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Autonomous Electron Tomography Reconstruction Using Bayesian Optimization

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Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada 2023年第1期29卷 1915-1916页

作者： Millsaps, William Schwartz, Jonathan Di, Zichao Wendy Jiang, Yi Hovden, Robert Department of Nuclear Engineering Radiological Sciences University of Michigan Ann Arbor MI United States Department of Materials Science and Engineering University of Michigan Ann Arbor MI United States Mathematics and Computer Science Division Argonne National Laboratory Lemont IL United States Advanced Photon Source Facility Argonne National Laboratory Lemont IL United States Applied Physics Program University of Michigan Ann Arbor MI United States

Antithetic Multilevel Particle Filters

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arXiv 2023年

作者： Jasra, Ajay Maama, Mohamed Ombao, Hernando Applied Mathematics and Computational Science Program United States Statistics Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this paper we consider the filtering of partially observed multi-dimensional diffusion processes that are observed regularly at discrete times. This is a challenging problem which requires the use of advanced numerical schemes based upon time-discretization of the diffusion process and then the application of particle filters. Perhaps the state-of-the-art method for moderate dimensional problems is the multilevel particle filter of [12]. This is a method that combines multilevel Monte Carlo and particle filters. The approach in that article is based intrinsically upon an Euler discretization method. We develop a new particle filter based upon the antithetic truncated Milstein scheme of [10]. We show that for a class of diffusion problems, for ϵ > 0 given, that the cost to produce a mean square error (MSE) in estimation of the filter, of O(ϵ2) is O(ϵ−2 log(ϵ)2). In the case of multidimensional diffusions with non-constant diffusion coefficient, the method of [12] has a cost of O(ϵ−2.5) to achieve the same MSE. We support our theory with numerical results in several examples. Copyright © 2023, The Authors. All rights reserved.

关键词： Mean square error

Unbiased Parameter Estimation for Partially Observed Diffusions

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arXiv 2023年

作者： Awadelkarim, Elsiddig Jasra, Ajay Ruzayqat, Hamza Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this article we consider the estimation of static parameters for partially observed diffusion process with discrete-time observations over a fixed time interval. In particular, we assume that one must time-discretize the partially observed diffusion process and work with the model with bias and consider maximizing the resulting log-likelihood. Using a novel double randomization scheme, based upon Markovian stochastic approximation we develop a new method to unbiasedly estimate the static parameters, that is, to obtain the maximum likelihood estimator with no time discretization bias. Under assumptions we prove that our estimator is unbiased and investigate the method in several numerical examples, showing that it can empirically out-perform existing unbiased *** Codes 60J22, 62M05, 65C40, 62M20 © 2023, CC BY.

关键词： Parameter estimation

Characteristic Mode Analysis of Nanostructures using Hydrodynamic Volume Integral Equation

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Characteristic Mode Analysis of Nanostructures using Hydrody...

Antennas and Propagation & USNC/URSI National Radio Science Meeting

作者： Meruyert Khamitova Ran Zhao Doolos Aibek uulu Hakan Bagci Electrical and Computer Engineering (ECE) Program Computer Electrical and Mathematical Science and Engineering (CEMSE) Division King Abdullah University of Science and Technology (KAUST) Thuwal Kingdom of Saudi Arabia School of Electronic Science and Engineering University of Electronic Science and Technology of China (UESTC) Chengdu Sichuan China Department of Mathematics and Natural Sciences University of Central Asia (UCA) Naryn Kyrgyzstan

ISBN: (数字)9798350369908

ISBN: (纸本)9798350369915

The characteristic mode analysis (CMA) is formulated and implemented for the hydrodynamic volume integral equation (HDVIE) that is used to mathematically model electromagnetic field interactions and conduction current dynamics on nanoantennas and nanoscatterers. The proposed method produces excitation-independent characteristic hydrodynamic currents and the corresponding modal significance curves, providing useful information that can be used to optimize the performance of a nanoantenna. Numerical results demonstrate the reliability and the applicability of the proposed approach.

关键词： Solid modeling Nanoantennas Integral equations Hydrodynamics Mathematical models Characteristic mode analysis Numerical models

Learner Action Patterns in the Problem-Solving Process Related to program Code Composition Based on Tracking System Activities 7

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Learner Action Patterns in the Problem-Solving Process Relat...

7th International Conference on Informatics and Computing, ICIC 2022

作者： Syahidi, Aulia Akhrian Supianto, Ahmad Afif Hirashima, Tsukasa Watanobe, Yutaka Politeknik Negeri Banjarmasin Smart City Information System Applied Undergraduate Program Banjarmasin City Indonesia Research Center for Data and Information Sciences Bandung City Indonesia Graduate School of Advanced Science and Engineering Hiroshima University Kagamiyama Learning Engineering Laboratory Higashihiroshima Japan University of Aizu Division of Information Systems Department of Computer Science and Engineering Fukushima AizuWakamatsu Japan

ISBN: (纸本)9798350345711

Learning activities are an indicator of the learner's desire to learn during the learning process. The pattern of learner action is related to learning activities. In this case, in extracting the learning process, it is necessary to collect a lot of data through analysis of the learning process. The purpose of this study is to recommend and report the performance of an activity tracking system equipped with visual artifacts as an educational data mining approach to analyze action patterns when learners complete the arrangement of program code lines in each programming problem. In this study, data were taken from activity recordings when learners used interactive learning media for a basic programming subject called TOLSYASUPI-EduMed which had problem-solving learning models embedded in their interactions. Learning Analytics is used as a method of this research and data relationships from learner actions during the learning process using the 'if-then' rule. Log data is used for recording and detecting activities carried out by learners. We confirm that the results of the study are based on the findings of the data relationship that if the lines of program code are too long (more than five lines) then almost all learners experience a bottleneck condition. The completion time of each question and the number of iterations in completing the program code lines for each question have also been recorded and have a pattern of connection between the data. The information that has been obtained is then forwarded to teachers or stakeholders as key information to make appropriate feedback to learners based on the results as a means of analyzing and evaluating the programming learning process. © 2022 IEEE.

关键词： Data mining

Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 959-973页

作者： Juexiao Zhou Bin Zhang Haoyang Li Longxi Zhou Zhongxiao Li Yongkang Long Wenkai Han Mengran Wang Huanhuan Cui Jingjing Li Wei Chen Xin Gao Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Shenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Academy for Advanced Interdisciplinary Studies Southern University of Science and TechnologyShenzhen 518055China

The accurate annotation of transcription start sites(TSSs)and their usage are critical for the mechanistic understanding of gene regulation in different biological *** fulfill this,specific high-throughput experimental technologies have been developed to capture TSSs in a genome-wide manner,and various computational tools have also been developed for in silico prediction of TSSs solely based on genomic *** of these computational tools cast the problem as a binary classification task on a balanced dataset,thus resulting in drastic false positive predictions when applied on the genome ***,we present Dee Re CT-TSS,a deep learningbased method that is capable of identifying TSSs across the whole genome based on both DNA sequence and conventional RNA sequencing *** show that by effectively incorporating these two sources of information,Dee Re CT-TSS significantly outperforms other solely sequence-based methods on the precise annotation of TSSs used in different cell ***,we develop a meta-learning-based extension for simultaneous TSS annotations on 10 cell types,which enables the identification of cell type-specific ***,we demonstrate the high precision of DeeReCT-TSS on two independent datasets by correlating our predicted TSSs with experimentally defined TSS chromatin *** source code for Dee Re CT-TSS is available at https://github.-com/Joshua Chou2018/Dee Re CT-TSS_release and https://***/biocode/tools/BT007316.

关键词： Transcription start site Machine learning Deep learning Meta-learning RNA sequencing

Molecular architecture of mammalian pyruvate dehydrogenase complex

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Protein & Cell 2025年第1期16卷 72-78页

作者： Maofei Chen Yutong Song Sensen Zhang Yitang Zhang Xudong Chen Minghui Zhang Meng Han Xin Gao Sai Li Maojun Yang Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological StructureSchool of Life SciencesTsinghua UniversityBeijing 100084China Ministry of Education Key Laboratory of Protein Science Tsinghua UniversityBeijing 100084China State Key Laboratory of Membrane Biology Tsinghua UniversityBeijing 100084China Department of Biochemistry and Molecular Biology School of Basic Medical SciencesShenzhen University Health Science CenterShenzhen 518060China Protein Research Technology Center Protein Chemistry and Omics PlatformSchool of Life SciencesTsinghua UniversityBeijing 100084China Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Kingdom of Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Kingdom of Saudi Arabia Cryo-EM Facility Center Southern University of Science and TechnologyShenzhen 518055China Beijing Life Science Academy Beijing 102209China

Dear Editor,Pyruvate dehydrogenase complex(PDHc) is a large multienzyme assembly(Mr = 4–10 million Daltons) consisting of three essential components: pyruvate dehydrogenase(E1p), dihydrolipoyl transacetylase(E2p), and dihydrolipoyl dehydrogenase(E3). These three enzymes perform distinct functions sequentially to catalyze the oxidative decarboxylation of pyruvate with formation of nicotinamide adenine dinucleotide(NADH) and acetyl-coenzyme A(Patel and Roche, 1990).

关键词： sequentially oxidative Dalton

Stochastic Dynamics and Probability Analysis for a Generalized Epidemic Model with Environmental Noise

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arXiv 2024年

作者： Boukanjime, Brahim Maama, Mohamed Laboratory of Mathematical Modeling and Economic Calculations Hassan First University of Settat Morocco Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Saudi Arabia

In this paper we consider a stochastic SEIQR (susceptible-exposed-infected-quarantined-recovered) epidemic model with a generalized incidence function. Using the Lyapunov method, we establish the existence and uniqueness of a global positive solution to the model, ensuring that it remains well-defined over time. Through the application of Young’s inequality and Chebyshev’s inequality, we demonstrate the concepts of stochastic ultimate boundedness and stochastic permanence, providing insights into the long-term behavior of the epidemic dynamics under random perturbations. Furthermore, we derive conditions for stochastic extinction, which describes scenarios where the epidemic may eventually die out, and V-geometric ergodicity, which indicates the rate at which the system’s state converges to its equilibrium. Finally, we perform numerical simulations to verify our theoretical results and assess the model’s behavior under different parameters. Copyright © 2024, The Authors. All rights reserved.

关键词： Stochastic models

Bayesian Parameter Inference for Partially Observed SDEs driven by Fractional Brownian Motion

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arXiv 2022年

作者： Maama, Mohamed Jasra, Ajay Ombao, Hernando Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955 Saudi Arabia Statistics Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955 Saudi Arabia

In this paper we consider Bayesian parameter inference for partially observed fractional Brownian motion (fBM) models. The approach we follow is to time-discretize the hidden process and then to design Markov chain Monte Carlo (MCMC) algorithms to sample from the posterior density on the parameters given data. We rely on a novel representation of the time discretization, which seeks to sample from an approximation of the posterior and then corrects via importance sampling;the approximation reduces the time (in terms of total observation time T) by O(T). This method is extended by using a multilevel MCMC method which can reduce the computational cost to achieve a given mean square error (MSE) versus using a single time discretization. Our methods are illustrated on simulated and real data. Copyright © 2022, The Authors. All rights reserved.

关键词： Mean square error