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arXiv 2024年

作者： Ho, Matthew Bartlett, Deaglan J. Chartier, Nicolas Cuesta-Lazaro, Carolina Ding, Simon Lapel, Axel Lemos, Pablo Lovell, Christopher C. Makinen, T. Lucas Modi, Chirag Pandya, Viraj Pandey, Shivam Perez, Lucia A. Wandelt, Benjamin Bryan, Greg L. UMR 7095 98 bis bd Arago ParisF-75014 France Center for the Gravitational-Wave Universe Astronomy Program Department of Physics and Astronomy Seoul National University Seoul08826 Korea Republic of Center for Astrophysics Harvard & Smithsonian 60 Garden St CambridgeMA02138 United States The NSF AI Institute for Artificial Intelligence and Fundamental Interactions United States Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Université de Montréal Montréal Canada Mila - Quebec Artificial Intelligence Institute Montréal Canada Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning Montréal Canada Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Institute of Cosmology and Gravitation University of Portsmouth Burnaby Road PortsmouthPO1 3FX United Kingdom & Astrophysics Group Imperial College London Blackett Laboratory Prince Consort Road LondonSW7 2AZ United Kingdom Center for Computational Mathematics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Columbia Astrophysics Laboratory Columbia University 550 West 120th Street New YorkNY10027 United States 4 place Jussieu ParisF-75252 Cedex 5 France

This paper presents the learning the Universe Implicit Likelihood Inference (LtU-ILI) pipeline, a codebase for rapid, user-friendly, and cutting-edge machine learning (ML) inference in astrophysics and cosmology. The pipeline includes software for implementing various neural architectures, training schemata, priors, and density estimators in a manner easily adaptable to any research workflow. It includes comprehensive validation metrics to assess posterior estimate coverage, enhancing the reliability of inferred results. Additionally, the pipeline is easily parallelizable and is designed for efficient exploration of modeling hyperparameters. To demonstrate its capabilities, we present real applications across a range of astrophysics and cosmology problems, such as: estimating galaxy cluster masses from X-ray photometry;inferring cosmology from matter power spectra and halo point clouds;characterizing progenitors in gravitational wave signals;capturing physical dust parameters from galaxy colors and luminosities;and establishing properties of semi-analytic models of galaxy formation. We also include exhaustive benchmarking and comparisons of all implemented methods as well as discussions about the challenges and pitfalls of ML inference in astronomical sciences. All code and examples are made publicly available at https://***/maho3/ltu-ili. © 2024, CC BY.

关键词： Cosmology

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SimBIG: Field-level Simulation-Based Inference of Galaxy Clustering

arXiv

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arXiv 2023年

作者： Lemos, Pablo Parker, Liam Hahn, ChangHoon Ho, Shirley Eickenberg, Michael Hou, Jiamin Massara, Elena Modi, Chirag Dizgah, Azadeh Moradinezhad Blancard, Bruno Régaldo-Saint Spergel, David Department of Physics Université de Montréal 1375 Avenue Thérèse-Lavoie-Roux MontréalQCH2V 0B3 Canada Mila - Quebec Artificial Intelligence Institute 6666 Rue Saint-Urbain MontréalQCH2S 3H1 Canada Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning Montréal Canada Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Physics Princeton University PrincetonNJ08544 United States Center for Cosmology and Particle Physics Department of Physics New York University New YorkNY10003 United States Department of Physics Carnegie Mellon University PittsburghPA15213 United States Center for Computational Mathematics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Astronomy University of Florida 211 Bryant Space Science Center GainesvilleFL32611 United States Max-Planck-Institut für Extraterrestrische Physik Postfach 1312 Giessenbachstrasse 1 Garching bei München85748 Germany Waterloo Centre for Astrophysics University of Waterloo 200 University Ave W WaterlooONN2L 3G1 Canada Department of Physics and Astronomy University of Waterloo 200 University Ave W WaterlooONN2L 3G1 Canada Département de Physique Théorique Université de Genève 24 quai Ernest Ansermet Genève 41211 Switzerland

We present the first simulation-based inference (SBI) of cosmological parameters from field-level analysis of galaxy clustering. Standard galaxy clustering analyses rely on analyzing summary statistics, such as the power spectrum, P, with analytic models based on perturbation theory. Consequently, they do not fully exploit the non-linear and non-Gaussian features of the galaxy distribution. To address these limitations, we use the SimBIG forward modelling framework to perform SBI using normalizing flows. We apply SimBIG to a subset of the BOSS CMASS galaxy sample using a convolutional neural network with stochastic weight averaging to perform massive data compression of the galaxy field. We infer constraints on (Equation presented) and (Equation presented). While our constraints on Ωm are in-line with standard P analyses, those on σ8 are 2.65× tighter. Our analysis also provides constraints on the Hubble constant H0 = 64.5 ± 3.8 km/s/Mpc from galaxy clustering alone. This higher constraining power comes from additional non-Gaussian cosmological information, inaccessible with P. We demonstrate the robustness of our analysis by showcasing our ability to infer unbiased cosmological constraints from a series of test simulations that are constructed using different forward models than the one used in our training dataset. This work not only presents competitive cosmological constraints but also introduces novel methods for leveraging additional cosmological information in upcoming galaxy surveys like DESI, PFS, and Euclid. © 2023, CC0.

关键词： Galaxies

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Strong gravitational lensing as a probe of dark matter

arXiv

引用

arXiv 2023年

作者： Vegetti, S. Birrer, S. Despali, G. Fassnacht, C.D. Gilman, D. Hezaveh, Y. Levasseur, L. Perreault McKean, J.P. Powell, D.M. O’Riordan, C.M. Vernardos, G. Max Planck Institut für Astrophysik Karl-Schwarzschild-Strasse 1 Garching MünchenD-85748 Germany Department of Physics and Astronomy Stony Brook University Stony BrookNY11794 United States Dipartimento di Fisica e Astronomia "A. Righi" Alma Mater Studiorum Università di Bologna Via Piero Gobetti 93/2 BolognaI-40129 Italy Institut für Theoretische Astrophysik Zentrum für Astronomie Heidelberg Universität Albert-Ueberle-Str. 2 Heidelberg69120 Germany Dept. of Physics and Astronomy University of California Davis 1 Shields Ave. DavisCA95616 United States Department of Astronomy and Astrophysics University of Toronto TorontoONM5S 3H4 Canada Department of Physics Université de Montréal Montréal Canada Mila - Quebec Artificial Intelligence Institute Montréal Canada Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning Montréal Canada Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Perimeter Institute for Theoretical Physics WaterlooONN2L 2Y5 Canada Kapteyn Astronomical Institute University of Groningen PO Box 800 AV Groningen9700 Netherlands ASTRON Netherlands Institute for Radio Astronomy PO Box 2 AA Dwingeloo7990 Netherlands Observatoire de Sauverny Versoix1290 Switzerland

Dark matter structures within strong gravitational lens galaxies and along their line of sight leave a gravitational imprint on the multiple images of lensed sources. Strong gravitational lensing provides, therefore, a key test of different dark matter models in a way that is independent of the baryonic content of matter structures on subgalactic scales. In this chapter, we describe how galaxy-scale strong gravitational lensing observations are sensitive to the physical nature of dark matter. We provide a historical perspective of the field, and review its current status. We discuss the challenges and advances in terms of data, treatment of systematic errors and theoretical predictions, that will enable one to deliver a stringent and robust test of different dark matter models in the near future. With the advent of the next generation of sky surveys, the number of known strong gravitational lens systems is expected to increase by several orders of magnitude. Coupled with high-resolution followup observations, these data will provide a key opportunity to constrain the properties of dark matter with strong gravitational lensing. Copyright © 2023, The Authors. All rights reserved.

关键词： Galaxies

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Brain Tumor Segmentation (BraTS) Challenge 2024: Meningioma Radiotherapy Planning Automated Segmentation

arXiv

引用

arXiv 2024年

作者： LaBella, Dominic Schumacher, Katherine Mix, Michael Leu, Kevin McBurney-Lin, Shan Nedelec, Pierre Villanueva-Meyer, Javier Shapey, Jonathan Vercauteren, Tom Chia, Kazumi Ivory, Marina Barfoot, Theodore Al-Salihi, Omar Leu, Justin Halasz, Lia Velichko, Yury Wang, Chunhao Kirkpatrick, John Floyd, Scott Reitman, Zachary J. Mullikin, Trey Bagci, Ulas Sachdev, Sean Hattangadi-Gluth, Jona A. Seibert, Tyler M. Farid, Nikdokht Puett, Connor Pease, Matthew W. Shiue, Kevin Anwar, Syed Muhammad Faghani, Shahriar Taylor, Peter Haider, Muhammad Ammar Warman, Pranav Albrecht, Jake Jakab, András Moassefi, Mana Chung, Verena Aristizabal, Alejandro Karargyris, Alexandros Kassem, Hasan Pati, Sarthak Sheller, Micah Coley, Aaron Huang, Christina Ghanta, Siddharth Schneider, Alex Sharp, Conrad Saluja, Rachit Kofler, Florian Lohmann, Philipp Vollmuth, Phillipp Gagnon, Louis Adewole, Maruf Li, Hongwei Bran Kazerooni, Anahita Fathi Tahon, Nourel Hoda Anazodo, Udunna Moawad, Ahmed W. Menze, Bjoern Linguraru, Marius George Aboian, Mariam Wiestler, Benedikt Baid, Ujjwal Conte, Gian-Marco Rauschecker, Andreas M. Nada, Ayman Abayazeed, Aly H. Huang, Raymond de Verdier, Maria Correia Rudie, Jeffrey D. Bakas, Spyridon Calabrese, Evan Department of Radiation Oncology Duke University Medical Center DurhamNC United States Department of Radiation Oncology SUNY Upstate Medical University SyracuseNY United States San FranciscoCA United States Department of Neurosurgery King’s College Hospital London United Kingdom School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Guy’s and St Thomas’ NHS Foundation Trust United Kingdom Department of Radiation Oncology University of Washington SeattleWA United States Department of Radiology Northwestern University EvanstonIL United States Department of Radiation Oncology Northwestern University EvanstonIL United States Department of Radiation Medicine and Applied Sciences University of California San Diego La Jolla CA United States Department of Radiology University of California San Diego La Jolla CA United States Department of Bioengineering University of California San Diego La Jolla CA United States Department of Neurological Surgery Indiana University School of Medicine IndianapolisIN United States Department of Radiation Oncology Indiana University IndianapolisIN United States Children’s National Hospital WashingtonDC United States George Washington University WashingtonDC United States Mayo Clinic RochesterMN United States CMH Lahore Medical College Lahore Pakistan Duke University Medical Center School of Medicine DurhamNC United States Sage Bionetworks United States University of Zürich Zürich Switzerland Artificial Intelligence Lab Department of Radiology Mayo Clinic RochesterMN United States MLCommons United States Factored AI United States Center For Federated Learning in Medicine Indiana University IndianapolisIN United States Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Medical Working Group MLCommons San FranciscoCA United States Intel United States Duke Universi

The 2024 Brain Tumor Segmentation Meningioma Radiotherapy (BraTS-MEN-RT) challenge aims to advance automated segmentation algorithms using the largest known multi-institutional dataset of 750 radiotherapy planning brain MRIs with expert-annotated target labels for patients with intact or postoperative meningioma that underwent either conventional external beam radiotherapy or stereotactic radiosurgery. Each case includes a defaced 3D post-contrast T1-weighted radiotherapy planning MRI in its native acquisition space, accompanied by a single-label "target volume" representing the gross tumor volume (GTV) and any at-risk postoperative site. Target volume annotations adhere to established radiotherapy planning protocols, ensuring consistency across cases and institutions. For preoperative meningiomas, the target volume encompasses the entire GTV and associated nodular dural tail, while for postoperative cases, it includes at-risk resection cavity margins as determined by the treating institution. Case annotations were reviewed and approved by expert neuroradiologists and radiation oncologists. Participating teams will develop, containerize, and evaluate automated segmentation models using this comprehensive dataset. Model performance will be assessed using an adapted lesion-wise Dice Similarity Coefficient and the 95% Hausdorff distance. The top-performing teams will be recognized at the Medical Image Computing and Computer Assisted Intervention Conference in October 2024. BraTS-MEN-RT is expected to significantly advance automated radiotherapy planning by enabling precise tumor segmentation and facilitating tailored treatment, ultimately improving patient outcomes. © 2024, CC BY.

关键词： Radiotherapy

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Why is the Winner the Best?

Why is the Winner the Best?

引用

Conference on Computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and post-processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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Generating Synthetic Computed Tomography for Radiotherapy: SynthRAD2023 Challenge Report

arXiv

引用

arXiv 2024年

作者： Huijben, Evi M.C. Terpstra, Maarten L. Galapon, Arthur Pai, Suraj Thummerer, Adrian Koopmans, Peter Afonso, Manya van Eijnatten, Maureen Gurney-Champion, Oliver Chen, Zeli Zhang, Yiwen Zheng, Kaiyi Li, Chuanpu Pang, Haowen Ye, Chuyang Wang, Runqi Song, Tao Fan, Fuxin Qiu, Jingna Huang, Yixing Ha, Juhyung Park, Jong Sung Alain-Beaudoin, Alexandra Bériault, Silvain Yu, Pengxin Guo, Hongbin Huang, Zhanyao Li, Gengwan Zhang, Xueru Fan, Yubo Liu, Han Xin, Bowen Nicolson, Aaron Zhong, Lujia Deng, Zhiwei Müller-Franzes, Gustav Khader, Firas Li, Xia Zhang, Ye Hémon, Cédric Boussot, Valentin Zhang, Zhihao Wang, Long Bai, Lu Wang, Shaobin Mus, Derk Kooiman, Bram Sargeant, Chelsea A.H. Henderson, Edward G.A. Kondo, Satoshi Kasai, Satoshi Karimzadeh, Reza Ibragimov, Bulat Helfer, Thomas Dafflon, Jessica Chen, Zijie Wang, Enpei Perko, Zoltan Maspero, Matteo Department of Biomedical Engineering Eindhoven University of Technology Eindhoven Netherlands Radiotherapy Department University Medical Center Utrecht Utrecht Netherlands Computational Imaging Group for MR Diagnostics & Therapy University Medical Center Utrecht Utrecht Netherlands Department of Radiation Oncology University Medical Center Groningen University of Groningen Groningen Netherlands GROW School for Oncology Maastricht University Medical Centre Maastricht Netherlands Department of Radiation Oncology LMU University Hospital LMU Munich Munich Germany Department of Radiation Oncology Radboud University Medical Center Nijmegen Netherlands Wageningen University & Research Wageningen Plant Research Wageningen Netherlands Department of Radiology and Nuclear Medicine Amsterdam UMC Location University of Amsterdam Amsterdam Netherlands Cancer Center Amsterdam Imaging and Biomarkers Amsterdam Netherlands School of Biomedical Engineering Southern Medical University Guangzhou China School of Integrated Circuits and Electronics Beijing Institute of Technology Beijing China School of Biomedical Engineering ShanghaiTech University Shanghai China Fudan University Shanghai China Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen Germany Indiana University Bloomington United States Advanced Development Engineering Elekta Ltd Montreal Canada Infervision Medical Technology Co. Ltd. Beijing China Department of Biomedical Engineering Shantou University China Independent researchers Department of Computer Science Vanderbilt University Nashville United States Australian e-Health Research Centre CSIRO HerstonQLD Australia Los AngelesCA United States University Hospital Aachen Aachen Germany Center for Proton Therapy Paul Scherrer Institut Villigen Switzerland Department of Computer Science ETH Zurich Zurich Switzerland University Rennes 1 CLCC Eugène Marquis INSERM LTSI Rennes France Subtle Medical Shanghai China MedMind Technology Co.

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information, while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (≥ 0.87/0.90) and gamma pass rates for photon (≥ 98.1%/99.0%) and proton (≥ 97.3%/97.0%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy. It showcased the growing capacity of deep learning to produce high-quality sCT, reducing reliance on conventional CT for treatment planning. © 2024, CC

关键词： Radiotherapy

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Constructing Impactful machine learning Research for Astronomy: Best Practices for Researchers and Reviewers

arXiv

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arXiv 2023年

作者： Huppenkothen, Daniela Ntampaka, Michelle Ho, Matthew Fouesneau, Morgan Nord, Brian Peek, J.E.G. Walmsley, Mike Wu, John F. Avestruz, C. Buck, Tobias Brescia, Massimo Finkbeiner, Douglas P. Goulding, Andy D. Kacprzak, T. Melchior, Peter Pasquato, Mario Ramachandra, Nesar Ting, Yuan-Sen van de Ven, Glenn Villar, Soledad Villar, V.A. Zinger, Elad SRON Netherlands Institute for Space Research Niels Bohrweg 4 Leiden2333CA Netherlands Anton Pannekoek Institute for Astronomy University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Space Telescope Science Institute BaltimoreMD21218 United States Department of Physics & Astronomy Johns Hopkins University BaltimoreMD21218 United States UMR 7095 98 bis bd Arago ParisF-75014 France Königstuhl 17 HeidelbergD-69117 Germany Fermi National Accelerator Laboratory P. O. Box 500 BataviaIL60510 United States Kavli Institute for Cosmological Physics University of Chicago ChicagoIL60637 United States Department of Astronomy and Astrophysics University of Chicago ChicagoIL60637 United States Jodrell Bank Centre for Astrophysics Department of Physics & Astronomy University of Manchester ManchesterM13 9PL United Kingdom Dunlap Institute for Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Leinweber Center for Theoretical Physics University of Michigan Ann ArborMI48109 United States Department of Physics University of Michigan Ann ArborMI48109 United States Universität Heidelberg Interdisziplinäres Zentrum für Wissenschaftliches Rechnen Im Neuenheimer Feld 205 Heidelberg69120 Germany Universität Heidelberg Zentrum für Astronomie Institut für Theoretische Astrophysik Albert-Ueberle-Straße 2 Heidelberg69120 Germany Department of Physics "E. Pancini " University Federico II of Napoli Via Cinthia 21 NapoliI-80126 Italy INAF Astronomical Observatory of Capodimonte Salita Moiariello 16 NapoliI-80131 Italy Department of Physics Harvard University 17 Oxford St. CambridgeMA02138 United States Harvard-Smithsonian Center for Astrophysics 60 Garden St. CambridgeMA02138 United States Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Swiss Data Science Center Paul Scherrer Institute Villigen5303 Switzerland Center for Statistics & Machine Learn

machine learning has rapidly become a tool of choice for the astronomical community. It is being applied across a wide range of wavelengths and problems, from the classification of transients to neural network emulators of cosmological simulations, and is shifting paradigms about how we generate and report scientific results. At the same time, this class of method comes with its own set of best practices, challenges, and drawbacks, which, at present, are often reported on incompletely in the astrophysical literature. With this paper, we aim to provide a primer to the astronomical community, including authors, reviewers, and editors, on how to implement machine learning models and report their results in a way that ensures the accuracy of the results, reproducibility of the findings, and usefulness of the method. Copyright © 2023, The Authors. All rights reserved.

关键词： machine learning

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analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge

arXiv

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arXiv 2024年

作者： LaBella, Dominic Baid, Ujjwal Khanna, Omaditya McBurney-Lin, Shan McLean, Ryan Nedelec, Pierre Rashid, Arif Tahon, Nourel Hoda Altes, Talissa Bhalerao, Radhika Dhemesh, Yaseen Godfrey, Devon Hilal, Fathi Floyd, Scott Janas, Anastasia Kazerooni, Anahita Fathi Kirkpatrick, John Kent, Collin Kofler, Florian Leu, Kevin Maleki, Nazanin Menze, Bjoern Pajot, Maxence Reitman, Zachary J. Rudie, Jeffrey D. Saluja, Rachit Velichko, Yury Wang, Chunhao Warman, Pranav Adewole, Maruf Albrecht, Jake Anazodo, Udunna Anwar, Syed Muhammad Bergquist, Timothy Chen, Sully Francis Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Khalili, Nastaran Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Liu, Xinyang Mahtabfar, Aria Meier, Zeke Moawad, Ahmed W. Mongan, John Piraud, Marie Shinohara, Russell Takeshi Wiggins, Walter F. Abayazeed, Aly H. Akinola, Rachel Jakab, András Bilello, Michel de Verdier, Maria Correia Crivellaro, Priscila Davatzikos, Christos Farahani, Keyvan Freymann, John Hess, Christopher Huang, Raymond Lohmann, Philipp Moassefi, Mana Pease, Matthew W. Vollmuth, Phillipp Sollmann, Nico Diffley, David Nandolia, Khanak K. Warren, Daniel I. Hussain, Ali Fehringer, Pascal Bronstein, Yulia Deptula, Lisa Stein, Evan G. Taherzadeh, Mahsa de Oliveira, Eduardo Portela Haughey, Aoife Kontzialis, Marinos Saba, Luca Turner, Benjamin Brüßeler, Melanie M.T. Ansari, Shehbaz Gkampenis, Athanasios Weiss, David Maximilian Mansour, Aya Shawali, Islam H. Yordanov, Nikolay Stein, Joel M. Hourani, Roula Moshebah, Mohammed Yahya Abouelatta, Ahmed Magdy Rizvi, Tanvir Willms, Klara Martin, Dann C. Okar, Abdullah D'Anna, Gennaro Taha, Ahmed Sharifi, Yasaman Faghani, Shahriar Kite, Dominic Pinho, Marco Haider, Muhammad Ammar Aristizabal, Alejandro Karargyris, Alexandros Kassem, Hasan Pati, Sarthak Sheller, Micah Alonso-Basanta, Michelle Villanueva-Meyer, Javier Rauschecker, Andreas M. Nada, Ayman Aboian, Mariam Flanders, Adam E. Wiestler, Benedikt Bakas, Spyridon Ca Duke University Medical Center Department of Radiation Oncology DurhamNC United States Division of Computational Pathology Department of Pathology Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Center for Federated Learning in Medicine Indiana University IndianapolisIN United States Department of Neurosurgery Thomas Jefferson University PhiladelphiaPA United States University of California San FranciscoCA United States Yale University New HavenCT United States Department of Radiation Oncology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States University of Missouri ColumbiaMO United States Department of Biostatistics and Health Data Science Indiana University School of Medicine IndianapolisIN United States Children's Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Helmholtz AI Helmholtz Munich Germany Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum rechts der Isar Technical University of Munich Germany San FranciscoCA United States Biomedical Image Analysis and Machine Learning Department of Quantitative Biomedicine University of Zurich Switzerland Department of Neuroradiology Technical University of Munich Munich Germany University of San Diego CA United States Cornell University IthacaNY United States Department of Radiology Northwestern University EvanstonIL United States Duke University Medical Center School of Medicine DurhamNC United States Lab Crestview Radiology Lagos Nigeria Sage Bionetworks United States McGill University MontrealQC Canada Children's National Hospital WashingtonDC United States George Washington University WashingtonDC United State

We describe the design and results from the BraTS 2023 Intracranial Meningioma Segmentation Challenge. The BraTS Meningioma Challenge differed from prior BraTS Glioma challenges in that it focused on meningiomas, which are typically benign extra-axial tumors with diverse radiologic and anatomical presentation and a propensity for multiplicity. Nine participating teams each developed deep-learning automated segmentation models using image data from the largest multi-institutional systematically expert annotated multilabel multi-sequence meningioma MRI dataset to date, which included 1000 training set cases, 141 validation set cases, and 283 hidden test set cases. Each case included T2, T2/FLAIR, T1, and T1Gd brain MRI sequences with associated tumor compartment labels delineating enhancing tumor, non-enhancing tumor, and surrounding non-enhancing T2/FLAIR hyperintensity. Participant automated segmentation models were evaluated and ranked based on a scoring system evaluating lesion-wise metrics including dice similarity coefficient (DSC) and 95% Hausdorff Distance. The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0.976, 0.976, and 0.964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0.899, 0.904, and 0.871, respectively. These results serve as state-of-the-art benchmarks for future pre-operative meningioma automated segmentation algorithms. Additionally, we found that 1286 of 1424 cases (90.3%) had at least 1 compartment voxel abutting the edge of the skull-stripped image edge, which requires further investigation into optimal pre-processing face anonymization steps. © 2024, CC BY.

关键词： Tumors

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TEMPLATES: Characterization of a Merger in the Dusty Lensing SPT0418-47 System

arXiv

引用

arXiv 2023年

作者： Cathey, Jared Gonzalez, Anthony H. Lower, Sidney Phadke, Kedar A. Spilker, Justin Aravena, Manuel Bayliss, Matthew Birkin, Jack E. Birrer, Simon Chapman, Scott Dahle, Håkon Hayward, Christopher C. Hezaveh, Yashar Hill, Ryley Hutchison, Taylor A. Kim, Keunho J. Mahler, Guillaume Marrone, Daniel P. Narayanan, Desika Navarre, Alexander Reuter, Cassie Rigby, Jane R. Sharon, Keren Solimano, Manuel Sulzenauer, Nikolaus Vieira, Joaquin Vizgan, David Department of Astronomy University of Florida 211 Bryant Space Sciences Center GainesvilleFL32611 United States Department of Astronomy University of Illinois 1002 West Green St. UrbanaIL61801 United States Center for AstroPhysical Surveys National Center for Supercomputing Applications 1205 West Clark Street UrbanaIL61801 United States Department of Physics and Astronomy George P. and Cynthia Woods Mitchell Institute for Fundamental Physics and Astronomy Texas A&M University 4242 TAMU College StationTX77843-4242 United States Núcleo de Astronomía Facultad de Ingeniería y Ciencias Universidad Diego Portales Av. Ejercito 441 Santiago Chile Department of Physics University of Cincinnati CincinnatiOH45221 United States Department of Physics and Astronomy Stony Brook University Stony BrookNY11794 United States Department of Physics and Atmospheric Science Dalhousie University HalifaxNSB3H 4R2 Canada NRC Herzberg Astronomy and Astrophysics 5071 West Saanich Rd VictoriaBCV9E 2E7 Canada Department of Physics and Astronomy University of British Columbia VancouverBCV6T1Z1 Canada Eureka Scientific Inc OaklandCA94602 United States Institute of Theoretical Astrophysics University of Oslo P.O. Box 1029 Blindern OsloNO-0315 Norway Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Physics Université de Montréal Montréal Canada Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning Montréal Canada Mila - Quebec Artificial Intelligence Institute Montréal Canada Observational Cosmology Lab NASA Goddard Space Flight Center Code 665 8800 Greenbelt Rd. GreenbeltMD20771 United States Centre for Extragalactic Astronomy Durham University South Road DurhamDH1 3LE United Kingdom Institute for Computational Cosmology Durham University South Road DurhamDH1 3LE United Kingdom Steward Observatory University of Arizona 933 North Cherry Avenue TucsonAZ85721

We present JWST and ALMA results for the lensing system SPT0418−47, which includes a strongly-lensed, dusty star-forming galaxy at redshift z = 4.225 and an associated multiply-imaged companion. JWST NIRCam and MIRI imaging observations presented in this paper were acquired as part of the Early Release Science program Targeting Extremely Magnified Panchromatic Lensed Arcs and Their Extended Star Formation (TEMPLATES). This data set provides robust, mutiwavelength detection of stellar light in both the main (SPT0418A) and companion (SPT0418B) galaxies, while the ALMA detection of [C II] emission confirms that SPT0418B lies at the same redshift as SPT0418A. From a source plane reconstruction, we infer that the projected physical separation of the two galaxies is 4.42 ±0.05 kpc. We derive total magnifications of µ = 29.5 ±1.2 and µ = 4.2 ±0.9 for SPT0418A and SPT0418B, respectively. We use both cigale and prospector to derive stellar masses. The stellar mass ratio of SPT0418A and SPT0418B is approximately 4 to 1 (4.5 ± 1.0 for cigale and 4.2+1.9−1.6 for prospector). We also see evidence of extended structure associated with SPT0418A in the lensing reconstruction that is suggestive of a tidal feature. Interestingly, the star formation rates and stellar masses of both galaxies are consistent with the main sequence of star-forming galaxies at this epoch, indicating that this ongoing interaction has not noticeably elevated the star formation levels. © 2023, CC BY.

关键词： Galaxies

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Multi-phase black-hole feedback and a bright [CII] halo in a Lo-BAL quasar at z ∼ 6.6

arXiv

引用

arXiv 2024年

作者： Bischetti, Manuela Choi, Hyunseop Fiore, Fabrizio Feruglio, Chiara Carniani, Stefano D’Odorico, Valentina Bañados, Eduardo Chen, Huanqing Decarli, Roberto Gallerani, Simona Hlavacek-Larrondo, Julie Lai, Samuel Leighly, Karen M. Mazzucchelli, Chiara Perreault-Levasseur, Laurence Tripodi, Roberta Walter, Fabian Wang, Feige Yang, Jinyi Zanchettin, Maria Vittoria Zhu, Yongda Dipartimento di Fisica Universitá di Trieste Sezione di Astronomia Via G.B. Tiepolo 11 TriesteI-34131 Italy INAF - Osservatorio Astronomico di Trieste Via G. B. Tiepolo 11 TriesteI–34131 Italy Département de Physique Université de Montréal Succ. Centre-Ville MontréalQCH3C 3J7 Canada Mila - Quebec Artificial Intelligence Institute MontréalQC Canada IFPU - Institut for fundamental physics of the Universe Via Beirut 2 Trieste34014 Italy Scuola Normale Superiore Piazza dei Cavalieri 7 PisaI-56126 Italy Max Planck Institut für Astronomie Königstuhl 17 HeidelbergD-69117 Germany Canadian Institute for Theoretical Astrophysics University of Toronto 60 St George St TorontoONM5R 2M8 Canada INAF - Osservatorio di Astrofisica e Scienza dello Spazio di Bologna via Gobetti 93/3 BolognaI-40129 Italy Research School of Astronomy and Astrophysics Australian National University CanberraACT2611 Australia Homer L. Dodge Department of Physics and Astronomy The University of Oklahoma 440 W. Brooks St. NormanOK73019 United States Núcleo de Astronomía de la Facultad de Ingeniería Universidad Diego Portales Av. Ejército Libertador 441 Santiago Chile Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning Montréal Canada Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States University of Ljubljana FMF Jadranska 19 1000 Slovenia Steward Observatory University of Arizona 933 N Cherry Avenue TucsonAZ85721 United States SISSA Via Bonomea 265 Trieste34136 Italy Department of Physics & Astronomy University of California RiversideCA92521 United States

Although the mass growth of supermassive black holes during the Epoch of Reionisation is expected to play a role in shaping the concurrent growth of their host-galaxies, observational evidence of feedback at z6 is still sparse. We perform the first multi-scale and multi-phase characterisation of black-hole driven outflows in the z ∼ 6.6 quasar J0923+0402 and assess how these winds impact the cold gas reservoir. We employ the SimBAL spectral synthesis to fit broad absorption line (BAL) features and find a powerful ionized outflow on 210 pc scale, with a kinetic power ∼ 2 − 100% of the quasar luminosity. ALMA observations of [CII] emission allow us to study the morphology and kinematics of the cold gas. We detect high-velocity [CII] emission, likely associated with a cold neutral outflow at ∼ 0.5−2 kpc scale in the host-galaxy, and a bright extended [CII] halo with a size of ∼ 15 kpc. For the first time at such an early epoch, we accurately constrain the outflow energetics in both the ionized and the atomic neutral gas phases. We find such energetics to be consistent with expectations for an efficient feedback mechanism, and both ejective and preventative feedback modes are likely at play. The scales and energetics of the ionized and atomic outflows suggest that they might be associated with different quasar accretion episodes. The results of this work indicate that strong black hole feedback is occurring in quasars at z 6 and is likely responsible for shaping the properties of the cold gas reservoir up to circum-galactic scales. © 2024, CC BY.

关键词： Galaxies

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