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ENIGMA-Meditation: Worldwide Consortium for Neuroscientific Investigations of Meditation Practices

Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 2025年第4期10卷 425-436页

作者： Ganesan, Saampras Barrios, Fernando A. Batta, Ishaan Bauer, Clemens C.C. Braver, Todd S. Brewer, Judson A. Brown, Kirk Warren Cahn, Rael Cain, Joshua A. Calhoun, Vince D. Cao, Lei Chetelat, Gaël Ching, Christopher R.K. Creswell, J. David Dagnino, Paulina Clara Davanger, Svend Davidson, Richard J. Deco, Gustavo Dutcher, Janine M. Escrichs, Anira Eyler, Lisa T. Fani, Negar Farb, Norman A.S. Fialoke, Suruchi Fresco, David M. Garg, Rahul Garland, Eric L. Goldin, Philippe Hafeman, Danella M. Jahanshad, Neda Kang, Yoona Khalsa, Sahib S. Kirlic, Namik Lazar, Sara W. Lutz, Antoine McDermott, Timothy J. Pagnoni, Giuseppe Piguet, Camille Prakash, Ruchika S. Rahrig, Hadley Reggente, Nicco Saccaro, Luigi F. Sacchet, Matthew D. Siegle, Greg J. Tang, Yi-Yuan Thomopoulos, Sophia I. Thompson, Paul M. Torske, Alyssa Treves, Isaac N. Tripathi, Vaibhav Tsuchiyagaito, Aki Turner, Matthew D. Vago, David R. Valk, Sofie Zeidan, Fadel Zalesky, Andrew Turner, Jessica A. King, Anthony P. Department of Biomedical Engineering The University of Melbourne Carlton VIC Australia Contemplative Studies Centre Melbourne School of Psychological Sciences The University of Melbourne Melbourne VIC Australia Systems Lab of Neuroscience Neuropsychiatry and Neuroengineering The University of Melbourne Parkville VIC Australia Universidad Nacional Autónoma de México Instituto de Neurobiolgía México Querétaro Mexico Center for Translational Research in Neuroimaging and Data Science: Georgia State University Georgia Institute of Technology and Emory University Atlanta GA United States Department of Psychology Northeastern University Boston Massachusetts Brain and Cognitive Science McGovern Institute for Brain Research Massachusetts Institute of Technology Cambridge Massachusetts Department of Psychological and Brain Sciences Washington University St. Louis Missouri Department of Behavioral and Social Sciences Brown University School of Public Health Providence Rhode Island Department of Psychology Carnegie Mellon University Pittsburgh PA United States University of Southern California Department of Psychiatry & Behavioral Sciences Los Angeles California University of Southern California Center for Mindfulness Science Los Angeles California Institute for Advanced Consciousness Studies Santa Monica California Department of Psychiatry and Behavioral Health The Ohio State University College of Medicine Columbus OH United States Normandie University Université de Caen Normandie INSERM U1237 Neuropresage Team Cyceron Caen France Imaging Genetics Center Mark and Mary Stevens Neuroimaging and Informatics Institute Keck School of Medicine of the University of Southern California Los Angeles California Desert-Pacific Mental Illness Research Education and Clinical Center VA San Diego Healthcare System San Diego California Computational Neuroscience Group Center for Brain and Cognition Department of Information and Communication Technologies Universitat Pompeu Fa

Meditation is a family of ancient and contemporary contemplative mind-body practices that can modulate psychological processes, awareness, and mental states. Over the last 40 years, clinical science has manualized meditation practices and designed various meditation interventions that have shown therapeutic efficacy for disorders including depression, pain, addiction, and anxiety. Over the past decade, neuroimaging has been used to examine the neuroscientific basis of meditation practices, effects, states, and outcomes for clinical and nonclinical populations. However, the generalizability and replicability of current neuroscientific models of meditation have not yet been established, because they are largely based on small datasets entrenched with heterogeneity along several domains of meditation (e.g., practice types, meditation experience, clinical disorder targeted), experimental design, and neuroimaging methods (e.g., preprocessing, analysis, task-based, resting-state, structural magnetic resonance imaging). These limitations have precluded a nuanced and rigorous neuroscientific phenotyping of meditation practices and their potential benefits. Here, we present ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis)–Meditation, the first worldwide collaborative consortium for neuroscientific investigations of meditation practices. ENIGMA-Meditation will enable systematic meta- and mega-analyses of globally distributed neuroimaging datasets of meditation using shared, standardized neuroimaging methods and tools to improve statistical power and generalizability. Through this powerful collaborative framework, existing neuroscientific accounts of meditation practices can be extended to generate novel and rigorous neuroscientific insights that account for multidomain heterogeneity. ENIGMA-Meditation will inform neuroscientific mechanisms that underlie therapeutic action of meditation practices on psychological and cognitive attributes, thereby advancing the f

关键词： Consortium ENIGMA Magnetic resonance imaging (MRI) Meditation Mindfulness Neuroimaging

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Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

arXiv

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arXiv 2023年

作者： Yang, Kaiyuan Musio, Fabio Ma, Yihui Juchler, Norman Paetzold, Johannes C. Al-Maskari, Rami Höher, Luciano Li, Hongwei Bran Hamamci, Ibrahim Ethem Sekuboyina, Anjany Shit, Suprosanna Huang, Houjing Prabhakar, Chinmay de la Rosa, Ezequiel Waldmannstetter, Diana Kofler, Florian Navarro, Fernando Menten, Martin Ezhov, Ivan Rueckert, Daniel Vos, Iris Ruigrok, Ynte Velthuis, Birgitta Kuijf, Hugo Hämmerli, Julien Wurster, Catherine Bijlenga, Philippe Westphal, Laura Bisschop, Jeroen Colombo, Elisa Baazaoui, Hakim Makmur, Andrew Hallinan, James Wiestler, Bene Kirschke, Jan S. Wiest, Roland Montagnon, Emmanuel Letourneau-Guillon, Laurent Galdran, Adrian Galati, Francesco Falcetta, Daniele Zuluaga, Maria A. Lin, Chaolong Zhao, Haoran Zhang, Zehan Ra, Sinyoung Hwang, Jongyun Park, Hyunjin Chen, Junqiang Wodzinski, Marek Müller, Henning Shi, Pengcheng Liu, Wei Ma, Ting Yalçin, Cansu Hamadache, Rachika E. Salvi, Joaquim Llado, Xavier Estrada, Uma Maria Lal-Trehan Abramova, Valeriia Giancardo, Luca Oliver, Arnau Liu, Jialu Huang, Haibin Cui, Yue Lin, Zehang Liu, Yusheng Zhu, Shunzhi Patel, Tatsat R. Tutino, Vincent M. Orouskhani, Maysam Wang, Huayu Mossa-Basha, Mahmud Zhu, Chengcheng Rokuss, Maximilian R. Kirchhoff, Yannick Disch, Nico Holzschuh, Julius Isensee, Fabian Maier-Hein, Klaus Sato, Yuki Hirsch, Sven Wegener, Susanne Menze, Bjoern Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Center for Computational Health Zurich University of Applied Sciences Zurich Switzerland Department of Neuroradiology University Hospital of Zurich Zurich Switzerland Department of Neurosurgery Zhongnan Hospital of Wuhan University Wuhan China Department of Computing Imperial College London London United Kingdom Helmholtz Center Munich Germany Athinoula A. Martinos Center for Biomedical Imaging Harvard Medical School Boston United States School of Medicine Technical University of Munich Munich Germany Department of Informatics Technical University of Munich Munich Germany Helmholtz AI Helmholtz Munich Munich Germany Image Sciences Institute UMC Utrecht Utrecht Netherlands Department of Neurology UMC Utrecht Utrecht Netherlands Department of Radiology UMC Utrecht Utrecht Netherlands Department of Clinical Neurosciences Division of Neurosurgery Geneva University Hospitals Geneva Switzerland Department of Neurology University Hospital of Zurich Zurich Switzerland Department of Physiology University of Toronto Toronto Canada Department of Neurosurgery University Hospital of Zurich Zurich Switzerland Department of Diagnostic Imaging National University Hospital Singapore Department of Diagnostic and Interventional Neuroradiology University Hospital Berne University of Berne Berne Switzerland Montreal Canada Universitat Pompeu Fabra Barcelona Spain EURECOM Biot France Institute of Medical Technology Peking University Health Science Center Beijing China Hangzhou Genlight Medtech Co. Ltd. Hangzhou China Department of Artificial Intelligence Sungkyunkwan University Seoul Korea Republic of Department of Electrical and Computer Engineering Sungkyunkwan University Seoul Korea Republic of Shanghai MediWorks Precision Instruments Co. Ltd. Shanghai China Institute of Informatics HES-SO Valais-Wallis Switzerland Department of Measurement and Electronics AGH University

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited public datasets with annotations on CoW anatomy, especially for CTA. Therefore we organized the TopCoW Challenge in 2023 with the release of an annotated CoW dataset. The TopCoW dataset was the first public dataset with voxel-level annotations for thirteen possible CoW vessel components, enabled by virtual-reality (VR) technology. It was also the first large dataset with paired MRA and CTA from the same patients. TopCoW challenge formalized the CoW characterization problem as a multiclass anatomical segmentation task with an emphasis on topological metrics. We invited submissions worldwide for the CoW segmentation task, which attracted over 140 registered participants from four continents. The top performing teams managed to segment many CoW components to Dice scores around 90%, but with lower scores for communicating arteries and rare variants. There were also topological mistakes for predictions with high Dice scores. Additional topological analysis revealed further areas for improvement in detecting certain CoW components and matching CoW variant topology accurately. TopCoW represented a first attempt at benchmarking the CoW anatomical segmentation task for MRA and CTA, both morphologically and topologically. © 2023, CC BY-NC-ND.

关键词： Large datasets

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Understanding metric-related pitfalls in image analysis validation

arXiv

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arXiv 2023年

作者： Reinke, Annika Tizabi, Minu D. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Kavur, A. Emre Rädsch, Tim Sudre, Carole H. Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Buettner, Florian Cardoso, M. Jorge Cheplygina, Veronika Chen, Jianxu Christodoulou, Evangelia Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian van Ginneken, Bram Glocker, Ben Godau, Patrick Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Isensee, Fabian Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kleesiek, Jens Kofler, Florian Kooi, Thijs Kopp-Schneider, Annette Kozubek, Michal Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rafelski, Susanne M. Rajpoot, Nasir Reyes, Mauricio Riegler, Michael A. Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. van Calster, Ben Varoquaux, Gaël Yaniv, Ziv R. Jäger, Paul F. Maier-Hein, Lena Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany NCT Heidelberg A Partnership Between DKFZ University Medical Center Heidelberg Germany Heidelberg Division of Medical Image Computing Germany Heidelberg Division of Intelligent Medical Systems Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montreal Canada Division of Computational Pathology Dept of Pathology & Laboratory Medicine Indiana University School of Medicine IU Health Information and Translational Sciences Building Indianapolis United States University of Pennsylvania Richards Medical Research Laboratories FL7 PhiladelphiaPA United States Department of Digital Medical Technologies Holon Institute of Technology Holon Israel European Federation for Medical Informatics Le Mont-sur-Lausanne Switzerland Center for Processing Speech and Images Department of Electrical Engineering KU Leuven Leuven Belgium partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt Marburg Germany Heidelberg Germany Goethe University Frankfurt Department of Medicine Germany Goethe University Frankfurt Department of Informatics Germany and Frankfurt Cancer Insititute Germany Department of Computer Science IT University of Copenhagen Copenhagen Denmark Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Dortmund Germany Imaging Platform Broad Institute of MIT and Harvard CambridgeMA United States Centre for Statistics in Medicine University of Oxford Oxford United Kingdom Center for Biomedical In

Validation metrics are key for tracking scientific progress and bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately. While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. While focused on biomedical image analysis, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. The work serves to enhance global comprehension of a key topic in image analysis validation. © 2023, CC BY.

关键词： computer vision

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Real-world occurrence, therapy, and outcome of patients with class 2 or 3 BRAF compared with class 1 BRAF-mutated cancers

ESMO Real World Data and Digital Oncology

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ESMO Real World Data and Digital Oncology 2024年 6卷 100075-100075页

作者： Pradervand, S. Freundler, N. Gosztonyi, B. Roncoroni, L. Achermann, R. Schwenk, T. de Fraipont, G. Garessus, J. Haefliger, S. Leichtle, A.B. Kiessling, M.K. Mueller-Focke, T. Krebs, F.S. Zoete, V. Tsantoulis, P. Michielin, O. Britschgi, C. Wicki, A. Centre Hospitalier Universitaire Vaudois – CHUV Department of Oncology Lausanne Department of Medical Oncology and Hematology University Hospital Zurich University of Zurich Department of Medical Informatics Universitätsspital Basel – USB Basel Oncology Hematology and Transfusion Medicine Kantonsspital Aarau Aarau Geneva University Hospitals – HUG Geneva Department of Medical Oncology Inselspital Bern University Hospital University of Bern Department of Clinical Chemistry Inselspital – Bern University Hospital and Center for Artificial Intelligence University of Bern Bern Computer-Aided Molecular Engineering Group Department of Oncology UNIL-CHUV Ludwig Institute for Cancer Research Lausanne Lausanne Molecular Modelling Group Swiss Institute of Bioinformatics Lausanne Swiss Group for Clinical Cancer Research (SAKK) Bern Switzerland

BackgroundBRAF V600 mutations are the epitome of targeted therapy. However, not much is known about non-V600 mutations. Using the new data infrastructure of the Swiss Personalized Oncology project of the Swiss Personalized Health Network (SPHN), we evaluated the fate of patients with cancer with non-V600 BRAF mutations in comparison to patients with class 1 mutations. Patients and methodsIn this retrospective observational multicenter study, we have assembled a cohort of 392 patients with class 1 and 154 patients with nonclass 1 BRAF mutations (76 colorectal cancers, 96 lung cancers, 297 melanomas, and 77 other cancers). We carried out outcome analyses between mutational classes and therapeutic subgroups. ResultsOverall survival (OS) did not differ significantly between patients with class 1 and nonclass 1 mutations. Upon treatment with BRAF/MEK inhibitors, patients with class 1 mutant melanoma showed numerically longer progression-free survival (PFS; 217 days) than patients with nonclass 1 mutant disease (73 days). Overall, in patients with class 2 or 3 mutations, BRAF and MEK inhibitors showed no benefit over other systemic therapies. However, specific class 2 mutations such as K601E may confer sensitivity to BRAF/MEK inhibitors, with two out of five patients achieving a PFS >400 days. ConclusionsThe diversity of BRAF mutations presents significant treatment challenges. Despite similar OS, nonclass 1 mutant tumors showed a trend toward lower PFS with BRAF/MEK blockade. Selected class 2 mutations may confer sensitivity to BRAF/MEK inhibitors. This highlights the rationale for a mutation, rather than class-specific, clinical approach against nonclass 1 BRAF-mutant tumors.

关键词： BRAF mutations precision oncology personalized treatment Swiss Personalized Health Network (SPHN)

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OncoReg: Medical Image Registration for Oncological Challenges

arXiv

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arXiv 2025年

作者： Heyer, Wiebke Elser, Yannic Berkel, Lennart Song, Xinrui Xu, Xuanang Yan, Pingkun Jia, Xi Duan, Jinming Li, Zi Mok, Tony C.W. Li, BoWen Staackmann, Christian Großbröhmer, Christoph Hansen, Lasse Hering, Alessa Sieren, Malte M. Heinrich, Mattias P. Institute of Medical Informatics University of Lübeck Lübeck Germany Institute of Radiology and Nuclear Medicine University Hospital Schleswig-Holstein Lübeck Germany Department of Biomedical Engineering Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute TroyNY United States School of Computer Science University of Birmingham Birmingham United Kingdom Division of Informatics Imaging and Data Sciences University of Manchester United Kingdom DAMO Academy Alibaba Group Hangzhou China Hangzhou Shengshi Technology Co. Ltd Hangzhou China Department of Radiation Oncology University Hospital Schleswig-Holstein Lübeck Germany EchoScout GmbH Lübeck Germany Radboud University Medical Center Nijmegen Netherlands Institute of Radiology and Nuclear Medicine Institute of Interventional Radiology University Hospital Schleswig-Holstein Lübeck Germany

In modern cancer research, the vast volume of medical data generated is often underutilised due to challenges related to patient privacy. The OncoReg Challenge addresses this issue by enabling researchers to develop and validate image registration methods through a two-phase framework that ensures patient privacy while fostering the development of more generalisable AI models. Phase one involves working with a publicly available dataset, while phase two focuses on training models on a private dataset within secure hospital networks. OncoReg builds upon the foundation established by the Learn2Reg Challenge by incorporating the registration of interventional cone-beam computed tomography (CBCT) with standard planning fan-beam CT (FBCT) images in radiotherapy. Accurate image registration is crucial in oncology, particularly for dynamic treatment adjustments in image-guided radiotherapy, where precise alignment is necessary to minimise radiation exposure to healthy tissues while effectively targeting tumours. This work details the methodology and data behind the OncoReg Challenge and provides a comprehensive analysis of the competition entries and results. Findings reveal that feature extraction plays a pivotal role in this registration task. A new method emerging from this challenge demonstrated its versatility, while established approaches continue to perform comparably to newer techniques. Both deep learning and classical approaches still play significant roles in image registration, with the combination of methods—particularly in feature extraction—proving most effective. © 2025, CC BY.

关键词： Deep learning

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Why is the winner the best?

arXiv

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arXiv 2023年

作者： Eisenmann, M. Reinke, A. Weru, V. Tizabi, M.D. Isensee, F. Adler, T.J. Ali, S. Andrearczyk, V. Aubreville, M. Baid, U. Bakas, S. Balu, N. Bano, S. Bernal, J. Bodenstedt, S. Casella, A. Cheplygina, V. Daum, M. de Bruijne, M. Depeursinge, A. Dorent, R. Egger, J. Ellis, D.G. Engelhardt, S. Ganz, M. Ghatwary, N. Girard, G. Godau, P. Gupta, A. Hansen, L. Harada, K. Heinrich, M. Heller, N. Hering, A. Huaulmé, A. Jannin, P. Kavur, A.E. Kodym, O. Kozubek, M. Li, J. Li, H. Ma, J. Martín-Isla, C. Menze, B. Noble, A. Oreiller, V. Padoy, N. Pati, S. Payette, K. Rädsch, T. Rafael-Patiño, J. Bawa, V. Singh Speidel, S. Sudre, C.H. van Wijnen, K. Wagner, M. Wei, D. Yamlahi, A. Yap, M.H. Yuan, C. Zenk, M. Zia, A. Zimmerer, D. Aydogan, D. Bhattarai, B. Bloch, L. Brüngel, R. Cho, J. Choi, C. Dou, Q. Ezhov, I. Friedrich, C.M. Fuller, C. Gaire, R.R. Galdran, A. Faura, Á. García Grammatikopoulou, M. Hong, S. Jahanifar, M. Jang, I. Kadkhodamohammadi, A. Kang, I. Kofler, F. Kondo, S. Kuijf, H. Li, M. Luu, M. Martinčič, T. Morais, P. Naser, M.A. Oliveira, B. Owen, D. Pang, S. Park, J. Park, S. Plotka, S. Puybareau, E. Rajpoot, N. Ryu, K. Saeed, N. Shephard, A. Shi, P. Štepec, D. Subedi, R. Tochon, G. Torres, H.R. Urien, H. Vilaça, J.L. Wahid, K.A. Wang, H. Wang, J. Wang, L. Wang, X. Wiestler, B. Wodzinski, M. Xia, F. Xie, J. Xiong, Z. Yang, S. Yang, Y. Zhao, Z. Maier-Hein, K. Jäger, P.F. Kopp-Schneider, A. Maier-Hein, L. Heidelberg Germany Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Germany Heidelberg Germany School of Computing Faculty of Engineering and Physical Sciences University of Leeds Leeds United Kingdom 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 University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington SeattleWA United States Department of Computer Science University College London London United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Biomedical Imaging Group Rotterdam Department of Radiology and Nuclear Medicine Erasmus MC Rotterdam Netherlands Department of Computer Science University of Copenhagen Copenhagen Denmark Sierre Switzerland Harvard Medical School Brigham and Women’s Hospital BostonMA United States School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Essen Germany University of Nebraska Medical Center OmahaNE United States Department of Internal Medicine III Heidelberg University Hospital Heidelberg Germany Neurobiology Research Unit Copenhagen University Hospital Rigshospitalet C

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 postprocessing (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. © 2023, CC BY.

关键词： Benchmarking

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BraTS-Path Challenge: Assessing Heterogeneous Histopathologic Brain Tumor Sub-regions

arXiv

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arXiv 2024年

作者： Bakas, Spyridon Thakur, Siddhesh P. Faghani, Shahriar Moassefi, Mana Baid, Ujjwal Chung, Verena Pati, Sarthak Innani, Shubham Baheti, Bhakti Albrecht, Jake Karargyris, Alexandros Kassem, Hasan Nasrallah, MacLean P. Ahrendsen, Jared T. Barresi, Valeria Gubbiotti, Maria A. Lpez, Giselle Y. Lucas, Calixto-Hope G. Miller, Michael L. Cooper, Lee A.D. Huse, Jason T. Bell, William R. Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Neurological Surgery Indiana University School of Medicine IndianapolisIN United States Department of Radiology and Imaging Sciences Indiana University School of Medicine IndianapolisIN United States Department of Biostatistics and Health Data Science Indiana University School of Medicine IndianapolisIN United States Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IndianapolisIN United States Medical Research Group MLCommons San FranciscoCA United States Department of Radiology Mayo Clinic MN United States Sage Bionetworks United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology Feinberg School of Medicine Northwestern University ChicagoIL United States Department of Diagnostics and Public Health University of Verona Verona Italy Division of Pathology and Laboratory Medicine Department of Anatomical Pathology University of Texas MD Anderson Cancer Center TX United States The Preston Robert Tisch Brain Tumor Center at Duke DurhamNC United States Department of Pathology Duke University School of Medicine DurhamNC United States Department of Neurosurgery Duke University Medical School DurhamNC United States Division of Neuropathology Department of Pathology Johns Hopkins University School of Medicine BaltimoreMD United States Department of Pathology and Cell Biology Columbia University Irving Medical Center New YorkNY United States Department of Translational Molecular Pathology University of Texas MD Anderson Cancer Center TX United States

Glioblastoma is the most common primary adult brain tumor, with a grim prognosis - median survival of 12-18 months following treatment, and 4 months otherwise. Glioblastoma is widely infiltrative in the cerebral hemispheres and well-defined by heterogeneous molecular and micro-environmental histopathologic profiles, which pose a major obstacle in treatment. Correctly diagnosing these tumors and assessing their heterogeneity is crucial for choosing the precise treatment and potentially enhancing patient survival rates. In the gold-standard histopathology-based approach to tumor diagnosis, detecting various morpho-pathological features of distinct histology throughout digitized tissue sections is crucial. Such "features" include the presence of cellular tumor, geographic necrosis, pseudopalisading necrosis, areas abundant in microvascular proliferation, infiltration into the cortex, wide extension in subcortical white matter, leptomeningeal infiltration, regions dense with macrophages, and the presence of perivascular or scattered lymphocytes. With these features in mind and building upon the main aim of the BraTS Cluster of Challenges https://***/brats2024, the goal of the BraTS-Path challenge is to provide a systematically prepared comprehensive dataset and a benchmarking environment to develop and fairly compare deep-learning models capable of identifying tumor sub-regions of distinct histologic profile. These models aim to further our understanding of the disease and assist in the diagnosis and grading of conditions in a consistent manner. © 2024, CC BY.

关键词： Tumors

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Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII

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Database 2023年第2023期2023卷 baad005-baad005页

作者： Leaman, Robert Islamaj, Rezarta Adams, Virginia Alliheedi, Mohammed A. Almeida, João Rafael Antunes, Rui Bevan, Robert Chang, Yung-Chun Erdengasileng, Arslan Hodgskiss, Matthew Ida, Ryuki Kim, Hyunjae Li, Keqiao Mercer, Robert E. Mertová, Lukrécia Mobasher, Ghadeer Shin, Hoo-Chang Sung, Mujeen Tsujimura, Tomoki Yeh, Wen-Chao Lu, Zhiyong National Center for Biotechnology Information (NCBI) National Library of Medicine National Institutes of Health 8600 Rockville Pike Bethesda 20894 MD United States Nvidia 2788 San Tomas Expressway Santa Clara 95051 CA United States Department of Computer Science Al Baha University 4781 King Fahd Rd Al Aqiq 65779 Saudi Arabia Department of Electronics Telecommunications and Informatics (DETI) Institute of Electronics and Informatics Engineering of Aveiro (IEETA) University of Aveiro Campus Universitário de Santiago Aveiro 3810-193 Portugal Department of Information and Communications Technologies University of A Coruña Camiño Do Lagar de Castro A Coruña 15008 Spain Informatics Department Medicines Discovery Catapult Alderley Park Block 35 Mereside Macclesfield SK10 4ZF United Kingdom Graduate Institute of Data Science Taipei Medical University No. 172-1 Section 2 Keelung Rd Da’an District Taipei City 106 Taiwan Department of Statistics Florida State University 117 N. Woodward Ave Tallahassee 32306 FL United States Computational Intelligence Laboratory Toyota Technological Institute 2-12-1 Hisakata Tempaku-ku Nagoya Aichi 468-8511 Japan Department of Computer Science and Engineering Korea University 145 Anam-ro Seongbuk-gu Seoul 02841 South Korea Department of Computer Science The University of Western Ontario Middlesex College Room 355 London N6A 5B7 ON Canada Scientific Databases and Visualization Group Heidelberg Institute for Theoretical Studies (HITS GGmbH) Schloss-Wolfsbrunnenweg 35 Heidelberg 69118 Germany Institute of Computer Science Heidelberg University Im Neuenheimer Feld 205 Heidelberg 69120 Germany Institute of Information Systems and Applications National Tsing Hua University No. 101 Section 2 Kuang-Fu Road Hsinchu 30013 Taiwan

The BioCreative National Library of Medicine (NLM)-Chem track calls for a community effort to fine-tune automated recognition of chemical names in the biomedical literature. Chemicals are one of the most searched biomedical entities in PubMed, and - as highlighted during the coronavirus disease 2019 pandemic - their identification may significantly advance research in multiple biomedical subfields. While previous community challenges focused on identifying chemical names mentioned in titles and abstracts, the full text contains valuable additional detail. We, therefore, organized the BioCreative NLM-Chem track as a community effort to address automated chemical entity recognition in full-text articles. The track consisted of two tasks: (i) chemical identification and (ii) chemical indexing. The chemical identification task required predicting all chemicals mentioned in recently published full-text articles, both span [i.e. named entity recognition (NER)] and normalization (i.e. entity linking), using Medical Subject Headings (MeSH). The chemical indexing task required identifying which chemicals reflect topics for each article and should therefore appear in the listing of MeSH terms for the document in the MEDLINE article indexing. This manuscript summarizes the BioCreative NLM-Chem track and post-challenge experiments. We received a total of 85 submissions from 17 teams worldwide. The highest performance achieved for the chemical identification task was 0.8672 F-score (0.8759 precision and 0.8587 recall) for strict NER performance and 0.8136 F-score (0.8621 precision and 0.7702 recall) for strict normalization performance. The highest performance achieved for the chemical indexing task was 0.6073 F-score (0.7417 precision and 0.5141 recall). This community challenge demonstrated that (i) the current substantial achievements in deep learning technologies can be utilized to improve automated prediction accuracy further and (ii) the chemical indexing task is substanti

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Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

arXiv

引用

arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

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Quantum speedup for track reconstruction in particle accelerators

引用

Physical Review D 2022年第7期105卷 076012-076012页

作者： D. Magano A. Kumar M. Kālis A. Locāns A. Glos S. Pratapsi G. Quinta M. Dimitrijevs A. Rivošs P. Bargassa J. Seixas A. Ambainis Y. Omar Physics of Information and Quantum Technologies Group Instituto de Telecomunicações Av. Rovisco Pais 1 1049-001 Lisboa Portugal Instituto Superior Técnico Universidade de Lisboa Av. Rovisco Pais 1 1049-001 Lisboa Portugal Department of Mathematics Clarkson University Potsdam New York 13699 USA Center for Quantum Computer Science Faculty of Computing University of Latvia Raiņa bulv. 19 R𝚤ga LV-1586 Latvia Institute of Theoretical and Applied Informatics Polish Academy of Sciences Bałtycka 5 44-100 Gliwice Poland Portuguese Quantum Institute Av. Rovisco Pais 1 1049-001 Lisboa Portugal Laboratório de Instrumentação e Física Experimental de Partículas Av. Pr. Gama Pinto 2 1649-003 Lisbon Portugal Center for Physics and Engineering of Advanced Materials Av. Rovisco Pais 1 1049-001 Lisbon Portugal

To investigate the fundamental nature of matter and its interactions, particles are accelerated to very high energies and collided inside detectors, producing a multitude of other particles that are scattered in all directions. As charged particles traverse the detector, they leave signals of their passage. The problem of track reconstruction is to recover the original trajectories from these signals. This challenging data analysis task will become even more demanding as the luminosity of future accelerators increases, leading to collision events with a more complex structure. We identify four fundamental routines present in every local tracking method and analyze how they scale in the context of a standard tracking algorithm. We show that for some of these routines we can reach a lower computational complexity with quantum search algorithms. Although the found quantum speedups are mild, this constitutes, to the best of our knowledge, the first rigorous evidence of a quantum advantage for a high-energy physics data processing task.

关键词： Quantum algorithms

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