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arXiv 2019年

作者： Roitershtein, Alexander Rastegar, Reza Chapkin, Robert S. Ivanov, Ivan Department of Statistics Texas A&M University College StationTX77843 United States Occidental Petroleum Corporation HoustonTX77046 United States Departments of Mathematics and Engineering University of Tulsa OK74104 United States Department of Nutrition and Food Science Program in Integrative Nutrition and Complex Diseases Texas A&M University College StationTX77843 United States Department of Veterinary Physiology and Pharmacology Texas A&M University College StationTX77843 United States

We study a generalized discrete-time multi-type Wright-Fisher population process. The mean-field dynamics of the stochastic process is induced by a general replicator difference equation. We prove several results regarding the asymptotic behavior of the model, focusing on the impact of the mean-field dynamics on it. One of the results is a limit theorem that describes sufficient conditions for an almost certain path to extinction, first eliminating the type which is the least fit at the mean-field equilibrium. The effect is explained by the metastability of the stochastic system, which under the conditions of the theorem spends almost all time before the extinction event in a neighborhood of the equilibrium. In addition to limit theorems, we propose a variation of Fisher's maximization principle, fundamental theorem of natural selection, for a completely general deterministic replicator dynamics and study implications of the deterministic maximization principle for the stochastic model. Copyright © 2019, The Authors. All rights reserved.

关键词： Stochastic systems

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clotFoam: An Open-Source Framework to Simulate Blood Clot Formation Under Arterial Flow

arXiv

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arXiv 2023年

作者： Montgomery, David Municchi, Federico Leiderman, Karin Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Department of Mechanical Engineering Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Department of Mathematics University of North Carolina at Chapel Hill 216 Lenoir Dr Chapel HillNC27599 United States Computational Medicine Program University of North Carolina at Chapel Hill 216 Lenoir Dr Chapel HillNC27599 United States

Blood clotting involves the coupled processes of platelet aggregation and coagulation. Simulating clotting under flow in complex geometries is challenging due to multiple temporal and spatial scales and high computational cost. clotFoam is an open-source software developed in OpenFOAM that employs a continuum model of platelet advection, diffusion, and aggregation in a dynamic fluid environment and a simplified coagulation model with proteins that advect, diffuse, and react within the fluid and with wall-bound species through reactive boundary conditions. Our framework provides the foundation on which one can build more complex models and perform reliable simulations in almost any computational domain. © 2023, CC BY.

关键词： Coagulation

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Spatial analysis of human development index by province in Indonesia 2018-2020

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AIP Conference Proceedings 2023年第1期2720卷

作者： Tuti Purwaningsih Rochmad Novian Inderanata Monica Rahma Fauziah Statistics Department Universitas Islam Indonesia Yogyakarta Indonesia Mechanical Engineering Vocational Education Department Universitas Sarjanawiyata Yogyakarta Indonesia Doctoral Program in Technology and Vocational Education Yogyakarta State University Yogyakarta Indonesia

This study aims to determine, explain and analyze the human development index or the so-called HDI. To find out the factors that affect the human development index. The Human Development Index is one indicator of the creation of development that is able to encourage economic growth. To measure the quality of human capital, the United Nations Development program (UNDP) introduced the concept of the quality of human capital which was named the Human Development Index or the Human Development Index (IPM). The human development index (HDI) is a strategic indicator that is widely used to see the efforts and performance of development programs as a whole in an area. In this case, HDI is considered as an illustration of the results of development programs that have been carried out several years earlier. Likewise, the progress of development programs in a period can be measured and indicated by the HDI at the beginning and end of the period. HDI is a measure to see the impact of regional development performance which has a very broad dimension, because it shows the quality of the population of an area in terms of life expectancy, intellectuality and decent living standards. The Human Development Index is one indicator of the creation of development that is able to encourage economic growth. To measure the quality of human capital, the United Nations Development program (UNDP) introduced the concept of the quality of human capital which was named the Human Development Index or the Human Development Index (IPM). The HDI provides a combined three-dimensional measure of human development, namely the health dimension measured by life expectancy, the education dimension measured by the level of adult literacy and average length of schooling and the purchasing power dimension which has a decent standard of living measured by purchasing power parity.

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Accelerating Real-Time Imaging for Radiotherapy: Leveraging Multi-GPU Training with PyTorch

Accelerating Real-Time Imaging for Radiotherapy: Leveraging ...

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International Conference on Machine Learning and Applications (ICMLA)

作者： Ruth Obe Brandt Kaufmann Kaelen Baird Sam Kadel Yasmin Soltani Mostafa Cham Matthias K. Gobbert Carlos A. Barajas Zhuoran Jiang Vijay R. Sharma Lei Ren Stephen W. Peterson Jerimy C. PoIf Dept. of Computer Science and of Software Engineering U. of Houston-Clear Lake USA Dept. of Mathematics and Statistics U. of San Francisco USA Dept. of Computer Science and of Mathematics Skidmore College USA Dept. of Computer Science and of Psychology Mount Holyoke College USA Dept. of Biomedical Engineering U. of Houston USA Dept. of Information Systems U. of Maryland Baltimore County Dept. of Mathematics and Statistics U. of Maryland Baltimore County Medical Physics Graduate Program Duke University USA Dept. of Radiation Oncology U. of Maryland School of Medicine USA Department of Radiation Oncology U. of Maryland School of Medicine USA Dept. of Physics U. of Cape Town South Africa H3D Inc. USA

Proton beam therapy is an advanced form of cancer radiotherapy that uses high-energy proton beams to deliver precise and targeted radiation to tumors. This helps to mit-igate unnecessary radiation exposure in healthy tissues. Real-time imaging of prompt gamma rays with Compton cameras has been suggested to improve therapy efficacy. However, the camera's non-zero time resolution leads to incorrect interaction classifications and noisy images that are insufficient for accurately assessing proton delivery in patients. To address the challenges posed by the Compton camera's image quality, machine learning techniques are employed to classify and refine the generated data. These machine-learning techniques include recurrent and feedforward neural networks. A PyTorch model was designed to improve the data captured by the Compton camera. This decision was driven by PyTorch's flexibility, powerful capabilities in handling sequential data, and enhanced G PU usage. This accelerates the model's computations on large-scale radiotherapy data. Through hyperparameter tuning, the validation accuracy of our PyTorch model has been improved from an initial 7 % to over 60 %. Moreover, the PyTorch Distributed Data Parallelism strategy was used to train the RNN models on multiple G PU s, which significantly reduced the training time with a minor impact on model accuracy.

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Visualizing structure and transitions in high-dimensional biological data (vol 54, pg 781, 2019)

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NATURE BIOTECHNOLOGY 2020年第1期38卷 108-108页

作者： Moon, Kevin R. van Dijk, David Wang, Zheng Gigante, Scott Burkhardt, Daniel B. Chen, William S. Yim, Kristina van den Elzen, Antonia Hirn, Matthew J. Coifman, Ronald R. Ivanova, Natalia B. Wolf, Guy Krishnaswamy, Smita Department of Mathematics and Statistics Utah State University Logan USA Cardiovascular Research Center section Cardiology Department of Internal Medicine Yale University New Haven USA Department of Computer Science Yale University New Haven USA School of Basic Medicine Qingdao University Qingdao China Yale Stem Cell Center Department of Genetics Yale University New Haven USA Computational Biology and Bioinformatics Program Yale University New Haven USA Department of Genetics Yale University New Haven USA Department of Computational Mathematics Science and Engineering Michigan State University East Lansing USA Department of Mathematics Michigan State University East Lansing USA Applied Mathematics Program Yale University New Haven USA Department of Genetics Center for Molecular Medicine University of Georgia Athens USA Department of Mathematics and Statistics Université de Montréal Montréal Canada Mila—Quebec Artificial Intelligence Institute Montréal Canada

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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EQTL AND MUTATIONAL ANALYSIS OF NB-LRR MEDIATED IMMUNITY TO POWDERY MILDEW

EQTL AND MUTATIONAL ANALYSIS OF NB-LRR MEDIATED IMMUNITY TO ...

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The 13th International Cereal Rusts and Powdery Mildews Conference(第13届国际禾谷类锈病与白粉病大会)

作者： Roger WISE Priyanka SURANA Greg FUERST Ruo XU Divya MISTRY Julie DICKERSON Dan NETTLETON Department of Statistics Iowa State UniversityAmesIowa 50011 Department of Plant Pathology and Microbiology Center for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011 Department of StatisticsIowa State UniversityAmesIowa 50011 Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011 Department of Electrical and Computer Engineering Iowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011 Bioinformatics and Computational Biology Graduate Program Iowa State UniversityAmesIowa 50011 Department of Plant Pathology and MicrobiologyCenter for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011 Department of Plant Pathology and Microbiology Center for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011 Bioinformatics and Computational Biology Graduate Program Iowa State UniversityAmesIowa 50011 Crop and Insect GeneticsGenomicsand Informatics Research UnitU.S.Department of Agriculture-Agricultural Research ServiceIowa State UniversityAmesIowa 50011 Crop and Insect Genetics Genomicsand Informatics Research UnitU.S.Department of Agriculture-Agricultural Research ServiceIowa State UniversityAmesIowa 50011

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On the approximability of random-hypergraph MAX-3-XORSAT problems with quantum algorithms

arXiv

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arXiv 2023年

作者： Kapit, Eliot Barton, Brandon A. Feeney, Sean Grattan, George Patnaik, Pratik Sagal, Jacob Carr, Lincoln D. Oganesyan, Vadim Department of Physics Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Quantum Engineering Program Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Physics and Astronomy College of Staten Island CUNY Staten IslandNY10314 United States Physics Program and Initiative for the Theoretical Sciences The Graduate Center CUNY New YorkNY10016 United States Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New YorkNY10010 United States

A canonical feature of the constraint satisfaction problems in NP is approximation hardness, where in the worst case, finding sufficient-quality approximate solutions is exponentially hard for all known methods. Fundamentally, the lack of any guided local minimum escape method ensures both exact and approximate classical approximation hardness, but the equivalent mechanism(s) for quantum algorithms are poorly understood. For algorithms based on Hamiltonian time evolution, we explore this question through the prototypically hard MAX-3-XORSAT problem class. We conclude that the mechanisms for quantum exact and approximation hardness are fundamentally distinct. We review known results from the literature, and identify mechanisms that make conventional quantum methods (such as Adiabatic Quantum Computing) weak approximation algorithms in the worst case. We construct a family of "spectrally filtered" quantum algorithms that escape these issues, and develop analytical theories for their performance. We show that, for random hypergraphs in the approximation-hard regime, if we define the energy to be E = Nunsat - Nsat, spectrally filtered quantum optimization will return states with E ≤ qmEGS (where EGS is the ground state energy) in sub-quadratic time, where conservatively, qm 0.59. This is in contrast to qm → 0 for the hardest instances with classical searches. We test all of these claims with extensive numerical simulations. We do not claim that this approximation guarantee holds for all possible hypergraphs, though our algorithm’s mechanism can likely generalize widely. These results suggest that quantum computers are more powerful for approximate optimization than had been previously assumed. © 2023, CC BY.

关键词： Constraint satisfaction problems

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Position: Bayesian deep learning is needed in the age of large-scale AI 24

Position: Bayesian deep learning is needed in the age of lar...

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Proceedings of the 41st International Conference on Machine Learning

作者： Theodore Papamarkou Maria Skoularidou Konstantina Palla Laurence Aitchison Julyan Arbel David Dunson Maurizio Filippone Vincent Fortuin Philipp Hennig José Miguel Hernández-Lobato Aliaksandr Hubin Alexander Immer Theofanis Karaletsos Mohammad Emtiyaz Khan Agustinus Kristiadi Yingzhen Li Stephan Mandt Christopher Nemeth Michael A. Osborne Tim G. J. Rudner David Rügamer Yee Whye Teh Max Welling Andrew Gordon Wilson Ruqi Zhang Department of Mathematics The University of Manchester Manchester UK Eric and Wendy Schmidt Center Broad Institute of MIT and Harvard Cambridge Spotify London UK Computational Neuroscience Unit University of Bristol Bristol UK Centre Inria de l'Université Grenoble Alpes Grenoble France Department of Statistical Science Duke University Statistics Program KAUST Saudi Arabia Helmholtz AI Munich Germany and Department of Computer Science Technical University of Munich Munich Germany and Munich Center for Machine Learning Munich Germany Tübingen AI Center University of Tübingen Tübingen Germany Department of Engineering University of Cambridge Cambridge UK Department of Mathematics University of Oslo Oslo Norway and Bioinformatics and Applied Statistics Norwegian University of Life Sciences Ås Norway Department of Computer Science ETH Zurich Switzerland Chan Zuckerberg Initiative California Center for Advanced Intelligence Project RIKEN Tokyo Japan Vector Institute Toronto Canada Department of Computing Imperial College London London UK Department of Computer Science UC Irvine Irvine Department of Mathematics and Statistics Lancaster University Lancaster UK Department of Engineering Science University of Oxford Oxford UK Center for Data Science New York University New York Munich Center for Machine Learning Munich Germany and Department of Statistics LMU Munich Munich Germany DeepMind London UK and Department of Statistics University of Oxford Oxford UK Informatics Institute University of Amsterdam Amsterdam Netherlands Courant Institute of Mathematical Sciences and Center for Data Science Computer Science Department New York University New York Department of Computer Science Purdue University West Lafayette

In the current landscape of deep learning research, there is a predominant emphasis on achieving high predictive accuracy in supervised tasks involving large image and language datasets. However, a broader perspective reveals a multitude of overlooked metrics, tasks, and data types, such as uncertainty, active and continual learning, and scientific data, that demand attention. Bayesian deep learning (BDL) constitutes a promising avenue, offering advantages across these diverse settings. This paper posits that BDL can elevate the capabilities of deep learning. It revisits the strengths of BDL, acknowledges existing challenges, and highlights some exciting research avenues aimed at addressing these obstacles. Looking ahead, the discussion focuses on possible ways to combine large-scale foundation models with BDL to unlock their full potential.

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Two-dimensional Bose-Hubbard model for helium on graphene

arXiv

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arXiv 2021年

作者： Yu, Jiangyong Lauricella, Ethan Elsayed, Mohamed Shepherd, Kenneth Nichols, Nathan S. Lombardi, Todd Kim, Sang Wook Wexler, Carlos Vanegas, Juan M. Lakoba, Taras Kotov, Valeri N. Del Maestro, Adrian Department of Physics University of Vermont BurlingtonVT05405 United States Materials Science Program University of Vermont BurlingtonVT05405 United States Department of Physics and Astronomy University of Missouri ColumbiaMO65211 United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05405 United States Department of Physics and Astronomy University of Tennessee KnoxvilleTN37996 United States Min H. Kao Department of Electrical Engineering and Computer Science University of Tennessee KnoxvilleTN37996 United States

An exciting development in the field of correlated systems is the possibility of realizing two-dimensional (2D) phases of quantum matter. For a systems of bosons, an example of strong correlations manifesting themselves in a 2D environment is provided by helium adsorbed on graphene. We construct the effective Bose-Hubbard model for this system which involves hard-core bosons (U ≈ ∞), repulsive nearest-neighbor (V > 0) and small attractive (V0 4He adsorbed on graphene deep in the commensurate solid phase with 1/3 of the sites on the dual triangular lattice occupied. Because the parameters of the effective Bose-Hubbard model are very sensitive to the exact lattice structure, this opens up an avenue to tune quantum phase transitions in this solid-state system. Copyright © 2021, The Authors. All rights reserved.

关键词： Hubbard model

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Non-invasive biopsy diagnosis of diabetic kidney disease via deep learning applied to retinal images: a population-based study

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The Lancet Digital Health 2025年第5期7卷 100868页

作者： Meng, Ziyao Guan, Zhouyu Yu, Shujie Wu, Yilan Zhao, Yaoning Shen, Jie Lim, Cynthia Ciwei Chen, Tingli Yang, Dawei Ran, An Ran He, Feng Hamzah, Haslina Singh, Sarkaaj Abd Raof, Anis Syazwani Lee-Boey, Jian Wen Samuel Lim, Soo-Kun Sun, Xufang Ge, Shuwang Xu, Gang Su, Hua Cheng, Yang Lu, Feng Liao, Xiaofei Jin, Hai Deng, Chenxin Ruan, Lei Zhang, Cuntai Wu, Chan Dai, Rongping Jin, Yixiao Wang, Wenxiao Li, Tingyao Liu, Ruhan Li, Jiajia Shu, Jia Lu, Yuwei Wang, Xiangning Wu, Qiang Qin, Yiming Tang, Jin Sheng, Xiaohua Jiao, Qiong Yang, Xiaokang Guo, Minyi McKay, Gareth J Hogg, Ruth E Liew, Gerald Chee, Evelyn Yi Lyn Hsu, Wynne Lee, Mong Li Szeto, Simon Luk, Andrea O Y Chan, Juliana C N Cheung, Carol Y Tan, Gavin Siew Wei Tham, Yih-Chung Cheng, Ching-Yu Sabanayagam, Charumathi Lim, Lee-Ling Jia, Weiping Li, Huating Sheng, Bin Wong, Tien Yin Shanghai Belt and Road International Joint Laboratory of Intelligent Prevention and Treatment for Metabolic Diseases Department of Computer Science and Engineering School of Electronic Information and Electrical Engineering Institute for Proactive Healthcare Shanghai Jiao Tong University Department of Endocrinology and Metabolism Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai Diabetes Institute Shanghai Clinical Centre for Diabetes Shanghai Key Laboratory of Diabetes Mellitus Shanghai China MOE Key Laboratory of AI School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai China Beijing Tsinghua Changgung Hospital Eye Center School of Clinical Medicine Tsinghua Medicine Tsinghua University Beijing China Medical Records and Statistics Office Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai China Department of Renal Medicine Singapore General Hospital SingHealth-Duke Academic Medical Centre Singapore Singapore Department of Ophthalmology Shanghai Health and Medical Center Wuxi China Department of Ophthalmology and Visual Sciences The Chinese University of Hong Kong Hong Kong Special Administrative Region China Singapore Eye Research Institute Singapore National Eye Centre Singapore Department of Medicine Faculty of Medicine Universiti Malaya Kuala Lumpur Malaysia Department of Ophthalmology Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Hubei Wuhan China Department of Nephrology Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China Department of Nephrology Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China Department of Ophthalmology Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China National Engineering Research Centre for Big Dat

Background: Improving the accessibility of screening diabetic kidney disease (DKD) and differentiating isolated diabetic nephropathy from non-diabetic kidney disease (NDKD) are two major challenges in the field of diabetes care. We aimed to develop and validate an artificial intelligence (AI) deep learning system to detect DKD and isolated diabetic nephropathy from retinal fundus images. Methods: In this population-based study, we developed a retinal image-based AI-deep learning system, DeepDKD, pretrained using 734 084 retinal fundus images. First, for DKD detection, we used 486 312 retinal images from 121 578 participants in the Shanghai Integrated Diabetes Prevention and Care System for development and internal validation, and ten multi-ethnic datasets from China, Singapore, Malaysia, Australia, and the UK (65 406 participants) for external validation. Second, to differentiate isolated diabetic nephropathy from NDKD, we used 1068 retinal images from 267 participants for development and internal validation, and three multi-ethnic datasets from China, Malaysia, and the UK (244 participants) for external validation. Finally, we conducted two proof-of-concept studies: a prospective real-world study with 3 months' follow-up to evaluate the effectiveness of DeepDKD in screening DKD;and a longitudinal analysis of the effectiveness of DeepDKD in differentiating isolated diabetic nephropathy from NDKD on renal function changes with 4·6 years' follow-up. Findings: For detecting DKD, DeepDKD achieved an area under the receiver operating characteristic curve (AUC) of 0·842 (95% CI 0·838–0·846) on the internal validation dataset and AUCs of 0·791–0·826 across external validation datasets. For differentiating isolated diabetic nephropathy from NDKD, DeepDKD achieved an AUC of 0·906 (0·825–0·966) on the internal validation dataset and AUCs of 0·733–0·844 across external validation datasets. In the prospective study, compared with the metadata model, DeepDKD could detect DKD wit

关键词： Deep learning

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