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arXiv 2024年

作者： Huang, Keke Wang, Yu Guang Li, Ming Liò, Pietro School of Computing National University of Singapore Singapore Institute of Natural Sciences School of Mathematical Sciences Zhangjiang Institute for Advanced Study Shanghai Jiao Tong University Shanghai China Shanghai AI Laboratory Shanghai China School of Mathematics and Statistics University of New South Wales Sydney Australia Zhejiang Institute of Optoelectronics Jinhua China Zhejiang Key Laboratory of Intelligent Education Technology and Application Zhejiang Normal University Jinhua China Department of Computer Science and Technology Cambridge University Cambridge United Kingdom

Spectral Graph Neural Networks (GNNs), alternatively known as graph filters, have gained increasing prevalence for heterophily graphs. Optimal graph filters rely on Laplacian eigendecomposition for Fourier transform. In an attempt to avert prohibitive computations, numerous polynomial filters have been proposed. However, polynomials in the majority of these filters are predefined and remain fixed across different graphs, failing to accommodate the varying degrees of heterophily. Addressing this gap, we demystify the intrinsic correlation between the spectral property of desired polynomial bases and the heterophily degrees via thorough theoretical analyses. Subsequently, we develop a novel adaptive heterophily basis wherein the basis vectors mutually form angles reflecting the heterophily degree of the graph. We integrate this heterophily basis with the homophily basis to construct a universal polynomial basis UniBasis, which devises a polynomial filter-based graph neural network – UniFilter. It optimizes the convolution and propagation in GNN, thus effectively limiting over-smoothing and alleviating over-squashing. Our extensive experiments, conducted on datasets with a diverse range of heterophily, support the superiority of UniBasis in the universality but also its proficiency in graph explanation. © 2024, CC BY-NC-SA.

关键词： Graph neural networks

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Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks

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Nucleic acids research 2023年第13期51卷 6578-6592页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Bo-Jia Chen Yu-Te Lin Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung 402 Taiwan. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Program in Integrative & Complex Diseases Department of Nutrition Texas A&M University College Station TX 77843 USA. Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA.

In this paper, we introduce Gene Knockout Inference (GenKI), a virtual knockout (KO) tool for gene function prediction using single-cell RNA sequencing (scRNA-seq) data in the absence of KO samples when only wild-type (WT) samples are available. Without using any information from real KO samples, GenKI is designed to capture shifting patterns in gene regulation caused by the KO perturbation in an unsupervised manner and provide a robust and scalable framework for gene function studies. To achieve this goal, GenKI adapts a variational graph autoencoder (VGAE) model to learn latent representations of genes and interactions between genes from the input WT scRNA-seq data and a derived single-cell gene regulatory network (scGRN). The virtual KO data is then generated by computationally removing all edges of the KO gene-the gene to be knocked out for functional study-from the scGRN. The differences between WT and virtual KO data are discerned by using their corresponding latent parameters derived from the trained VGAE model. Our simulations show that GenKI accurately approximates the perturbation profiles upon gene KO and outperforms the state-of-the-art under a series of evaluation conditions. Using publicly available scRNA-seq data sets, we demonstrate that GenKI recapitulates discoveries of real-animal KO experiments and accurately predicts cell type-specific functions of KO genes. Thus, GenKI provides an in-silico alternative to KO experiments that may partially replace the need for genetically modified animals or other genetically perturbed systems.

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How universal polynomial bases enhance spectral graph neural networks: heterophily, over-smoothing, and over-squashing 24

How universal polynomial bases enhance spectral graph neural...

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Proceedings of the 41st International Conference on Machine Learning

作者： Keke Huang Yu Guang Wang Ming Li Pietro Liò School of Computing National University of Singapore Singapore Institute of Natural Sciences School of Mathematical Sciences Zhangjiang Institute for Advanced Study Shanghai Jiao Tong University Shanghai China and Shanghai AI Laboratory Shanghai China and School of Mathematics and Statistics University of New South Wales Sydney Australia Zhejiang Institute of Optoelectronics Jinhua China and Zhejiang Key Laboratory of Intelligent Education Technology and Application Zhejiang Normal University Jinhua China Department of Computer Science and Technology Cambridge University Cambridge UK

Spectral Graph Neural Networks (GNNs), alternatively known as graph filters, have gained increasing prevalence for heterophily graphs. Optimal graph filters rely on Laplacian eigendecomposition for Fourier transform. In an attempt to avert prohibitive computations, numerous polynomial filters have been proposed. However, polynomials in the majority of these filters are predefined and remain fixed across different graphs, failing to accommodate the varying degrees of heterophily. Addressing this gap, we demystify the intrinsic correlation between the spectral property of desired polynomial bases and the heterophily degrees via thorough theoretical analyses. Subsequently, we develop a novel adaptive heterophily basis wherein the basis vectors mutually form angles reflecting the heterophily degree of the graph. We integrate this heterophily basis with the homophily basis to construct a universal polynomial basis UniBasis, which devises a polynomial filter-based graph neural network - UniFilter. It optimizes the convolution and propagation in GNN, thus effectively limiting over-smoothing and alleviating over-squashing. Our extensive experiments, conducted on datasets with a diverse range of heterophily, support the superiority of UniBasis in the universality but also its proficiency in graph explanation.

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Probing the long-range structure of the Tcc+ with the strong and electromagnetic decays

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Physical Review D 2021年第5期104卷 L051502-L051502页

作者： Lu Meng Guang-Juan Wang Bo Wang Shi-Lin Zhu Ruhr-Universität Bochum Fakultät für Physik und Astronomie Institut für Theoretische Physik II D-44780 Bochum Germany Advanced Science Research Center Japan Atomic Energy Agency Tokai Ibaraki 319-1195 Japan School of Physical Science and Technology Hebei University Baoding 071002 China Key Laboratory of High-precision Computation and Application of Quantum Field Theory of Hebei Province Baoding 071002 China School of Physics and Center of High Energy Physics Peking University Beijing 100871 China

Very recently, the LHCb Collaboration reported the doubly charmed tetraquark state Tcc+ below the D*+D0 threshold about 273 keV. As a very near-threshold state, its long-distance structure is very important. In the molecular scheme, we relate the coupling constants of Tcc+ with D*0D+ and D*+D0 to its binding energy and mixing angle of two components with a coupled-channel effective field theory. With the coupling constants, we investigate the kinetically allowed strong decays Tcc+→D0D0π+, Tcc+→D+D0π0 and radiative decays D+D0γ. Our results show that the decay width of Tcc+→D0D0π+ is the largest one, which is just the experimental observation channel. Our theoretical total strong and radiative widths are in favor of the Tcc+ as a |D*+D0⟩ dominated bound state. The total strong and radiative width in the single channel limit and isospin singlet limit are given as 59.7−4.4+4.6 keV and 46.7−2.9+2.7 keV, respectively. Our calculation is cutoff-independent and without prior isospin assignment. The absolute partial widths and ratios of the different decay channels can be used to test the structure of Tcc+ state when the updated experimental results are available.

关键词： Bound states Effective field theory Particle decays Mesons

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Revisit the isospin violating decays of X(3872)

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Physical Review D 2021年第9期104卷 094003-094003页

In this work, we revisit the isospin violating decays of X(3872) in a coupled-channel effective field theory. In the molecular scheme, the X(3872) is interpreted as the bound state of D¯*0D0/D¯0D*0 and D*−D+/D−D*+ channels. In a cutoff-independent formalism, we relate the coupling constants of X(3872) with the two channels to the molecular wave function. The isospin violating decays of X(3872) are obtained by two equivalent approaches, which amend some deficiencies about this issue in literature. In the quantum field theory approach, the isospin violating decays arise from the coupling constants of X(3872) to two dimeson channels. In the quantum mechanics approach, the isospin violating is attributed to wave functions at the origin. We illustrate that how to cure the insufficient results in literature. Within the comprehensive analysis, we bridge the isospin violating decays of X(3872) to its inner structure. Our results show that the proportion of the neutral channel in X(3872) is over 80%. As a by-product, we calculate the strong decay width of X(3872)→D¯0D0π0 and radiative one X(3872)→D¯0D0γ. The strong decay width and radiative decay width are about 30 keV and 10 keV, respectively, for the binding energy from −300 keV to −50 keV.

关键词： Particle decays Particle interactions Mesons Effective field theory

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Coupled chemical reactions: Effects of electric field, diffusion, and boundary control

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Physical Review E 2023年第6期108卷 064413-064413页

作者： Shixin Xu Robert Eisenberg Zilong Song Huaxiong Huang Zu Chongzhi Center for Mathematics and Computational Sciences Duke Kunshan University 8 Duke Ave Kunshan Jiangsu 215316 China Department of Applied Mathematics Illinois Institute of Technology Chicago Illinois 60616 USA and Department of Physiology and Biophysics Rush University Chicago Ilinois 60612 USA Math and Statistics Department Utah State University Old Main Hill Logan Utah 84322 USA Research Center for Mathematics Advanced Institute of Natural Sciences Beijing Normal University Zhuhai Guangdong 519088 China Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science BNU-HKBU United International College Zhuhai Guangdong 519088 China Laboratory of Mathematics and Complex Systems MOE Beijing Normal University Beijing 100875 China and Department of Mathematics and Statistics York University Toronto Ontario Canada M3J 1P3

Chemical reactions involve the movement of charges, and this paper presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical thermodynamics principles. It encompasses both electrostatics and chemical reactions within consistently defined energetic and dissipative functionals. Furthermore, the energy variation method is extended to account for open systems that involve the input and output of charge and mass. Such open systems have the capability to convert one form of input energy into another form of output energy. In particular, a two-domain model is developed to study a reaction system with self-regulation and internal switching, which plays a vital role in the electron transport chain of mitochondria responsible for ATP generation—a crucial process for sustaining life. Simulations are conducted to explore the influence of electric potential on reaction rates and switching dynamics within the two-domain system. It shows that the electric potential inhibits the oxidation reaction while accelerating the reduction reaction.

关键词： Continuum mechanics Dissipative dynamics Electric field effects

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Experimental Identification of Non-Abelian Topological Orders on a Quantum Simulator

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Physical Review Letters 2017年第8期118卷 080502-080502页

作者： Keren Li Yidun Wan Ling-Yan Hung Tian Lan Guilu Long Dawei Lu Bei Zeng Raymond Laflamme State Key Laboratory of Low-Dimensional Quantum Physics and Department of Physics Tsinghua University Beijing 100084 China Institute for Quantum Computing and Department of Physics and Astronomy University of Waterloo Waterloo N2L 3G1 Ontario Canada Department of Physics and Center for Field Theory and Particle Physics Fudan University Shanghai 200433 China Collaborative Innovation Center of Advanced Microstructures Nanjing University Nanjing 210093 China Perimeter Institute for Theoretical Physics Waterloo N2L 2Y5 Ontario Canada State Key Laboratory of Surface Physics and Department of Physics Fudan University 220 Handan Road Shanghai 200433 China Department of Mathematics & Statistics University of Guelph Guelph Nag 2W1 Ontario Canada Canadian Institute for Advanced Research Toronto M5G 1Z8 Ontario Canada

Topological orders can be used as media for topological quantum computing—a promising quantum computation model due to its invulnerability against local errors. Conversely, a quantum simulator, often regarded as a quantum computing device for special purposes, also offers a way of characterizing topological orders. Here, we show how to identify distinct topological orders via measuring their modular S and T matrices. In particular, we employ a nuclear magnetic resonance quantum simulator to study the properties of three topologically ordered matter phases described by the string-net model with two string types, including the Z2 toric code, doubled semion, and doubled Fibonacci. The third one, non-Abelian Fibonacci order is notably expected to be the simplest candidate for universal topological quantum computing. Our experiment serves as the basic module, built on which one can simulate braiding of non-Abelian anyons and ultimately, topological quantum computation via the braiding, and thus provides a new approach of investigating topological orders using quantum computers.

关键词： Anyons Fractionalization Quantum simulation Topological quantum computing Nuclear magnetic resonance

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[email protected] 3 core-shell fillers improved high temperature energy storage density of P(VDF-HFP) based nanocomposites

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Composites Science and Technology 2022年 229卷

作者： Zhongcan Luo Zhanwen Ye Bo Duan Guodong Li Kaiyuan Li Zijian Yang Shiqing Nie Tianwei Chen Ling Zhou Pengcheng Zhai Hubei Key Laboratory of Theory and Application of Advanced Materials Mechanics Wuhan University of Technology Wuhan 430070 PR China School of Optical and Electronic Information Huazhong University of Science and Technology Wuhan 430074 PR China

The emerging industry has put forward stricter requirements for the operating temperature of electrostatic capacitors. Improving the high temperature breakdown strength is the key issue to enhance the thermal stability of polymer-based nanocomposites. In this study, the nanoparticles which is composed of high heat conductivity coefficient core (SiC) and high dielectric constant shell (BaTiO 3 ) were prepared and used as fillers, with the purpose of improving breakdown strength (E b ) and discharged energy storage density (U dis ) of P(VDF-HFP)-based nanocomposites at high temperature. Compared with the pure polymer, the composite films, especially the films with 7.5 wt% fillers, showed great enhancements in breakdown strength and discharged energy storage density at high temperature. The average E b reached 1524.6 kV/cm at 120 °C, which was 1.84 times of the contrast. The U dis at 120 °C was 2.05 J/cm 3 (1700 kV/cm), which increased by 569.4% than that of pure polymer (at 700 kV/cm, 0.36 J/cm 3 ). The improvement of thermal performance and Young's modulus of materials was contributing to the enhancements of thermal breakdown strength and electromechanical breakdown strength at high temperature. This study provides an effective way to prepare dielectric composites for high-temperature environment application.

关键词： Core-shell particle Thermal stability High temperature breakdown strength Energy storage density

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Preface

Engineering Applications of Computational Methods

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Engineering applications of Computational Methods 2023年 13卷 V页

作者： Wen, Chih-Yung Jiang, Yazhong Shi, Lisong Department of Aeronautical and Aviation Engineering Faculty of Engineering The Hong Kong Polytechnic University Hong Kong Hubei Key Laboratory of Theory and Application of Advanced Materials Mechanics School of Science Wuhan University of Technology Hubei Wuhan China

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General One-loop Generating Function by IBP relations

arXiv

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arXiv 2024年

作者： Hu, Chang Feng, Bo Shen, Jiyuan Zhang, Yaobo College of Physics Science and Technology Hebei University Baoding071002 China Hebei Key Laboratory of High-precision Computation and Application of Quantum Field Theory Baoding071002 China Hebei Research Center of the Basic Discipline for Computational Physics Baoding071002 China School of Fundamental Physics and Mathematical Sciences Hangzhou Institute for Advanced Study UCAS Hangzhou310024 China University of Chinese Academy of Sciences Beijing100049 China Beijing Computational Science Research Center Beijing100193 China Peng Huanwu Center for Fundamental Theory Anhui Hefei230026 China Institute of Theoretical Physics Chinese Academy of Sciences Beijing100190 China School of Physics Ningxia University Yinchuan750002 China

In this paper, we have studied the general generating function of reduction for one-loop integrals with arbitrary tensor structure in the numerator and arbitrary power distribution of propagators in the denominator. Using IBP relations, we have established the partial differential equations for these generating functions and solved them analytically with compact form. These results provide useful information for the analytical structure of reduction coefficients and guidance for applying the generating function method to reductions of higher loop integrals. © 2024, CC BY.

关键词： Choquet integral

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