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arXiv 2025年

作者： Barron, Ryan Eren, Maksim E. Truong, Duc P. Matuszek, Cynthia Wendelberger, James Dorn, Mary F. Alexandrov, Boian Theoretical Division Los Alamos National Laboratory United States Information Systems and Modeling Los Alamos National Laboratory United States Department of Computer Science and Electrical Engineering University of Maryland Baltimore County United States Computer Computational and Statistical Sciences Los Alamos National Laboratory United States

Missing link prediction is a method for network analysis, with applications in recommender systems, biology, social sciences, cybersecurity, information retrieval, and Artificial Intelligence (AI) reasoning in Knowledge Graphs. Missing link prediction identifies unseen but potentially existing connections in a network by analyzing the observed patterns and relationships. In proliferation detection, this supports efforts to identify and characterize attempts by state and non-state actors to acquire nuclear weapons or associated technology - a notoriously challenging but vital mission for global security. Dimensionality reduction techniques like Non-Negative Matrix Factorization (NMF) and Logistic Matrix Factorization (LMF) are effective but require selection of the matrix rank parameter, that is, of the number of hidden features, k, to avoid over/under-fitting. We introduce novel Weighted (WNMFk), Boolean (BNMFk), and Recommender (RNMFk) matrix factorization methods, along with ensemble variants incorporating logistic factorization, for link prediction. Our methods integrate automatic model determination for rank estimation by evaluating stability and accuracy using a modified bootstrap methodology and uncertainty quantification (UQ), assessing prediction reliability under random perturbations. Additionally, we incorporate Otsu threshold selection and k-means clustering for Boolean matrix factorization, comparing them to coordinate descent-based Boolean thresholding. Our experiments highlight the impact of rank k selection, evaluate model performance under varying test-set sizes, and demonstrate the benefits of UQ for reliable predictions using abstention. We validate our methods on three synthetic datasets (Boolean and Gaussian distributed) and benchmark them against LMF and symmetric LMF (symLMF) on five real-world protein-protein interaction networks, showcasing an improved prediction performance. Copyright © 2025, The Authors. All rights reserved.

关键词： Non-negative matrix factorization

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Implementing a 3D multigrid algorithm on Fujitsu's vector parallel supercomputer 1

Implementing a 3D multigrid algorithm on Fujitsu's vector pa...

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1st Aizu International Symposium on Parallel Algorithms/Architecture Synthesis, AISPAS 1995

作者： Wang, I. Lung, H. Katsumata, Y. Ishigai, T. Scientific and Engineering Applications Fujitsu Systenis Business of America Inc. Santa ClaraCA95054 United States Computational Engineering Applications Supercomputer Systems Department Science Systems Division Fujitsu Limited Chiba261 Japan

ISBN: (纸本)081867038X

Multigrid algorithms are well adopted by many engineering applications programs on the traditional sequential computers due to their good convergence behavior. In order to convert those existing resources to the field of parallel computing in a timely manner, an effective parallelization methodology should be set up to ease the conversion efforts and to take advantage of the power of parallel processing at the same time. We demonstrate how domain decomposition can be applied to the multigrid algorithm by means of a simple three-dimensional problem which is solved by a V-cycle scheme. The sequential code in FORTRAN provided by NASA NAS, known as the NAS multigrid parallel benchmark test, is being used in our current study. We have concluded that the parallelization methodology presented here would greatly reduce conversion efforts in the process of parallelization and would obtain very good performance and scalability on the Fujitsu's VPP500 computers. Fujiisa's VPP500 uses Fujitsu's well-known vector supercomputer as its processing element (PE) each rated at 1.6 GFLOPS. Also, the highly efficient crossbar network serves as the inter-PE highway has been rated at 800 MB/s. Both technologies have been implemented an Fujatsu's products and widely accepted in ihe supercomputing industry for decades. Fujitsu's VPP Fortran compiler also gives us much flexibility in the parallelizalion and provides a smooth conversion environment for this research. © 1995 IEEE.

关键词： Domain decomposition methods

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Artificial intelligence for modelling infectious disease epidemics

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Nature 2025年第8051期638卷 623-635页

作者： Kraemer, Moritz U. G. Tsui, Joseph L.-H. Chang, Serina Y. Lytras, Spyros Khurana, Mark P. Vanderslott, Samantha Bajaj, Sumali Scheidwasser, Neil Curran-Sebastian, Jacob Liam Semenova, Elizaveta Zhang, Mengyan Unwin, H. Juliette T. Watson, Oliver J. Mills, Cathal Dasgupta, Abhishek Ferretti, Luca Scarpino, Samuel V. Koua, Etien Morgan, Oliver Tegally, Houriiyah Paquet, Ulrich Moutsianas, Loukas Fraser, Christophe Ferguson, Neil M. Topol, Eric J. Duchêne, David A. Stadler, Tanja Kingori, Patricia Parker, Michael J. Dominici, Francesca Shadbolt, Nigel Suchard, Marc A. Ratmann, Oliver Flaxman, Seth Holmes, Edward C. Gomez-Rodriguez, Manuel Schölkopf, Bernhard Donnelly, Christl A. Pybus, Oliver G. Cauchemez, Simon Bhatt, Samir Pandemic Sciences Institute University of Oxford Oxford United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Electrical Engineering and Computer Science University of California Berkeley Berkeley CA United States UCSF UC Berkeley Joint Program in Computational Precision Health Berkeley CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Section of Epidemiology Department of Public Health University of Copenhagen Copenhagen Denmark Oxford Vaccine Group University of Oxford and NIHR Oxford Biomedical Research Centre Oxford United Kingdom Department of Epidemiology and Biostatistics Imperial College London London United Kingdom Department of Computer Science University of Oxford Oxford United Kingdom School of Mathematics University of Bristol Bristol United Kingdom MRC Centre for Global Infectious Disease Analysis School of Public Health Imperial College London London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Doctoral Training Centre University of Oxford Oxford United Kingdom Institute for Experiential AI Northeastern University MA Boston Thailand Santa Fe Institute Santa Fe NM United States World Health Organization Regional Office for Africa Brazzaville Congo WHO Hub for Pandemic and Epidemic Intelligence Health Emergencies Programme World Health Organization Berlin Germany Centre for Epidemic Response and Innovation (CERI) School for Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa African Institute for Mathematical Sciences (AIMS) South Africa Muizenberg Cape Town South Africa Genomics England London United Kingdom Scripps Research La Jolla CA United States Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland The Ethox Centre Nuffield

Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. Artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social science, have the potential to transform the scope and power of infectious disease epidemiology. Here we consider the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science. We first outline how recent advances in AI can accelerate breakthroughs in answering key epidemiological questions and we discuss specific AI methods that can be applied to routinely collected infectious disease surveillance data. Second, we elaborate on the social context of AI for infectious disease epidemiology, including issues such as explainability, safety, accountability and ethics. Finally, we summarize some limitations of AI applications in this field and provide recommendations for how infectious disease epidemiology can harness most effectively current and future developments in AI. © Springer Nature Limited 2025.

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Implementing a 3D multigrid algorithm on Fujitsu's vector parallel supercomputer

Implementing a 3D multigrid algorithm on Fujitsu's vector pa...

引用

Aizu International Symposium on Parallel Algorithms/Architecture Synthesis

作者： J. Wang H. Lung Y. Katsumata T. Ishigai Scientific and Engineering Applications Fujitsu Systenis Business of America Inc. Santa Clara CA USA Computational Engineering Applications Supercomputer Systems Department Science Systems Division Fujitsu Laboratories Limited Chiba Japan

关键词： Parallel processing Power engineering and energy Application software Power engineering computing Convergence NASA Benchmark testing Sequential analysis Scalability Concurrent computing

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Modern deep learning in bioinformatics

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Journal of Molecular Cell Biology 2020年第11期12卷 823-827页

作者： Haoyang Li Shuye Tian Yu Li Qiming Fang Renbo Tan Yijie Pan Chao Huang Ying Xu Xin Gao Cancer Systems Biology Center The China-Japan Union HospitalJilin UniversityChangchun 130033China MOE Key Laboratory of Symbolic Computation and Knowledge Engineering College of Computer Science and TechnologyJilin UniversityChangchun 130012China Department of Biology Southern University of Science and TechnologyShenzhen 518055China Computational Bioscience Research Center(CBRC) Computer Electrical and Mathematical Sciences and Engineering(CEMSE)DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955Saudi Arabia School of Computer Science and Technology Hangzhou Dianzi UniversityHangzhou 310018China Ningbo Institute of Information Technology Application Chinese Academy of SciencesNingbo 315040China Computational Systems Biology Lab Department of Biochemistry and Molecular Biology and Institute of BioinformaticsUniversity of GeorgiaAthensGA 30602USA

Deep learning(DL)has shown explosive growth in its application to bioinformatics and has demonstrated thrillingly promising power to mine the complex relationship hidden in large-scale biological and biomedical data.A number of comprehensive reviews have been published on such applications,ranging from high-level reviews with future perspectives to those mainly serving as tutorials.

关键词： has such she

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Weighted dynamic time warping for time series classification

Weighted dynamic time warping for time series classification

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作者： Jeong, Young-Seon Jeong, Myong K. Omitaomu, Olufemi A. Department of Industrial and Systems Engineering Rutgers University 640 Bartholomew Road Piscataway NJ 08854 United States Rutgers Center for Operations Research Rutgers University Piscataway NJ United States Department of Industrial and Systems Engineering KAIST Daejon Korea Republic of Geographic Information Science and Technology Group Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak Ridge TN United States

Dynamic time warping (DTW), which finds the minimum path by providing non-linear alignments between two time series, has been widely used as a distance measure for time series classification and clustering. However, DTW does not account for the relative importance regarding the phase difference between a reference point and a testing point. This may lead to misclassification especially in applications where the shape similarity between two sequences is a major consideration for an accurate recognition. Therefore, we propose a novel distance measure, called a weighted DTW (WDTW), which is a penalty-based DTW. Our approach penalizes points with higher phase difference between a reference point and a testing point in order to prevent minimum distance distortion caused by outliers. The rationale underlying the proposed distance measure is demonstrated with some illustrative examples. A new weight function, called the modified logistic weight function (MLWF), is also proposed to systematically assign weights as a function of the phase difference between a reference point and a testing point. By applying different weights to adjacent points, the proposed algorithm can enhance the detection of similarity between two time series. We show that some popular distance measures such as DTW and Euclidean distance are special cases of our proposed WDTW measure. We extend the proposed idea to other variants of DTW such as derivative dynamic time warping (DDTW) and propose the weighted version of DDTW. We have compared the performances of our proposed procedures with other popular approaches using public data sets available through the UCR Time Series Data Mining Archive for both time series classification and clustering problems. The experimental results indicate that the proposed approaches can achieve improved accuracy for time series classification and clustering problems. © 2010 Elsevier Ltd. All rights reserved.

关键词： Time series

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Generating the Local Oscillator “Locally” in Continuous-Variable Quantum Key Distribution Based on Coherent Detection

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Physical Review X 2015年第4期5卷 041009-041009页

作者： Bing Qi Pavel Lougovski Raphael Pooser Warren Grice Miljko Bobrek Quantum Information Science Group Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831-6418 USA Department of Physics and Astronomy The University of Tennessee Knoxville Tennessee 37996-1200 USA RF Communications and Intelligent Systems Group Electrical and Electronics Systems Research Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831-6006 USA

Continuous-variable quantum key distribution (CV-QKD) protocols based on coherent detection have been studied extensively in both theory and experiment. In all the existing implementations of CV-QKD, both the quantum signal and the local oscillator (LO) are generated from the same laser and propagate through the insecure quantum channel. This arrangement may open security loopholes and limit the potential applications of CV-QKD. In this paper, we propose and demonstrate a pilot-aided feedforward data recovery scheme that enables reliable coherent detection using a “locally” generated LO. Using two independent commercial laser sources and a spool of 25-km optical fiber, we construct a coherent communication system. The variance of the phase noise introduced by the proposed scheme is measured to be 0.04 (rad2), which is small enough to enable secure key distribution. This technology also opens the door for other quantum communication protocols, such as the recently proposed measurement-device-independent CV-QKD, where independent light sources are employed by different users.

关键词： Quantum cryptography

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Guest Editorial: Special issue on computational methods and artificial intelligence applications in low-carbon energy systems

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IET Renewable Power Generation 2024年第3期18卷 303-305页

作者： Wang, Yishen Zhou, Fei Guerrero, Josep M. Baker, Kyri Chen, Yize Wang, Hao Xu, Bolun Xu, Qianwen Zhu, Hong Agwan, Utkarsha State Grid Laboratory of Grid Advanced Computing and Applications State Grid Smart Grid Research Institute Co. Ltd. Beijing China Department of Energy Technology Aalborg University Aalborg Denmark Department of Civil Environmental and Architectural Engineering University of Colorado-Boulder BoulderCO United States Guangzhou China Department of Data Science and AI Monash University ClaytonVIC Australia Department of Earth and Environmental Engineering Columbia University New YorkNY United States Electric Power and Energy Systems Division KTH Royal Institute of Technology Stockholm Sweden State Grid Jiangsu Electric Power Co. Ltd. Nanjing China Department of Electrical Engineering and Computer Sciences University of California - Berkeley BerkeleyCA United States

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Graph Pyramid Autoformer for Long- Term Traffic Forecasting 22

Graph Pyramid Autoformer for Long- Term Traffic Forecasting

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22nd IEEE International Conference on Machine Learning and applications, ICMLA 2023

作者： Zhong, Weiheng Mallick, Tanwi MacFarlane, Jane Meidani, Hadi Balaprakash, Prasanna University of Illinois at Urbana-Champaign Department of Civil Environmental Engineering ChampaignIL United States Mathematics and Computer Science Division Argonne National Laboratory LemontIL United States Sustainable Energy Systems Group Lawrence Berkeley National Laboratory BerkeleyCA United States Computing and Computational Sciences Directorate Oak Ridge National Laboratory Oak RidgeTN United States

ISBN: (纸本)9798350345346

Accurate traffic forecasting is vital to an intelligent transportation system. Although many deep learning models have achieved state-of-art performance for short-term traffic forecasting of up to 1 hour, long-term traffic forecasting that spans multiple hours remains a major challenge. To that end, we develop Graph Pyramid Autoformer (GPA), an attention-based spatial-temporal graph neural network that uses a novel pyramid autocorrelation attention mechanism. It enables learning from long temporal sequences on graphs and improves long-term traffic forecasting accuracy. We demonstrate the efficacy of the GPA using two benchmark traffic datasets: Los Angeles' METR-LA and the Bay Area's PEMS-BAY. Notably, our model has outperformed a range of existing state-of-the-art methods, delivering up to a 25 % improvement in the accuracy of long-term traffic forecasts. Our code is available at: https://***/WeiheneZlExplainable-Graph-Autoformer. © 2023 IEEE.

关键词： Graph Neural Network Long-term forecasting Pyramid Autocorrelation attention

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A Communication-Efficient Decentralized Newton's Method with Provably Faster Convergence

arXiv

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arXiv 2022年

作者： Liu, Huikang Zhang, Jiaojiao So, Anthony Man-Cho Ling, Qing The Research Institute for Interdisciplinary Sciences School of Information Management and Engineering Shanghai University of Finance and Economics China The Division of Decision and Control Systems School of Electrical Engineering and Computer Science Kth Royal Institute of Technology Sweden The Department of Systems Engineering and Engineering Management The Chinese University of Hong Kong Hong Kong The School of Computer Science and Engineering Guangdong Province Key Laboratory of Computational Science Sun Yat-Sen University China The Pazhou Lab China

In this paper, we consider a strongly convex finite-sum minimization problem over a decentralized network and propose a communication-efficient decentralized Newton's method for solving it. The main challenges in designing such an algorithm come from three aspects: (i) mismatch between local gradients/ Hessians and the global ones;(ii) cost of sharing second-order information;(iii) tradeoff among computation and communication. To handle these challenges, we first apply dynamic average consensus (DAC) so that each node is able to use a local gradient approximation and a local Hessian approximation to track the global gradient and Hessian, respectively. Second, since exchanging Hessian approximations is far from communication-efficient, we require the nodes to exchange the compressed ones instead and then apply an error compensation mechanism to correct for the compression noise. Third, we introduce multistep consensus for exchanging local variables and local gradient approximations to balance between computation and communication. With novel analysis, we establish the globally linear (resp., asymptotically super-linear) convergence rate of the proposed method when m is constant (resp., tends to infinity), where m ≥ 1 is the number of consensus inner steps. To the best of our knowledge, this is the first super-linear convergence result for a communication-efficient decentralized Newton's method. Moreover, the rate we establish is provably faster than those of first-order methods. Our numerical results on various applications corroborate the theoretical findings. Copyright © 2022, The Authors. All rights reserved.

关键词： Newton-Raphson method

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