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Verification of Operational Numerical Weather Prediction Model Forecasts of Precipitation Using Satellite Rainfall Estimates over Africa

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arXiv 2022年

作者： Wang, Yan Gueye, Moussa Greybush, Steven J. Greatrex, Helen Whalen, Andrew J. Ssentongo, Paddy Zhang, Fuqing Jenkins, Gregory S. Schiff, Steven J. Department of Meteorology and Atmospheric Science The Pennsylvania State University University ParkPA United States Department of Geography Department of Statistics The Pennsylvania State University University ParkPA United States Institute for Computational and Data Sciences The Pennsylvania State University University ParkPA United States Center for Neural Engineering Center for Infectious Disease Dynamics The Pennsylvania State University University ParkPA United States Public Health Science The Pennsylvania State University University ParkPA United States Department of Neurosurgery Engineering Science and Mechanics and Physics The Pennsylvania State University University ParkPA United States Department of Neurosurgery Massachusetts General Hospital Harvard University MA United States Kaolack Senegal

Rainfall is an important variable to be able to monitor and forecast across Africa, due to its impact on agriculture, food security, climate related diseases and public health. Numerical Weather Models (NWM) are an important component of this work, due to their complete spatial coverage, high resolution, and ability to forecast into the future. In this study, we seek to evaluate the spatiotemporal skill of short-term rainfall forecasts of rainfall across Africa. Specifically, the European Centre for Medium-Range Weather Forecasts (ECMWF) and the National centers for Environmental Prediction-Global Forecast System (NCEP-GFS) forecast models are verified by Rainfall Estimates 2.0 (RFE2) and African Rainfall Climatology Version 2 (ARC2), which are fused products of satellite and in-situ observations and are commonly used in analysis of African rainfall. We found that the model rainfall forecasts show good consistency with the satellite rainfall observations in spatial distribution over Africa on the seasonal timescale. Evaluation metrics show high spatial and seasonal variations over the African continent, including a strong link to the location of the inter-tropical convergence zone (ITCZ) and topographically enhanced precipitation. The rainfall forecasts at one week aggregation time are improved against daily forecasts. © 2022, CC BY-NC-ND.

关键词： Rain

An optimal algorithm for strict circular seriation

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arXiv 2021年

作者： Armstrong, Santiago Guzmán, Cristóbal Long, Carlos A. Sing Institute for Mathematical and Computational Engineering Pontificia Universidad Católica de Chile Santiago Chile Anid - Millennium Science Initiative Program Millennium Nucleus Center for the Discovery of Structures in Complex Data Santiago Chile Department of Applied Mathematics University of Twente Netherlands Institute for Biological and Medical Engineering Pontificia Universidad Católica de Chile Santiago Chile

We study the problem of circular seriation, where we are given a matrix of pairwise dissimilarities between n objects, and the goal is to find a circular order of the objects in a manner that is consistent with their dissimilarity. This problem is a generalization of the classical linear seriation problem where the goal is to find a linear order, and for which optimal O(n2) algorithms are known. Our contributions can be summarized as follows. First, we introduce circular Robinson matrices as the natural class of dissimilarity matrices for the circular seriation problem. Second, for the case of strict circular Robinson dissimilarity matrices we provide an optimal O(n2) algorithm for the circular seriation problem. Finally, we propose a statistical model to analyze the well-posedness of the circular seriation problem for large n. In particular, we establish O(log(n)/n) rates on the distance between any circular ordering found by solving the circular seriation problem to the underlying order of the model, in the Kendall-tau *** Codes 68R01, 05C85, 05C50, 05C25, 65C20 Copyright © 2021, The Authors. All rights reserved.

关键词： Trees (mathematics)

Magnetic-resonance-based electrical property mapping using global maxwell tomography with an 8-channel head coil at 7 Tesla: A simulation study

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arXiv 2020年

作者： Giannakopoulos, Ilias I. Serrallés, José E.C. Daniel, Luca Sodickson, Daniel K. Polimeridis, Athanasios G. White, Jacob K. Lattanzi, Riccardo Skoltech Center for Computational Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow143026 Russia Research Laboratory of Electronics Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Department of Radiology New York University School of Medicine New YorkNY United States Q Bio CA94063 United States

Objective: Global Maxwell Tomography (GMT) is a recently introduced volumetric technique for noninvasive estimation of electrical properties (EP) from magnetic resonance measurements. Previous work evaluated GMT using ideal radiofrequency (RF) excitations. The aim of this simulation study was to assess GMT performance with a realistic RF coil. Methods: We designed a transmit-receive RF coil with 8 decoupled channels for 7T head imaging. We calculated the RF transmit field (B1+) inside heterogeneous head models for different RF shimming approaches, and used them as input for GMT to reconstruct EP for all voxels. Results: Coil tuning/decoupling remained relatively stable when the coil was loaded with different head models. Mean error in EP estimation changed from 7.5% to 9.5% and from 4.8% to 7.2% for relative permittivity and conductivity, respectively, when changing head model without re-tuning the coil. Results slightly improved when an SVD-based RF shimming algorithm was applied, in place of excitation with one coil at a time. Despite errors in EP, RF transmit field (B1+) and absorbed power could be predicted with less than 0.5% error over the entire head. GMT could accurately detect a numerically inserted tumor. Conclusion: This work demonstrates that GMT can reliably reconstruct EP in realistic simulated scenarios using a tailored 8-channel RF coil design at 7T. Future work will focus on construction of the coil and optimization of GMT's robustness to noise, to enable in-vivo GMT experiments. Significance: GMT could provide accurate estimations of tissue EP, which could be used as biomarkers and could enable patient-specific estimation of RF power deposition, which is an unsolved problem for ultrahigh-field magnetic resonance imaging. Copyright © 2020, The Authors. All rights reserved.

关键词： Integral equations

Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

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arXiv 2023年

作者： Takaba, Kenichiro Pulido, Iván Behara, Pavan Kumar Cavender, Chapin E. Friedman, Anika J. Henry, Michael M. MacDermott-Opeskin, Hugo Iacovella, Christopher R. Nagle, Arnav M. Payne, Alexander Matthew Shirts, Michael R. Mobley, David L. Chodera, John D. Wang, Yuanqing Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Pharmaceuticals Research Center Advanced Drug Discovery Asahi Kasei Pharma Corporation Shizuoka410-2321 Japan Center for Neurotherapeutics Department of Pathology and Laboratory Medicine University of California IrvineCA92697 United States Skaggs School of Pharmacy and Pharmaceutical Sciences University of California 9500 Gilman Drive La Jolla San DiegoCA92093 United States Department of Chemical and Biological Engineering University of Colorado Boulder BoulderCO80309 United States Open Molecular Software Foundation DavisCA95618 United States Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Department of Pharmaceutical Sciences University of California IrvineCA92697 United States Tri-Institutional Ph.D. Program in Chemical Biology Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University New YorkNY10004 United States

The development of reliable and extensible molecular mechanics (MM) force fields—fast, empirical models characterizing the potential energy surface of molecular systems—is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest. © 2023, CC BY.

关键词： Quantum chemistry

Contour integral methods for nonlinear eigenvalue problems: A systems theoretic approach

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arXiv 2020年

作者： Brennan, Michael C. Embree, Mark Gugercin, Serkan Center for Computational Engineering Massachusetts Institute of Technology CambridgeMA02139-4307 United States Department of Mathematics Division of Computational Modeling and Data Analytics Academy of Integrated Science Virginia Tech BlacksburgVA24061 United States

Contour integral methods for nonlinear eigenvalue problems seek to compute a subset of the spectrum in a bounded region of the complex plane. We briefly survey this class of algorithms, establishing a relationship to system realization techniques in control theory. This connection motivates a new general framework for contour integral methods (for linear and nonlinear eigenvalue problems), building on recent developments in multi-point rational interpolation of dynamical systems. These new techniques, which replace the usual Hankel matrices with Loewner matrix pencils, incorporate general interpolation schemes and permit ready recovery of eigenvectors. Because the main computations (the solution of linear systems associated with contour integration) are identical for these Loewner methods and the traditional Hankel approach, a variety of new eigenvalue approximations can be explored with modest additional work. Numerical examples illustrate the potential of this approach. We also discuss how the concept of filter functions can be employed in this new framework, and show how contour methods enable a data-driven modal truncation method for model *** Codes 15A18, 65F15, 93B20, 93B30 15A18, 65F15, 93B20, 93B30 15A18, 65F15, 93B20, 93B30 Copyright © 2020, The Authors. All rights reserved.

关键词： Eigenvalues and eigenfunctions

Adaptive test allocation for outbreak detection and tracking in social contact networks

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arXiv 2020年

作者： Batlle, Pau Bruna, Joan Fernandez-Granda, Carlos Preciado, Victor M. Courant Institute of Mathematical Sciences Center for Data Science New York University NY United States Department of Electrical and Systems Engineering Applied Mathematics and Computational Science University of Pennsylvania PA United States

We present a general framework for adaptive allocation of viral tests in social contact networks. We pose and solve several complementary problems. First, we consider the design of a social sensing system whose objective is the early detection of a novel epidemic outbreak. In particular, we propose an algorithm to select a subset of individuals to be tested in order to detect the onset of an epidemic outbreak as fast as possible. We pose this problem as a hitting time probability maximization problem and use submodularity optimization techniques to derive explicit quality guarantees for the proposed solution. Second, once an epidemic outbreak has been detected, we consider the problem of adaptively distributing viral tests over time in order to maximize the information gained about the current state of the epidemic. We formalize this problem in terms of information entropy and mutual information and propose an adaptive allocation strategy with quality guarantees. For these problems, we derive analytical solutions for any stochastic compartmental epidemic model with Markovian dynamics, as well as efficient Monte-Carlo-based algorithms for non-Markovian dynamics. Finally, we illustrate the performance of the proposed framework in numerical experiments involving a model of Covid-19 applied to a real human contact network. Copyright © 2020, The Authors. All rights reserved.

关键词： Epidemiology

Finding shortest and nearly shortest path nodes in large substantially incomplete networks

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arXiv 2022年

作者： Kitsak, Maksim Ganin, Alexander Elmokashfi, Ahmed Cui, Hongzhu Eisenberg, Daniel A. Alderson, David L. Korkin, Dmitry Linkov, Igor Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology Delft Netherlands Network Science Institute Northeastern University BostonMA02115 United States Department of Systems and Information Engineering University of Virginia CharlottesvilleVA22904 United States U.S. Army Engineer Research and Development Center Contractor Concord MA01742 United States Simula Metropolitan Center for Digital Engineering Oslo Norway Bioinformatics and Computational Biology Program Worcester Polytechnic Institute WorcesterMA01609 United States Institute for Genomic Medicine Columbia University Medical Center New YorkNY United States Operations Research Department Naval Postgraduate School MontereyCA93943 United States Data Science Program Worcester Polytechnic Institute WorcesterMA01609 United States Computer Science Department Worcester Polytechnic Institute WorcesterMA01609 United States U.S. Army Engineer Research and Development Center Environmental Laboratory Concord MA01742 United States

Dynamic processes on networks, be it information transfer in the Internet, contagious spreading in a social network, or neural signaling, take place along shortest or nearly shortest paths. Unfortunately, our maps of most large networks are substantially incomplete due to either the highly dynamic nature of networks, or high cost of network measurements, or both, rendering traditional path finding methods inefficient. We find that shortest paths in large real networks, such as the network of protein-protein interactions (PPI) and the Internet at the autonomous system (AS) level, are not random but are organized according to latent-geometric rules. If nodes of these networks are mapped to points in latent hyperbolic spaces, shortest paths in them align along geodesic curves connecting endpoint nodes. We find that this alignment is sufficiently strong to allow for the identification of shortest path nodes even in the case of substantially incomplete networks. We demonstrate the utility of latent-geometric path finding in problems of cellular pathway reconstruction and communication security. Copyright © 2022, The Authors. All rights reserved.

关键词： Proteins

Author Correction: Employing fingerprinting of medicinal plants by means of LC-MS and machine learning for species identification task

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Scientific reports 2020年第1期10卷 11482页

作者： Pavel Kharyuk Dmitry Nazarenko Ivan Oseledets Igor Rodin Oleg Shpigun Andrey Tsitsilin Mikhail Lavrentyev Skolkovo Institute of Science and Technology Center for Computational and Data-Intensive Science and Engineering Moscow 143026 Russia. kharyuk.pavel@***. Institute of Numerical Mathematics of the Russian Academy of Sciences Moscow 119991 Russia. kharyuk.pavel@***. Lomonosov Moscow State University Faculty of Chemistry Moscow 119991 Russia. dmitro.nazarenko@***. Skolkovo Institute of Science and Technology Center for Computational and Data-Intensive Science and Engineering Moscow 143026 Russia. Institute of Numerical Mathematics of the Russian Academy of Sciences Moscow 119991 Russia. Lomonosov Moscow State University Faculty of Chemistry Moscow 119991 Russia. All-Russian Research Institute of Medicinal and Aromatic Plants (VILAR) Moscow 117216 Russia. Saratov State University Department of Botanics and Ecology Saratov 410012 Russia.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Heavy metals prediction in coastal marine sediments using hybridized machine learning models with metaheuristic optimization algorithm

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Chemosphere 2024年 352卷 141329页

作者： Yaseen, Zaher Mundher Melini Wan Mohtar, Wan Hanna Homod, Raad Z. Alawi, Omer A. Abba, Sani I. Oudah, Atheer Y. Togun, Hussein Goliatt, Leonardo Ul Hassan Kazmi, Syed Shabi Tao, Hai Civil and Environmental Engineering Department King Fahd University of Petroleum and Minerals Dhahran 31261 Saudi Arabia Interdisciplinary Research Center for Membranes and Water Security King Fahd University of Petroleum & Minerals (KFUPM) Dhahran Saudi Arabia Department of Civil Engineering Faculty of Engineering and Built Environment Universiti Kebangsaan Malaysia UKM Selangor Bangi 43600 Malaysia Environmental Management Centre Institute of Climate Change Universiti Kebangsaan Malaysia Selangor UKM Bangi 43600 Malaysia Department of Oil and Gas Engineering Basrah University for Oil and Gas Basra Iraq Department of Thermofluids School of Mechanical Engineering Universiti Teknologi Malaysia UTM Skudai Johor Bahru 81310 Malaysia Department of Computer Sciences College of Education for Pure Science University of Thi-Qar Nasiriyah 64001 Iraq Information and Communication Technology Research Group Scientific Research Center Al-Ayen University Nasiriyah 64001 Iraq Department of Mechanical Engineering College of Engineering University of Baghdad Baghdad Iraq Computational and Applied Mechanics Department Federal University of Juiz de Fora 36036-900 Brazil Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention and Guangdong Provincial Key Laboratory of Marine Biotechnology Shantou University Shantou 515063 China School of Computer and Information Qiannan Normal University for Nationalities Guizhou Duyun 558000 China Institute of Big Data Application and Artificial Intelligence Qiannan Normal University for Nationalities Guizhou Duyun 558000 China Faculty of Data Science and Information Technology INTI International University 71800 Malaysia

This study proposes different standalone models viz: Elman neural network (ENN), Boosted Tree algorithm (BTA), and f relevance vector machine (RVM) for modeling arsenic (As (mg/kg)) and zinc (Zn (mg/kg)) in marine sediments owing to anthropogenic activities. A heuristic algorithm based on the potential of RVM and a flower pollination algorithm (RVM-FPA) was developed to improve the prediction performance. Several evaluation indicators and graphical methods coupled with visualized cumulative probability function (CDF) were used to evaluate the accuracy of the models. Akaike (AIC) and Schwarz (SCI) information criteria based on Dickey-Fuller (ADF) and Philip Perron (PP) tests were introduced to check the reliability and stationarity of the data. The prediction performance in the verification phase indicated that RVM-M2 (PBAIS = -o.0465, MAE = 0.0335) and ENN-M2 (PBAIS = 0.0043, MAE = 0.0322) emerged as the best model for As (mg/kg) and Zn (mg/kg), respectively. In contrast with the standalone approaches, the simulated hybrid RVM-FPA proved merit and the most reliable, with a 5 % and 18 % predictive increase for As (mg/kg) and Zn (mg/kg), respectively. The study's findings validated the potential for estimating complex HMs through intelligent data-driven models and heuristic optimization. The study also generated valuable insights that can inform the decision-makers and stockholders for environmental management strategies. © 2024 Elsevier Ltd

关键词： Artificial intelligence Heavy metals Sensitivity analysis Soil contamination