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arXiv 2021年

作者： Wang, Qizhou Yao, Jiangchao Gong, Chen Liu, Tongliang Gong, Mingming Yang, Hongxia Han, Bo Department of Computer Science Hong Kong Baptist University Hong Kong Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of MoE School of Computer Science and Engineering Nanjing University of Science and Technology China Data Analytics and Intelligence Lab Alibaba Group China Department of Computing Hong Kong Polytechnic University Hong Kong Trustworthy Machine Learning Lab School of Computer Science University of Sydney Australia School of Mathematics and Statistics University of Melbourne Australia

machine learning in the context of noise is a challenging but practical setting to plenty of real-world applications. Most of the previous approaches in this area focus on the pairwise relation (casual or correlational relationship) with noise, such as learning with noisy labels. However, the group noise, which is parasitic on the coarse-grained accurate relation with the fine-grained uncertainty, is also universal and has not been well investigated. The challenge under this setting is how to discover true pairwise connections concealed by the group relation with its fine-grained noise. To overcome this issue, we propose a novel Max-Matching method for learning with group noise. Specifically, it utilizes a matching mechanism to evaluate the relation confidence of each object (cf. Figure 1) w.r.t. the target, meanwhile considering the Non-IID characteristics among objects in the group. Only the most confident object is considered to learn the model, so that the fine-grained noise is mostly dropped. The performance on a range of real-world datasets in the area of several learning paradigms demonstrates the effectiveness of Max-Matching. Copyright © 2021, The Authors. All rights reserved.

关键词： machine learning

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Hierarchical Bayesian approach for adaptive integration of Bragg peaks in time-of-flight neutron scattering data

arXiv

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arXiv 2024年

作者： Reshniak, Viktor Wang, Xiaoping Zhang, Guannan Liu, Siyan Yin, Junqi Data Analysis and Machine Learning Group Oak Ridge National Laboratory 1 Bethel Valley Rd Oak RidgeTN37830 United States Single Crystal Diffraction Oak Ridge National Laboratory 1 Bethel Valley Rd Oak RidgeTN37830 United States Computational Earth Sciences Group Oak Ridge National Laboratory 1 Bethel Valley Rd Oak RidgeTN37830 United States Analytics and AI Methods at Scale Oak Ridge National Laboratory 1 Bethel Valley Rd Oak RidgeTN37830 United States

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) operates in the event mode. Time-of-flight (TOF) information about each detected neutron is collected separately and saved as a descriptive entry in a database enabling unprecedented accuracy of the collected experimental data. Nevertheless, the common data processing pipeline still involves the binning of data to perform analysis and feature extraction. For weak reflections, improper binning leads to sparse histograms with low signal-to-noise ratios, rendering them uninformative. In this study, we propose the Bayesian approach for the identification of Bragg peaks in TOF diffraction data. The method is capable of adaptively handling the varying sampling rates found in different regions of the reciprocal space. Unlike histogram fitting methods, our approach focuses on estimating the true neutron flux function. We accomplish this by employing a profile fitting algorithm based on the event-level likelihood, along with a multiresolution histogram-level prior. By using this approach, we ensure that there is no loss of information due to data reduction in strong reflections and that the search space is appropriately restricted for weak reflections. To demonstrate the effectiveness of our proposed model, we apply it to real experimental data collected at the TOPAZ single crystal diffractometer at SNS. Copyright © 2024, The Authors. All rights reserved.

关键词： Diffraction

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Big data: Prospects and Challenges

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Vikalpa 2015年第1期40卷 74 - 96页

作者： Janakiraman Moorthy Rangin Lahiri Neelanjan Biswas Dipyaman Sanyal Jayanthi Ranjan Krishnadas Nanath Pulak Ghosh (Coordinator) Director and Professor of Marketing at the Institute of Management Technology Dubai. Earlier he was Professor of Marketing at the IIM Calcutta and IIM Lucknow. He received his PhD from IIM Ahmedabad. His recent research papers were published in the leading scholarly ournals such as Marketing Science British Food Journal Journal of Information Technology Case and Application Research Journal of Database Marketing & Customer Strategy Management. He has wide experience in the banking and investment industry. He was earlier the Global Research and Project Director of the Institute for Customer Relationship Management Atlanta USA. He was the Convener of the prestigious CAT Exam 2011. e-mail: Practice Director leading Atos India's CRM practice while supporting Strategic Business Development for North American Market. With an experience of more than 15 years Rangin has worked extensively as a Business Consultant in Information Technology (Sales Automation Marketing & Service Management area) Customer Data Management and CRM Analytics. e-mail: Business Consultant at Atos with extensive experience in Business Analysis Risk Management Analytics Business Development Presales Solution Ideation on Enterprise Data Management Enterprise Reference Data and Master Data Management area. e-mail: founder and CEO of dono consulting a boutique quantitative analytics and investment research firm. He has worked for leading financial firms in New York and India including Dow Jones Blackstone Sorin Capital (VP Quantitative Modeling) and Thomson Reuters (Head of Real Estate Analytics). A CFA charter holder and Commonwealth Scholar Deep has an MS (Applied Economics) from University of Texas Dallas and an MA (Economics) from Jadavpur University e-mail: Professor in the Information Systems Group of the Institute of Management Technology Ghaziabad. Her PhD is in the field of data mining from Jamia Millia Islamia Central University India. She has published five edited books. She is serving on the editorial b

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Correction to: Development and clinical validation of inertial sensor-based gait-clustering methods in Parkinson's disease

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Journal of neuroengineering and rehabilitation 2019年第1期16卷 98页

作者： An Nguyen Nils Roth Nooshin Haji Ghassemi Julius Hannink Thomas Seel Jochen Klucken Heiko Gassner Bjoern M Eskofier Machine Learning and Data Analytics Lab Department of Computer Science Friedrich-Alexander-University Erlangen-Nürnberg (FAU) Carl-Thiersch-Straße 2b 91052 Erlangen Germany. an.nguyen@fau.de. Machine Learning and Data Analytics Lab Department of Computer Science Friedrich-Alexander-University Erlangen-Nürnberg (FAU) Carl-Thiersch-Straße 2b 91052 Erlangen Germany. Control Systems Group Department of Electrical Engineering and Computer Science Technische Universität Berlin (TUB) Einsteinufer 17 10587 Berlin Germany. Department of Molecular Neurology University Hospital Erlangen Friedrich-Alexander University Erlangen-Nürnberg (FAU) Schwabachanlage 6 91054 Erlangen Germany.

The original article [1] contained an error whereby Fig. 6 contained a minor shading glitch affecting its presentation. This has now been corrected.

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A Digital Twin to overcome long-time challenges in Photovoltaics

arXiv

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arXiv 2023年

作者： Lüer, Larry Peters, Marius Smith, Ana Sunčana Dorschky, Eva Eskofier, Bjoern M. Liers, Frauke Franke, Jörg Sjarov, Martin Brossog, Matthias Guldi, Dirk Maier, Andreas Brabec, Christoph J. Friedrich-Alexander-Universität Erlangen-Nürnberg Martensstrasse 7 Erlangen91058 Germany Immerwahrstraße 2 Erlangen91058 Germany PULS Group Department of Physics Friedrich-Alexander-Universität Erlangen-Nürnberg IZNF Erlangen Germany Division of Physical Chemistry Ruđer Bošković Institute Bijenička cesta 54 Zagreb Croatia Machine Learning and Data Analytics Lab Friedrich-Alexander-Universität Erlangen-Nürnberg Carl-Thiersch-Straße 2b Bayern Erlangen91052 Germany Friedrich-Alexander-Universität Erlangen-Nürnberg Cauerstr. 11 Erlangen91058 Germany Friedrich-Alexander-Universität Erlangen-Nürnberg Egerlandstr. 7 Erlangen91058 Germany Department of Chemistry and Pharmacy Friedrich-Alexander-Universität Erlangen-Nürnberg Egerlandstr. 3 Erlangen91058 Germany Informatics Department Friedrich-Alexander-Universität Erlangen-Nürnberg Martenstr. 3 Erlangen91058 Germany

The recent successes of emerging photovoltaics (PV) such as organic and perovskite solar cells are largely driven by innovations in material science. However, closing the gap to commercialization still requires significant innovation to match contradicting requirements such as performance, longevity and recyclability. The rate of innovation, as of today, is limited by a lack of design principles linking chemical motifs to functional microscopic structures, and by an incapacity to experimentally access microscopic structures from investigating macroscopic device properties. Both limitations in turn are caused by an individualist approach to learning, not being able to produce consistent datasets large enough to find patterns and physical laws leading us to breakthrough innovations. In this work, we envision a layout of a Digital Twin for PV materials aimed at removing both limitations. The layout combines machine learning approaches, as performed in materials acceleration platforms (MAPs), with mathematical models derived from the underlying physics and digital twin concepts from the engineering world. This layout will allow using high-throughput (HT) experimentation in MAPs to improve the parametrization of quantum chemical and solid-state models. In turn, the improved and generalized models can be used to obtain the crucial structural parameters from HT data. HT experimentation will thus yield a detailed understanding of generally valid structure-property relationships, enabling inverse molecular design, that is, predicting the optimal chemical structure and process conditions to build PV devices satisfying a multitude of requirements at the same time. After motivating our proposed layout of the digital twin with causal relationships in material science, we discuss the current state of the enabling technologies such as model-based inference of hidden parameters, already being able to yield insight from HT data today. However, we identify the multiscale nature of PV

关键词： machine learning

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Harnessing multimodal approaches for depression detection using large language models and facial expressions

Npj mental health research

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Npj mental health research 2024年第1期3卷 66页

作者： Misha Sadeghi Robert Richer Bernhard Egger Lena Schindler-Gmelch Lydia Helene Rupp Farnaz Rahimi Matthias Berking Bjoern M Eskofier Machine Learning and Data Analytics Lab (MaD Lab) Department Artificial Intelligence in Biomedical Engineering (AIBE) Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Erlangen 91052 Germany. misha.sadeghi@fau.de. Machine Learning and Data Analytics Lab (MaD Lab) Department Artificial Intelligence in Biomedical Engineering (AIBE) Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Erlangen 91052 Germany. Chair of Visual Computing (LGDV) Department of Computer Science Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Erlangen 91058 Germany. Chair of Clinical Psychology and Psychotherapy (KliPs) Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Erlangen 91052 Germany. Translational Digital Health Group Institute of AI for Health Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg 85764 Germany.

Detecting depression is a critical component of mental health diagnosis, and accurate assessment is essential for effective treatment. This study introduces a novel, fully automated approach to predicting depression severity using the E-DAIC dataset. We employ Large Language Models (LLMs) to extract depression-related indicators from interview transcripts, utilizing the Patient Health Questionnaire-8 (PHQ-8) score to train the prediction model. Additionally, facial data extracted from video frames is integrated with textual data to create a multimodal model for depression severity prediction. We evaluate three approaches: text-based features, facial features, and a combination of both. Our findings show the best results are achieved by enhancing text data with speech quality assessment, with a mean absolute error of 2.85 and root mean square error of 4.02. This study underscores the potential of automated depression detection, showing text-only models as robust and effective while paving the way for multimodal analysis.

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Complementary App-Based Yoga Home Exercise Therapy for Patients With Axial Spondyloarthritis: Usability Study

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JMIR Formative Research 2024年 8卷 e57185页

作者： Grube, Lara Petit, Pascal Vuillerme, Nicolas Nitschke, Marlies Nwosu, Obioma Bertrand Knitza, Johannes Krusche, Martin Seifer, Ann-Kristin Eskofier, Bjoern Schett, Georg Morf, Harriet Department of Internal Medicine 3- Rheumatology & Immunology Universitätsklinikum Erlangen Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen Germany Deutsches Zentrum Immuntherapie Universitätsklinikum Erlangen Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen Germany AGEIS Université Grenoble Alpes Grenoble France Institut Universitaire de France Paris France LabCom Telecom4Health Orange Labs & Université Grenoble Alpes CNRS Inria Grenoble France Machine Learning and Data Analytics Lab Department Artificial Intelligence in Biomedical Engineering (AIBE) Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen Germany Institute for Digital Medicine University Hospital of Giessen and Marburg Philipps-University Marburg Marburg Germany III. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany Translational Digital Health Group Institute of AI for Health German Research Center for Environmental Health Helmholtz Zentrum München Neuherberg Germany

Background: Axial spondyloarthritis (AS) is a chronic inflammatory rheumatic disease characterized by potentially disabling inflammation of the spine and adjacent joints. Regular exercise is a cornerstone of treatment. However, patients with AS currently have little support. YogiTherapy (MaD Lab) is an app developed to support patients with AS by providing instructions for yoga-based home exercise therapy. Objective: This study aimed to evaluate the usability and acceptance of the newly designed YogiTherapy app for patients with AS. Methods: Patients completed the User Version of the Mobile Application Rating Scale (uMARS) and net promoter score (NPS) questionnaires after the app introduction. Wilcoxon Mann-Whitney rank sum test, chi-square test for count data, and correlation analysis were conducted to examine the usability of the app, acceptance, and patient characteristics. Results: A total of 65 patients with AS (33, 51% female;age: mean 43.3, SD 13.6 years) were included in the study from May 2022 to June 2023. Subsequently, the data were analyzed. Usability was rated moderate, with a mean uMARS of 3.35 (SD 0.47) points on a scale from 0 to 5. The highest-rated uMARS dimension was information (mean 3.88, SD 0.63), followed by functionality (mean 3.84, SD 0.87). Females reported a significantly higher uMARS total score than males (mean 3.47, SD 0.48 vs mean 3.23, SD 0.45;P=.03, Vargha and Delaney A [VDA] 0.66, 95% CI 0.53-0.77). The mean average of the NPS was 6.23 (SD 2.64) points (on a scale from 0 to 10), based on 43% (26/65 nonpromoters, 42% (25/65) indifferent, and 15% (9/65) promoters. A total of 7% (5/65) of those surveyed did not answer the question. When applying the NPS formula, the result is –26%. The NPS showed a positive correlation with the usage of mobile apps (r=0.39;P=.02). uMARS functionality was significantly higher rated by patients younger than 41 years (mean 4.17, SD 0.55 vs mean 3.54, SD 1;P<.001;VDA 0.69, 95% CI 0.56-0.80). Patients consi

关键词： adjacent joints ankylosing spondylitis app apps axial spondylarthritis chronic correlation analysis DHA digital health application digital therapeutics DTx eHealth exercise home exercise joint joints patient patient acceptance patients physical exercise rheumatic disease self-assessment spine spondyloarthritis therapy usability usability study Yoga YogiTherapy

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Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes

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ImmunoInformatics 2023年 9卷

作者： Christian A Balbin Janelle Nunez-Castilla Vitalii Stebliankin Prabin Baral Masrur Sobhan Trevor Cickovski Ananda Mohan Mondal Giri Narasimhan Prem Chapagain Kalai Mathee Jessica Siltberg-Liberles Department of Biological Sciences College of Arts Science and Education Florida International University Miami United States Bioinformatics Research Group (BioRG) Knight Foundation School of Computing and Information Sciences Florida International University Miami United States Department of Physics College of Arts Science and Education Florida International University Miami United States Machine Learning and Data Analytics Group (MLDAG) Knight Foundation School of Computing and Information Sciences Florida International University Miami United States Biomolecular Sciences Institute Florida International University Miami United States Department of Human and Molecular Genetics Herbert Wertheim College of Medicine Florida International University Miami United States

Upon infection, foreign antigenic proteins stimulate the host's immune system to produce antibodies targeting the pathogen. These antibodies bind to regions on the antigen called epitopes. Structural similarity (molecular mimicry) of epitopes between an infecting pathogen and host proteins or other pathogenic proteins the host has previously encountered can impact the host immune response to the pathogen and may lead to cross-reactive antibodies. The ability to identify potential regions of molecular mimicry in a pathogen can illuminate immune effects which are especially important to pathogen treatment and vaccine design. Here we present Epitopedia, a software pipeline that facilitates the identification of regions that may exhibit potential three-dimensional molecular mimicry between an antigenic pathogen protein and known immune epitopes as catalogued by the Immune Epitope database (IEDB). Epitopedia is open-source software released under the MIT license and is freely available on GitHub, including a Docker container with all other software dependencies preinstalled. We performed an analysis describing how various secondary structure states, identity between pentapeptide pairs, and identity between the parent sequences of pentapeptide pairs affects RMSD. We found that pentapeptides pairs in a helical conformation had considerably lower RMSD values than those in extended or coil conformations. We also found that RMSD is significantly increased when pentapeptide pairs are from non-homologous sequences.

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Why is the Winner the Best?

Why is the Winner the Best?

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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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Biomedical image analysis competitions: The state of current participation practice

arXiv

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arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

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