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arXiv 2021年

作者： Zhang, Linfeng Wang, Han Muniz, Maria Carolina Panagiotopoulos, Athanassios Z. Car, Roberto Weinan, E. DP Technology Beijing China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China HEDPS CAPT College of Engineering Peking University Beijing100871 China Department of Chemical and Biological Engineering Princeton University PrincetonNJ08544 United States Department of Chemistry Department of Physics Program in Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States School of Mathematical Sciences Peking University Beijing100871 China AI for Science Institute Beijing China Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make possible molecular simulations with the accuracy of quantum mechanical density functional theory, at a cost only moderately higher than that of empirical force fields. However, the majority of these models lack explicit long-range interactions and fail to describe properties that derive from the Coulombic tail of the forces. To overcome this limitation we extend the DP model by approximating the long-range electrostatic interaction between ions (nuclei+core electrons) and valence electrons with that of distributions of spherical Gaussian charges located at ionic and electronic sites. The latter are rigorously defined in terms of the centers of the maximally localized Wannier distributions, whose dependence on the local atomic environment is modeled accurately by a deep neural network. In the deep potential long-range (DPLR) model, the electrostatic energy of the Gaussian charge system is added to short-range interactions that are represented as in the standard DP model. The resulting potential energy surface is smooth and possesses analytical forces and virial. Missing effects in the standard DP scheme are recovered, improving on accuracy and predictive power. By including long-range electrostatics, DPLR correctly extrapolates to large systems the potential energy surface learned from quantum mechanical calculations on smaller systems. We illustrate the approach with three examples, the potential energy profile of the water dimer, the free energy of interaction of a water molecule with a liquid water slab, and the phonon dispersion curves of the NaCl crystal. © 2021, CC BY.

关键词： Electrostatics

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Special issue on genome wide association study

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Quantitative Biology 2021年第2期9卷 105-106页

作者： Lin Hou Qiongshi Lu Can Yang Hongyu Zhao Center for Statistical Science Department of Industrial EngineeringMOE Key Laboratory of BioinformaticsSchool of Life SciencesTsinghua UniversityBeijing 100084China Department of Biostatistics and Medical Informatics Department of StatisticsCenter for Demography of Health and AgingUniversity of Wisconsin-MadisonWl 53726USA Department of Mathematics the Hong Kong University of Science and TechnologyHong KongChina Department of Biostatistics Yale School of Public HealthNew HavenCT 06510USA Department of Genetics Yale UniversityNew HavenCT 06510USA Program of Computational Biology and Bioinformatics Yale UniversityNew HavenCT 06510USA

Since the first success of genome wide association study(GWAS)was reported in 2005 by Hoh and colleagues on the identification of a major gene for age related macular degeneration,many thousands of published studies have reported reproducible association signals between hundreds of thousands of genetic variants and thousands of traits and diseases in the past 16 *** is a growing number of biobanks with up to one million participants developed across the world to facilitate genetic studies of complex traits through ***,many consortium projects have been initiated to collect diverse types of data that have proved very valuable for integrated analysis of GWAS *** rich data present both great opportunities and challenges to scientists on data management,computation,analysis,integration,and *** special issue of Quantitative Biology collects nine papers that cover major progresses,challenges,and future directions for GWAS analysis.

关键词： hundreds GWAS initiated

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Hybrid Auxiliary Field Quantum Monte Carlo for Molecular Systems

arXiv

引用

arXiv 2022年

作者： Chen, Yixiao Zhang, Linfeng Weinan, E. Car, Roberto Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Center for Machine Learning Research School of Mathematical Sciences Peking University Beijing100084 China Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States

We propose a quantum Monte Carlo approach to solve the many-body Schrödinger equation for the electronic ground state. The method combines optimization from variational Monte Carlo and propagation from auxiliary field quantum Monte Carlo, in a way that significantly alleviates the sign problem. In application to molecular systems, we obtain highly accurate results for configurations dominated by either dynamic or static electronic correlation. Copyright © 2022, The Authors. All rights reserved.

关键词： Monte Carlo methods

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computational models of astrocyte function at glutamatergic synapses

arXiv

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arXiv 2024年

作者： Lenk, Kerstin Denizot, Audrey Genocchi, Barbara Seppälä, Ippa Taheri, Marsa Nadkarni, Suhita Institute of Neural Engineering Graz University of Technology Graz Austria BioTechMed Graz8010 Austria Theoretical Sciences Visiting Program Okinawa Institute of Science and Technology Graduate University Onna Japan Okinawa Institute of Science and Technology Computational Neuroscience Unit Onna-Son Japan AIstroSight Inria Hospices Civils de Lyon Université Claude Bernard Lyon 1 Villeurbanne France University of Lyon LIRIS UMR5205 Villeurbanne France Faculty of Medicine and Health Technology Tampere University Tampere Finland Department of Psychology and Speech-Language Pathology University of Turku Turku Finland Department of Neurobiology University of California Los AngelesCA United States Department of Biology Indian Institute of Science Education and Research Pune India

At tripartite synapses, astrocytes are in close contact with neurons and contribute to various functions, from synaptic transmission, maintenance of ion homeostasis and glutamate uptake to metabolism. However, disentangling the precise contribution of astrocytes to those phenomena and the underlying biochemical mechanisms is remarkably challenging. This notably results from their highly ramified morphology, the nanoscopic size of the majority of astrocyte processes, and the poorly understood information encoded by their spatiotemporally diverse calcium signals. This book chapter presents selected computational models of the involvement of astrocytes in glutamatergic transmission. The goal of this chapter is to present representative models of astrocyte function in conjunction with the biological questions they can investigate. © 2024, CC BY-NC-SA.

关键词： Calcium

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Anomalous suppression of large-scale density fluctuations in classical and quantum spin liquids

arXiv

引用

arXiv 2025年

作者： Chen, Duyu Samajdar, Rhine Jiao, Yang Torquato, Salvatore Materials Research Laboratory University of California Santa BarbaraCA93106 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Center for Theoretical Science Princeton University PrincetonNJ08544 United States Materials Science and Engineering Arizona State University TempeAZ85287 United States Department of Physics Arizona State University TempeAZ85287 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Materials Institute Princeton University PrincetonNJ08540 United States Program in Applied and Computational Mathematics PrincetonNJ08544 United States

Classical spin liquids (CSLs) are intriguing states of matter that do not exhibit long-range magnetic order and are characterized by an extensive ground-state degeneracy. Adding quantum fluctuations, which induce dynamics between these different classical ground states, can give rise to quantum spin liquids (QSLs). QSLs are highly entangled quantum phases of matter characterized by fascinating emergent properties, such as fractionalized excitations and topological order. One such exotic quantum liquid is the Z2 QSL, which can be regarded as a resonating valence bond (RVB) state formed from superpositions of dimer coverings of an underlying lattice. In this work, we unveil a hidden large-scale structural property of archetypal CSLs and QSLs known as hyperuniformity, i.e., normalized infinite-wavelength density fluctuations are completely suppressed in these systems. In particular, we first demonstrate that classical ensembles of close-packed dimers and their corresponding quantum RVB states are perfectly hyperuniform in general. Subsequently, we focus on a ruby-lattice spin liquid that was recently realized in a Rydberg-atom quantum simulator, and show that the QSL remains effectively hyperuniform even in the presence of a finite density of spinon and vison excitations, as long as the dimer constraint is still largely preserved. Moreover, we demonstrate that metrics based on the framework of hyperuniformity can be used to distinguish the QSL from other proximate quantum phases. These metrics can help identify potential QSL candidates, which can then be further analyzed using more advanced, computationally-intensive quantum numerics to confirm their status as true QSLs. © 2025, CC BY-NC-ND.

关键词： Quantum entanglement

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The effects of surface fossil magnetic fields on massive star evolution: V. Models at low metallicity

arXiv

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arXiv 2024年

作者： Keszthelyi, Z. Puls, J. Chiaki, G. Nagakura, H. Ud-Doula, A. Takiwaki, T. Tominaga, N. Center for Computational Astrophysics Division of Science National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan LMU München Universitätssternwarte Scheinerstr. 1 München81679 Germany National Institute of Technology Kochi College 200-1 Monobe Kochi Nankoku783-8508 Japan Penn State Scranton 120 Ridge View Drive DunmorePA18512 United States Astronomical Science Program Graduate Institute for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Department of Physics Faculty of Science and Engineering Konan University 8-9-1 Okamoto Hyogo Kobe658-8501 Japan

At metallicities lower than that of the Small Magellanic Cloud, it remains essentially unexplored how fossil magnetic fields, forming large-scale magnetospheres, could affect the evolution of massive stars, thereby impacting the fundamental building blocks of the early Universe. We extend our stellar evolution model grid with representative calculations of main-sequence, single-star models with initial masses of 20 and 60 M☉, including appropriate changes for low-metallicity environments (Z = 10−3–10−6). We scrutinise the magnetic, rotational, and chemical properties of the models. When lowering the metallicity, the rotational velocities can become higher and the tendency towards quasi-chemically homogeneous evolution increases. While magnetic fields aim to prevent the development of this evolutionary channel, the weakening stellar winds lead to less efficient magnetic braking in our models. Since the stellar radius is almost constant during a blueward evolution caused by efficient chemical mixing, the surface magnetic field strength remains unchanged in some models. We find core masses at the terminal-age main sequence between 22 and 52 M☉ for initially 60 M☉ models. This large difference is due to the vastly different chemical and rotational evolution. We conclude that in order to explain chemical species and, in particular, high nitrogen abundances in the early Universe, the adopted stellar models need to be under scrutiny. The assumptions regarding wind physics, chemical mixing, and magnetic fields will strongly impact the model predictions. © 2024, CC BY.

关键词： Giant stars

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Artificial intelligence for geoscience:Progress,challenges,and perspectives

引用

The Innovation 2024年第5期5卷 136-160,135页

作者： Tianjie Zhao Sheng Wang Chaojun Ouyang Min Chen Chenying Liu Jin Zhang Long Yu Fei Wang Yong Xie Jun Li Fang Wang Sabine Grunwald Bryan MWong Fan Zhang Zhen Qian Yongjun Xu Chengqing Yu Wei Han Tao Sun Zezhi Shao Tangwen Qian Zhao Chen Jiangyuan Zeng Huai Zhang Husi Letu Bing Zhang Li Wang Lei Luo Chong Shi Hongjun Su Hongsheng Zhang Shuai Yin Ni Huang Wei Zhao Nan Li Chaolei Zheng Yang Zhou Changping Huang Defeng Feng Qingsong Xu Yan Wu Danfeng Hong Zhenyu Wang Yinyi Lin Tangtang Zhang Prashant Kumar Antonio Plaza Jocelyn Chanussot Jiabao Zhang Jiancheng Shi Lizhe Wang Aerospace Information Research Institute Chinese Academy of SciencesBeijing 100094China School of Computer Science China University of GeosciencesWuhan 430078China State Key Laboratory of Mountain Hazards and Engineering Resilience Institute of Mountain Hazards and EnvironmentChinese Academy of SciencesChengdu 610299China Key Laboratory of Virtual Geographic Environment(Ministry of Education of PRC) Nanjing Normal UniversityNanjing 210023China Data Science in Earth Observation Technical University of Munich80333 MunichGermany The National Key Laboratory of Water Disaster Prevention Yangtze Institute for Conservation and DevelopmentHohai UniversityNanjing 210098China Institute of Computing Technology Chinese Academy of SciencesBeijing 100190China School of Geographical Sciences Nanjing University of Information Science and TechnologyNanjing 210044China State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China Soil Water and Ecosystem Sciences DepartmentUniversity of FloridaPO Box 110290GainesvilleFLUSA Materials Science Engineering Program Cooperating Faculty Member in the Department of Chemistry and Department of Physics Astronomy University of CaliforniaCaliforniaRiversideCA 92521USA Institute of Remote Sensing and Geographical Information System School of Earth and Space SciencesPeking UniversityBeijing 100871China Key Laboratory of Computational Geodynamics University of Chinese Academy of SciencesBeijing 100049China International Research Center of Big Data for Sustainable Development Goals Beijing 100094China College of Geography and Remote Sensing Hohai UniversityNanjing 211100China Department of Geography The University of Hong KongHong Kong 999077SARChina Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control Nanjing 210044China School of Environmental Science and Engineering Nanjing University of Information Science&TechnologyNanjing 210044China Collaborative Inno

This paper explores the evolution of geoscientific inquiry,tracing the progression from traditional physics-based models to modern data-driven approaches facilitated by significant advancements in artificial intelligence(AI)and data collection *** models,which are grounded in physical and numerical frameworks,provide robust explanations by explicitly reconstructing underlying physical ***,their limitations in comprehensively capturing Earth’s complexities and uncertainties pose challenges in optimization and real-world *** contrast,contemporary data-driven models,particularly those utilizing machine learning(ML)and deep learning(DL),leverage extensive geoscience data to glean insights without requiring exhaustive theoretical *** techniques have shown promise in addressing Earth science-related ***,challenges such as data scarcity,computational demands,data privacy concerns,and the“black-box”nature of AI models hinder their seamless integration into *** integration of physics-based and data-driven methodologies into hybrid models presents an alternative *** models,which incorporate domain knowledge to guide AI methodologies,demonstrate enhanced efficiency and performance with reduced training data *** review provides a comprehensive overview of geoscientific research paradigms,emphasizing untapped opportunities at the intersection of advanced AI techniques and *** examines major methodologies,showcases advances in large-scale models,and discusses the challenges and prospects that will shape the future landscape of AI in *** paper outlines a dynamic field ripe with possibilities,poised to unlock new understandings of Earth’s complexities and further advance geoscience exploration.

关键词： Earth utilizing landscape

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Scalable privacy-preserving cancer type prediction with homomorphic encryption

arXiv

引用

arXiv 2022年

作者： Sarkar, Esha Chielle, Eduardo Gursoy, Gamze Chen, Leo Gerstein, Mark Maniatakos, Michail Tandon School of Engineering New York University Brooklyn United States Department of Electrical and Computer Engineering New York University Abu Dhabi Abu Dhabi United Arab Emirates Program in Computational Biology and Bioinformatics Yale University New Haven United States Department of Computer Science Yale University New Haven United States

Machine Learning (ML) alleviates the challenges of high-dimensional data analysis and improves decision making in critical applications like healthcare. Effective cancer/tumor classification from high-dimensional genetic mutation data can be useful for cancer diagnosis and treatment, if the distinguishable patterns between cancer/tumor types are identified. At the same time, analysis of high-dimensional data is computationally expensive and is often outsourced to cloud services. Privacy concerns in outsourced ML, especially in the field of genetics, motivate the use of encrypted computation, like Homomorphic Encryption (HE). But restrictive overheads of encrypted computation deter its usage. In this work, we explore the challenges of privacy preserving cancer detection using a real-world dataset consisting of more than 2 million genetic information for several cancer types. Since the data is inherently high-dimensional, we explore smaller ML models for cancer prediction to enable fast inference in the privacy preserving domain. We develop a solution for privacy preserving cancer inference which first leverages the domain knowledge on somatic mutations to efficiently encode genetic mutations and then uses statistical tests for feature selection. Our logistic regression model, built using our novel encoding scheme, achieves 0.98 micro-average area under curve with 13% higher test accuracy than similar studies. We exhaustively test our model’s predictive capabilities by analyzing the genes used by the model. Furthermore, we propose a fast matrix multiplication algorithm that can efficiently handle high-dimensional data. Experimental results show that, even with 40,000 features, our proposed matrix multiplication algorithm can speed up concurrent inference of multiple individuals by approximately 10x and inference of a single individual by approximately 550x, in comparison to standard matrix multiplication. © 2022, CC BY.

关键词： Clustering algorithms

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Opportunities and Challenges from Using Animal Videos in Reinforcement Learning for Navigation

arXiv

引用

arXiv 2022年

作者： Giammarino, Vittorio Queeney, James Carstensen, Lucas C. Hasselmo, Michael E. Paschalidis, Ioannis Ch. Division of Systems Engineering Boston University BostonMA02215 United States Center for Systems Neuroscience Department of Psychological and Brain Sciences Graduate Program for Neuroscience Boston University BostonMA02215 United States College of Engineering Hariri Institute for Computing & Computational Science & Engineering Boston University BostonMA02215 United States

We investigate the use of animal videos (observations) to improve Reinforcement Learning (RL) efficiency and performance in navigation tasks with sparse rewards. Motivated by theoretical considerations, we make use of weighted policy optimization for off-policy RL and describe the main challenges when learning from animal videos. We propose solutions and test our ideas on a series of 2D navigation tasks. We show how our methods can leverage animal videos to improve performance over RL algorithms that do not leverage such observations. © 2022, CC BY.

关键词： Reinforcement learning

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HYPER-REALIST RENDERING: A THEORETICAL FRAMEWORK

arXiv

引用

arXiv 2024年

作者： Akleman, Ergun Kurt, Murat Akleman, Derya Bruins, Gary Deng, Sitong Subramanian, Meena Visual Computing & Computational Media School of PVFA Computer Science and Engineering College of Engineering Texas A&M University College StationTX77831 United States International Computer Institute Ege University Izmir Turkey Department of Statistics Texas A&M University College StationTX77831 United States Visualization Program Department of Architecture Texas A&M University College StationTX77831 United States Department of Visualization Texas A&M University College StationTX77831 United States

This is the first paper in a series on hyper-realist rendering. In this paper, we introduce the concept of hyper-realist rendering and present a theoretical framework to obtain hyper-realist images. We are using the term Hyper-realism as an umbrella word that captures all types of visual artifacts that can evoke an impression of reality. The hyper-realist artifacts are visual representations that are not necessarily created by following logical and physical principles and can still be perceived as representations of reality. This idea stems from the principles of representational arts, which attain visually acceptable renderings of scenes without implementing strict physical laws of optics and materials. The objective of this work is to demonstrate that it is possible to obtain visually acceptable illusions of reality by employing such artistic approaches. With representational art methods, we can even obtain an alternate illusion of reality that looks more real even when it is not real. This paper demonstrates that it is common to create illusions of reality in visual arts with examples of paintings by representational artists. We propose an approach to obtain expressive local and global illuminations to obtain these stylistic illusions with a set of well-defined and formal methods. Our formalism is based on four principles: (1) colors and textures must be represented by algebraically complete structures, (2) we should allow impossible and inconsistent shapes in scene concepts, (3) we have to decompose illumination and shading, and (4) we must build our shading functions using statistic-based methods instead of physics-based methods. We claim that these principles allow us to develop simple methods since we can avoid algebraic inconsistencies. Using such simple methods, it can be possible to significantly speed up modeling and rendering algorithms by focusing only on essential elements that can create illusions of reality. © 2024, CC BY.

关键词： Formal methods

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