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ORCIDHugo J. W. L. Aerts
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- affiliation: Harvard Medical School, Boston, MA, USA
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Journal Articles
- 2024
[j13]Keno K. Bressem
, Jens-Michalis Papaioannou, Paul Grundmann, Florian Borchert, Lisa C. Adams, Leonhard Liu, Felix Busch, Lina Xu, Jan P. Loyen, Stefan Markus Niehues, Moritz Augustin, Lennart Grosser, Marcus R. Makowski, Hugo J. W. L. Aerts, Alexander Löser:
medBERT.de: A comprehensive German BERT model for the medical domain. Expert Syst. Appl. 237(Part C): 121598 (2024)- [j12]Shan Chen, Yingya Li, Sheng Lu, Hoang Van, Hugo J. W. L. Aerts, Guergana K. Savova, Danielle S. Bitterman:
Evaluating the ChatGPT family of models for biomedical reasoning and classification. J. Am. Medical Informatics Assoc. 31(4): 940-948 (2024) - [j11]Marco Guevara, Shan Chen, Spencer Thomas, Tafadzwa L. Chaunzwa, Idalid Franco, Benjamin H. Kann, Shalini Moningi, Jack M. Qian, Madeleine Goldstein, Susan Harper, Hugo J. W. L. Aerts, Paul J. Catalano, Guergana K. Savova, Raymond H. Mak, Danielle S. Bitterman:
Large language models to identify social determinants of health in electronic health records. npj Digit. Medicine 7(1) (2024) - 2023
- [j10]Felix Busch, Lina Xu, Dmitry Sushko, Matthias Weidlich, Daniel Truhn, Gustav Müller-Franzes, Maurice M. Heimer, Stefan Markus Niehues, Marcus R. Makowski, Markus Hinsche, Janis Lucas Vahldiek, Hugo J. W. L. Aerts, Lisa C. Adams, Keno K. Bressem:
Dual center validation of deep learning for automated multi-label segmentation of thoracic anatomy in bedside chest radiographs. Comput. Methods Programs Biomed. 234: 107505 (2023) - [j9]Anna Zapaishchykova, Divyanshu Tak, Aidan Boyd, Zezhong Ye, Hugo J. W. L. Aerts, Benjamin H. Kann:
SegmentationReview: A Slicer3D extension for fast review of AI-generated segmentations. Softw. Impacts 17: 100536 (2023) - 2021
- [j8]Roman Zeleznik, Jakob Weiss, Jana Taron, Christian V. Guthier, Danielle S. Bitterman, Cindy Hancox, Benjamin H. Kann, Daniel W. Kim, Rinaa S. Punglia, Jeremy Bredfeldt, Borek Foldyna, Parastou Eslami, Michael T. Lu, Udo Hoffmann, Raymond H. Mak, Hugo J. W. L. Aerts:
Deep-learning system to improve the quality and efficiency of volumetric heart segmentation for breast cancer. npj Digit. Medicine 4 (2021) - 2016
- [j7]Petr Smirnov, Zhaleh Safikhani, Nehme Hachem, Dong Wang, Adrian She, Catharina Olsen, Mark Freeman, Heather Marie Selby, Deena M. A. Gendoo, Patrick Grossmann, Andrew H. Beck, Hugo J. W. L. Aerts, Mathieu Lupien, Anna Goldenberg, Benjamin Haibe-Kains:
PharmacoGx: an R package for analysis of large pharmacogenomic datasets. Bioinform. 32(8): 1244-1246 (2016) - [j6]Tina Kapur, Steve Pieper, Andriy Fedorov, Jean-Christophe Fillion-Robin, Michael Halle, Lauren O'Donnell, Andras Lasso, Tamas Ungi, Csaba Pinter, Julien Finet, Sonia Pujol, Jagadeesan Jayender, Junichi Tokuda, Isaiah Norton, Raúl San José Estépar, David T. Gering, Hugo J. W. L. Aerts, Marianna Jakab, Nobuhiko Hata, Luiz Ibáñez, Daniel J. Blezek, Jim Miller, Stephen R. Aylward, W. Eric L. Grimson, Gabor Fichtinger, William M. Wells III, William E. Lorensen, William J. Schroeder, Ron Kikinis:
Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience. Medical Image Anal. 33: 176-180 (2016) - [j5]Zhaleh Safikhani, Nehme Hachem, Petr Smirnov, Mark Freeman, Anna Goldenberg, Nicolai J. Birkbak, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains:
Safikhani et al. reply. Nat. 540(7631): E2-E4 (2016) - 2015
- [j4]Diana M. Hendrickx, Hugo J. W. L. Aerts, Florian Caiment, Dominic Clark, Timothy M. D. Ebbels, Chris T. A. Evelo, Hans Gmuender, Dennie G. A. J. Hebels, Ralf Herwig, Jürgen Hescheler, Danyel G. J. Jennen, Marlon J. A. Jetten, Stathis Kanterakis, Hector C. Keun, Vera Matser, John P. Overington, Ekaterina Pilicheva, Ugis Sarkans, Marcelo P. Segura-Lepe, Isaia Sotiriadou, Timo Wittenberger, Clemens Wittwehr, Antonella Zanzi, Jos C. S. Kleinjans:
diXa: a data infrastructure for chemical safety assessment. Bioinform. 31(9): 1505-1507 (2015) - 2013
- [j3]Simon Papillon-Cavanagh, Nicolas De Jay, Nehme Hachem, Catharina Olsen, Gianluca Bontempi, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains:
Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity. J. Am. Medical Informatics Assoc. 20(4): 597-602 (2013) - [j2]Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai J. Birkbak, Andrew C. Jin, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush:
Inconsistency in large pharmacogenomic studies. Nat. 504(7480): 389-393 (2013) - [j1]Yuhua Gu, Virendra Kumar, Lawrence O. Hall, Dmitry B. Goldgof, Ching-Yen Li, René Korn, Claus Bendtsen, Emmanuel Rios Velazquez, Andre Dekker, Hugo J. W. L. Aerts, Philippe Lambin, Xiuli Li, Jie Tian, Robert A. Gatenby, Robert J. Gillies:
Automated delineation of lung tumors from CT images using a single click ensemble segmentation approach. Pattern Recognit. 46(3): 692-702 (2013)
Conference and Workshop Papers
- 2024
- [c4]Jack Gallifant, Shan Chen, Pedro Moreira, Nikolaj Munch, Mingye Gao, Jackson Pond, Leo Anthony Celi, Hugo J. W. L. Aerts, Thomas Hartvigsen, Danielle S. Bitterman:
Language Models are Surprisingly Fragile to Drug Names in Biomedical Benchmarks. EMNLP (Findings) 2024: 12448-12465 - [c3]Anna Zapaishchykova, Benjamin H. Kann, Divyanshu Tak, Zezhong Ye, Daphne A. Haas-Kogan, Hugo J. W. L. Aerts:
SynthBrainGrow: Synthetic Diffusion Brain Aging for Longitudinal MRI Data Generation in Young People. DGM4MICCAI@MICCAI 2024: 75-86 - 2022
- [c2]Darrin W. Byrd, Dennis Bontempi, Hao Yang, Hugo J. W. L. Aerts, Binzhang Zhao, Andrey Fedorov, Lawrence H. Schwartz, Tavis Allison, Chaya Moscowitz, Paul E. Kinahan:
Using virtual clinical trials to determine the accuracy of AI-based quantitative imaging biomarkers in oncology trials using standard-of-care CT. Medical Imaging: Image Perception, Observer Performance, and Technology Assessment 2022 - 2008
- [c1]Guillaume Janssens, Jonathan Orban de Xivry, Hugo J. W. L. Aerts, Geert Bosmans, Andre L. A. J. Dekker, Benoît Macq:
Improving physical behavior in image registration. ICIP 2008: 2952-2955
Informal and Other Publications
- 2024
- [i21]Lisa Adams, Felix Busch, Tianyu Han, Jean-Baptiste Excoffier, Matthieu Ortala, Alexander Löser, Hugo J. W. L. Aerts, Jakob Nikolas Kather, Daniel Truhn, Keno K. Bressem:
LongHealth: A Question Answering Benchmark with Long Clinical Documents. CoRR abs/2401.14490 (2024) - [i20]Yining Zha, Benjamin H. Kann, Zezhong Ye, Anna Zapaishchykova, John He, Shu-Hui Hsu, Jonathan E. Leeman, Kelly J. Fitzgerald, David E. Kozono, Raymond H. Mak, Hugo J. W. L. Aerts:
Magnetic resonance delta radiomics to track radiation response in lung tumors receiving stereotactic MRI-guided radiotherapy. CoRR abs/2402.16619 (2024) - [i19]Anna Zapaishchykova, Benjamin H. Kann, Divyanshu Tak, Zezhong Ye, Daphne A. Haas-Kogan, Hugo J. W. L. Aerts:
SynthBrainGrow: Synthetic Diffusion Brain Aging for Longitudinal MRI Data Generation in Young People. CoRR abs/2405.00682 (2024) - [i18]Shan Chen, Jack Gallifant, Mingye Gao, Pedro Moreira, Nikolaj Munch, Ajay Muthukkumar, Arvind Rajan, Jaya Kolluri, Amelia Fiske, Janna Hastings, Hugo J. W. L. Aerts, Brian Anthony, Leo Anthony Celi, William G. La Cava, Danielle S. Bitterman:
Cross-Care: Assessing the Healthcare Implications of Pre-training Data on Language Model Bias. CoRR abs/2405.05506 (2024) - [i17]Hartmut Häntze, Lina Xu, Felix J. Dorfner, Leonhard Donle, Daniel Truhn, Hugo J. W. L. Aerts, Mathias Prokop, Bram van Ginneken, Alessa Hering, Lisa C. Adams, Keno K. Bressem:
MRSegmentator: Robust Multi-Modality Segmentation of 40 Classes in MRI and CT Sequences. CoRR abs/2405.06463 (2024) - [i16]Felix J. Dorfner, Janis Lucas Vahldiek, Leonhard Donle, Andrei Zhukov, Lina Xu, Hartmut Häntze, Marcus R. Makowski, Hugo J. W. L. Aerts, Fabian Proft, Valeria Rios Rodriguez, Judith Rademacher, Mikhail Protopopov, Hildrun Haibel, Torsten Diekhoff, Murat Torgutalp, Lisa C. Adams, Denis Poddubnyy, Keno K. Bressem:
Incorporating Anatomical Awareness for Enhanced Generalizability and Progression Prediction in Deep Learning-Based Radiographic Sacroiliitis Detection. CoRR abs/2405.07369 (2024) - [i15]Jack Gallifant, Shan Chen, Pedro Moreira, Nikolaj Munch, Mingye Gao, Jackson Pond, Leo Anthony Celi, Hugo J. W. L. Aerts, Thomas Hartvigsen, Danielle S. Bitterman:
Language Models are Surprisingly Fragile to Drug Names in Biomedical Benchmarks. CoRR abs/2406.12066 (2024) - [i14]Raffi Hagopian, Timothy Strebel, Simon Bernatz, Gregory A Myers, Erik Offerman, Erick Zúniga, Cy Y. Kim, Angie T. Ng, James A Iwaz, Sunny P. Singh, Evan P. Carey, Michael J. Kim, R. Spencer Schaefer, Jeannie Yu, Amilcare Gentili, Hugo J. W. L. Aerts:
Artificial Intelligence-Based Opportunistic Coronary Calcium Screening in the Veterans Affairs National Healthcare System. CoRR abs/2409.09968 (2024) - [i13]Shan Chen, Mingye Gao, Kuleen Sasse, Thomas Hartvigsen, Brian Anthony, Lizhou Fan, Hugo J. W. L. Aerts, Jack Gallifant, Danielle S. Bitterman:
Wait, but Tylenol is Acetaminophen... Investigating and Improving Language Models' Ability to Resist Requests for Misinformation. CoRR abs/2409.20385 (2024) - 2023
- [i12]Keno K. Bressem, Jens-Michalis Papaioannou, Paul Grundmann, Florian Borchert, Lisa C. Adams, Leonhard Liu, Felix Busch, Lina Xu, Jan P. Loyen, Stefan Markus Niehues, Moritz Augustin, Lennart Grosser, Marcus R. Makowski, Hugo J. W. L. Aerts, Alexander Löser:
MEDBERT.de: A Comprehensive German BERT Model for the Medical Domain. CoRR abs/2303.08179 (2023) - [i11]Shan Chen, Marco Guevara, Nicolas Ramirez, Arpi Murray, Jeremy L. Warner, Hugo J. W. L. Aerts, Timothy A. Miller, Guergana K. Savova, Raymond H. Mak, Danielle S. Bitterman:
Natural language processing to automatically extract the presence and severity of esophagitis in notes of patients undergoing radiotherapy. CoRR abs/2303.13722 (2023) - [i10]Shan Chen, Yingya Li, Sheng Lu, Hoang Van, Hugo J. W. L. Aerts, Guergana K. Savova, Danielle S. Bitterman:
Evaluation of ChatGPT Family of Models for Biomedical Reasoning and Classification. CoRR abs/2304.02496 (2023) - [i9]Deepa Krishnaswamy, Dennis Bontempi, Vamsi Thiriveedhi, Davide Punzo, David A. Clunie, Christopher P. Bridge, Hugo J. W. L. Aerts, Ron Kikinis, Andrey Fedorov:
Enrichment of the NLST and NSCLC-Radiomics computed tomography collections with AI-derived annotations. CoRR abs/2306.00150 (2023) - [i8]Marco Guevara, Shan Chen, Spencer Thomas, Tafadzwa L. Chaunzwa, Idalid Franco, Benjamin H. Kann, Shalini Moningi, Jack M. Qian, Madeleine Goldstein, Susan Harper, Hugo J. W. L. Aerts, Guergana K. Savova, Raymond H. Mak, Danielle S. Bitterman:
Large Language Models to Identify Social Determinants of Health in Electronic Health Records. CoRR abs/2308.06354 (2023) - [i7]Karim Lekadir, Aasa Feragen, Abdul Joseph Fofanah, Alejandro F. Frangi, Alena Buyx, Anais Emelie, Andrea Lara, Antonio R. Porras, An-Wen Chan, Arcadi Navarro, Ben Glocker, Benard Ohene Botwe, Bishesh Khanal, Brigit Beger, Carol C. Wu, Celia Cintas, Curtis P. Langlotz, Daniel Rueckert, Deogratias Mzurikwao, Dimitrios I. Fotiadis, Doszhan Zhussupov, Enzo Ferrante, Erik Meijering, Eva Weicken, Fabio A. González, Folkert W. Asselbergs, Fred W. Prior, Gabriel P. Krestin, Gary S. Collins, Geletaw Sahle Tegenaw, Georgios Kaissis, Gianluca Misuraca, Gianna Tsakou, Girish Dwivedi, Haridimos Kondylakis, Harsha Jayakody, Henry C. Woodruff, Hugo J. W. L. Aerts, Ian Walsh, Ioanna Chouvarda, Irène Buvat, Islem Rekik, James S. Duncan, Jayashree Kalpathy-Cramer, Jihad Zahir, Jinah Park, John Mongan, Judy W. Gichoya, Julia A. Schnabel, et al.:
FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare. CoRR abs/2309.12325 (2023) - [i6]Shan Chen, Marco Guevara, Shalini Moningi, Frank Hoebers, Hesham Elhalawani, Benjamin H. Kann, Fallon E. Chipidza, Jonathan Leeman, Hugo J. W. L. Aerts, Timothy A. Miller, Guergana K. Savova, Raymond H. Mak, Maryam Lustberg, Majid Afshar, Danielle S. Bitterman:
The impact of using an AI chatbot to respond to patient messages. CoRR abs/2310.17703 (2023) - 2022
- [i5]Lisa C. Adams, Felix Busch, Daniel Truhn, Marcus R. Makowski, Hugo J. W. L. Aerts, Keno K. Bressem:
What Does DALL-E 2 Know About Radiology? CoRR abs/2209.13696 (2022) - 2021
- [i4]Zezhong Ye, Jack M. Qian, Ahmed Hosny, Roman Zeleznik, Deborah Plana, Jirapat Likitlersuang, Zhongyi Zhang, Raymond H. Mak, Hugo J. W. L. Aerts, Benjamin H. Kann:
Deep learning-based detection of intravenous contrast in computed tomography scans. CoRR abs/2110.08424 (2021) - 2019
- [i3]Ahmed Hosny, Michael Schwier, Christoph Berger, Evin Pinar Örnek, Mehmet Turan, Phi V. Tran, Leon Weninger, Fabian Isensee, Klaus H. Maier-Hein, Richard McKinley, Michael T. Lu, Udo Hoffmann, Bjoern H. Menze, Spyridon Bakas, Andriy Fedorov, Hugo J. W. L. Aerts:
ModelHub.AI: Dissemination Platform for Deep Learning Models. CoRR abs/1911.13218 (2019) - 2018
- [i2]Michael Schwier, Joost van Griethuysen, Mark G. Vangel, Steve Pieper, Sharon Peled, Clare M. Tempany, Hugo J. W. L. Aerts, Ron Kikinis, Fiona M. Fennessy, Andrey Fedorov:
Repeatability of Multiparametric Prostate MRI Radiomics Features. CoRR abs/1807.06089 (2018) - 2017
- [i1]Martin Vallières, Emily Kay-Rivest, Léo Jean Perrin, Xavier Liem, Christophe Furstoss, Hugo J. W. L. Aerts, Nader Khaouam, Phuc Felix Nguyen-Tan, Chang-Shu Wang, Khalil Sultanem, Jan Seuntjens, Issam El-Naqa:
Radiomics strategies for risk assessment of tumour failure in head-and-neck cancer. CoRR abs/1703.08516 (2017)
Coauthor Index
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