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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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Joint modeling of received power, mean delay, and delay spread for wideband radio channels

arXiv

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arXiv 2020年

作者： Bharti, Ayush Adeogun, Ramoni Cai, Xuesong Fan, Wei Briol, François-Xavier Clavier, Laurent Pedersen, Troels The Department of Electronic Systems Aalborg University Denmark The Department of Statistical Science University College London The Data-Centric Engineering Programme The Alan Turing Institute London United Kingdom IMT Lille Douai University of Lille CNRS UMR 8520 LilleF-59000 France

We propose a multivariate log-normal distribution to jointly model received power, mean delay, and root mean square (rms) delay spread of wideband radio channels, referred to as the standardized temporal moments. The model is validated using experimental data collected from five different measurement campaigns (four indoor and one outdoor scenario). We observe that the received power, the mean delay, and the rms delay spread are correlated random variables, and therefore, should be simulated jointly. Joint models are able to capture the structure of the underlying process, unlike the independent models considered in the literature. The proposed model of the multivariate log-normal distribution is found to be a good fit for a large number of wideband data-sets. Copyright © 2020, The Authors. All rights reserved.

关键词： Millimeter waves

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Erratum: "Controlling species densities in structurally perturbed intransitive cycles with higher-order interactions" [Chaos 32(10), 103122 (2022)]

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Chaos (Woodbury, N.Y.) 2023年第4期33卷 049901页

作者： Sourin Chatterjee Sayantan Nag Chowdhury Dibakar Ghosh Chittaranjan Hens Department of Mathematics and Statistics Indian Institute of Science Education and Research Kolkata West Bengal 741246 India. Physics and Applied Mathematics Unit Indian Statistical Institute 203 B. T. Road Kolkata 700108 India. Technology Innovation Hub (TIH) IDEAS (Institute of Data Engineering Analytics and Science Foundation) @ Indian Statistical Institute 203 B. T. Road Kolkata 700108 India. International Institute of Information Technology Gachibowli Hyderabad 500032 India.

Recently, we noticed Figs. 4 and 5 were interchanged in Ref. 1, although their respective captions remain correct (Figs. 1 and 2). A typing mistake in mathemati

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Operational Research: Methods and Applications

arXiv

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arXiv 2023年

作者： Petropoulos, Fotios Laporte, Gilbert Aktas, Emel Alumur, Sibel A. Archetti, Claudia Ayhan, Hayriye Battarra, Maria Bennell, Julia A. Bourjolly, Jean-Marie Boylan, John E. Breton, Michèle Canca, David Charlin, Laurent Chen, Bo Cicek, Cihan Tugrul Cox, Louis Anthony Currie, Christine S.M. Demeulemeester, Erik Ding, Li Disney, Stephen M. Ehrgott, Matthias Eppler, Martin J. Erdogan, Güneş Fortz, Bernard Franco, L. Alberto Frische, Jens Greco, Salvatore Gregory, Amanda J. Hämäläinen, Raimo P. Herroelen, Willy Hewitt, Mike Holmström, Jan Hooker, John N. Işık, Tugçe Johnes, Jill Kara, Bahar Y. Karsu, Özlem Kent, Katherine Köhler, Charlotte Kunc, Martin Kuo, Yong-Hong Letchford, Adam N. Leung, Janny Li, Dong Li, Haitao Lienert, Judit Ljubić, Ivana Lodi, Andrea Lozano, Sebastián Lurkin, Virginie Martello, Silvano McHale, Ian G. Midgley, Gerald Morecroft, John D.W. Mutha, Akshay Oguz, Ceyda Petrovic, Sanja Pferschy, Ulrich Psaraftis, Harilaos N. Rose, Sam Saarinen, Lauri Salhi, Said Song, Jing-Sheng Sotiros, Dimitrios Stecke, Kathryn E. Strauss, Arne K. Tarhan, Istenç Thielen, Clemens Toth, Paolo Van Woensel, Tom Vanden Berghe, Greet Vasilakis, Christos Vaze, Vikrant Vigo, Daniele Virtanen, Kai Wang, Xun Weron, Rafal White, Leroy Yearworth, Mike Yıldırım, E. Alper Zaccour, Georges Zhao, Xuying School of Management University of Bath Bath United Kingdom Makridakis Open Forecasting Center University of Nicosia Nicosia Cyprus Department of Decision Sciences HEC Montréal Montreal Canada Molde University College Molde Norway Cranfield School of Management Cranfield University Cranfield United Kingdom Department of Management Sciences University of Waterloo Waterloo Canada ESSEC Business School in Paris Department of Information Systems Decision Sciences and Statistics Cergy France H. Milton Stewart School of Industrial and Systems Engineering Georgia Institute of Technology Atlanta United States Centre for Decision Research Leeds University Business School University of Leeds Leeds United Kingdom Université du Québec à Montréal Montreal Canada Centre for Marketing Analytics and Forecasting Lancaster University Management School Lancaster University Lancaster United Kingdom School of Engineering Department of Industrial Engineering and Management Science I University of Seville Seville Spain Mila-Quebec AI Institute Montreal Canada Warwick Business School University of Warwick Coventry United Kingdom Department of Industrial Engineering Atilim University Ankara Turkey Department of Business Analytics University of Colorado School of Business Denver United States Cox Associates Denver United States Mathematical Sciences University of Southampton Southampton United Kingdom Faculty of Economics and Business Research Center for Operations Management KU Leuven Leuven Belgium Durham University Business School Durham University Durham United Kingdom Center for Simulation Analytics and Modelling University of Exeter Business School Exeter United Kingdom Department of Management Science Lancaster University Management School Lancaster University Lancaster United Kingdom University of St. Gallen St. Gallen Switzerland HEC - Management School of the University of Liège Liège Belgium Département d'Informatique Université Libre de Bruxelles Bruss

Throughout its history, Operational Research has evolved to include a variety of methods, models and algorithms that have been applied to a diverse and wide range of contexts. This encyclopedic article consists of two main sections: methods and applications. The first aims to summarise the up-to-date knowledge and provide an overview of the state-of-the-art methods and key developments in the various subdomains of the field. The second offers a wide-ranging list of areas where Operational Research has been applied. The article is meant to be read in a nonlinear fashion. It should be used as a point of reference or first-port-of-call for a diverse pool of readers: academics, researchers, students, and practitioners. The entries within the methods and applications sections are presented in alphabetical order. The authors dedicate this paper to the 2023 Turkey/Syria earthquake victims. We sincerely hope that advances in OR will play a role towards minimising the pain and suffering caused by this and future catastrophes. © 2023, CC BY.

关键词： Decision making

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DriveSOTIF: Advancing Perception SOTIF Through Multimodal Large Language Models

arXiv

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arXiv 2025年

作者： Huang, Shucheng Shi, Freda Sun, Chen Zhong, Jiaming Ning, Minghao Yang, Yufeng Lu, Yukun Wang, Hong Khajepour, Amir MVSLab Department of Mechanical and Mechatronics Engineering University of Waterloo 200 University Ave West WaterlooONN2L3G1 Canada CompLING Lab David R. Cheriton School of Computer Science University of Waterloo Vector Institute 200 University Ave West WaterlooONN2L3G1 Canada Department of Data and Systems Engineering University of Hong Kong Pok Fu Lam Hong Kong School of Vehicle and Mobility Tsinghua University Beijing100084 China

Human drivers naturally possess the ability to perceive driving scenarios, predict potential hazards, and react instinctively due to their spatial and causal intelligence, which allows them to perceive, understand, predict, and interact with the 3D world both spatially and temporally. Autonomous vehicles, however, lack these capabilities, leading to challenges in effectively managing perception-related Safety of the Intended Functionality (SOTIF) risks, particularly in complex and unpredictable driving conditions. To address this gap, we propose an approach that fine-tunes multimodal language models (MLLMs) on a customized dataset specifically designed to capture perception-related SOTIF scenarios. Model benchmarking demonstrates that this tailored dataset enables the models to better understand and respond to these complex driving situations. Additionally, in real-world case studies, the proposed method correctly handles challenging scenarios that even human drivers may find difficult. Real-time performance tests further indicate the potential for the models to operate efficiently in live driving environments. This approach, along with the dataset generation pipeline, shows significant promise for improving the identification, cognition, prediction, and reaction to SOTIF-related risks in autonomous driving systems. The dataset and information are available: https://***/s95huang/*** © 2025, CC BY-NC-ND.

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NTIRE 2023 Challenge on Light Field Image Super-Resolution: dataset, Methods and Results

arXiv

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arXiv 2023年

作者： Wang, Yingqian Wang, Longguang Liang, Zhengyu Yang, Jungang Timofte, Radu Guo, Yulan Jin, Kai Wei, Zeqiang Yang, Angulia Guo, Sha Gao, Mingzhi Zhou, Xiuzhuang Van Duong, Vinh Huu, Thuc Nguyen Yim, Jonghoon Jeon, Byeungwoo Liu, Yutong Cheng, Zhen Xiao, Zeyu Xu, Ruikang Xiong, Zhiwei Liu, Gaosheng Jin, Manchang Yue, Huanjing Yang, Jingyu Gao, Chen Zhang, Shuo Chang, Song Lin, Youfang Chao, Wentao Wang, Xuechun Wang, Guanghui Duan, Fuqing Xia, Wang Wang, Yan Xia, Peiqi Wang, Shunzhou Lu, Yao Cong, Ruixuan Sheng, Hao Yang, Da Chen, Rongshan Wang, Sizhe Cui, Zhenglong Chen, Yilei Lu, Yongjie Cai, Dongjun An, Ping Salem, Ahmed Ibrahem, Hatem Yagoub, Bilel Kang, Hyun-Soo Zeng, Zekai Wu, Heng National University of Defense Technology China Aviation University of Air Force China University of Würzburg Germany ETH Zürich Switzerland The Shenzhen Campus of Sun Yat-Sen University Sun Yat-Sen University China Bigo Technology Pte. Ltd Singapore Smart Medical Innovation Lab Beijing University of Posts and Telecommunications China Global Explorer Ltd. Suzhou China National Engineering Research Center of Visual Technology School of Computer Science Peking University China School of Artificial Intelligence Beijing University of Posts and Telecommunications China Department of Electrical and Computer Engineering Sungkyunkwan University Korea Republic of University of Science and Technology of China China School of Electrical and Information Engineering Tianjin University China Beijing Key Lab of Traffic Data Analysis and Mining School of Computer and Information Technology Beijing Jiaotong University China Beijing Normal University China Toronto Metropolitan University Canada Beijing Institute of Technology China Shenzhen MSU-BIT University China State Key Laboratory of Virtual Reality Technology and Systems School of Computer Science and Engineering Beihang University China Beihang Hangzhou Innovation Institute Yuhang China Faculty of Applied Sciences Macao Polytechnic University China School of Communication and Information Engineering Shanghai University China School of Information and Communication Engineering Chungbuk National University Korea Republic of Guangdong University of Technology China

In this report, we summarize the first NTIRE challenge on light field (LF) image super-resolution (SR), which aims at super-resolving LF images under the standard bicubic degradation with a magnification factor of 4. This challenge develops a new LF dataset called NTIRE-2023 for validation and test, and provides a toolbox called BasicLFSR to facilitate model development. Compared with single image SR, the major challenge of LF image SR lies in how to exploit complementary angular information from plenty of views with varying disparities. In total, 148 participants have registered the challenge, and 11 teams have successfully submitted results with PSNR scores higher than the baseline method LF-InterNet [1]. These newly developed methods have set new state-of-the-art in LF image SR, e.g., the winning method achieves around 1 dB PSNR improvement over the existing state-of-the-art method DistgSSR [2]. We report the solutions proposed by the participants, and summarize their common trends and useful tricks. We hope this challenge can stimulate future research and inspire new ideas in LF image SR. © 2023, CC BY-SA.

关键词： Image enhancement

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Lessons Learned from Assessing Trustworthy AI in Practice

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Digital Society 2023年第3期2卷 1-25页

作者： Vetter, Dennis Amann, Julia Bruneault, Frédérick Coffee, Megan Düdder, Boris Gallucci, Alessio Gilbert, Thomas Krendl Hagendorff, Thilo van Halem, Irmhild Hickman, Eleanore Hildt, Elisabeth Holm, Sune Kararigas, Georgios Kringen, Pedro Madai, Vince I. Wiinblad Mathez, Emilie Tithi, Jesmin Jahan Westerlund, Magnus Wurth, Renee Zicari, Roberto V. Computational Vision and Artificial Intelligence Lab Goethe University Frankfurt Frankfurt Am Main Germany Z-Inspection® Initiative Venice Italy Health Ethics and Policy Lab ETH Zurich Zurich Switzerland Strategy and Innovation Careum Foundation Zurich Switzerland Philosophie Departement Collège André-Laurendeau Montréal Canada École Des Médias Université du Québec À Montréal Montréal Canada Department of Medicine Division of Infectious Diseases and Immunology New York University Grossman School of Medicine New York City USA Department of Computer Science University of Copenhagen Copenhagen Denmark Digital Life Initiative Cornell Tech New York City USA Cluster of Excellence “Machine Learning: New Perspectives for Science” University of Tuebingen Tuebingen Germany School of Law University of Bristol Bristol UK Center for the Study of Ethics in the Professions Illinois Institute of Technology Chicago USA Department of Business Management and Analytics Arcada University of Applied Sciences Helsinki Finland Department of Food & Resource Economics University of Copenhagen Copenhagen Denmark Department of Physiology Faculty of Medicine University of Iceland Reykjavik Iceland QUEST Centre for Responsible Research Berlin Institute of Health Charité Universitätsmedizin Berlin Berlin Germany Faculty of Computing Engineering and the Built Environment School of Computing and Digital Technology Birmingham City University Birmingham UK Parallel Computing Labs Intel Santa Clara USA School of Economics Innovation and Technology Kristiania University College Oslo Norway Data Science Graduate School Seoul National University Seoul South Korea

Building artificial intelligence (AI) systems that adhere to ethical standards is a complex problem. Even though a multitude of guidelines for the design and development of such trustworthy AI systems exist, these guidelines focus on high-level and abstract requirements for AI systems, and it is often very difficult to assess if a specific system fulfills these requirements. The Z-Inspection® process provides a holistic and dynamic framework to evaluate the trustworthiness of specific AI systems at different stages of the AI lifecycle, including intended use, design, and development. It focuses, in particular, on the discussion and identification of ethical issues and tensions through the analysis of socio-technical scenarios and a requirement-based framework for ethical and trustworthy AI. This article is a methodological reflection on the Z-Inspection® process. We illustrate how high-level guidelines for ethical and trustworthy AI can be applied in practice and provide insights for both AI researchers and AI practitioners. We share the lessons learned from conducting a series of independent assessments to evaluate the trustworthiness of real-world AI systems, as well as key recommendations and practical suggestions on how to ensure a rigorous trustworthiness assessment throughout the lifecycle of an AI system. The results presented in this article are based on our assessments of AI systems in the healthcare sector and environmental monitoring, where we used the framework for trustworthy AI proposed in the Ethics Guidelines for Trustworthy AI by the European Commission’s High-Level Expert Group on AI. However, the assessment process and the lessons learned can be adapted to other domains and include additional frameworks.

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Predicting tipping phenomenon in a conceptual airfoil structure under extreme flight environment

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Journal of Sound and Vibration 2025年

作者： Jinzhong Ma Dengyan Li Ruifang Wang Qi Liu Yong Xu Tomasz Kapitaniak Jürgen Kurths School of Mathematics and Statistics Shanxi University Taiyuan 030006 China Key Laboratory of Complex Systems and Data Science of Ministry of Education Shanxi University Taiyuan 030006 China Department of Systems and Control Engineering Tokyo Institute of Technology Tokyo 152-8552 Japan School of Mathematics and Statistics Northwestern Polytechnical University Xi’an 710072 China MOE Key Laboratory for Complexity Science in Aerospace Northwestern Polytechnical University Xi’an 710072 China Division of Dynamics Lodz University of Technology Stefanowskiego 1/15 90-924 Lodz Poland Potsdam Institute for Climate Impact Research Potsdam 14412 Germany Department of Physics Humboldt University at Berlin Berlin 12489 Germany

This paper investigates the tipping phenomenon in a conceptual airfoil system subjected to both periodic excitation and extreme random loads modeled by non-Gaussian Lévy noise. Firstly, the effects of main parameters of Lévy noise on the tipping phenomenon are uncovered. It is found that an increased noise intensity or a reduced stability index can induce the tipping phenomenon to take place before the bifurcation point of the corresponding deterministic system. Moreover, large rises and jumps in Lévy noise can more easily lead to catastrophic high-amplitude oscillations than the ideal Gaussian white noise. Then, the residence probability of the airfoil system remaining in high-amplitude oscillations is given to further quantify the likelihood of the tipping phenomenon induced by Lévy noise. To realize the prediction of these catastrophic high-amplitude oscillations, a concept of the high-risk region is defined based on the residence probability. Finally, the ranges of the related parameters, where Lévy noise-induced tipping phenomenon may occur, are approximately quantified. These findings may provide theoretical guidance for engineers in preventing catastrophic tipping phenomena in airfoil structures, thereby enhancing the safety of aircraft operations in extreme environments.

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A first-order primal-dual method for nonconvex constrained optimization based on the augmented Lagrangian

arXiv

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arXiv 2020年

作者： Zhu, Daoli Zhao, Lei Zhang, Shuzhong Antai College of Economics and Management and Sino-US Global Logistics Institute Shanghai Jiao Tong University Shanghai200030 China School of Naval Architecture Ocean and Civil Engineering Shanghai Jiao Tong University Shanghai200030 China Department of Industrial and Systems Engineering University of Minnesota MinneapolisMN55455 United States School of Data Science Shenzhen Research Institute of Big Data Chinese University of Hong Kong Shenzhen Hong Kong

Nonlinearly constrained nonconvex and nonsmooth optimization models play an increasingly important role in machine learning, statistics and data analytics. In this paper, based on the augmented Lagrangian function we introduce a flexible first-order primal-dual method, to be called nonconvex auxiliary problem principle of augmented Lagrangian (NAPP-AL), for solving a class of nonlinearly constrained nonconvex and nonsmooth optimization problems. We demonstrate that NAPP-AL converges to a stationary solution at the rate of o(1/√k), where k is the number of iterations. Moreover, under an additional error bound condition (to be called VP-EB in the paper), we further show that the convergence rate is in fact linear. Finally, we show that the famous Kurdyka-Lojasiewicz property and the metric subregularity imply the afore-mentioned VP-EB *** Codes 90C30, 90C26. Copyright © 2020, The Authors. All rights reserved.

关键词： Constrained optimization

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

arXiv

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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

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