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1st Challenge on Head and Neck Tumor Segmentation for MRI-Guided Applications, HNTS-MRG 2024, Held in Conjunction with 27th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2024

作者： Wahid, Kareem A. Dede, Cem El-Habashy, Dina M. Kamel, Serageldin Rooney, Michael K. Khamis, Yomna Abdelaal, Moamen R. A. Ahmed, Sara Corrigan, Kelsey L. Chang, Enoch Dudzinski, Stephanie O. Salzillo, Travis C. McDonald, Brigid A. Mulder, Samuel L. McCullum, Lucas Alakayleh, Qusai Sjogreen, Carlos He, Renjie Mohamed, Abdallah S. R. Lai, Stephen Y. Christodouleas, John P. Schaefer, Andrew J. Naser, Mohamed A. Fuller, Clifton D. Department of Radiation Oncology The University of Texas MD Anderson Cancer HoustonTX United States Department of Imaging Physics The University of Texas MD Anderson Cancer HoustonTX United States Transitional Year Program Corewell Health Wiliam Beaumont Royal OakMI United States Department of Radiation Oncology University of Maryland School of Medicine BaltimoreMD United States Department of Clinical Oncology and Nuclear Medicine Faculty of Medicine Alexandria University Alexandria Egypt UT MD Anderson Cancer CenterUTHealth Houston Graduate School of Biomedical Sciences Houston United States Department of Radiation Oncology Baylor College of Medicine HoustonTX United States Department of Head and Neck Surgery The University of Texas MD Anderson Cancer HoustonTX United States Elekta AtlantaGA United States Department of Computational Applied Mathematics and Operations Research Rice University HoustonTX United States

ISBN: (纸本)9783031832734

Magnetic resonance (MR)-guided radiation therapy (RT) is enhanc- ing head and neck cancer (HNC) treatment through superior soft tissue con- trast and longitudinal imaging capabilities. However, manual tumor segmentation remains a significant challenge, spurring interest in artificial intelligence (AI)- driven automation. To accelerate innovation in this field, we present the Head and Neck Tumor Segmentation for MR-Guided Applications (HNTS-MRG) 2024 Challenge, a satellite event of the 27th International Conference on Medical Image Computing and Computer Assisted Intervention. This challenge addresses the scarcity of large, publicly available AI-ready adaptive RT datasets in HNC and explores the potential of incorporating multi-timepoint data to enhance RT auto- segmentation performance. Participants tackled two HNC segmentation tasks: automatic delineation of primary gross tumor volume (GTVp) and gross metastatic regional lymph nodes (GTVn) on pre-RT (Task 1) and mid-RT (Task 2) T2- weighted scans. The challenge provided 150 HNC cases for training and 50 for final testing hosted on *** using a Docker submission framework. In total, 19 independent teams from across the world qualified by submitting both their algorithms and corresponding papers, resulting in 18 submissions for Task 1 and 15 submissions for Task 2. Evaluation using the mean aggregated Dice Simi- larity Coefficient showed top-performing AI methods achieved scores of 0.825 in Task 1 and 0.733 in Task 2. These results surpassed clinician interobserver vari- ability benchmarks, marking significant strides in automated tumor segmentation for MR-guided RT applications in HNC. © The Author(s) 2025.

关键词： Deep learning

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Viscosity in water from first-principles and deep-neural-network simulations

arXiv

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arXiv 2022年

作者： Malosso, Cesare Zhang, Linfeng Car, Roberto Baroni, Stefano Tisi, Davide SISSA - Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States DP Technology Beijing100080 China Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States CNR Istituto Officina dei Materiali SISSA Unit Trieste34136 Italy

We report on an extensive study of the viscosity of liquid water at near-ambient conditions, performed within the Green-Kubo theory of linear response and equilibrium ab initio molecular dynamics (AIMD), based on density-functional theory (DFT). In order to cope with the long simulation times necessary to achieve an acceptable statistical accuracy, our ab initio approach is enhanced with deep-neural-network potentials (NNP). This approach is first validated against AIMD results, obtained by using the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and paying careful attention to crucial, yet often overlooked, aspects of the statistical data analysis. Then, we train a second NNP to a dataset generated from the Strongly Constrained and Appropriately Normed (SCAN) functional. Once the error resulting from the imperfect prediction of the melting line is offset by referring the simulated temperature to the theoretical melting one, our SCAN predictions of the shear viscosity of water are in very good agreement with experiments. Copyright © 2022, The Authors. All rights reserved.

关键词： Deep neural networks

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On the importance of assessing topological convergence in Bayesian phylogenetic inference

arXiv

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arXiv 2024年

作者： Brusselmans, Marius Carvalho, Luiz Max Hong, Samuel L. Gao, Jiansi Matsen, Frederick A. Rambaut, Andrew Lemey, Philippe Suchard, Marc A. Dudas, Gytis Baele, Guy Department of Microbiology Immunology and Transplantation Rega Institute KU Leuven Leuven Belgium School of Applied Mathematics Getulio Vargas Foundation Praia de Botafogo 190 Rio de Janeiro22250-900 Brazil Computational Biology Program Fred Hutchinson Cancer Center SeattleWA98109 United States Howard Hughes Medical Institute Computational Biology Program Fred Hutchinson Cancer Research Center SeattleWA United States Department of Genome Sciences University of Washington SeattleWA United States Department of Statistics University of Washington SeattleWA United States Institute of Ecology and Evolution University of Edinburgh EdinburghEH9 3FL United Kingdom Department of Biostatistics Fielding School of Public Health University of California Los AngelesCA90095 United States Institute of Biotechnology Life Sciences Center Vilnius University Vilnius Lithuania

Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of the generated samples. Within the field of phylogenetics, one frequently adopted diagnostic approach is to evaluate the effective sample size (ESS) and to investigate trace graphs of the sampled parameters. A major limitation of these approaches is that they are developed for continuous parameters and therefore incompatible with a crucial parameter in these inferences: the tree topology. Several recent advancements have aimed at extending these diagnostics to topological space. In this reflection paper, we present two case studies – one on Ebola virus and one on HIV – illustrating how these topological diagnostics can contain information not found in standard diagnostics, and how decisions regarding which of these diagnostics to compute can impact inferences regarding MCMC convergence and mixing. Our results show the importance of running multiple replicate analyses and of carefully assessing topological convergence using the output of these replicate analyses. To this end, we illustrate different ways of assessing and visualizing the topological convergence of these replicates. Given the major importance of detecting convergence and mixing issues in Bayesian phylogenetic analyses, the lack of a unified approach to this problem warrants further action, especially now that additional tools are becoming available to researchers. © 2024, CC BY-SA.

关键词： Phylogenetic

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Publisher's Note: “Reacting and non-reacting, three-dimensional shear layers with spanwise stretching” [Phys. Fluids 34, 123602 (2022)]

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Physics of Fluids 2023年第1期35卷

作者： Jonathan L. Palafoutas William A. Sirignano 1Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08540 USA 2Department of Mechanical and Aerospace Engineering University of California Irvine Irvine California 92697 USA

This article was published online on 2 December 2022 with errors throughout the paper. All the derivative terms had the wrong denominator; the denominators were

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Ferroelectric transistors based on shear-transformation-mediated rhombohedral-stacked molybdenum disulfide

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Nature Electronics 2024年第1期7卷 29-38页

作者： Yang, Tilo H. Liang, Bor-Wei Hu, Hsiang-Chi Chen, Fu-Xiang Ho, Sheng-Zhu Chang, Wen-Hao Yang, Liu Lo, Han-Chieh Kuo, Tzu-Hao Chen, Jyun-Hong Lin, Po-Yen Simbulan, Kristan Bryan Luo, Zhao-Feng Chang, Alice Chinghsuan Kuo, Yi-Hao Ku, Yu-Seng Chen, Yi-Cheng Huang, You-Jia Chang, Yu-Chen Chiang, Yu-Fan Lu, Ting-Hua Lee, Min-Hung Li, Kai-Shin Wu, Menghao Chen, Yi-Chun Lin, Chun-Liang Lan, Yann-Wen Department of Physics National Taiwan Normal University Taipei Taiwan Taiwan Semiconductor Research Institute National Applied Research Laboratories Hsinchu Taiwan Department of Electrophysics National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Physics National Cheng Kung University Tainan Taiwan School of Physics Huazhong University of Science and Technology Wuhan China Institute of Cellular and Organismic Biology Academia Sinica Taipei Taiwan Department of Mathematics and Physics University of Santo Tomas Manila Philippines Program for Semiconductor Devices Materials and Hetero-integration Graduate School of Advanced Technology National Taiwan University Taipei Taiwan Hsinchu Taiwan Department of Physics National Taiwan University Taipei Taiwan Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States

To develop low-power, non-volatile computing-in-memory device using ferroelectric transistor technologies, ferroelectric channel materials with scaled thicknesses are required. Two-dimensional semiconductors, such as molybdenum disulfide (MoS2), equipped with sliding ferroelectricity could provide an answer. However, achieving switchable electric polarization in epitaxial MoS2 remains challenging due to the absence of mobile domain boundaries. Here we show that polarity-switchable epitaxial rhombohedral-stacked (3R) MoS2 can be used as a ferroelectric channel in ferroelectric memory transistors. We show that a shear transformation can spontaneously occur in 3R MoS2 epilayers, producing heterostructures with stable ferroelectric domains embedded in a highly dislocated and unstable non-ferroelectric matrix. This diffusionless phase transformation process produces mobile screw dislocations that enable collective polarity control of 3R MoS2 via an electric field. Polarization–electric-field measurements reveal a switching field of 0.036 V nm−1 for shear-transformed 3R MoS2. Our sliding ferroelectric transistors are non-volatile memory units with thicknesses of only two atomic layers and exhibit an average memory window of 7 V with an applied voltage of 10 V, retention times greater than 104 seconds and endurance greater than 104 cycles. © 2023, The Author(s), under exclusive licence to Springer Nature Limited.

关键词： Molybdenum disulfide

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DeePN2: A deep learning-based non-Newtonian hydrodynamic model

arXiv

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arXiv 2021年

作者： Fang, Lidong Ge, Pei Zhang, Lei Weinan, E. Lei, Huan Department of Computational Mathematics Science and Engineering Michigan State University MI48824 United States School of Mathematical Sciences Institute of Natural Sciences and MOE-LSC Shanghai Jiao Tong University 800 Dongchuan Road Shanghai200240 China Center for Machine Learning Research School of Mathematical Sciences Peking University Beijing100871 China AI for Science Institute Beijing100080 China Department of Mathematics and Program in Applied and Computational Mathematics Princeton University NJ08544 United States Department of Statistics and Probability Michigan State University MI48824 United States

A long standing problem in the modeling of non-Newtonian hydrodynamics of polymeric flows is the availability of reliable and interpretable hydrodynamic models that faithfully encode the underlying micro-scale polymer dynamics. The main complication arises from the long polymer relaxation time, the complex molecular structure and heterogeneous interaction. DeePN2, a deep learning-based non-Newtonian hydrodynamic model, has been proposed and has shown some success in systematically passing the micro-scale structural mechanics information to the macro-scale hydrodynamics for suspensions with simple polymer conformation and bond potential. The model retains a multi-scaled nature by mapping the polymer configurations into a set of symmetry-preserving macro-scale features. The extended constitutive laws for these macro-scale features can be directly learned from the kinetics of their micro-scale counterparts. In this paper, we develop DeePN2 using more complex micro-structural models. We show that DeePN2 can faithfully capture the broadly overlooked viscoelastic differences arising from the specific molecular structural mechanics without human intervention. © 2021, CC BY.

关键词： Non Newtonian flow

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Scalable Multiscale-Spectral Gfem for Composite Aero-Structures

SSRN

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SSRN 2022年

作者： Bénézech, Jean Seelinger, Linus Bastian, Peter Butler, Richard Dodwell, Timothy Ma, Chupeng Scheichl, Robert Material & Structure Research Centre University of Bath BathBA2 7AY United Kingdom Institute for Applied Mathematics and Interdisciplinary Center for Scientific Computing Heidelberg University Heidelberg Germany Institute of Data Science and AI University of Exeter DigiLab Exeter United Kingdom Department of Mathematical Sciences University of Bath Bath United Kingdom Institute of Scientific Research Great Bay University Dongguan China

Ill-conditioned and multiscale partial differential equations (PDEs) arise in many fields. It is a very challenging problem to compute a resolved, fine-scale solution or to find a robust low-dimensional approximation. In this paper, the first large-scale application of multiscale-spectral generalized finite element methods (MS-GFEM) to composite aero-structures is presented. A problem-specific coarse space generated from local eigenproblems yields a spectral element-type method with excellent approximation properties at low basis size, even for challenging multiscale problems. The implementation of the framework in the DUNE software package, as well as a detailed description of all components of the method are presented and exemplified on a composite laminated beam under compressive loading. The excellent parallel scalability of the method, as well as its superior performance compared to the related, previously introduced GenEO method are demonstrated on two realistic application cases. Further, by allowing low-cost approximate solves for closely related models or geometries this efficient, novel technology provides the basis for future applications in optimisation or uncertainty quantification on challenging problems in composite aero-structures. © 2022, The Authors. All rights reserved.

关键词： Finite element method

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Heat transport in liquid water from first-principles and deep-neural-network simulations

arXiv

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arXiv 2021年

作者： Tisi, Davide Zhang, Linfeng Bertossa, Riccardo Wang, Han Car, Roberto Baroni, Stefano SISSA - Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Huayuan Road 6 Beijing100088 China Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States CNR Istituto Officina Dei Materiali SISSA Unit Trieste34136 Italy

We compute the thermal conductivity of water within linear response theory from equilibrium molecular dynamics simulations, by adopting two different approaches. In one, the potential energy surface (PES) is derived on the fly from the electronic ground state of density functional theory (DFT) and the corresponding analytical expression is used for the energy flux. In the other, the PES is represented by a deep neural network (DNN) trained on DFT data, whereby the PES has an explicit local decomposition and the energy flux takes a particularly simple expression. By virtue of a gauge invariance principle, established by Marcolongo, Umari, and Baroni, the two approaches should be equivalent if the PES were reproduced accurately by the DNN model. We test this hypothesis by calculating the thermal conductivity, at the GGA (PBE) level of theory, using the direct formulation and its DNN proxy, finding that both approaches yield the same conductivity, in excess of the experimental value by approximately 60%. Besides being numerically much more efficient than its direct DFT counterpart, the DNN scheme has the advantage of being easily applicable to more sophisticated DFT approximations, such as meta-GGA and hybrid functionals, for which it would be hard to derive analytically the expression of the energy flux. We find in this way, that a DNN model, trained on meta-GGA (SCAN) data, reduce the deviation from experiment of the predicted thermal conductivity by about 50%, leaving the question open as to whether the residual error is due to deficiencies of the functional, to a neglect of nuclear quantum effects in the atomic dynamics, or, likely, to a combination of the two. Copyright © 2021, The Authors. All rights reserved.

关键词： Deep neural networks

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Generating Function for Projected Entangled-Pair States

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PRX Quantum 2024年第1期5卷 010335-010335页

作者： Wei-Lin Tu Laurens Vanderstraeten Norbert Schuch Hyun-Yong Lee Naoki Kawashima Ji-Yao Chen Faculty of Science and Technology Keio University 3-14-1 Hiyoshi Kohoku-ku Yokohama 223-8522 Japan Center for Nonlinear Phenomena and Complex Systems Université Libre de Bruxelles B-1050 Bruxelles Belgium University of Vienna Faculty of Physics Boltzmanngasse 5 Wien 1090 Austria University of Vienna Faculty of Mathematics Oskar-Morgenstern-Platz 1 Wien 1090 Austria Division of Display and Semiconductor Physics Korea University Sejong 30019 Korea Department of Applied Physics Graduate School Korea University Sejong 30019 Korea Interdisciplinary Program in E·ICT-Culture-Sports Convergence Korea University Sejong 30019 Korea Institute for Solid State Physics The University of Tokyo Kashiwa Chiba 277-8581 Japan Trans-scale Quantum Science Institute The University of Tokyo Bunkyo Tokyo 113-0033 Japan Center for Neutron Science and Technology Guangdong Provincial Key Laboratory of Magnetoelectric Physics and Devices School of Physics Sun Yat-sen University Guangzhou 510275 China

Diagrammatic summation is a common bottleneck in modern applications of projected entangled-pair states, especially in computing low-energy excitations of a two-dimensional quantum many-body system. To solve this problem, here we extend the generating-function approach for tensor-network diagrammatic summation, a scheme previously proposed in the context of matrix product states. Taking the form of a one-particle excitation, we show that the excited state can be computed efficiently in the generating-function formalism, which can further be used in evaluating the dynamical structure factor of the system. Our benchmark results for the spin-1/2 transverse-field Ising model and Heisenberg model on the square lattice provide a desirable accuracy, showing good agreement with known results. We then study the spin-1/2J1-J2 model on the same lattice and investigate the dynamical properties of the putative gapless spin liquid phase. We conclude with a discussion on generalizations to multiparticle excitations.

关键词： Quasiparticles & collective excitations Quantum many-body systems Quantum spin models Strongly correlated systems Many-body techniques Projected entangled pair states Tensor network methods

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Scanning protocol influence on relative electron Density-CT number calibrations and radiotherapy dose calculation for a Halcyon Linac

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Radiation Physics and Chemistry 2025年 236卷

作者： Thanh Tai, Duong Nhu Tuyen, Pham Duc Tuan, Hoang Hung, Hoang T.P. Kandemir, Recep Omer, Hiba Sulieman, Abdelmoneim Bradley, David Chow, James C.L. Department of Medical Physics Faculty of Medicine Nguyen Tat Thanh University 298-300A Nguyen Tat Thanh Street Ward 13 District 4 Ho Chi Minh City Viet Nam Department of Radiation Oncology University Medical Shing Mark Hospital Dong Nai 810000 Viet Nam Danang Irradiation Facility Research and Development Center for Radiation Technology VINATOM 550000 Da Nang Viet Nam Dokuz Eylül University Institute of Health Sciences Department of Medical Physics Izmir Turkey Dokuz Eylül University Vocational School of Health Services The Program of Radiotherapy Izmir Turkey Department of Radiological Sciences College of Applied Medical Sciences Imam Abdulrahman Bin Faisal University P. O. Box 1982 Dammam34212 Saudi Arabia Department of Radiological Sciences College of Applied Medical Sciences King Saud Bin Abdulaziz University for Health Sciences Al Ahsa Saudi Arabia Imaging Physics Section Research and Innovation Department King Faisal Specialist Hospital & Research Center Riyadh Saudi Arabia Applied Radiation Physics and Technologies Group Sunway University 46150 PJ Malaysia School of Mathematics and Physics University of Surrey GuildfordGU2 7XH United Kingdom Department of Radiation Oncology University of Toronto TorontoONN5T 1P5 Canada Radiation Medicine Program Princess Margaret Cancer Centre University Health Network ONM5G 1X6 Canada

Tissue Relative Electron Density (RED), typically determined via computation of CT-based Hounsfield unit (HU) values, has an accuracy which is affected by the choice of CT scanning parameters. The influence of these on the RED-CT number calibration curves is of importance, not least concerning variations in CT x-ray tube voltage and current. The purpose of this study was to examine the effect of variations in CT x-ray tube voltage and current on the calibration curves of RED - CT number conversion, with the aim of improving the accuracy of dose calculation in radiotherapy treatment planning. An electron density phantom CIRS have been conducted at 200 mAs, for tube voltages of 80, 110, and 130 kVp, corresponding images being calibrated in terms of RED-CT number conversion curves. Subsequent treatment plans have been generated, identified in terms of the applied tube voltages, the 130 kVp plan being designated the reference plan. The remaining plans have been compared to the reference plan via analysis of isodose distribution and dose. The influence of tube voltage were being found to be greatest for high-density substances such as bone in comparison to low-density materials. Conversely, the CT number of a titanium rod has been consistent, regardless of the choice of tube voltage or current. The effect of tube current variation on the calibration curves has been minor at higher tube voltages but more pronounced using lower voltages and current. The presence in the phantom of plugs of high-density materials has resulted in beam hardening artefacts, impacting on the RED values for other plugs. In achieving accurate dose calculation for radiotherapy treatment plans the work underscores the need to account for effects of CT scanning parameters on the RED-CT number conversion curves. Further emphasized is the importance of careful selection of imaging protocols in seeking to minimize beam hardening artefacts and to ensure accurate determination of RED. The study demonstrat

关键词： X ray tubes

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