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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Implicit Asymptotic Preserving Method for Linear Transport Equations

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Communications in computational Physics 2017年第6期22卷 157-181页

作者： Qin Li Li Wang Mathematics Department University of Wisconsin-Madison480 Lincoln Dr.MadisonWI 53705USA Departments of Mathematics and Computational Data-Enabled Science and Engineering Program State University of New York at Buffalo244 Mathematics BuildingBuffaloNY 14260USA The Optimization Group TheWisconsin Institute ofDiscoveryMadisonWI 53715USA

The computation of the radiative transfer equation is expensive mainly due to two stiff terms:the transport term and the collision *** stiffness in the former comes from the fact that particles(such as photons)travel at the speed of light,while that in the latter is due to the strong scattering in the optically thick *** study the fully implicit scheme for this equation to account for the *** main challenge in the implicit treatment is the coupling between the spacial and angular coordinates that requires the large size of the to-be-inverted matrix,which is also ill-conditioned and not necessarily *** main idea is to utilize the spectral structure of the ill-conditioned matrix to construct a pre-conditioner,which,along with an exquisite split of the spatial and angular dependence,significantly improve the condition number and allows a matrix-free *** also design a fast solver to compute this pre-conditioner explicitly in *** method is shown to be efficient in both diffusive and free streaming limit,and the computational cost is comparable to the state-of-the-art *** examples including anisotropic scattering and two-dimensional problems are provided to validate the effectiveness of our method.

关键词： Implicitmethod asymptotic preserving pre-conditioner diffusive regime free streaming limit

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Automated, high throughput exploration of process–structure–property relationships using the MapReduce paradigm

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Materials Discovery 2015年 1卷 21-28页

作者： Wodo, Olga Zola, Jaroslaw Sarath Pokuri, Balaji Sesha Du, Pengfei Ganapathysubramanian, Baskar University at Buffalo Materials Design and Innovation Department Buffalo United States University at Buffalo Mechanical and Aerospace Engineering Department Buffalo United States University at Buffalo Computational and Data-Enabled Science and Engineering Program Buffalo United States University at Buffalo Computer Science and Engineering Department Buffalo United States University at Buffalo Biomedical Informatics Department Buffalo United States Iowa State University Mechanical Engineering Department Ames United States Iowa State University Electrical and Computer Engineering Department Ames United States

The microstructure of a material intimately affects the performance of a device made from this material. The microstructure, in turn, is affected by the processing pathway used to fabricate the device. This forms the process–structure–property triangle that is central to material science. There has been increasing interest to comprehensively understand and subsequently exploit process–structure–property (PSP) relationships to design processing pathways that result in tailored microstructures exhibiting optimal properties. However, unraveling process–structure–property relationships usually requires systematic and tedious combinatorial search of process and system variables to identify the microstructures that are produced. This is further complicated by the necessity to interrogate the properties of the huge set of corresponding microstructures. Motivated by this challenge, we focus on developing a generic methodology to establish and explore PSP pathways. We leverage recent advances in high performance computing (HPC) and high throughput computing (HTC) with the premise that a domain expert should be able to focus on domain specific PSP problems while the highly specialized HPC/HTC knowledge needed to approach such problems should be hidden from the domain expert. Our hypothesis is that PSP exploration can be naturally formulated in terms of a standard paradigm in cloud computing, namely the MapReduce programming model. We show how reformulating PSP exploration into a MapReduce workflow enables us to take advantage of advances in cloud computing while requiring minimal specialized knowledge of HPC. We illustrate this generic approach by exploring PSP relationships relevant to organic photovoltaics. We focus on identifying microstructural traits that correlate with specific properties of the photovoltaic process: exciton generation, exciton dissociation and charge generation. We integrate a graph-based microstructure characterization tool, and a microstructure-aware

关键词： Drift diffusion model High throughput analysis MapReduce paradigm Organic solar cells Process–structure–processing Thermal annealing

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Dimension reduction of dynamical systems on networks with leading and non-leading eigenvectors of adjacency matrices

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Physical Review Research 2022年第2期4卷 023257-023257页

作者： Naoki Masuda Prosenjit Kundu Department of Mathematics State University of New York at Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo New York 14260-5030 USA

Dimension reduction techniques for dynamical systems on networks are considered to promote our understanding of the original high-dimensional dynamics. One strategy of dimension reduction is to derive a low-dimensional dynamical system whose behavior approximates the observables of the original dynamical system that are weighted linear summations of the state variables at the different nodes. Recently proposed methods use the leading eigenvector of the adjacency matrix of the network as the mixture weights to obtain such observables. In the present study, we explore performances of this type of one-dimensional reductions of dynamical systems on networks when we use non-leading eigenvectors of the adjacency matrix as the mixture weights. Our theory predicts that non-leading eigenvectors can be more efficient than the leading eigenvector and enables us to select the eigenvector minimizing the error. We numerically verify that the optimal non-leading eigenvector outperforms the leading eigenvector for some dynamical systems and networks. We also argue that, despite our theory, it is practically better to use the leading eigenvector as the mixture weights to avoid misplacing the bifurcation point too distantly and to be resistant against dynamical noise.

关键词： Network resilience

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Accuracy of a one-dimensional reduction of dynamical systems on networks

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Physical Review E 2022年第2期105卷 024305-024305页

作者： Prosenjit Kundu Hiroshi Kori Naoki Masuda Department of Mathematics State University of New York at Buffalo Buffalo New York 14260-2900 USA Department of Complexity Science and Engineering The University of Tokyo Chiba 277-8561 Japan Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo New York 14260-5030 USA

Resilience is an ability of a system with which the system can adjust its activity to maintain its functionality when it is perturbed. To study resilience of dynamics on networks, Gao et al. [Nature (London) 530, 307 (2016)] proposed a theoretical framework to reduce dynamical systems on networks, which are high dimensional in general, to one-dimensional dynamical systems. The accuracy of this one-dimensional reduction relies on three approximations in addition to the assumption that the network has a negligible degree correlation. In the present study, we analyze the accuracy of the one-dimensional reduction assuming networks without degree correlation. We do so mainly through examining the validity of the individual assumptions underlying the method. Across five dynamical system models, we find that the accuracy of the one-dimensional reduction hinges on the spread of the equilibrium value of the state variable across the nodes in most cases. Specifically, the one-dimensional reduction tends to be accurate when the dispersion of the node's state is small. We also find that the correlation between the node's state and the node's degree, which is common for various dynamical systems on networks, is unrelated to the accuracy of the one-dimensional reduction.

关键词： Complex systems Dynamics of networks Network resilience

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Metapopulation models imply non-Poissonian statistics of interevent times

arXiv

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arXiv 2021年

作者： dos Reis, Elohim Fonseca Masuda, Naoki Department of Mathematics State University of New York at Buffalo BuffaloNY United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY United States

Interevent times in temporal contact data from humans and animals typically obey heavy-tailed distributions, and this property impacts contagion and other dynamical processes on networks. We theoretically show that distributions of interevent times heavier-tailed than exponential distributions are a consequence of the most basic metapopulation model used in epidemiology and ecology, in which individuals move from a patch to another according to the simple random walk. Our results hold true irrespectively of the network structure and also for more realistic mobility rules such as high-order random walks and the recurrent mobility patterns used for modeling human dynamics. Copyright © 2021, The Authors. All rights reserved.

关键词： Random processes

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Opinion dynamics on tie-decay networks

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Physical Review Research 2021年第2期3卷 023249-023249页

作者： Kashin Sugishita Mason A. Porter Mariano Beguerisse-Díaz Naoki Masuda Department of Mathematics State University of New York at Buffalo Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo New York 14260-5030 USA and Faculty of Science and Engineering Waseda University 169-8555 Tokyo Japan

In social networks, interaction patterns typically change over time. We study opinion dynamics on tie-decay networks in which tie strength increases instantaneously when there is an interaction and decays exponentially between interactions. Specifically, we formulate continuous-time Laplacian dynamics and a discrete-time DeGroot model of opinion dynamics on these tie-decay networks, and we carry out numerical computations for the continuous-time Laplacian dynamics. We examine the speed of convergence by studying the spectral gaps of combinatorial Laplacian matrices of tie-decay networks. First, we compare the spectral gaps of the Laplacian matrices of tie-decay networks that we construct from empirical data with the spectral gaps for corresponding randomized and aggregate networks. We find that the spectral gaps for the empirical networks tend to be smaller than those for the randomized and aggregate networks. Second, we study the spectral gap as a function of the tie-decay rate and time. Intuitively, we expect small tie-decay rates to lead to fast convergence because the influence of each interaction between two nodes lasts longer for smaller decay rates. Moreover, as time progresses and more interactions occur, we expect eventual convergence. However, we demonstrate that the spectral gap need not decrease monotonically with respect to the decay rate or increase monotonically with respect to time. Our results highlight the importance of the interplay between the times that edges strengthen and decay in temporal networks.

关键词： Network structure Social networks Consensus & non-consensus models

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Metapopulation models imply non-Poissonian statistics of interevent times

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Physical Review Research 2022年第1期4卷 013050-013050页

作者： Elohim Fonseca dos Reis Naoki Masuda Department of Mathematics State University of New York at Buffalo Buffalo 14260-2900 New York USA Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo 14260-5030 New York USA Faculty of Science and Engineering Waseda University Tokyo 169-8555 Japan

Interevent times in temporal contact data from humans and animals typically obey heavy-tailed distributions, which impacts contagion and other dynamical processes on networks. We theoretically show that distributions of interevent times heavier-tailed than exponential distributions are a consequence of the most basic metapopulation model used in epidemiology and ecology, in which individuals move from one patch to another according to the simple random walk. Our results hold true irrespective of the network structure and also for more realistic mobility rules such as high-order random walks and the recurrent mobility patterns used for modeling human dynamics.

关键词： Continuous-time random walk Population dynamics Networks & random structures Social networks Diffusion & random walks Markovian processes Non-Markovian processes

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Early Warnings for Multistage Transitions in Dynamics on Networks

arXiv

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arXiv 2022年

作者： MacLaren, Neil G. Kundu, Prosenjit Masuda, Naoki Department of Mathematics State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States

Successfully anticipating sudden major changes in complex systems is a practical concern. Such complex systems often form a heterogeneous network, which may show multistage transitions in which some nodes experience a regime shift earlier than others as an environment gradually changes. Here we investigate early warning signals for networked systems undergoing a multistage transition. We found that knowledge of both the ongoing multistage transition and network structure enables us to calculate effective early warning signals for multistage transitions. Furthermore, we found that small subsets of nodes could anticipate transitions as well as or even better than using all the nodes. Even if we fix the network and dynamical system, no single best subset of nodes provides good early warning signals, and a good choice of sentinel nodes depends on the tipping direction and the current stage of the dynamics within a multistage transition, which we systematically characterize. © 2022, CC BY.

关键词： Dynamics

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Randomizing hypergraphs preserving degree correlation and local clustering

arXiv

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arXiv 2021年

作者： Nakajima, Kazuki Shudo, Kazuyuki Masuda, Naoki Department of Mathematical and Computing Science Tokyo Institute of Technology Japan Department of Mathematics State University of New York Buffalo United States Computational and Data-Enabled Science and Engineering Program State University of New York Buffalo United States Faculty of Science and Engineering Waseda University Japan

Many complex systems involve direct interactions among more than two entities and can be represented by hypergraphs, in which hyperedges encode higher-order interactions among an arbitrary number of nodes. To analyze structures and dynamics of given hypergraphs, a solid practice is to compare them with those for randomized hypergraphs that preserve some specific properties of the original hypergraphs. In the present study, we propose a family of such reference models for hypergraphs, called the hyper dk-series, by extending the so-called dk-series for dyadic networks to the case of hypergraphs. The hyper dk-series preserves up to the individual node’s degree, node’s degree correlation, node’s redundancy coefficient, and/or the hyperedge’s size depending on the parameter values. Furthermore, we numerically find that higher-order hyper dk-series more accurately preserves the shortest path length and degree distribution of the one-mode projection of the original hypergraph, which the method does not intend to preserve. We also apply the hyper dk-series to numerical simulations of epidemic spreading and evolutionary game dynamics on empirical social hypergraphs. We find that the hyperedge’s size affects these dynamics more than any of the node’s properties and that the node’s degree correlation and redundancy in the empirical hypergraphs promote cooperation. Copyright © 2021, The Authors. All rights reserved.

关键词： Redundancy

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