Publications

Jonas Teuwen

2024

Artificial Intelligence-Enhanced Breast MRI

Investigative Radiology
R. Lo Gullo, E. Marcus, J. Huayanay, S. Eskreis-Winkler, S. Thakur, J. Teuwen, K. Pinker, 2024

doi abstract
On retrospective k-space subsampling schemes for deep MRI reconstruction

Magnetic Resonance Imaging
G. Yiasemis, C. I. Sánchez, J. Sonke, J. Teuwen, 2024

doi preprints abstract
Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer

The Journal of Pathology
C. A. Jahangir, D. B. Page, G. Broeckx, C. A. Gonzalez, C. Burke, C. Murphy, J. S. Reis‐Filho, A. Ly, P. W. Harms, R. R. Gupta, M. Vieth, A. I. Hida, M. Kahila, Z. Kos, P. J. Van Diest, S. Verbandt, J. Thagaard, R. Khiroya, K. Abduljabbar, G. Acosta Haab, B. Acs, S. Adams, J. S. Almeida, I. Alvarado‐Cabrero, F. Azmoudeh‐Ardalan, S. Badve, N. B. Baharun, E. R. Bellolio, V. Bheemaraju, K. R. Blenman, L. Botinelly Mendonça Fujimoto, O. Burgues, A. Chardas, M. C. U. Cheang, F. Ciompi, L. A. Cooper, A. Coosemans, G. Corredor, F. L. Dantas Portela, F. Deman, S. Demaria, S. N. Dudgeon, M. Elghazawy, C. Fernandez‐Martín, S. Fineberg, S. B. Fox, J. M. Giltnane, S. Gnjatic, P. I. Gonzalez‐Ericsson, A. Grigoriadis, N. Halama, M. G. Hanna, A. Harbhajanka, S. N. Hart, J. Hartman, S. Hewitt, H. M. Horlings, Z. Husain, S. Irshad, E. A. Janssen, T. R. Kataoka, K. Kawaguchi, A. I. Khramtsov, U. Kiraz, P. Kirtani, L. L. Kodach, K. Korski, G. Akturk, E. Scott, A. Kovács, A. Lænkholm, C. Lang‐Schwarz, D. Larsimont, J. K. Lennerz, M. Lerousseau, X. Li, A. Madabhushi, S. K. Maley, V. Manur Narasimhamurthy, D. K. Marks, E. S. Mcdonald, R. Mehrotra, S. Michiels, D. Kharidehal, F. U. A. A. Minhas, S. Mittal, D. A. Moore, S. Mushtaq, H. Nighat, T. Papathomas, F. Penault‐Llorca, R. D. Perera, C. J. Pinard, J. C. Pinto‐Cardenas, G. Pruneri, L. Pusztai, N. M. Rajpoot, B. L. Rapoport, T. T. Rau, J. M. Ribeiro, D. Rimm, A. Vincent‐Salomon, J. Saltz, S. Sayed, E. Hytopoulos, S. Mahon, K. P. Siziopikou, C. Sotiriou, A. Stenzinger, M. A. Sughayer, D. Sur, F. Symmans, S. Tanaka, T. Taxter, S. Tejpar, J. Teuwen, E. A. Thompson, T. Tramm, W. T. Tran, J. Van Der Laak, G. E. Verghese, G. Viale, N. Wahab, T. Walter, Y. Waumans, H. Y. Wen, W. Yang, Y. Yuan, J. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, E. Specht Stovgaard, R. Salgado, W. M. Gallagher, A. Rahman, 2024

doi abstract
To deform or not: treatment-aware longitudinal registration for breast DCE-MRI during neoadjuvant chemotherapy via unsupervised keypoints detection
L. Han, T. Tan, T. Zhang, Y. Gao, X. Wang, V. Longo, S. Ventura-Díaz, A. D'Angelo, J. Teuwen, R. Mann, 2024

ArXiv abstract
Equivariant Multiscale Learned Invertible Reconstruction for Cone Beam CT
N. Moriakov, J. Sonke, J. Teuwen, 2024

ArXiv abstract
Deep Cardiac MRI Reconstruction with ADMM

Statistical Atlases and Computational Models of the Heart. Regular and CMRxRecon Challenge Papers
G. Yiasemis, N. Moriakov, J. Sonke, J. Teuwen, 2024

doi preprints abstract
Artificial intelligence and explanation: How, why, and when to explain black boxes

European Journal of Radiology
E. Marcus, J. Teuwen, 2024

doi abstract
IMPORTANT-Net: Integrated MRI multi-parametric increment fusion generator with attention network for synthesizing absent data

Information Fusion
T. Zhang, T. Tan, L. Han, X. Wang, Y. Gao, J. Van Dijk, A. Portaluri, A. Gonzalez-Huete, A. D’Angelo, C. Lu, J. Teuwen, R. Beets-Tan, Y. Sun, R. Mann, 2024, 108

doi preprints abstract
Nodule detection and generation on chest X-rays: NODE21 Challenge

IEEE Transactions on Medical Imaging
E. Sogancioglu, B. Van Ginneken, F. Behrendt, M. Bengs, A. Schlaefer, M. Radu, D. Xu, K. Sheng, F. Scalzo, E. Marcus, S. Papa, J. Teuwen, E. T. Scholten, S. Schalekamp, N. Hendrix, C. Jacobs, W. Hendrix, C. I. Sánchez, K. Murphy, 2024

doi preprints abstract
Optimizing CycleGAN design for CBCT-to-CT translation: insights into 2D vs 3D modeling, patch size, and the need for tailored evaluation metrics

Medical Imaging 2024: Image Processing
I. Hadzic, S. Pai, V. Trier Taasti, D. Bontempi, I. Zhovannik, R. Canters, J. J. Sonke, A. Dekker, J. Teuwen, A. Traverso, 2024

doi abstract
The state-of-the-art in Cardiac MRI Reconstruction: Results of the CMRxRecon Challenge in MICCAI 2023
J. Lyu, C. Qin, S. Wang, F. Wang, Y. Li, Z. Wang, K. Guo, C. Ouyang, M. Tänzer, M. Liu, L. Sun, M. Sun, Q. Li, Z. Shi, S. Hua, H. Li, Z. Chen, Z. Zhang, B. Xin, D. N. Metaxas, G. Yiasemis, J. Teuwen, L. Zhang, W. Chen, Y. Pang, X. Liu, A. Razumov, D. V. Dylov, Q. Dou, K. Yan, Y. Xue, Y. Du, J. Dietlmeier, C. Garcia-Cabrera, Z. A. Hemidi, N. Vogt, Z. Xu, Y. Zhang, Y. Chu, W. Chen, W. Bai, X. Zhuang, J. Qin, L. Wu, G. Yang, X. Qu, H. Wang, C. Wang, 2024

ArXiv abstract
Application of deep learning on mammographies to discriminate between low and high-risk DCIS for patient participation in active surveillance trials.

Cancer imaging: the official publication of the International Cancer Imaging Society
S. Alaeikhanehshir, M. M. Voets, F. H. van Duijnhoven, E. H. Lips, E. J. Groen, M. C. J. van Oirsouw, S. E. Hwang, J. Y. Lo, J. Wesseling, R. M. Mann, J. Teuwen, 2024, 24;(1):48

PubMed abstract
AI Applications to Breast MRI: Today and Tomorrow.

Journal of magnetic resonance imaging: JMRI
R. Lo Gullo, J. Brunekreef, E. Marcus, L. K. Han, S. Eskreis-Winkler, S. B. Thakur, R. Mann, K. Groot Lipman, J. Teuwen, K. Pinker, 2024

PubMed abstract
Abstract 4951: Integrative multi-omic machine learning model predicts neoadjuvant immunotherapy response using molecular data and deep learning-derived features from digital pathology

Cancer Research
L. V. Leek, V. Botha, V. A. Baxi, J. Teuwen, H. M. Horlings, S. D. Chasalow, J. V. D. Haar, L. F. Wessels, A. Debroy, E. E. Voest, 2024, 84;(6_Supplement):4951-4951

doi abstract
End-to-end Adaptive Dynamic Subsampling and Reconstruction for Cardiac MRI
G. Yiasemis, J. Sonke, J. Teuwen, 2024

ArXiv abstract

2023

Constrained Empirical Risk Minimization: Theory and Practice
E. Marcus, R. Sheombarsing, J. Sonke, J. Teuwen, 2023

ArXiv abstract
STAPLER: Efficient learning of TCR-peptide specificity prediction from full-length TCR-peptide data
B. P. Y. Kwee, M. Messemaker, E. Marcus, G. Oliveira, W. Scheper, C. J. Wu, J. Teuwen, T. N. Schumacher, 2023

doi abstract
Predicting up to 10 year breast cancer risk using longitudinal mammographic screening history
X. Wang, T. Tan, Y. Gao, R. Su, T. Zhang, L. Han, J. Teuwen, A. D’Angelo, C. A. Drukker, M. K. Schmidt, R. Beets-Tan, N. Karssemeijer, R. Mann, 2023

doi abstract
Visualize what you learn: a well-explainable joint-learning framework based on multi-view mammograms and associated reports
Y. Gao, H. Zhou, X. Wang, T. Zhang, R. Tan, L. Han, L. Estacio, A. D’Angelo, J. Teuwen, R. Mann, T. Tan, 2023

doi abstract
RadioLOGIC, a healthcare model for processing electronic health records and decision-making in breast disease

Cell Reports Medicine
T. Zhang, T. Tan, X. Wang, Y. Gao, L. Han, L. Balkenende, A. D’Angelo, L. Bao, H. M. Horlings, J. Teuwen, R. G. Beets-Tan, R. M. Mann, 2023

doi abstract
Spatial analyses of immune cell infiltration in cancer: current methods and future directions. A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer

The Journal of Pathology
D. B. Page, G. Broeckx, C. A. Jahangir, S. Verbandt, R. R. Gupta, J. Thagaard, R. Khiroya, Z. Kos, K. Abduljabbar, G. Acosta Haab, B. Acs, J. S. Almeida, I. Alvarado‐Cabrero, F. Azmoudeh‐Ardalan, S. Badve, N. B. Baharun, E. R. Bellolio, V. Bheemaraju, K. R. Blenman, L. Botinelly Mendonça Fujimoto, O. Burgues, M. C. U. Cheang, F. Ciompi, L. A. Cooper, A. Coosemans, G. Corredor, F. L. Dantas Portela, F. Deman, S. Demaria, S. N. Dudgeon, M. Elghazawy, S. Ely, C. Fernandez‐Martín, S. Fineberg, S. B. Fox, W. M. Gallagher, J. M. Giltnane, S. Gnjatic, P. I. Gonzalez‐Ericsson, A. Grigoriadis, N. Halama, M. G. Hanna, A. Harbhajanka, A. Hardas, S. N. Hart, J. Hartman, S. Hewitt, A. I. Hida, H. M. Horlings, Z. Husain, E. Hytopoulos, S. Irshad, E. A. Janssen, M. Kahila, T. R. Kataoka, K. Kawaguchi, D. Kharidehal, A. I. Khramtsov, U. Kiraz, P. Kirtani, L. L. Kodach, K. Korski, A. Kovács, A. Laenkholm, C. Lang‐Schwarz, D. Larsimont, J. K. Lennerz, M. Lerousseau, X. Li, A. Ly, A. Madabhushi, S. K. Maley, V. Manur Narasimhamurthy, D. K. Marks, E. S. Mcdonald, R. Mehrotra, S. Michiels, F. U. A. A. Minhas, S. Mittal, D. A. Moore, S. Mushtaq, H. Nighat, T. Papathomas, F. Penault‐Llorca, R. D. Perera, C. J. Pinard, J. C. Pinto‐Cardenas, G. Pruneri, L. Pusztai, A. Rahman, N. M. Rajpoot, B. L. Rapoport, T. T. Rau, J. S. Reis‐Filho, J. M. Ribeiro, D. Rimm, A. Salomon, M. Salto‐Tellez, J. Saltz, S. Sayed, K. P. Siziopikou, C. Sotiriou, A. Stenzinger, M. A. Sughayer, D. Sur, F. Symmans, S. Tanaka, T. Taxter, S. Tejpar, J. Teuwen, E. A. Thompson, T. Tramm, W. T. Tran, J. Van Der Laak, P. J. Van Diest, G. E. Verghese, G. Viale, M. Vieth, N. Wahab, T. Walter, Y. Waumans, H. Y. Wen, W. Yang, Y. Yuan, S. Adams, J. M. S. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, R. Salgado, E. Specht Stovgaard, G. Akturk, N. Bouchmaa, 2023

doi abstract
Improving Lesion Volume Measurements on Digital Mammograms
N. Moriakov, J. Peters, R. Mann, N. Karssemeijer, J. V. Dijck, M. Broeders, J. Teuwen, 2023

ArXiv abstract
Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer

The Journal of Pathology
J. Thagaard, G. Broeckx, D. B. Page, C. A. Jahangir, S. Verbandt, Z. Kos, R. Gupta, R. Khiroya, K. Abduljabbar, G. Acosta Haab, B. Acs, G. Akturk, J. S. Almeida, I. Alvarado‐Cabrero, M. Amgad, F. Azmoudeh‐Ardalan, S. Badve, N. B. Baharun, E. Balslev, E. R. Bellolio, V. Bheemaraju, K. R. Blenman, L. Botinelly Mendonça Fujimoto, N. Bouchmaa, O. Burgues, A. Chardas, M. Chon U Cheang, F. Ciompi, L. A. Cooper, A. Coosemans, G. Corredor, A. B. Dahl, F. L. Dantas Portela, F. Deman, S. Demaria, J. Doré Hansen, S. N. Dudgeon, T. Ebstrup, M. Elghazawy, C. Fernandez‐Martín, S. B. Fox, W. M. Gallagher, J. M. Giltnane, S. Gnjatic, P. I. Gonzalez‐Ericsson, A. Grigoriadis, N. Halama, M. G. Hanna, A. Harbhajanka, S. N. Hart, J. Hartman, S. Hauberg, S. Hewitt, A. I. Hida, H. M. Horlings, Z. Husain, E. Hytopoulos, S. Irshad, E. A. Janssen, M. Kahila, T. R. Kataoka, K. Kawaguchi, D. Kharidehal, A. I. Khramtsov, U. Kiraz, P. Kirtani, L. L. Kodach, K. Korski, A. Kovács, A. Laenkholm, C. Lang‐Schwarz, D. Larsimont, J. K. Lennerz, M. Lerousseau, X. Li, A. Ly, A. Madabhushi, S. K. Maley, V. Manur Narasimhamurthy, D. K. Marks, E. S. Mcdonald, R. Mehrotra, S. Michiels, F. U. A. A. Minhas, S. Mittal, D. A. Moore, S. Mushtaq, H. Nighat, T. Papathomas, F. Penault‐Llorca, R. D. Perera, C. J. Pinard, J. C. Pinto‐Cardenas, G. Pruneri, L. Pusztai, A. Rahman, N. M. Rajpoot, B. L. Rapoport, T. T. Rau, J. S. Reis‐Filho, J. M. Ribeiro, D. Rimm, A. Roslind, A. Vincent‐Salomon, M. Salto‐Tellez, J. Saltz, S. Sayed, E. Scott, K. P. Siziopikou, C. Sotiriou, A. Stenzinger, M. A. Sughayer, D. Sur, S. Fineberg, F. Symmans, S. Tanaka, T. Taxter, S. Tejpar, J. Teuwen, E. A. Thompson, T. Tramm, W. T. Tran, J. Van Der Laak, P. J. Van Diest, G. E. Verghese, G. Viale, M. Vieth, N. Wahab, T. Walter, Y. Waumans, H. Y. Wen, W. Yang, Y. Yuan, R. M. Zin, S. Adams, J. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, R. Salgado, E. Specht Stovgaard, 2023, 260;(5):498-513

doi abstract
Development, validation, and simplification of a scanner‐specific CT simulator

Medical Physics
S. A. M. Tunissen, L. J. Oostveen, N. Moriakov, J. Teuwen, K. Michielsen, E. J. Smit, I. Sechopoulos, 2023

doi abstract
vSHARP: variable Splitting Half-quadratic ADMM algorithm for Reconstruction of inverse-Problems
G. Yiasemis, N. Moriakov, J. Sonke, J. Teuwen, 2023

ArXiv abstract
Synthesis of Contrast-Enhanced Breast MRI Using T1- and Multi-b-Value DWI-Based Hierarchical Fusion Network with Attention Mechanism

Lecture Notes in Computer Science
T. Zhang, L. Han, A. D’Angelo, X. Wang, Y. Gao, C. Lu, J. Teuwen, R. Beets-Tan, T. Tan, R. Mann, 2023

doi abstract
Beyond the AJR: A Breakthrough in the Use of Artificial Intelligence for Mammography in Screening for Breast Cancer

American Journal of Roentgenology
R. M. Mann, J. Teuwen, 2023

doi
End‐to‐end memory‐efficient reconstruction for cone beam CT

Medical Physics
N. Moriakov, J. Sonke, J. Teuwen, 2023, 12;(50):7579-7593

doi preprints abstract
Kandinsky Conformal Prediction: Efficient Calibration of Image Segmentation Algorithms
J. Brunekreef, E. Marcus, R. Sheombarsing, J. Sonke, J. Teuwen, 2023

ArXiv abstract
JSSL: Joint Supervised and Self-supervised Learning for MRI Reconstruction
G. Yiasemis, N. Moriakov, C. I. Sánchez, J. Sonke, J. Teuwen, 2023

ArXiv abstract
Synthesis-based imaging-differentiation representation learning for multi-sequence 3D/4D MRI

Medical Image Analysis
L. Han, T. Tan, T. Zhang, Y. Huang, X. Wang, Y. Gao, J. Teuwen, R. Mann, 2023

doi abstract
Clinicopathological and prognostic value of calcification morphology descriptors in ductal carcinoma in situ of the breast: a systematic review and meta-analysis

Insights into Imaging
M. M. Van Leeuwen, S. Doyle, A. W. Van Den Belt–Dusebout, S. Van Der Mierden, C. E. Loo, R. M. Mann, J. Teuwen, J. Wesseling, 2023, 14;(1)

doi abstract
Deep learning-based breast region segmentation in raw and processed digital mammograms: generalization across views and vendors

Journal of Medical Imaging
S. D. Verboom, M. Caballo, J. Peters, J. Gommers, D. Van Den Oever, M. J. M. Broeders, J. Teuwen, I. Sechopoulos, 2023, 11;(01)

doi abstract

2022

FlowNet-PET: Unsupervised Learning to Perform Respiratory Motion Correction in PET Imaging
T. O'Briain, C. Uribe, K. M. Yi, J. Teuwen, I. Sechopoulos, M. Bazalova-Carter, 2022

ArXiv abstract
Evaluation of deep learning-based multiparametric MRI oropharyngeal primary tumor auto-segmentation and investigation of input channel effects: Results from a prospective imaging registry

Clinical and Translational Radiation Oncology
K. A. Wahid, S. Ahmed, R. He, L. V. Van Dijk, J. Teuwen, B. A. Mcdonald, V. Salama, A. S. Mohamed, T. Salzillo, C. Dede, N. Taku, S. Y. Lai, C. D. Fuller, M. A. Naser, 2022, 32

doi preprints
DeepSMILE: Contrastive self-supervised pre-training benefits MSI and HRD classification directly from H&E whole-slide images in colorectal and breast cancer

Medical Image Analysis
Y. Schirris, E. Gavves, I. Nederlof, H. M. Horlings, J. Teuwen, 2022, 79

doi
Application of Deep Learning in Breast Cancer Imaging

Seminars in Nuclear Medicine
L. Balkenende, J. Teuwen, R. M. Mann, 2022, 52;(5):584-596

doi
Multi-Coil MRI Reconstruction Challenge—Assessing Brain MRI Reconstruction Models and Their Generalizability to Varying Coil Configurations

Frontiers in Neuroscience
Y. Beauferris, J. Teuwen, D. Karkalousos, N. Moriakov, M. Caan, G. Yiasemis, L. Rodrigues, A. Lopes, H. Pedrini, L. Rittner, M. Dannecker, V. Studenyak, F. Gröger, D. Vyas, S. Faghih-Roohi, A. Kumar Jethi, J. Chandra Raju, M. Sivaprakasam, M. Lasby, N. Nogovitsyn, W. Loos, R. Frayne, R. Souza, 2022, 16

doi preprints abstract
DIRECT: Deep Image REConstruction Toolkit

Journal of Open Source Software
G. Yiasemis, N. Moriakov, D. Karkalousos, M. Caan, J. Teuwen, 2022, 7;(73):4278

doi
Deep MRI reconstruction with radial subsampling

Medical Imaging 2022: Physics of Medical Imaging
G. Yiasemis, C. Zhang, C. I. Sánchez, J. Sonke, J. Teuwen, 2022

doi preprints
Prediction of Upstaging in Ductal Carcinoma in Situ Based on Mammographic Radiomic Features

Radiology
R. Hou, L. J. Grimm, M. A. Mazurowski, J. R. Marks, L. M. King, C. C. Maley, T. Lynch, M. Van Oirsouw, K. Rogers, N. Stone, M. Wallis, J. Teuwen, J. Wesseling, E. S. Hwang, J. Y. Lo, 2022, 303;(1):54-62

doi
Exploiting the Dixon Method for a Robust Breast and Fibro-Glandular Tissue Segmentation in Breast MRI

Diagnostics
R. Samperna, N. Moriakov, N. Karssemeijer, J. Teuwen, R. M. Mann, 2022, 12;(7):1690

doi abstract
Deep learning-based breast tissue segmentation in digital mammography: generalization across views and vendors

Medical Imaging 2022: Image Processing
S. D. Verboom, M. Caballo, M. J. M. Broeders, J. Teuwen, I. Sechopoulos, 2022

doi
Tumor tracking in 4D CT images for adaptive radiotherapy

Medical Imaging 2022: Image Processing
P. S. Kronemeijer, E. Gavves, J. Sonke, J. Teuwen, 2022

doi
Mammary duct detection using self-supervised encoders

Medical Imaging 2022: Computer-Aided Diagnosis
S. Doyle, F. Dal Canton, J. Wesseling, C. I. Sánchez, J. Teuwen, 2022

doi
Breast imaging and deep learning: past, present, and future

Advances in Magnetic Resonance Technology and Applications
S. Eskreis-Winkler, J. Teuwen, S. Benson, 2022

doi
Recurrent variational network: A deep learning inverse problem solver applied to the task of accelerated mri reconstruction

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)
G. Yiasemis, J. Sonke, C. Sánchez, J. Teuwen, 2022

url preprints
Federated learning enables big data for rare cancer boundary detection.

Nature communications
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url abstract
WeakSTIL: weak whole-slide image level stromal tumor infiltrating lymphocyte scores are all you need

Medical Imaging 2022: Digital and Computational Pathology
Y. Schirris, M. Engelaer, A. Panteli, H. M. Horlings, E. Gavves, J. Teuwen, 2022

doi preprints
Prediction of histological grade and molecular subtypes of invasive breast cancer using mammographic growth rate in screening

European Journal of Cancer
J. Peters, N. Moriakov, J. Van Dijck, S. Elias, E. Lips, J. Wesseling, R. Mann, J. Teuwen, M. Caballo, M. Broeders, 2022, 175

doi