Jiang Research Institute of Trustworthy Autonomous Systems SUSTech Shenzhen China Department of Computer Science and Engineering SUSTech Shenzhen China Center for High Performance Computing and Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Computer School Beijing Information Science and Technology University Beijing China Singapore

As an affordable and convenient eye scan, fundus photography holds the potential for preventing vision impairment, especially in resource-limited regions. However, fundus image degradation is common under intricate imaging environments, impacting following diagnosis and treatment. Consequently, image quality assessment (IQA) and enhancement (IQE) are essential for ensuring the clinical value and reliability of fundus images. While existing reviews offer some overview of this field, a comprehensive analysis of the interplay between IQA and IQE, along with their clinical deployment challenges, is lacking. This paper addresses this gap by providing a thorough review of fundus IQA and IQE algorithms, research advancements, and practical applications. We outline the fundamentals of the fundus photography imaging system and the associated interferences, and then systematically summarize the paradigms in fundus IQA and IQE. Furthermore, we discuss the practical challenges and solutions in deploying IQA and IQE, as well as offer insights into potential future research directions. Copyright © 2025, The Authors. All rights reserved.

关键词： Photography

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COph100: A comprehensive fundus image registration dataset from infants constituting the "RIDIRP" database

arXiv

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arXiv 2025年

作者： Hu, Yan Gong, Mingdao Qiu, Zhongxi Liu, Jiabao Shen, Hongli Yuan, Mingzhen Zhang, Xiaoqing Li, Heng Lu, Hai Liu, Jiang Research Institute of Trustworthy Autonomous Systems Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen China Beijing Tongren Eye Center Beijing Tongren Hospital Capital Medical University Beijing Ophthalmology and Visual Sciences Key Laboratory Beijing China Center for High Performance Computing and Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China

Retinal image registration is vital for diagnostic therapeutic applications within the field of ophthalmology. Existing public datasets, focusing on adult retinal pathologies with high-quality images, have limited number of image pairs and neglect clinical challenges. To address this gap, we introduce COph100, a novel and challenging dataset known as the Comprehensive Ophthalmology Retinal Image Registration dataset for infants with a wide range of image quality issues constituting the public "RIDIRP" database1. COph100 consists of 100 eyes, each with 2 to 9 examination sessions, amounting to a total of 491 image pairs carefully selected from the publicly available dataset. We manually labeled the corresponding ground truth image points and provided automatic vessel segmentation masks for each image. We have assessed COph100 in terms of image quality and registration outcomes using state-of-the-art algorithms. This resource enables a robust comparison of retinal registration methodologies and aids in the analysis of disease progression in infants, thereby deepening our understanding of pediatric ophthalmic conditions. Copyright © 2025, The Authors. All rights reserved.

关键词： Image registration

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CircRNA Profiles Analysis of Neuroblastoma for Identification of Drug Targets

IEEE Transactions on Computational Biology and Bioinformatic...

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IEEE Transactions on Computational Biology and bioinformatics 2025年第2期22卷 433-443页

作者： Jingjing Zhang Zhen Ju Huiling Zhang Haiping Zhang Rui Zhou Godfrey Chi-Fung Chan Jintao Meng Wenhui Xi Yanjie Wei Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China University of Chinese Academy of Sciences Beijing China South China Agricultural University Guangzhou China Department of Paediatrics & Adolescent Medicine Li Ka Shing Faculty of Medicine The University of Hong Kong Hong Kong China Center for High Performance Computing and Key Laboratory for Quantitative Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China

Neuroblastoma is a prevalent pediatric tumor with a low 5-year survival rate among high-risk patients, and the prognosis remains poor despite available therapeutic interventions. Therefore, identifying novel and effective therapeutic targets is critical for improving outcomes in these patients. In this study, we performed an integrative analysis of two neuroblastoma circRNA sequencing datasets to identify potential drug targets. By comparing circRNA expression levels between neuroblastoma tissues and adjacent normal tissues, we identified differentially expressed circRNAs and subsequently predicted 30 hub circRNAs through Weighted Gene Co-expression Network Analysis. To elucidate the functional roles of these circRNAs, we investigated their interactions with RNA-binding proteins. The results suggest that hsa_circ_0051680 and hsa_circ_0006107 may influence neuroblastoma progression through interactions with FUS and IGF2BP1, respectively. Furthermore, we analyzed the translational potential of the hub circRNAs, revealing that six circRNAs encode proteins with complex secondary structures. Molecular docking analysis identified five high-affinity complexes between circRNA-encoded proteins (hsa_circ_0000786, hsa_circ_0005087, hsa_circ_0006867) and their corresponding ligands. These circRNA-derived proteins present promising novel drug targets for both the diagnosis and treatment of neuroblastoma.

关键词： Proteins Correlation bioinformatics Sequential analysis Computational biology Databases Translation Prediction algorithms Pediatrics Encoding

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Autism Spectrum Disorder Classification with Interpretability in Children Based on Structural MRI Features Extracted Using Contrastive Variational Autoencoder

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Big Data Mining and Analytics 2024年第3期7卷 781-793页

作者： Ruimin Ma Ruitao Xie Yanlin Wang Jintao Meng Yanjie Wei Yunpeng Cai Wenhui Xi Yi Pan Shenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhen 518055China University of Chinese Academy of Sciences Beijing 100049China Shenzhen Key Laboratory of Intelligent Bioinformatics and with Center for High Performance ComputingShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Autism Spectrum Disorder(ASD)is a highly disabling mental disease that brings significant impairments of social interaction ability to the patients,making early screening and intervention of ASD *** the development of the machine learning and neuroimaging technology,extensive research has been conducted on machine classification of ASD based on structural Magnetic Resonance Imaging(s-MRI).However,most studies involve with datasets where participants'age are above 5 and lack *** this paper,we propose a machine learning method for ASD classification in children with age range from 0.92 to 4.83 years,based on s-MRI features extracted using Contrastive Variational AutoEncoder(CVAE).78 s-MRIs,collected from shenzhen Children's Hospital,are used for training CVAE,which consists of both ASD-specific feature channel and common-shared feature *** ASD participants represented by ASD-specific features can be easily discriminated from Typical Control(TC)participants represented by the common-shared *** case of degraded predictive accuracy when data size is extremely small,a transfer learning strategy is proposed here as a potential ***,we conduct neuroanatomical interpretation based on the correlation between s-MRI features extracted from CVAE and surface area of different cortical regions,which discloses potential biomarkers that could help target treatments of ASD in the future.

关键词： Autism Spectrum Disorder(ASD)classification Contrastive Variational AutoEncoder(CVAE) transfer learning neuroanatomical interpretation

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Accumulative Time Based Ranking Method to Reputation Evaluation in Information Networks

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Journal of Computer Science & Technology 2022年第4期37卷 960-974页

作者： Hao Liao Qi-Xin Liu Ze-Cheng Huang Ke-Zhong Lu Chi Ho Yeung Yi-Cheng Zhang National Engineering Laboratory on Big Data System Computing Technology College of Computer Science and SoftwareEngineeringShenzhen UniversityShenzhen 518060China Guangdong Province Key Laboratory of Popular High Performance Computers Shenzhen UniversityShenzhen 518060China Guangdong Province Engineering Center of China-Made High Performance Data Computing System College of ComputerScience and Software EngineeringShenzhen UniversityShenzhen 518060China Institute of Big Data Intelligent Management and Decision Shenzhen UniversityShenzhen 518060China Department of Science and Environmental Studies The Education University of Hong KongHong Kong 999077China Department of Physics University of FribourgFribourg 1700Switzerland

Due to over-abundant information on the Web, information filtering becomes a key task for online users to obtain relevant suggestions and how to extract the most related item 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 take into account the growth record of the network to identify the evolution of the reputation of users and the quality of items, by incorporating two behavior weighting factors which can capture the hidden facts on reputation and quality dynamics for each user and item respectively. Our proposed ATR algorithm mainly combines the iterative approach to rank user reputation and item quality with temporal dependence compared with other reputation evaluation methods. We show that our algorithm outperforms other benchmark ranking algorithms in terms of precision and robustness on empirical datasets from various online retailers and the citation datasets among research publications. Therefore, our proposed method has the capability to effectively evaluate user reputation and item quality.

关键词： temporal network behavior dynamics reputation evaluation ranking algorithm

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Medical image registration and its application in retinal images:a review

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Visual computing for Industry,Biomedicine,and Art 2024年第1期7卷 142-164页

作者： Qiushi Nie Xiaoqing Zhang Yan Hu Mingdao Gong Jiang Liu Research Institute of Trustworthy Autonomous Systems and Department of Computer Science and Engineering Southern University of Science and TechnologyShenzhen 518055China Center for High Performance Computing and Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Singapore Eye Research Institute Singapore 169856Singapore State Key Laboratory of Ophthalmology Optometry and Visual ScienceEye HospitalWenzhou Medical UniversityWenzhou 325027China

Medical image registration is vital for disease diagnosis and treatment with its ability to merge diverse informa-tion of images,which may be captured under different times,angles,or *** several surveys have reviewed the development of medical image registration,they have not systematically summarized the existing med-ical image registration *** this end,a comprehensive review of these methods is provided from traditional and deep-learning-based perspectives,aiming to help audiences quickly understand the development of medical image *** particular,we review recent advances in retinal image registration,which has not attracted much *** addition,current challenges in retinal image registration are discussed and insights and prospects for future research provided.

关键词： Computer-aided diagnosis Medical image registration Deep learning Generative model Transformer Retina

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Adaptive Wavelet Filters as Practical Texture Feature Amplifiers for Parkinson’s Disease Screening in OCT

arXiv

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arXiv 2025年

作者： Zhang, Xiaoqing Shi, Hanfeng Li, Xiangyu Ye, Haili Xu, Tao Li, Na Hu, Yan Lv, Fan Chen, Jiangfan Liu, Jiang Center for High Performance Computing and Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Research Institute of Trustworthy Autonomous Systems Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen518055 China State Key Laboratory of Ophthalmology Optometry and Vision Science Wenzhou Medical University Wenzhou China Centre for Computational Science and Mathematical Modelling Coventry University Coventry United Kingdom School of Computer Science University of Nottingham Ningbo China Ningbo315100 China School of Ophthalmology and Optometry Wenzhou Medical University Wenzhou325035 China Department of Electronic and Information Engineering Changchun University Changchun130022 China

Parkinson’s disease (PD) is a prevalent neurodegenerative disorder globally. The eye’s retina is an extension of the brain and has great potential in PD screening. Recent studies have suggested that texture features extracted from retinal layers can be adopted as biomarkers for PD diagnosis under optical coherence tomography (OCT) images. Frequency domain learning techniques can enhance the feature representations of deep neural networks (DNNs) by decomposing frequency components involving rich texture features. Additionally, previous works have not exploited texture features for automated PD screening in OCT. Motivated by the above analysis, we propose a novel Adaptive Wavelet Filter (AWF) that serves as the Practical Texture Feature Amplifier to fully leverage the merits of texture features to boost the PD screening performance of DNNs with the aid of frequency domain learning. Specifically, AWF first enhances texture feature representation diversities via channel mixer, then emphasizes informative texture feature representations with the well-designed adaptive wavelet filtering token mixer. By combining the AWFs with the DNN stem, AWFNet is constructed for automated PD screening. Additionally, we introduce a novel Balanced Confidence (BC) Loss by mining the potential of sample-wise predicted probabilities of all classes and class frequency prior, to further boost the PD screening performance and trustworthiness of AWFNet. The extensive experiments manifest the superiority of our AWFNet and BC over state-of-the-art methods in terms of PD screening performance and trustworthiness. © 2025, CC BY-NC-SA.

关键词： Neurodegenerative diseases

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Fast truss decomposition in memory 10th

Fast truss decomposition in memory

引用

10th International Conference on Security, Privacy and Anonymity in Computation, Communication and Storage, SpaCCS 2017

作者： Xing, Yuxuan Xiao, Nong Lu, Yutong Li, Ronghua Yu, Songping Gao, Siqi State Key Laboratory of High Performance Computing National University of Defense Technology Changsha China National Supercomputer Center in Guangzhou Sun Yat-sen University Guangzhou China Guangdong Province Key Laboratory of Popular High Performance Computers Shenzhen University Shenzhen China

ISBN: (纸本)9783319723945

The k-truss is a type of cohesive subgraphs proposed for the analysis of massive network. Existing in-memory algorithms for computing k-truss are inefficient for searching and parallel. We propose a novel traversal algorithm for truss decomposition: it effectively reduces computation complexity, we fully exploit the parallelism thanks to the optimization, and overlap IO and computation for a better performance. Our experiments on real datasets verify that it is 2x–5x faster than the exiting fastest in-memory algorithm. © Springer International Publishing AG 2017.

关键词： Trusses

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Identification of key Genes as Potential Drug Targets for Gastric Cancer

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Tsinghua Science and Technology 2023年第4期28卷 649-664页

作者： Md.Tofazzal Hossain Md.Selim Reza Yin Peng Shengzhong Feng Yanjie Wei Center for High Performance Computing Joint Engineering Research Center for Health Big Data Intelligent Analysis TechnologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China School of Computer Science and Technology University of Chinese Academy of SciencesBeijing 100049China Department of Statistics Bangabandhu Sheikh Mujibur Rahman Science and Technology UniversityGopalganj 8100Bangladesh Guangdong Provincial Key Laboratory for Genome Stability and Disease Prevention and Regional Immunity and Diseases Department of PathologyShenzhen UniversityShenzhen 518060China

Gastric cancer(GC)is one of the most common cancers and ranks the third in cancer mortality all over the *** goal of this study was to identify potential hub-genes,highlighting their functions,signaling pathways,and candidate drugs for the treatment of GC *** used publicly available next generation sequencing(NGS)data to identify differentially expressed(DE)*** top DE genes were mapped to STRING database to construct the protein-protein interaction(PPI)network and top hub genes were selected for further *** found a total of 1555 DE genes with 870 upregulated and 685 downregulated genes in *** selected the top 400(200 upregulated and 200 downregulated)genes to construct a PPI network and extracted the top 15 hub *** gene ontology(GO)term and kyoto encyclopedia of genes and genomes(KEGG)pathway enrichment analyses of the 15 hub genes exposed some important functions and signaling pathways that were significantly associated with GC *** survival analysis of the hub genes disclosed that the lower expressions of the three hub genes CDH2,COL4A1,and COL5A2 were associated with better survival of GC *** three genes might be the candidate biomarkers for the diagnosis and treatment of ***,we considered 3 key proteins(genomic biomarkers)(COL4A1,CDH2,and CO5A2)as the drug target proteins(receptors),performed their docking analysis with the 102 meta-drug agents,and found Everolimus,Docetaxel,Lanreotide,Venetoclax,Temsirolimus,and Nilotinib as the top ranked 6 candidate drugs with respect to our proposed target proteins for the treatment against GC ***,the proposed drugs might play vital role for the treatment against GC patients.

关键词： gastric cancer hub genes candidate genes molecular docking candidate drugs

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A Heuristic Sparsification Method to Improve the performance of Neural Networks on Autism Spectrum Disorder Identification Tasks 13

A Heuristic Sparsification Method to Improve the Performance...

引用

13th International Conference on Information Science and Technology, ICIST 2023

作者： Zhang, Fangyu Wei, Yanjie Lin, Zhenli Pan, Yi Liu, Jin Centre for High Performance Computing Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Department of Ophthalmology Shenzhen University General Hospital Shenzhen China Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China School of Computer Science and Engineering Central South University Changsha China

ISBN: (纸本)9798350313925

Deep learning (DL) has been widely used in the detection of neurological diseases such as Autism spectrum disorder (ASD). Most studies in this field manually designed and adjusted the hyperparameters of DL models, but due to the huge search space, few studies have attempted to optimize the topology of neural networks which is another important factor related to the performance of DL models. This paper proposes a heuristic sparsification method named the Evolutionary Connection Sparsification Algorithm (ECSA) which is used to optimize the topology of fully connected neural networks (FC-NNs) and generate the corresponding sparsely connected neural networks (SC-NNs). The algorithm is based on the workflow of the genetic algorithm but with improved coding strategy, fitness evaluation approach, crossover and mutation operator, and including an effective convergence acceleration strategy. Experiments show that the SC-NNs generated by ECSA significantly outperform the original FC-NNs in terms of accuracy, F1-score, and AUC, and the model complexities are greatly reduced. © 2023 IEEE.

关键词： Topology

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