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55th IEEE Conference on Decision and Control, CDC 2016

作者： Wang, Chu Li, Qianxiao Weinan, E. Chazelle, Bernard Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Nokia Bell Labs 600 Mountain Avenue Murray HillNJ07974 United States Department of Mathematics Program in Applied and Computational Mathematics Princeton University NJ08540 United States Department of Computer Science Princeton University PrincetonNJ08540 United States

ISBN: (纸本)9781509018376

The classic Hegselmann-Krause (HK) model for opinion dynamics consists of a set of agents on the real line, each one instructed to move, at every time step, to the mass center of the agents within a fixed distance R. In this work, we investigate the effects of noise in the continuous-time version of the model as described by its mean-field Fokker-Planck equation. In the presence of a finite number of agents, the system exhibits a phase transition from order to disorder as the noise increases. We introduce an order parameter to track the phase transition and resolve the corresponding phase diagram. The system undergoes a phase transition for small R but none for larger R. Based on the stability analysis of the mean-field equation, we derive the existence of a forbidden zone for the disordered phase to emerge. We also provide a theoretical explanation for the well-known 2R conjecture, which states that, for a random initial distribution in a fixed interval, the final configuration consists of clusters separated by a distance of roughly 2R. Our theoretical analysis confirms previous simulations and predicts properties of the noisy HK model in higher dimension. © 2016 IEEE.

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Leveraging undecided cases in chart-reviewed phenotypes to enhance EHR-based association studies

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Journal of Biomedical Informatics 2025年 166卷 104839页

作者： Jian, Xinyao Zhang, Dazheng Yu, Zehao Xu, Hua Bian, Jiang Wu, Yonghui Tong, Jiayi Chen, Yong University of Pennsylvania Perelman School of Medicine PhiladelphiaPA United States Department of Biostatistics Epidemiology and Informatics Perelman School of Medicine The University of Pennsylvania PhiladelphiaPA United States Department of Health Outcomes and Biomedical Informatics College of Medicine University of Florida GainesvilleFL United States Department of Biomedical Informatics and Data Science School of Medicine Yale University New HavenCT United States Department of Biostatistics and Health Data Science School of Medicine Indiana University IndianapolisIN United States Regenstreif Institute Indianapolis IndianaIN United States Cancer Informatics Shared Resource University of Florida Health Cancer Center GainesvilleFL United States Department of Biostatistics Johns Hopkins Bloomberg School of Public Health BaltimoreMD United States The Graduate Group in Applied Mathematics and Computational Science School of Arts and Sciences University of Pennsylvania PhiladelphiaPA United States Leonard Davis Institute of Health Economics PhiladelphiaPA United States PhiladelphiaPA United States PhiladelphiaPA United States

Objectives: In electronic health record (EHR)-based association studies, phenotyping algorithms efficiently classify patient clinical outcomes into binary categories but are susceptible to misclassification errors. The gold standard, manual chart review, involves clinicians determining the true disease status based on their assessment of health records. These clinicians-labeled phenotypes are labor-intensive and typically limited to a small subset of patients, potentially introducing a third "undecided" category when phenotypes are indeterminate. We aim to effectively integrate the algorithm-derived and chart-reviewed outcomes when both are available in EHR-based association studies. Material and Methods: We propose an augmented estimation method that combines the binary algorithm-derived phenotypes for the entire cohort with the trinary chart-reviewed phenotypes for a small, selected subset. Additionally, a cost-effective outcome-dependent sampling strategy is used to address the rare disease scenarios. The proposed trinary chart-reviewed phenotype integrated cost-effective augmented estimation (TriCA) was evaluated across a wide range of simulation settings and real-world applications, including using EHR data on Alzheimer's disease and related dementias (ADRD) from the OneFlorida + Clinical Research Network, and using cohort data on second breast cancer events (SBCE) from the Kaiser Permanente Washington. Results: Compared to estimation based on random sampling, our augmented method improved mean square error by up to 28.3% in simulation studies;compared to estimation using only trinary chart-reviewed phenotypes, our method improved efficiency by up to 33.3% in ADRD data and 50.8% in SBCE data. Discussion: Our simulation studies and real-world applications demonstrate that, compared to existing methods, the proposed method provides unbiased estimates with higher statistical efficiency. Conclusion: The proposed method effectively combined binary algorithm-derived

关键词： Clinical research

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One-shot distributed ridge regression in high dimensions 37

One-shot distributed ridge regression in high dimensions

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37th International Conference on Machine Learning, ICML 2020

作者： Dobriban, Edgar Sheng, Yue Wharton Statistics Department University of Pennsylvania PhiladelphiaPA United States Graduate Group in Applied Mathematics and Computational Science University of Pennsylvania PhiladelphiaPA United States

ISBN: (纸本)9781713821120

To scale up data analysis, distributed and parallel computing approaches are increasingly needed. Here we study a fundamental problem in this area: How to do ridge regression in a distributed computing environment? We study one-shot methods constructing weighted combinations of ridge regression estimators computed on each machine. By analyzing the mean squared error in a high dimensional model where each predictor has a small effect, we discover several new phenomena including that the efficiency depends strongly on the signal strength, but does not degrade with many workers, the risk decouples over machines, and the unexpected consequence that the optimal weights do not sum to unity. We also propose a new optimally weighted one-shot ridge regression algorithm. Our results are supported by simulations and real data analysis. © 2020 37th International Conference on Machine Learning, ICML 2020. All rights reserved.

关键词： Mean square error

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Dynamical properties of particulate composites derived from ultradense stealthy hyperuniform sphere packings

arXiv

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arXiv 2025年

作者： Vanoni, Carlo Kim, Jaeuk Steinhardt, Paul J. Torquato, Salvatore Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Stealthy hyperuniform (SHU) many-particle systems are distinguished by a structure factor that vanishes not only at zero wavenumber (as in "standard" hyperuniform systems) but also across an extended range of wavenumbers near the origin. We generate disordered SHU packings of identical and ‘nonoverlapping’ spheres in d-dimensional Euclidean space using a modified collective-coordinate optimization algorithm that incorporates a soft-core repulsive potential between particles in addition to the standard stealthy pair potential. Compared to SHU packings without soft-core repulsions, these SHU packings are ultradense with packing fractions ranging from 0.67-0.86 for d = 2 and 0.47-0.63 for d = 3, spanning a broad spectrum of structures depending on the stealthiness parameter χ. We consider two-phase media composed of hard particles derived from ultradense SHU packings (phase 2) embedded in a matrix phase (phase 1), with varying stealthiness parameter χ and packing fractions . Our main objective is the estimation of the dynamical physical properties of such two-phase media, namely, the effective dynamic dielectric constant and the time-dependent diffusion spreadability, which is directly related to nuclear magnetic relaxation in fluid-saturated porous media. We show through spreadability that two-phase media derived from ultradense SHU packings exhibit faster interphase diffusion due to the higher packing fractions achievable compared to media obtained without soft-core repulsion. The imaginary part of the effective dynamic dielectric constant of SHU packings vanishes at a small wavenumber, implying perfect transparency for the corresponding wavevectors. While a larger packing fraction yields a smaller transparency interval, we show that it also displays a reduced height of the attenuation peak. We also obtain cross-property relations between transparency characteristics and long-time behavior of the spreadability for such two-phase media, showing that one leads to infor

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Threshold and decay properties of transient isolated turbulent band in plane Couette flow

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applied mathematics and Mechanics(English Edition) 2019年第10期40卷 1449-1456页

作者： Jianzhou LU Jianjun TAO Weitao ZHOU Xiangming XIONG CAPT-HEDPS SKLTCS Collaborative Innovation Center of IFSA Department of Mechanics and Engineering Science College of Engineering Peking University Beijing 100871 China The Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 U. S.A.

By direct numerical simulations of the plane Couette flow (PCF) in a large computational domain, it is shown that an isolated turbulent band decays monotonically at low Reynolds numbers but experiences transient growth before the eventual relaminarization at moderate Reynolds numbers. The lower bound Reynolds number of the transient-growth regime is determined as 286. The width, length, and tilt angle of the iso- lated band structure are defined based on the disturbance kinetic energy in the mid-plane, and the geometric characteristics of the band can be described with a tilted rectangle. It is illustrated that before its eventual fragmentation, the isolated turbulent band decays in a style of longitudinal contraction, where the center, width, and tilt angle of the band keep almost constant but the band length contracts with a statistically constant velocity.

关键词： plane Couette flow (PCF) subcritical transition turbulent band

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Analysis of Sparse Quasi-Newton Updates with Positive Definite Matrix Completion

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Journal of the Operations Research Society of China 2014年第1期2卷 39-56页

作者： Yu-Hong Dai Nobuo Yamashita State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesP.O.Box 2719Beijing 100080People’s Republic of China Department of Applied Mathematics and Physics Graduate School of InformaticsKyoto UniversityKyoto 606-8501Japan

Based on the idea of maximum determinant positive definite matrix completion,Yamashita(Math Prog 115(1):1–30,2008)proposed a new sparse quasi-Newton update,called MCQN,for unconstrained optimization problems with sparse Hessian *** exchange of the relaxation of the secant equation,the MCQN update avoids solving difficult subproblems and overcomes the ill-conditioning of approximate Hessian ***,local and superlinear convergence results were only established for the MCQN update with the DFP *** this paper,we extend the convergence result to the MCQN update with the whole Broyden’s convex *** results are also reported,which suggest some efficient ways of choosing the parameter in the MCQN update the Broyden’s family.

关键词： Quasi-Newton method Large-scale problems Sparsity Positive definite matrix completion Superlinear convergence

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Homogenization of Maxwell's equations in periodic composites: Boundary effects and dispersion relations

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Physical Review E 2012年第6期85卷 066603-066603页

作者： Vadim A. Markel John C. Schotland []Department of Radiology and Graduate Group in Applied Mathematics and Computational Science University of Pennsylvania Philadelphia Pennsylvania 19104 USA

We consider the problem of homogenizing the Maxwell equations for periodic composites. The analysis is based on Bloch-Floquet theory. We calculate explicitly the reflection coefficient for a half space and derive and implement a computationally efficient continued-fraction expansion for the effective permittivity. Our results are illustrated by numerical computations for the case of two-dimensional systems. The homogenization theory of this paper is designed to predict various physically measurable quantities rather than to simply approximate certain coefficients in a partial differential equation.

关键词： HOMOGENIZATION (Differential equations) MAXWELL equations DISPERSION relations BOUNDARY value problems PERMITTIVITY NUMERICAL analysis PARTIAL differential equations

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Single-scattering optical tomography: Simultaneous reconstruction of scattering and absorption

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Physical Review E 2010年第1期81卷 016602-016602页

作者： Lucia Florescu Vadim A. Markel John C. Schotland Department of Bioengineering and Graduate Group in Applied Mathematics and Computational Science University of Pennsylvania Philadelphia Pennsylvania 19104 USA

We report theory and numerical simulations that demonstrate the feasibility of simultaneous reconstruction of the three-dimensional scattering and absorption coefficients of a mesoscopic system using angularly resolved measurements of scattered light. Image reconstruction is based on the inversion of a generalized (broken ray) Radon transform relating the scattering and absorption coefficients of the medium to angularly resolved intensity measurements. Although the single-scattering approximation to the radiative transport equation (RTE) is used to devise the image reconstruction method, there is no assumption that only singly scattered light is measured. That is, no physical mechanism for separating single-scattered photons from the rest of the multiply-scattered light (e.g., time gating) is employed in the proposed experiments. Numerical examples of image reconstruction are obtained using samples of optical depth of up to 3.2. The forward data are obtained from numerical solution of the RTE, accounting for all orders of scattering.

关键词： Image reconstruction

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Biomedical data and AI

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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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Hydrogen-Bonding Interactions from Nucleobase-Decorated Supramolecular Polymer: Synthesis, Self-Assembly and Biomedical Applications

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ACS Biomaterials science and Engineering 2024年第1期10卷 234-254页

作者： Ilhami, Fasih Bintang Birhan, Yihenew Simegniew Cheng, Chih-Chia Department of Natural Science Faculty of Mathematics and Natural Science Universitas Negeri Surabaya Surabaya60231 Indonesia Department of Chemistry College of Natural and Computational Sciences Debre Markos University Debre Markos00000 Ethiopia Graduate Institute of Applied Science and Technology National Taiwan University of Science and Technology Taipei10607 Taiwan

The fabrication of supramolecular materials for biomedical applications such as drug delivery, bioimaging, wound-dressing, adhesion materials, photodynamic/photothermal therapy, infection control (as antibacterial), etc. has grown tremendously, due to their unique properties, especially the formation of hydrogen bonding. Nevertheless, void space in the integration process, lack of feasibility in the construction of supramolecular materials of natural origin in living biological systems, potential toxicity, the need for complex synthesis protocols, and costly production process limits the actual application of nanomaterials for advanced biomedical applications. On the other hand, hydrogen bonding from nucleobases is one of the strategies that shed light on the blurred deployment of nanomaterials in medical applications, given the increasing reports of supramolecular polymers that promote advanced technologies. Herein, we review the extensive body of literature about supramolecular functional biomaterials based on nucleobase hydrogen bonding pertinent to different biomedical applications. It focuses on the fundamental understanding about the synthesis, nucleobase-decorated supramolecular architecture, and novel properties with special emphasis on the recent developments in the assembly of nanostructures via hydrogen-bonding interactions of nucleobase. Moreover, the challenges, plausible solutions, and prospects of the so-called hydrogen bonding interaction from nucleobase for the fabrication of functional biomaterials are outlined. © 2023 American Chemical Society

关键词： Hydrogen bonds

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