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Predicting circRNA-Disease Associations by Using Multi-Biomolecular Networks Based on Variational Graph Auto-Encoder with Attention Mechanism

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Chinese Journal of Electronics 2024年第6期33卷 1526-1537页

作者： Jing YANG Xiujuan LEI Yi PAN School of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology

CircRNA-disease association(CDA) can provide a new direction for the treatment of diseases. However,traditional biological experiment is time-consuming and expensive, this urges us to propose the reliable computational model to predict the associations between circRNAs and diseases. And there is existing more and more evidence indicates that the combination of multi-biomolecular information can improve the prediction accuracy. We propose a novel computational model for CDA prediction named MBCDA, we collect the multi-biomolecular information including circRNA, disease, miRNA and lncRNA based on 6 databases, and construct three heterogeneous network among them, then the multi-heads graph attention networks are applied to these three networks to extract the features of circRNAs and diseases from different views, the obtained features are put into variational graph auto-encoder(VGAE) network to learn the latent distributions of the nodes, a fully connected neural network is adopted to further process the output of VGAE and uses sigmoid function to obtain the predicted probabilities of circRNA-disease *** a result, MBCDA achieved the values of AUC and AUPR under 5-fold cross-validation of 0.893 and 0.887. MBCDA was applied to the analysis of the top-25 predicted associations between circRNAs and diseases, these experimental results show that our proposed MBCDA is a powerful computational model for CDA prediction.

关键词： Knowledge engineering Attention mechanisms computational modeling Biological system modeling Predictive models Feature extraction Heterogeneous networks Topology Data mining Diseases

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Engineering hyaluronic acid-based nanoassemblies for monoclonal antibody delivery-design,characterization,and biological insights

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Nano Research 2024年第10期17卷 9111-9125页

作者： Ana M.López-Estévez Y.Zhang María Medel Iker Arriaga Lucía Sanjurjo Cristian Huck-Iriart Nicola G.A.Abrescia María J.Vicent Defang Ouyang Dolores Torres María José Alonso Center for Research in Molecular Medicine and Chronic Diseases(CiMUS) University of Santiago de CompostelaSantiago de Compostela 15782Spain Department of Pharmacology Pharmacy and Pharmaceutical TechnologySchool of PharmacyUniversity of Santiago de CompostelaSantiago de Compostela 15782Spain Health Research Institute of Santiago de Compostela(IDIS) Santiago de Compostela 15782Spain State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences(ICMS)University of MacaoMacao 999078China Polymer Therapeutics Laboratory and CIBERONC Prince Felipe Research Centre Valencia E-46012Spain Structure and Cell Biology of Viruses Lab CIC bioGUNEBasque Research and Technology Alliance(BRTA)Derio 48160Spain ALBA Synchrotron Light Source Experiments DivisionCerdanyola del VallèsBarcelona 08290Spain IKERBASQUE Basque Foundation for ScienceBilbao 48009Spain

The current spotlight of cancer therapeutics is shifting towards personalized medicine with the widespread use of monoclonal antibodies(mAbs).Despite their increasing potential,mAbs have an intrinsic limitation related to their inability to cross cell membranes and reach intracellular *** offers promising solutions to overcome this limitation,however,formulation challenges *** challenges are the limited loading capacity(often insufficient to achieve clinical dosing),the complex formulation methods,and the insufficient characterization of mAb-loaded ***,we present a new nanocarrier consisting of hyaluronic acid-based nanoassemblies(HANAs)specifically designed to entrap mAbs with a high efficiency and an outstanding loading capacity(50%,w/w).HANAs composed by an mAb,modified HA and phosphatidylcholine(PC)resulted in sizes of~100 nm and neutral surface *** modeling identified the principal factors governing the high affinity of mAbs with the amphiphilic HA and *** composition and structural configuration were analyzed using the orthogonal techniques cryogenic transmission electron microscopy(cryo-TEM),asymmetrical flow field-flow fractionation(AF4),and small-angle X-ray scattering(SAXS).These techniques provided evidence of the formation of core-shell nanostructures comprising an aqueous core surrounded by a bilayer consisting of phospholipids and amphiphilic *** vitro experiments in cancer cell lines and macrophages confirmed HANAs’low toxicity and ability to transport mAbs to the intracellular *** reproducibility of this assembling process at industrial-scale batch sizes and the long-term stability was *** conclusion,these results underscore the suitability of HANAs technology to load and deliver biologicals,which holds promise for future clinical translation.

关键词： monoclonal antibody nanoparticles hyaluronic acid characterization particle size computational modeling

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Development of a High-Resolution computational Model for Investigating the Flow Around and Inside Traditional Five-Hole Probes

Development of a High-Resolution Computational Model for Inv...

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AIAA SciTech Forum

作者： Jeong, Dahae Guimaraes, Tamara Penn State Univ Dept Mech Engn University Pk PA 16802 USA

ISBN: (数字)9781624107115

ISBN: (纸本)9781624107115

Pressure probes are amongst the most used instruments for measuring pressure and velocities in fluid flows. Five-hole probes have five holes at the tip aligned with the flow, which are calibrated for various speeds and angles in both the pitch and yaw directions in order to generate a calibration map, then used for calculating flow velocities and angles when the probe is subject to the flow of study. Real flows may include particulates, such as dirt, sand, combustion residues, as well as different gas compositions, which may affect the performance of the probe by potentially clogging one of more of the holes, for example. In this work, numerical analyses of a hemispherical straight probe in pre-determined flows are performed to investigate the development of flow over the surface and internally to the probe channels. A commercial software is used to analyze the region near the head of the probe, where there is low turbulence and a favorable pressure gradient. The present work shows the characteristics of the flow development inside the entrance of the channels, furthermore, bringing insight into the impact of the channels on the flow around the probe head and the differences in the pressure data depending on pitch and yaw angles. Developing a high-resolution computational model will lead us to perform further computational studies to investigate the influence of different build parameters of the probe (such as head shape, surface roughness and positioning of holes) involving in the quality of the acquired data. It is expected that these results will bring great insight on methodology to study the flow behavior around multi-hole probes and correlations between acquired data and build parameters of the probe in airflow in addition to creating a powerful tool to decrease calibration costs by offering a computational alternative.

关键词： computational modeling Yaw Pressure Coefficient Surface Roughness Pressure Probes Flow Separation Turbulence Models Separated Flows Kinematic Viscosity computational Fluid Dynamics

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Latent-Factorization-of-Tensors-Incorporated Battery Cycle Life Prediction

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IEEE/CAA Journal of Automatica Sinica 2025年第3期12卷 633-635页

作者： Minzhi Chen Li Tao Jungang Lou Xin Luo the College of Computer and Information Science Southwest University the Huzhou Yangtze Delta Region Institute of Intelligent Transportation the School of Information Engineering Huzhou University IEEE

Dear Editor,This letter presents a latent-factorization-of-tensors (LFT)-incorporated battery cycle life prediction framework. Data-driven prognosis and health management (PHM) for battery pack (BP) can boost the safety and sustainability of a battery management system (BMS),which relies heavily on the quality of the measured BP data like the voltage (V), current (I), and temperature (T).

关键词： Batteries Tensors Prognostics and health management Data models Degradation Battery charge measurement Vectors Distributed databases computational modeling Buildings

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The Unsung Hero of the Electric Vehicle Revolution: The role of computational electromagnetics in electric machine design and analysis

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IEEE ELECTRIFICATION MAGAZINE 2023年第4期11卷 64-68页

作者： Aliprantis, Dionysios Pekarek, Steven Purdue Univ W Lafayette IN 47907 USA

The electrification of transportation hinges on a number of core technologies, such as power electronics and energy storage. In this article, the spotlight is on electric machines (EMs), a term that encompasses all electromechanical energy conversion devices, i.e., motors and generators. computational electromagnetics, like the finite element method (FEM), play a vital role in a modern EM design workflow. Such methods have been under development for decades, however, with recent advances in computing, they are now mainstream. One of their key features is that they allow us to search a design space with unprecedented accuracy. But perhaps more importantly in today's rapidly changing landscape, they are accelerating the pace of innovation, reducing prototyping costs and the time it takes to go from concept to product.

关键词： Technological innovation Sea surface Quantum computing computational modeling System performance Transportation computational electromagnetics

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Knowledge As Not Only Justified True Beliefs in Vision

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IEEE/CAA Journal of Automatica Sinica 2025年第2期12卷 297-299页

作者： Wenbo Zheng Fei-Yue Wang IEEE School of Computer Science and Artificial Intelligence Wuhan University of Technology Sanya Science and Education Innovation Park of Wuhan University of Technology the State Key Laboratory for Management and Control of Complex Systems Institute of Automation Chinese Academy of Sciences

computational knowledge vision [1] is emphasized as a novel perspective or field in this paper. It first proposes the visual hierarchy and its connection to knowledge, stating that knowledge is a justified true belief. To further the previous research, we concisely summarize our recent works and suggest a new direction that knowledge is also a thought framework in vision.

关键词： computational modeling Visualization Artificial intelligence Data models Visual perception Visual databases Training data

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computational Models for In-Vehicle User Interface Design: A Systematic Literature Review 24

Computational Models for In-Vehicle User Interface Design: A...

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16th International Conference on Automotive User Interfaces and Interactive Vehicular Applications (AutomotiveUI)

作者： Lorenz, Martin Amorim, Tiago Dey, Debargha Sadeghi, Mersedeh Ebel, Patrick Univ Leipzig ScaDS AI Leipzig Germany Univ Cologne Cologne Germany Cornell Tech New York NY USA

ISBN: (纸本)9798400705106

In this review, we analyze the current state of the art of computational models for in-vehicle User Interface (UI) design. Driver distraction, often caused by drivers performing Non Driving Related Tasks (NDRTs), is a major contributor to vehicle crashes. Accordingly, in-vehicle UIs must be evaluated for their distraction potential. computational models are a promising solution to automate this evaluation, but are not yet widely used, limiting their real-world impact. We systematically review the existing literature on computational models for NDRTs to analyze why current approaches have not yet found their way into practice. We found that while many models are intended for UI evaluation, they focus on small and isolated phenomena that are disconnected from the needs of automotive UI designers. In addition, very few approaches make predictions detailed enough to inform current design processes. Our analysis of the state of the art, the identified research gaps, and the formulated research potentials can guide researchers and practitioners toward computational models that improve the automotive UI design process.

关键词： computational modeling user interfaces literature review cognitive modeling automated driving

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Model Checking Computation Tree Logic over Multi-Valued Decision Processes and Its Reduction Techniques

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Chinese Journal of Electronics 2024年第6期33卷 1399-1411页

作者： Wuniu LIU Junmei WANG Qing HE Yongming LI School of Mathematics and Statistics Shaanxi Normal University School of Computer Science Shaanxi Normal University

Model checking computation tree logic based on multi-valued possibility measures has been studied by Li et al. on Information Sciences in 2019. However, the previous work did not consider the nondeterministic choices inherent in systems represented by multi-valued Kripke structures(MvKSs). This nondeterminism is crucial for accurate system modeling, decision making, and control capabilities. To address this limitation, we draw inspiration from the generalization of Markov chains to Markov decision processes in probabilistic systems. By integrating nondeterminism into MvKS, we introduce multi-valued decision processes(MvDPs) as a framework for modeling MvKSs with nondeterministic choices. We investigate the problems of model checking over MvDPs. Verifying properties are expressed by using multi-valued computation tree logic based on schedulers. Our primary objective is to leverage fixpoint techniques to determine the maximum and minimum possibilities of the system satisfying temporal *** allows us to identify the optimal or worst-case schedulers for decision making or control purposes. We aim to develop reduction techniques that enhance the efficiency of model checking, thereby reducing the associated time complexity. We mathematically demonstrate three reduction techniques that improve model checking performance in most scenarios.

关键词： Statistical analysis computational modeling Scalability Markov decision processes Decision making Model checking Systems modeling Probabilistic logic Mathematical models Time complexity

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QoS-Aware Computation Offloading in LEO Satellite Edge Computing for IoT:A Game-Theoretical Approach

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Chinese Journal of Electronics 2024年第4期33卷 875-885页

作者： Ying CHEN Jintao HU Jie ZHAO Geyong MIN School of Computer Science Beijing Information Science and Technology University University of Exeter

Low earth orbit(LEO) satellite edge computing can overcome communication difficulties in harsh environments, which lack the support of terrestrial communication infrastructure. It is an indispensable option for achieving worldwide wireless communication coverage in the future. To improve the quality-of-service(QoS) for Internet-of-things(IoT) devices, we combine LEO satellite edge computing and ground communication systems to provide network services for IoT devices in harsh environments. We study the QoS-aware computation offloading(QCO) problem for IoT devices in LEO satellite edge computing. Then we investigate the computation offloading strategy for IoT devices that can minimize the total QoS cost of all devices while satisfying multiple constraints, such as the computing resource constraint, delay constraint, and energy consumption constraint. We formulate the QoSaware computation offloading problem as a game model named QCO game based on the non-cooperative competition game among IoT devices. We analyze the finite improvement property of the QCO game and prove that there is a Nash equilibrium for the QCO game. We propose a distributed QoS-aware computation offloading(DQCO) algorithm for the QCO game. Experimental results show that the DQCO algorithm can effectively reduce the total QoS cost of IoT devices.

关键词： Satellites Costs computational modeling Low earth orbit satellites Quality of service Games Nash equilibrium

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Guest Editorial: Special Issue on Emerging computational Intelligence Techniques to Address Challenges in Biomedical Data and Imaging

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IEEE TRANSACTIONS ON EMERGING TOPICS IN computational INTELLIGENCE 2023年第2期7卷 292-294页

作者： Tanveer, M. Lin, Chin-Teng Ting, Chuan-Kang Andreu-Perez, Javier Indian Inst Technol Indore Dept Math Simrol India Univ Technol Sydney Computat Intelligence & Brain Comp Interface Lab Ultimo NSW 2007 Australia Natl Tsing Hua Univ Dept Power Mech Engn Hsinchu 300 Taiwan Univ Essex Sch Comp Sci & Elect Engn Colchester Essex England

The papers in this special section focus on emerging computational intelligent techniques to address the challenges in biomedical data and image processing.

关键词： Special issues and sections Biomedical imaging computational intelligence Computed tomography computational modeling Bioinformatics Deep learning Data mining

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