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A structural variation genotyping algorithm enhanced by CNV quantitative transfer

Frontiers of computer science 2022年第6期16卷 159-165页

作者： Tian ZHENG Xinyang QIAN Jiayin WANG Department of Computer Science and Technology School of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an710049China Institute of Data Science and Information Quality Shaanxi Engineering Research Center of Medical and Health Big DataXi’an Jiaotong UniversityXi’an710049China

Genotyping of structural variations considering copy number variations(CNVs)is an infancy and challenging ***,a prevalent form of critical genetic variations that cause abnormal copy numbers of large genomic regions in cells,often affect transcription and contribute to a variety of *** characteristics of CNVs often lead to the ambiguity and confusion of existing genotyping features and algorithms,which may cause heterozygous variations to be erroneously genotyped as homozygous variations and seriously affect the accuracy of downstream *** the allelic copy number increases,the error rate of genotyping increases *** instances with different copy numbers play an auxiliary role in the genotyping classification problem,but some will seriously interfere with the accuracy of the *** by these,we propose a transfer learning-based method to genotype structural variations accurately considering *** method first divides the instances with different allelic copy numbers and trains the basic machine learning framework with different genotype *** maximizes the weights of the instances that contribute to classification and minimizes the weights of the instances that hinder correct *** adjusting the weights of the instances with different allelic copy numbers,the contribution of all the instances to genotyping can be maximized,and the genotyping errors of heterozygote variations caused by CNVs can be *** applied the proposed method to both the simulated and real datasets,and compared it to some popular algorithms including GATK,Facets and *** experimental results demonstrate that the proposed method outperforms the others in terms of accuracy,stability and *** source codes have been uploaded at github/TrinaZ/CNVtransfer for academic use only.

关键词： genotyping copy number variations transfer earning

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Enhancing Knee Contact Force Prediction Using Transformer Networks: A Comparative Study with Lstm and Mlp

SSRN

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SSRN 2025年

作者： Xu, Fashu Wang, Junqing Tong, Bingkui Fang, Xuyi Zhang, Hui Deng, Tao Wei, Qu Nie, Yong Li, Kang Department of Orthopedic Surgery West China Biomedical Big Data Center West China Hospital Sichuan University Sichuan Chengdu China Department of Orthopedic Surgery Orthopedic Research Institute West China Hospital Sichuan University Sichuan Chengdu China State Key Laboratory of Robotics Shenyang Institute of Automation Chinese Academy of Sciences Liaoning Shenyang China College of Computer Science Sichuan University Sichuan Chengdu China College of Electrical Engineering Sichuan University Sichuan Chengdu China School of Mechanical Engineering Sichuan University Sichuan Chengdu China

Background and objectiveKnee contact force (KCF) is pivotal in both the study and degenerative pathologies like Knee Osteoarthritis. Traditionally, they are primarily estimated using musculoskeletal modeling and machine learning predictive algorithms. However, musculoskeletal modeling is limited by intricate experimental protocols, prohibitive equipment cost, and scalability challenges. While machine learning methods, though computationally efficient, exhibit suboptimal predictive accuracy. This study innovatively developed a Transformer model for predicting KCF, benchmarked against long short-term memory (LSTM) and multilayer perceptron (MLP) *** comprehensive database was constructed with gait data from 513 participants, incorporating three degrees of freedom of hip, knee flexion/extension, and ankle dorsiflexion/plantarflexion, constituting four input combinations for the models. Contact forces derived from OpenSim served as the ground truth. Root mean square error (RMSE) and coefficient of determination (R2) were used to evaluate the performance of *** results indicated that the Transformer model demonstrated superior performance, achieving a significantly lower mean root mean square error of 0.02 body weight (BW) compared to MLP (0.54 BW) and LSTM (0.45 BW). Furthermore, the mean R2 of the Transformer network (0.99) was markedly superior to that of MLP (0.45) and LSTM (0.58).ConclusionsThe application of Transformer networks significantly improved the accuracy of KCF prediction, addressing the limitations of traditional musculoskeletal modeling and existing machine learning approaches, which was of paramount importance in both clinical practice and biomechanical research. © 2025, The Authors. All rights reserved.

关键词： Mean square error

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A Consensus Privacy Metrics Framework for Synthetic data

arXiv

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arXiv 2025年

作者： Pilgram, Lisa Dankar, Fida K. Drechsler, Jörg Elliot, Mark Domingo-Ferrer, Josep Francis, Paul Kantarcioglu, Murat Kong, Linglong Malin, Bradley Muralidhar, Krishnamurty Myles, Puja Prasser, Fabian Raisaro, Jean Louis Yan, Chao El Emam, Khaled School of Epidemiology and Public Health University of Ottawa ON Canada CHEO Research Institute ON Canada Department of Nephrology and Medical Intensive Care Charité – Universitätsmedizin Berlin Berlin Germany Department for Statistical Methods Institute for Employment Research Nuernberg Germany Institute for Statistics Ludwig-Maximilians-Universität Munich Germany Joint Program in Survey Methodology University of Maryland United States The Cathie Marsh Institute Research School of Social Sciences University of Manchester Manchester United Kingdom Department of Computer Engineering and Mathematics Universitat Rovira i Virgili Catalonia Tarragona Spain Max Planck Institute for Software Systems Germany Department of Computer Science Virginia Tech United States Department of Mathematical and Statistical Sciences University of Alberta Alberta Canada Department of Biomedical Informatics Vanderbilt University Medical Center NashvilleTN United States Department of Biostatistics Vanderbilt University Medical Center NashvilleTN United States Department of Computer Science Vanderbilt University NashvilleTN United States Department of Marketing and Supply Chain Management University of Oklahoma Oklahoma United States Medicines and Healthcare products Regulatory Agency London United Kingdom Berlin Institute of Health at Charité Universitätsmedizin Berlin Medical Informatics Group Berlin Germany Biomedical Data Science Center University Hospital Lausanne Lausanne Switzerland

Synthetic data generation is one approach for sharing individual-level data. However, to meet legislative requirements, it is necessary to demonstrate that the individuals’ privacy is adequately protected. There is no consolidated standard for measuring privacy in synthetic data. Through an expert panel and consensus process, we developed a framework for evaluating privacy in synthetic data. Our findings indicate that current similarity metrics fail to measure identity disclosure, and their use is discouraged. For differentially private synthetic data, a privacy budget other than close to zero was not considered interpretable. There was consensus on the importance of membership and attribute disclosure, both of which involve inferring personal information about an individual without necessarily revealing their identity. The resultant framework provides precise recommendations for metrics that address these types of disclosures effectively. Our findings further present specific opportunities for future research that can help with widespread adoption of synthetic data. © 2025, CC BY.

关键词： Differential privacy

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Synthesis of churros-like V2Se9 nanostructures for ultrasensitive electrochemical detection of oxalic acid in urine with portable point-of-care diagnostic devices

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Biosensors and Bioelectronics 2025年 285卷 117589页

作者： Shi, Peizheng Ye, Chen Sun, Zhuang Sun, Kaiqiang Zhao, Ningbin Pourfakhr, Mahan Cai, Tao Nishimura, Kazuhito Jiang, Nan Tsai, Hsu-Sheng Wu, Lidong Wu, Wenqi Yu, Jiancheng Fu, Li Xu, Lixin Chen, Jun Lin, Cheng-Te College of Materials Science and Engineering Zhejiang University of Technology Hangzhou310014 China Qianwan Institute of CNITECH Ningbo315336 China State Key Laboratory of Advanced Marine Materials Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of Sciences Beijing100049 China Department of Bioengineering University of California Los AngelesCA90095 United States School of Physics Harbin Institute of Technology Harbin150001 China Key Laboratory of Control of Quality and Safety for Aquatic Products Chinese Academy of Fishery Sciences Beijing100141 China Department of Urology The Second Affiliated Hospital of Guangzhou Medical University Guangdong 510260 China Guangdong Key Laboratory of Urology Guangzhou Medical University Guangdong 511495 China Institute of Mass Spectrometry Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application Ningbo University Ningbo315211 China Zhenhai Institute of Mass Spectrometry Ningbo315211 China Faculty of Electrical Engineering and Computer Science Ningbo University Ningbo315211 China College of Materials and Environmental Engineering Hangzhou Dianzi University Hangzhou310018 China

The binding of oxalic acid (OA) with metal ions, particularly calcium ions, is a key factor in kidney stone formation, as it produces insoluble calcium oxalate, which crystallizes and accumulates in the kidneys. Consequently, OA in urine is commonly considered a significant biomarker for clinical diagnosis and early screening of kidney stones. This study reports churros-like V2Se9 nanostructures synthesized using a solvothermal method (high pressure and temperature) for sensitive and selective electrochemical detection of OA in urine. The electrodes made of churros-like V2Se9 hybridized with reduced graphene oxide (rGO) for OA recognition, demonstrated a linear range from 20 nM to 4 mM, with an extremely low detection limit of 9.7 nM. To enable fast, user friendly, and accurate point-of-care testing (POCT) for OA in urine samples, we designed and developed a portable workstation integrated with smartphone for data visualization. This is the first study to utilize the V2Se9 system for highly sensitive biosensor applications, highlighting its potential to advance screening techniques for key indicators of kidney stones by incorporating novel transition metal chalcogenide nanomaterials in POCT devices. © 2025 Elsevier B.V.

关键词： Electrochemical biosensors

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Video Stabilization via Prediction with Time-Series Network and Image Inpainting with Pyramid Fusion

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Chinese Journal of Electronics 2021年第6期30卷 1103-1110页

作者： CHENG Keyang LI Shichao RONG Lan WANG Wenshan SHI Wenxi ZHAN Yongzhao School of Computer Science and Communication Engineering Jiangsu University Jiangsu Province Big Data Ubiquitous Perception and Intelligent Agricultural Application Engineering Research Center Cyber Space Security Academy of Jiangsu University National Engineering Laboratory for Public Safety Risk Perception and Control by Big Data Xinjiang Lianhaichuangzhi Information Technology Co. Ltd.

Due to the poor filling effect of the video image defect commonly used in the video stabilization field, the video is seemed still unstable after the image stabilization process, which seriously affects the visual effect. To solve this problem, we improve a video stabilization method based on time-series network prediction and pyramid fusion restoration is proposed to optimize the visual effect after image *** flow of the proposed method is as follows: First,it is adaptive to determine whether the defect of the corresponding frame at the current time needs padding inpainting. Then, for the frame that needs to be inpainting,the frames generated before the current moment are sent to the model combining the convolutional neural networks and the gate recurrent unit to predict the part to be filled. Next the current defect image and the complete image to be filled are brought into the Laplacian pyramid reconstruction, and the improved weighted optimal suture is introduced for splicing during the fusion. Finally, the video frame is cut after reconstruction. The method is tested on a data set composed of videos commonly used in the field of video stabilization. The experimental results show that the average peak signal to noise ratio of the method is 2 to 5 d B higher than that of the comparison algorithm, and the average structural similarity index is improved by about 2% to 7% compared with the contrast algorithm.

关键词： image restoration image sequences video frame cutting improved weighted optimal suture gate recurrent unit video signal processing video stabilization method image fusion Laplacian pyramid reconstruction padding inpainting image resolution neural nets convolutional neural networks video image defect pyramid fusion restoration image inpainting visual effect optimization image reconstruction time-series network prediction image stabilization process

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The role of 4D flow MRI in deep vein thrombosis research

Meta-Radiology

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Meta-Radiology 2025年第1期3卷

作者： Li, Meizhi Wu, Shangjie Liang, Xiao Gao, Chuanqi Hu, Muhua Chen, Zhu He, Pei Jia, Tingting Xiong, Li Department of Pulmonary and Critical Care Medicine The Second Xiangya Hospital of Central South University Changsha China Department of Medical Administration The Second Xiangya Hospital of Central South University Changsha China Clinical Medical Research Center for Pulmonary and Critical Care Medicine in Hunan Province Changsha China Hunan Research Centre for Evidence-based Medicine The Second Xiangya Hospital of Central South University Changsha China Department of Biomedical Engineering School of Basic Medical Science Central South University Changsha China Department of Radiology Second Xiangya Hospital Central South University Changsha China Hunan Key Laboratory for Super Microstructure and Ultrafast Process School of Physics and Electronics Central South University Changsha China National Engineering Research Center for Medical Big Data Application Technology and Big Data Institute Central South University Changsha China General Surgery Department of Second Xiangya Hospital Central South University Changsha China General Surgery Intelligent Healthcare Division of Clinical Medical Research Center of Hunan Province Changsha China

Four-dimensional (4D) flow Magnetic Resonance Imaging (MRI) technology has emerged as a valuable tool in angiography, offering unique insights into the hemodynamics and flow patterns. This research aims to explore the role of 4D flow MRI in advancing our understanding of Deep Vein Thrombosis (DVT), covering its applications in diagnosing, characterizing and mechanism of DVT, as well as its potential for guiding treatment strategies. The qualitative and quantitative information provided by 4D flow MRI enables a comprehensive assessment of blood flow in different vascular regions, shedding light on the relationship between hemodynamic changes and the onset and progression of vascular diseases. Nevertheless, most quantitative research findings for 4D hemodynamic indicators are lacking, and their use is mainly limited to examining arterial conditions. More exploration will be necessary to determine their applicability in studying venous vessels. © 2025 The Authors

关键词： 4D flow MRI Deep vein thrombosis Image analysis algorithms Noninvasive imaging

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Blockchain Based Secured Load Balanced Task Scheduling Approach for Fitness Service

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computers, Materials & Continua 2022年第5期71卷 2599-2616页

作者： Muhammad Ibrahim Faisal Jamil YunJung Lee DoHyeun Kim Big Data Research Center Department of Computer Science and StatisticsJeju National UniversityKoreaJeju-si63243Korea Department of Computer Engineering(and Advanced Technology Research Institute) Jeju National UniversityJeju 63243Korea

In recent times,the evolution of blockchain technology has got huge attention from the research community due to its versatile applications and unique security *** IoT has shown wide adoption in various applications including smart cities,healthcare,trade,business,*** these applications,fitness applications have been widely considered for smart fitness *** users of the fitness system are increasing at a high rate thus the gym providers are constantly extending the fitness ***,scheduling such a huge number of requests for fitness exercise is a big ***,the user fitness data is critical thus securing the user fitness data from unauthorized access is also *** overcome these issues,this work proposed a blockchain-based load-balanced task scheduling approach.A thorough analysis has been performed to investigate the applications of IoT in the fitness industry and various scheduling *** proposed scheduling approach aims to schedule the requests of the fitness users in a load-balanced way that maximize the acceptance rate of the users’requests and improve resource *** performance of the proposed task scheduling approach is compared with the state-of-the-art approaches concerning the average resource utilization and task rejection *** obtained results confirm the efficiency of the proposed scheduling *** investigating the performance of the blockchain,various experiments are performed using the Hyperledger Caliper concerning latency,throughput,resource *** Solo approach has shown an improvement of 32%and 26%in throughput as compared to Raft and Solo-Raft approaches *** obtained results assert that the proposed architecture is applicable for resource-constrained IoT applications and is extensible for different IoT applications.

关键词： Load balancing resource scheduling task scheduling Internet of things blockchain fitness applications

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A robust black carbon prediction model derived from observational datasets in the Yangtze River Delta region, China

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Environmental Pollution 2025年 377卷 126361页

作者： Duan, Lian Fung, Pak Lun Fu, Qingyan Chen, Jia Huo, Juntao Huang, Kan Wang, Guochen Zaidan, Martha Arbayani Guo, Zhigang Hussein, Tareq Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention Department of Environmental Science & Engineering Fudan University Shanghai200438 China Faculty of Science University of Helsinki UHEL PL 64 HelsinkiFI-00014 Finland Shanghai Academy of Environmental Sciences Shanghai200233 China Shanghai Environmental Monitoring Center Shanghai200030 China Department of Physics School of Science University of Jordan Amman11942 Jordan Key Laboratory of Geoscience Big Data and Deep Resource of Zhejiang Province Department of Atmospheric Sciences School of Earth Sciences Zhejiang University Hangzhou310027 China Department of Computer Science Faculty of Science University of Helsinki UHEL PL 64 HelsinkiFI-00014 Finland Shanghai200062 China IRDR ICoE on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health Fudan University Shanghai200433 China Observation and Research Station of Huaniaoshan East China Sea Ocean-Atmosphere Integrated Ecosystem Ministry of Natural Resources China

Black carbon (BC) is a short-lived pollutant with significant environment and human health impacts. Monitoring BC is important, but its spatial coverage is limited. Therefore, predicting BC concentration is crucial in densely populated regions like the Yangtze River Delta (YRD). This study explores the machine learning (ML) models, including IAP, LASSO, RF, and SNN, to develop a robust BC prediction model for the YRD, based on BC behavior at the Dianshan Lake (DSL) site. The annual BC concentration at DSL was 1.37 μg/m3, mainly from liquid fuel combustion (68 %), biomass burning (16 %), and coal combustion contributing (16 %). The ML model was first trained with DSL data (June 2021–June 2022) and then applied to other YRD sites in four scenarios based on air mass trajectories. The SNN model had R2 values over 0.80 for all scenarios at the DSL site. The model performed better during peak traffic periods, highlighting traffic's impact on BC levels. These models were applied to the YRD sites with R2 from 0.45 to 0.84. Hangzhou (HZ, 0.75–0.81), Nanjing (NJ, 0.78–0.80), and Pudong (PD, 0.76–0.84) showed the highest results. This suggests the model effectively captures BC concentrations from sources with similar emissions and meteorological conditions. © 2025 Elsevier Ltd

关键词： River pollution

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Intelligent Personality Assessment and Verification from Handwriting using Machine Learning

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International Journal of Information Technology (Singapore) 2024年第7期16卷 4541-4546页

作者： Mishra, Pradeep Kumar Mishra, Gouri Sankar Abidi, Ali Imam Kumar, Rajiv Sahoo, Ashok Kumar Maini, Tarun Department of Computer Science and Application SSET Sharda University Department of Computer Science and Engineering SSET Sharda University NVIDIA AI Learning & amp Research Center Department of Applied Computational Science and Engineering G L Bajaj Institute of Technology and Management Greater Noida Graphic Era Hill University School of Computer Science and Engineering Galgotias University

It is possible to tell a lot about a person just by looking at their handwriting. The way someone writes might tell you a lot about who, they are as a person. There has been a lot of study on the possibility of deducing aspects of a person’s character from their handwriting. In this piece, we’ll look at the different personality qualities and how they might be utilized to make an evaluation. The report includes a dataset showing a correlation between several traits of personality. The Big Five Personality Traits are mapped using handwritten personality data. It was suggested that a comparison table should be used to spot distinctive character quirks. The article includes a review of previous studies and an assessment of the current status of the topic. Handwriting embodies have both creativity and expressiveness. © Bharati Vidyapeeth's Institute of computer applications and Management 2024.

关键词： Agreeableness Conscientiousness Extraversion Neuroticism Openness

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Classification of Awareness in Disorders of Consciousness Using Common Spatial Pattern

Classification of Awareness in Disorders of Consciousness Us...

引用

International Winter Workshop on Brain-computer Interface (BCI)

作者： Chaewon Lee Sunho Lee Jitka Annen Ji-Hoon Jeong Marcello Massimini Silvia Casarotto Melanie Boly Olivier Bodart Aurore Thibaut Mario Rosanova Steven Laureys Olivia Gosseries Minji Lee Dept. Data Science The Catholic University of Korea Bucheon Republic of Korea Dept. Biomedical Software Engineering The Catholic University of Korea Bucheon Republic of Korea Dept. GIGA-Research & Neurology University and University Hospital of Liege Liege Belgium Dept. Data Analysis University of Ghent Ghent Belgium Dept. Computer Science Chungbuk National University Cheongju Republic of Korea Dept. Biomedical and Clinical Sciences “L. Sacco” University of Milan Milan Italy Dept. Psychiatry Wisconsin Institute for Sleep and Consciousness University of Wisconsin Madison USA Coma Science Group GIGA-Consciousness GIGA Research Center University of Liège Liège Belgium Centre du Cerveau Neurology department University Hospital of Liège Liège Belgium

ISBN: (数字)9798331521929

ISBN: (纸本)9798331521936

Advances in intensive care have improved the survival rate of patients with severe acute brain injury, but diagnostic errors for patients with disorders of consciousness are still high. Accurate diagnosis of these patients is very important because effective treatment can vary depending on the diagnosis. In this study, we propose a framework for classifying unresponsive wakefulness syndrome and minimally conscious state, focusing on awareness. In particular, power spectral density and common spatial patterns were used together, considering that spatial information is a key feature in consciousness. The 16 patients with unresponsive wakefulness syndrome and 14 with minimally conscious state underwent resting-state electroencephalography measurements. In addition, we compared the performance by utilizing each frequency (delta, theta, alpha, beta, gamma bands) related to consciousness. As a result, the highest accuracy of 95.06% was achieved by the EEGNet classifier, especially in the beta frequency band. We demonstrated that spatial information is very important in consciousness, as we observed that classification performance improved when common spatial patterns were used. These results provide insight into various frameworks for diagnosing patients with disorders of consciousness and may help patients survive by increasing the diagnosis rate in the future.

关键词： Deep learning Accuracy Biological system modeling Pattern classification Focusing Signal processing Brain modeling Particle measurements Electroencephalography Robustness

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