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The Large Language Models on Biomedical Data Analysis: A Survey

IEEE Journal of Biomedical and Health Informatics 2025年第6期29卷 4486-4497页

作者： Lan, Wei Tang, Zhentao Liu, Mingyang Chen, Qingfeng Peng, Wei Chen, Yiping Phoebe Pan, Yi Guangxi University School of Computer Electronic and Information Nanning530004 China Kunming University of Science and Technology Faculty of Information Engineering and Automation Kunming650500 China La Trobe University Department of Computer Science and Information Technology MelbourneVIC3086 Australia Chinese Academy of Sciences Shenzhen Institute of Advanced Technology Shenzhen518055 China

With the rapid development of Large Language Model (LLM) technology, it has become an indispensable force in biomedical data analysis research. However, biomedical researchers currently have limited knowledge about LLM. Therefore, there is an urgent need for a summary of LLM applications in biomedical data analysis. Herein, we propose this review by summarizing the latest research work on LLM in biomedicine. In this review, LLM techniques are first outlined. We then discuss biomedical datasets and frameworks for biomedical data analysis, followed by a detailed analysis of LLM applications in genomics, proteomics, transcriptomics, radiomics, single-cell analysis, medical texts and drug discovery. Finally, the challenges of LLM in biomedical data analysis are discussed. In summary, this review is intended for researchers interested in LLM technology and aims to help them understand and apply LLM in biomedical data analysis research. © 2013 IEEE.

关键词： Data consistency

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Data-Driven Group Formation control of Cyber-Physical Systems via Distributed Cloud Computing

IEEE Transactions on Industrial Cyber-Physical Systems

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IEEE Transactions on Industrial Cyber-Physical Systems 2025年 3卷 341-350页

作者： Ren, Hongru Long, Yinren Li, Hongyi Huang, Tingwen Guangdong University of Technology School of Automation Guangdong-Hong Kong Joint Laboratory for Intelligent Decision and Cooperative Control Guangdong Provincial Key Laboratory for Intelligent Decision and Cooperative Control Guangzhou510006 China Southwest University College of Electronic and Information Engineering Chongqing400715 China Shenzhen University of Advanced Technology Faculty of Computer Science and Control Engineering Shenzhen518055 China

This paper investigates the group formation control problem for cyber-physical systems (CPSs) with random communication constraints. The distributed cloud computing system is constructed to divide agents into groups and establish communication between agents. A data-driven predictive control strategy is proposed by combining networked predictive control and model-free adaptive control method. The desired group formation control performance can be achieved and the three-channel random communication constraints of CPSs are actively compensated. Thisstrategy does not require the system model and relies solely on the system's I/O data for adaptive learning. Further analyses concludes the conditions for simultaneous reach stability and group formation of the closed-loop CPSs using the data-driven predictive control strategy. The effectiveness of the proposed strategy is validated by simulation results. © 2023 IEEE.

关键词： Distributed cloud

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Diversity and Freshness-Aware Regret Minimizing Set Queries 29th

Diversity and Freshness-Aware Regret Minimizing Set Queries

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29th International Computing and Combinatorics Conference, COCOON 2023

作者： Guo, Hongjie Li, Jianzhong Shen, Fangyao Gao, Hong Faculty of Computing Harbin Institute of Technology Heilongjiang Harbin China School of Computer Science and Technology Zhejiang Normal University Zhejiang Jinhua China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China

ISBN: (纸本)9783031491924

Multi-criteria decision-making often involves selecting a small representative set from a database. A recently proposed method is the regret minimization set (RMS) queries. It aims to rectify the shortcomings of needing a utility function in top-k queries and the overly large result size of skyline queries. However, the existing definition of RMS only ensures one result under any utility function, and do not consider the diversity and freshness of the returned results. In this paper, we define a strong regret set, which guarantees the utility value error of k data points under any utility function. Given this new definition, we propose two problems, namely the Minimum Size problem and the Max-sum Diversity and Freshness problem. Both proposed problems have been proven to be NP-hard. Correspondingly, we devise approximation algorithms for them, and analyze algorithms’ time complexities and the approximation ratios of the solutions obtained. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.

关键词： Approximation algorithms

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Analysis and Classification of Fake News Using Sequential Pattern Mining

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Big Data Mining and Analytics 2024年第3期7卷 942-963页

作者： M.Zohaib Nawaz M.Saqib Nawaz Philippe Fournier-Viger Yulin He College of Computer Science and Software Engineering Shenzhen UniversityShenzhen 518060 Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ) Shenzhen 518107China Department of Computer Science Faculty of Computing and Information TechnologyUnivesity of SargodhaSargodha 40100Pakistan

Disinformation,often known as fake news,is a major issue that has received a lot of attention *** researchers have proposed effective means of detecting and addressing *** machine and deep learning based methodologies for classification/detection of fake news are content-based,network(propagation)based,or multimodal methods that combine both textual and visual *** introduce here a framework,called FNACSPM,based on sequential pattern mining(SPM),for fake news analysis and *** this framework,six publicly available datasets,containing a diverse range of fake and real news,and their combination,are first transformed into a proper ***,algorithms for SPM are applied to the transformed datasets to extract frequent patterns(and rules)of words,phrases,or linguistic *** obtained patterns capture distinctive characteristics associated with fake or real news content,providing valuable insights into the underlying structures and commonalities of ***,the discovered frequent patterns are used as features for fake news *** framework is evaluated with eight classifiers,and their performance is assessed with various *** experiments were performed and obtained results show that FNACSPM outperformed other state-of-the-art approaches for fake news classification,and that it expedites the classification task with high accuracy.

关键词： disinformation fake news sequential pattern mining(SPM) frequent patterns classification

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ScCADE: A Superior Tool for Predicting Perturbation Responses in Single-Cell Gene Expression Using Contrastive Learning and Attention Mechanisms

ScCADE: A Superior Tool for Predicting Perturbation Response...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Ou, Jingfeng Li, Jiawei Xia, Zhiliang Dai, Shurui Ding, Yulian Guo, Yan Jiang, Limin Tang, Jijun Southern University of Science and Technology College of Engineering Shenzhen518055 China Shenzhen University of Advanced Technology Faculty of Computer Science and Control Engineering Shenzhen518107 China Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology Shenzhen518055 China University of Miami Department of Public Health Sciences MiamiFL33136 United States

ISBN: (纸本)9798350386226

The advent of single-cell transcriptomics has revolutionized our ability to analyze cellular heterogeneity and dynamics at a fine resolution, yet covering the vast array of potential perturbations remains challenging due to biological variability. To address this, we propose scCADE, a novel computational approach utilizing contrastive learning and an attention mechanism to decouple gene expression signatures and predict cellular responses to perturbations. scCADE excels in predicting responses in cells to perturbations observed in other cells but not yet seen in the target cells. Through rigorous ablation studies and validation across three datasets involving drug and gene editing perturbations, scCADE consistently outperformed existing methods, underscoring its efficacy and potential to advance genomics and personalized medicine by accurately forecasting responses to novel perturbations. © 2024 IEEE.

关键词： Contrastive Learning

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A Digital Twin and Consensus Empowered Cooperative control Framework for Platoon-Based Autonomous Driving

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清华大学学报自然科学版（英文版） 2025年第3期30卷 1096-1111页

作者： Jiayu Cao Supeng Leng Kai Xiong Xiaosha Chen School of Information and Communication Engineering University of Electronic Science and Technology of ChinaChengdu 611731China Shenzhen Institute for Advanced Study University of Electronic Science and Technology of ChinaShenzhen 518110China College of Computer Science and Technology and also with College of Data Science Taiyuan University of TechnologyTaiyuan 030024China

Platoon-based autonomous driving is indispensable for traffic automation,but it confronts substantial constraints in rugged terrains with unreliable links and scarce communication *** paper proposes a novel hierarchical Digital Twin(DT)and consensus empowered cooperative control framework for safe driving in harsh ***,leveraging intra-platoon information exchange,one platoon-level DT is constructed on the leader and multiple vehicle-level DTs are distributed among platoon *** leader first makes critical platoon-driving decisions based on the platoon-level ***,considering the impact of unreliable links on the platoon-level DT accuracy and the consequent risk of unsafe decision-making,a distributed consensus scheme is proposed to negotiate critical decisions *** successful negotiation,vehicles proceed to execute critical decisions,relying on their vehicle-level ***,a Space-Air-Ground-Integrated-Network(SAGIN)enabled information exchange is utilized to update the platoon-level DT for subsequent safe decision-making in scenarios with unreliable links,no roadside units,and obstructed ***,based on this framework,an adaptive platooning scheme is designed to minimize total delay and ensure driving *** results indicate that our proposed scheme improves driving safety by 21.1％and reduces total delay by 24.2％in harsh areas compared with existing approaches.

关键词： platoon autonomous driving distributed consensus digital twin space-air-ground integrated network

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Target-oriented Reference Construction for supervised cell type identification in scRNA-seq

Target-oriented Reference Construction for supervised cell t...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Wei, Xin Ma, Wenjing Wu, Zhijin Wu, Hao Brown University Department of Biostatistics United States University of Michigan Department of Biostatistics Ann Arbor United States Shenzhen University of Advanced Technology Faculty of Computer Science and Control Engineering Shenzhen China Chinese Academy of Sciences Shenzhen Institute of Advanced Technology Shenzhen China

ISBN: (纸本)9798350386226

Cell type identification is a crucial step in single-cell RNA-seq (scRNA-seq) data analysis. The supervised cell type identification method is a preferred solution due to its accuracy and efficiency. The performance of such methods highly depends on the quality of the reference data. Although there are many supervised cell type identification tools, no method currently exists for constructing reference data. Here, we develop Target-Oriented Reference Construction (TORC), a widely applicable strategy for constructing references based on target datasets in scRNA-seq supervised cell type identification. TORC focuses on alleviating differences in cell type composition between the reference and target sets. Extensive benchmarks on simulated and real data analyses demonstrate consistent improvements in cell type identification with TORC. © 2024 IEEE.

关键词： Self-supervised learning

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Memristive effects on an improved discrete Rulkov neuron model

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science China(Technological sciences) 2023年第11期66卷 3153-3163页

作者： BAO Han LI KeXin MA Jun HUA ZhongYun XU Quan BAO BoCheng School of Microelectronics and Control Engineering Changzhou UniversityChangzhou 213159China Department of Physics Lanzhou University of TechnologyLanzhou 730050China School of Computer Science and Technology Harbin Institute of TechnologyShenzhenShenzhen 518055China

A change in neuronal-action potential can generate a magnetically induced current during the release and propagation of intracellular *** better characterize the electromagnetic-induction effect,this paper presents an improved discrete Rulkov(ID-Rulkov)neuron model by coupling a discrete model of a memristor with sine memductance into a discrete Rulkov neuron *** ID-Rulkov neuron model possesses infinite invariant points,and its memristor-induced stability effect is evaluated by detecting the routes of period-doubling and Neimark-Sacker *** investigated the memristor-induced dynamic effects on the neuron model using bifurcation plots and firing ***,we theoretically expounded the memristor initial-boosting mechanism of infinite coexisting *** results show that the ID-Rulkov neuron model can realize diverse neuron firing patterns and produce hyperchaotic attractors that are nondestructively boosted by the initial value of the memristor,indicating that the introduced memristor greatly benefits the original neuron *** hyperchaotic attractors initially boosted by the memristor were verified by hardware experiments based on a hardware *** addition,pseudorandom number generators are designed using the ID-Rulkov neuron model,and their high randomness is demonstrated based onstrict test results.

关键词： neuron model invariant point memristive effect complex dynamics pseudorandom number generators

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Privacy Enhanced Mobile User Authentication Method Using Motion Sensors

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computer Modeling in engineering & sciences 2024年第3期138卷 3013-3032页

作者： Chunlin Xiong Zhengqiu Weng Jia Liu Liang Gu Fayez Alqahtani Amr Gafar Pradip Kumar Sharma Shenzhen Institutes of Advanced Technology Chinese Academy of SciencesShenzhen518052China Sangfor Technologies Inc. Shenzhen518055China School of Data Science and Artificial Intelligence Wenzhou University of TechnologyWenzhou325035China College of Computer Science&Technology Zhejiang University of TechnologyHangzhou310023China Software Engineering Department College of Computer and Information SciencesKing Saud UniversityRiyadh12372Saudi Arabia Math&Computer Science Department Faculty of ScienceMenofia UniversityShebin El-KomEgypt Computing Science Department University of AberdeenAberdeenUK

With the development of hardware devices and the upgrading of smartphones,a large number of users save privacy-related information in mobile devices,mainly smartphones,which puts forward higher demands on the protection of mobile users’privacy *** present,mobile user authenticationmethods based on humancomputer interaction have been extensively studied due to their advantages of high precision and non-perception,but there are still shortcomings such as low data collection efficiency,untrustworthy participating nodes,and lack of *** this end,this paper proposes a privacy-enhanced mobile user authentication method with motion sensors,which mainly includes:(1)Construct a smart contract-based private chain and federated learning to improve the data collection efficiency of mobile user authentication,reduce the probability of the model being bypassed by attackers,and reduce the overhead of data centralized processing and the risk of privacy leakage;(2)Use certificateless encryption to realize the authentication of the device to ensure the credibility of the client nodes participating in the calculation;(3)Combine Variational Mode Decomposition(VMD)and Long Short-TermMemory(LSTM)to analyze and model the motion sensor data of mobile devices to improve the accuracy of model *** experimental results on the real environment dataset of 1513 people show that themethod proposed in this paper can effectively resist poisoning attacks while ensuring the accuracy and efficiency of mobile user authentication.

关键词： Mobile authentication blockchain federated learning smart contract certificateless encryption VMD LSTM

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FUSION-BASED ALGORITHM FOR X-RAY PHASE CONTRAST IMAGING TECHNIQUES

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UPB Scientific Bulletin, Series A: Applied Mathematics and Physics 2024年第3期86卷 157-176页

作者： Rasinar, Cezara Safca, Nicoleta Cotorceanu, Elena Ciobanu, Ionut Stefanoiu, Dan Faculty of Automatic Control and Computer Science National University of Science and Technology POLITEHNICA Bucharest Romania Magurele Romania National University of Science and Technology POLITEHNICA Bucharest Romania Faculty of Chemical Engineering and Biotechnologies National University of Science and Technology POLITEHNICA Bucharest Romania

Phase Contrast X-ray Imaging represents a technique that has shown remarkable potential in the research field, by providing better visualization of soft tissue, high-contrast images, and high spatial resolution. In the phase contrast imaging technique, the extraction of the three images represented by attenuation, differential phase contrast, and dark-field contrast is essential, providing, in a specific way, information about the nature of the analyzed tissue. This paper introduces a new method based on the three acquired images merging while adjusting the weighting factors, aiming to identify the interest object and to extract the information provided by each contrast channel. In this regard, a fusion-based algorithm was applied to images acquired, using a 5.66 m long Interferometer Talbot-Lau with ultrahigh sensitivity of 0.84 µradians and mean energy of 30 keV. The obtained results are quite promising, as shown in the end of the article. © 2024, Politechnica university of Bucharest. All rights reserved.

关键词： Interferometers

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