Respiratory Motion Correction in Emission Tomography Image Reconstruction. - Mauricio Reyes 001; Grégoire Malandain; Pierre Malick Koulibaly; Miguel Ángel González Ballester; Jacques Darcourt (MICCAI (2), 2005)

On the adequacy of principal factor analysis for the study of shape variability. - Miguel Ángel González Ballester; Marius George Linguraru; Mauricio Reyes Aguirre; Nicholas Ayache (Image Processing, 2005)

Respiratory Motion Compensation in Emission Tomography. (Compensation du mouvement respiratoire en tomographie d'émission). - Mauricio Reyes Aguirre (2005)

Statistical Shape Analysis via Principal Factor Analysis. - Mauricio Reyes 001; Marius George Linguraru; Kostas Marias; Nicholas Ayache; Lutz-Peter Nolte; Miguel Ángel González Ballester (ISBI, 2007)

Statistical Shape Space Analysis Based on Level Sets. - Nina Kozic; Miguel Ángel González Ballester; Moritz Tannast; Lutz-Peter Nolte; Mauricio Reyes 001 (MIAR, 2008)

Hierarchical Markov Random Fields Applied to Model Soft Tissue Deformations on Graphics Hardware. - Christof Seiler; Philippe Büchler; Lutz-Peter Nolte; Mauricio Reyes 001; Rasmus R. Paulsen (Recent Advances in the 3D Physiological Human, 2009)

Population-Specific Evaluation of Implant Bone Fitting Using PCA Shape Space and Level Sets. - Nina Kozic; Miguel Ángel González Ballester; Philippe Büchler; Nils Reimers 002; Lutz-Peter Nolte; Marius George Linguraru; Mauricio Reyes 001 (ISBI, 2009)

Anatomical Variability of Organs Via Principal Factor Analysis from the Construction of an Abdominal Probabilistic Atlas. - Mauricio Reyes 001; Miguel Ángel González Ballester; Zhixi Li; Nina Kozic; See Chin; Ronald M. Summers; Marius George Linguraru (ISBI, 2009)

Conditional Variability of Statistical Shape Models Based on Surrogate Variables. - Rémi Blanc; Mauricio Reyes 001; Christof Seiler; Gábor Székely (MICCAI (1), 2009)

Multi-modal diffeomorphic demons registration based on point-wise mutual information. - Huanxiang Lu; Mauricio Reyes 001; Amira Serijovic; Stefan Weber 002; Yasuo Sakurai; Hitoshi Yamagata; Philippe C. Cattin (ISBI, 2010)

Parametric regression of 3D medical images through the exploration of non-parametric regression models. - Christof Seiler; Xavier Pennec; Mauricio Reyes 001 (ISBI, 2010)

Automated Intervertebral Disc Detection from Low Resolution, Sparse MRI Images for the Planning of Scan Geometries. - Xiao Dong; Huanxiang Lu; Yasuo Sakurai; Hitoshi Yamagata; Guoyan Zheng; Mauricio Reyes 001 (MLMI, 2010)

Anatomically-Driven Soft-Tissue Simulation Strategy for Cranio-Maxillofacial Surgery Using Facial Muscle Template Model. - Hyungmin Kim 001; Philipp Jürgens; Lutz-Peter Nolte; Mauricio Reyes 001 (MICCAI (1), 2010)

Optimisation of orthopaedic implant design using statistical shape space analysis based on level sets. - Nina Kozic; Stefan Weber 002; Philippe Büchler; Christian Lutz; Nils Reimers 002; Miguel Ángel González Ballester; Mauricio Reyes 001 (Medical Image Anal., 2010)

Segmentation of brain tumor images based on atlas-registration combined with a Markov-Random-Field lesion growth model. - Stefan Bauer; Lutz-Peter Nolte; Mauricio Reyes 001 (ISBI, 2011)

Diffusion weighted imaging distortion correction using hybrid multimodal image registration. - Huanxiang Lu; Philippe C. Cattin; Lutz-Peter Nolte; Mauricio Reyes 001 (ISBI, 2011)

Fully Automatic Segmentation of Brain Tumor Images Using Support Vector Machine Classification in Combination with Hierarchical Conditional Random Field Regularization. - Stefan Bauer; Lutz-Peter Nolte; Mauricio Reyes 001 (MICCAI (3), 2011)

Minimization of Intra-Operative Shaping of Orthopaedic Fixation Plates: A Population-Based Design. - Habib Bousleiman; Lucas E. Ritacco; Lutz-Peter Nolte; Mauricio Reyes 001 (MICCAI (2), 2011)

Geometry-Aware Multiscale Image Registration via OBBTree-Based Polyaffine Log-Demons. - Christof Seiler; Xavier Pennec; Mauricio Reyes 001 (MICCAI (2), 2011)

Femur specific polyaffine model to regularize the log-domain demons registration. - Christof Seiler; Xavier Pennec; Lucas E. Ritacco; Mauricio Reyes 001 (Image Processing, 2011)

Population-Based Design of Mandibular Plates Based on Bone Quality and Morphology. - Habib Bousleiman; Christof Seiler; Tateyuki Iizuka; Lutz-Peter Nolte; Mauricio Reyes 001 (MICCAI (1), 2012)

Simultaneous Multiscale Polyaffine Registration by Incorporating Deformation Statistics. - Christof Seiler; Xavier Pennec; Mauricio Reyes 001 (MICCAI (2), 2012)

Evaluation of a portable image overlay projector for the visualisation of surgical navigation data: phantom studies. - Kate A. Gavaghan; Thiago Oliveira-Santos; Matthias Peterhans; Mauricio Reyes 001; H. Kim; Sylvain Anderegg; Stefan Weber 002 (Int. J. Comput. Assist. Radiol. Surg., 2012)

Skull-stripping for Tumor-bearing Brain Images - Stefan Bauer; Lutz-Peter Nolte; Mauricio Reyes 001 (CoRR, 2012)

Interest points localization for brain image using landmark-annotated atlas. - Huanxiang Lu; Lutz-Peter Nolte; Mauricio Reyes 001 (Int. J. Imaging Syst. Technol., 2012)

Statistical model based shape prediction from a combination of direct observations and various surrogates: Application to orthopaedic research. - Rémi Blanc; Christof Seiler; Gábor Székely; Lutz-Peter Nolte; Mauricio Reyes 001 (Medical Image Anal., 2012)

Capturing the multiscale anatomical shape variability with polyaffine transformation trees. - Christof Seiler; Xavier Pennec; Mauricio Reyes 001 (Medical Image Anal., 2012)

Multiscale Modeling for Image Analysis of Brain Tumor Studies. - Stefan Bauer; Christian May; Dimitra D. Dionysiou; Georgios S. Stamatakos; Philippe Büchler; Mauricio Reyes 001 (IEEE Trans. Biomed. Eng., 2012)

Accuracy improvement in Cranio-Maxillofacial soft tissue simulation using a muscle embedded meshing approach. - Kamal Shahim; Orcun Goksel; Philipp Jürgens; Mauricio Reyes 001 (EMBC, 2013)

Integrated Spatio-Temporal Segmentation of Longitudinal Brain Tumor Imaging Studies. - Stefan Bauer; Jean Tessier; Oliver Krieter; Lutz-Peter Nolte; Mauricio Reyes 001 (MCV, 2013)

Prediction of Cranio-Maxillofacial Surgical Planning Using an Inverse Soft Tissue Modelling Approach. - Kamal Shahim; Philipp Jürgens; Philippe C. Cattin; Lutz-Peter Nolte; Mauricio Reyes 001 (MICCAI (1), 2013)

Hierarchical segmentation-assisted multimodal registration for MR brain images. - Huanxiang Lu; Roland Beisteiner; Lutz-Peter Nolte; Mauricio Reyes 001 (Comput. Medical Imaging Graph., 2013)

Integrated segmentation of brain tumor images for radiotherapy and neurosurgery. - Stefan Bauer; Huanxiang Lu; Christian May; Lutz-Peter Nolte; Philippe Büchler; Mauricio Reyes 001 (Int. J. Imaging Syst. Technol., 2013)

Towards automatic MRI volumetry for treatment selection in acute ischemic stroke patients. - Stefan Bauer; Pascal P. Gratz; Jan Gralla; Mauricio Reyes 001; Roland Wiest (EMBC, 2014)

Interactive segmentation of MR images from brain tumor patients. - Stefan Bauer; Nicole Porz; Raphael Meier; Alessia Pica; Johannes Slotboom; Roland Wiest; Mauricio Reyes 001 (ISBI, 2014)

Generalized Multiresolution Hierarchical Shape Models via Automatic Landmark Clusterization. - Juan J. Cerrolaza; Arantxa Villanueva; Mauricio Reyes 001; Rafael Cabeza; Miguel Ángel González Ballester; Marius George Linguraru (MICCAI (3), 2014)

Spatially Varying Registration Using Gaussian Processes. - Thomas Gerig; Kamal Shahim; Mauricio Reyes 001; Thomas Vetter; Marcel Lüthi (MICCAI (2), 2014)

Patient-Specific Semi-supervised Learning for Postoperative Brain Tumor Segmentation. - Raphael Meier; Stefan Bauer; Johannes Slotboom; Roland Wiest; Mauricio Reyes 001 (MICCAI (1), 2014)

Patient Specific Simulation for Planning of Cochlear Implantation Surgery. - Sergio Vera; Frederic Pérez; Clara Balust; Ramon Trueba; Jordi Rubió; Raul Calvo; Xavier Mazaira; Anandhan Dhanasingh; Livia Barazzetti; Mauricio Reyes 001; Mario Ceresa; Jens Fagertun; et al. (CLIP@MICCAI, 2014)

3D Face Reconstruction from Video Using 3D Morphable Model and Silhouette. - Christian Baumberger; Mauricio Reyes 001; Mihai Constantinescu; Radu Olariu; Edilson de Aguiar; Thiago Oliveira-Santos (SIBGRAPI, 2014)

Facial nerve image enhancement from CBCT using supervised learning technique. - Ping Lu 003; Livia Barazzetti; Vimal Chandran; Kate A. Gavaghan; Stefan Weber 002; Nicolas Gerber; Mauricio Reyes 001 (EMBC, 2015)

Correction tool for Active Shape Model based lumbar muscle segmentation. - Waldo Valenzuela; Stephen J. Ferguson; Dominika Ignasiak; Gaelle Diserens; Peter Vermathen; Chris Boesch; Mauricio Reyes 001 (EMBC, 2015)

Prediction of Trabecular Bone Anisotropy from Quantitative Computed Tomography Using Supervised Learning and a Novel Morphometric Feature Descriptor. - Vimal Chandran; Philippe Zysset; Mauricio Reyes 001 (MICCAI (1), 2015)

Segmenting the Ischemic Penumbra: A Decision Forest Approach with Automatic Threshold Finding. - Richard McKinley; Levin Häni; Roland Wiest; Mauricio Reyes 001 (Brainles@MICCAI, 2015)

Parameter Learning for CRF-Based Tissue Segmentation of Brain Tumors. - Raphael Meier; Venetia Karamitsou; Simon Habegger; Roland Wiest; Mauricio Reyes 001 (Brainles@MICCAI, 2015)

Automatic multi-resolution shape modeling of multi-organ structures. - Juan J. Cerrolaza; Mauricio Reyes 001; Ronald M. Summers; Miguel Ángel González Ballester; Marius George Linguraru (Medical Image Anal., 2015)

The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS). - Bjoern H. Menze; András Jakab; Stefan Bauer; Jayashree Kalpathy-Cramer; Keyvan Farahani; Justin S. Kirby; Yuliya Burren; Nicole Porz; Johannes Slotboom; Roland Wiest; Levente Lanczi; Elizabeth R. Gerstner; et al. (IEEE Trans. Medical Imaging, 2015)

Super-Resolution Classification Improves Facial Nerve Segmentation from CBCT Imaging. - Ping Lu 003; Livia Barazzetti; Vimal Chandran; Kate A. Gavaghan; Stefan Weber 002; Nicolas Gerber; Mauricio Reyes 001 (CURAC, 2016)

Advanced Design System for Infantile Cranium Shape Model Growth Prediction. - Kamal Shahim; Mauricio Reyes 001; Ruben Simon; Philipp Jürgens; Christoph Blecher (MIAR, 2016)

Nabla-net: A Deep Dag-Like Convolutional Architecture for Biomedical Image Segmentation. - Richard McKinley; Rik Wepfer; Tom Gundersen; Franca Wagner; Andrew Chan; Roland Wiest; Mauricio Reyes 001 (BrainLes@MICCAI, 2016)

CRF-Based Brain Tumor Segmentation: Alleviating the Shrinking Bias. - Raphael Meier; Urspeter Knecht; Roland Wiest; Mauricio Reyes 001 (BrainLes@MICCAI, 2016)

High-Throughput Glomeruli Analysis of μ CT Kidney Images Using Tree Priors and Scalable Sparse Computation. - Carlos Correa Shokiche; Philipp Baumann; Ruslan Hlushchuk; Valentin Djonov; Mauricio Reyes 001 (MICCAI (2), 2016)

Towards Uncertainty-Assisted Brain Tumor Segmentation and Survival Prediction. - Alain Jungo; Richard McKinley; Raphael Meier; Urspeter Knecht; Luis Vera; Julián Pérez-Beteta; David Molina-García; Víctor M. Pérez-García; Roland Wiest; Mauricio Reyes 001 (BrainLes@MICCAI, 2017)

Pooling-Free Fully Convolutional Networks with Dense Skip Connections for Semantic Segmentation, with Application to Brain Tumor Segmentation. - Richard McKinley; Alain Jungo; Roland Wiest; Mauricio Reyes 001 (BrainLes@MICCAI, 2017)

Perturb-and-MPM: Quantifying Segmentation Uncertainty in Dense Multi-Label CRFs. - Raphael Meier; Urspeter Knecht; Alain Jungo; Roland Wiest; Mauricio Reyes 001 (CoRR, 2017)

Fast and uncertainty-aware cerebral cortex morphometry estimation using random forest regression. - Yannick Suter; Christian Rummel; Roland Wiest; Mauricio Reyes 001 (ISBI, 2018)

Magnetic Resonance Fingerprinting Reconstruction via Spatiotemporal Convolutional Neural Networks. - Fabian Balsiger; Amaresha Shridhar Konar; Shivaprasad Chikop; Vimal Chandran; Olivier Scheidegger; Sairam Geethanath; Mauricio Reyes 001 (MLMIR@MICCAI, 2018)

On the Effect of Inter-observer Variability for a Reliable Estimation of Uncertainty of Medical Image Segmentation. - Alain Jungo; Raphael Meier; Ekin Ermis; Marcela Blatti-Moreno; Evelyn Herrmann; Roland Wiest; Mauricio Reyes 001 (MICCAI (1), 2018)

Efficient Active Learning for Image Classification and Segmentation Using a Sample Selection and Conditional Generative Adversarial Network. - Dwarikanath Mahapatra; Behzad Bozorgtabar; Jean-Philippe Thiran; Mauricio Reyes 001 (MICCAI (2), 2018)

Automatic Brain Tumor Grading from MRI Data Using Convolutional Neural Networks and Quality Assessment. - Sérgio Pereira; Raphael Meier; Victor Alves; Mauricio Reyes 001; Carlos A. Silva 002 (MLCN/DLF/iMIMIC@MICCAI, 2018)

Enhancing Clinical MRI Perfusion Maps with Data-Driven Maps of Complementary Nature for Lesion Outcome Prediction. - Adriano Pinto; Sérgio Pereira; Raphael Meier; Victor Alves; Roland Wiest; Carlos A. Silva 002; Mauricio Reyes 001 (MICCAI (3), 2018)

Deep Learning Versus Classical Regression for Brain Tumor Patient Survival Prediction. - Yannick Suter; Alain Jungo; Michael Rebsamen; Urspeter Knecht; Evelyn Herrmann; Roland Wiest; Mauricio Reyes 001 (BrainLes@MICCAI (2), 2018)

Patient-specific estimation of detailed cochlear shape from clinical CT images. - Hans Martin Kjer; Jens Fagertun; Wilhelm Wimmer; Nicolas Gerber; Sergio Vera; Livia Barazzetti; Nerea Mangado Lopez; Mario Ceresa; Gemma Piella; Thomas Stark; Martin Stauber; Mauricio Reyes 001; et al. (Int. J. Comput. Assist. Radiol. Surg., 2018)

Uncertainty-driven Sanity Check: Application to Postoperative Brain Tumor Cavity Segmentation. - Alain Jungo; Raphael Meier; Ekin Ermis; Evelyn Herrmann; Mauricio Reyes 001 (CoRR, 2018)

Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge. - Spyridon Bakas; Mauricio Reyes 001; András Jakab; Stefan Bauer; Markus Rempfler; Alessandro Crimi; Russell Takeshi Shinohara; Christoph Berger; Sung Min Ha; Martin Rozycki; Marcel Prastawa; Esther Alberts; et al. (CoRR, 2018)

Enhancing interpretability of automatically extracted machine learning features: application to a RBM-Random Forest system on brain lesion segmentation. - Sérgio Pereira; Raphael Meier; Richard McKinley; Roland Wiest; Victor Alves; Carlos A. Silva 002; Mauricio Reyes 001 (Medical Image Anal., 2018)

Highly Accurate Facial Nerve Segmentation Refinement From CBCT/CT Imaging Using a Super-Resolution Classification Approach. - Ping Lu 003; Livia Barazzetti; Vimal Chandran; Kate A. Gavaghan; Stefan Weber 002; Nicolas Gerber; Mauricio Reyes 001 (IEEE Trans. Biomed. Eng., 2018)

Learning Shape Representation on Sparse Point Clouds for Volumetric Image Segmentation. - Fabian Balsiger; Yannick Soom; Olivier Scheidegger; Mauricio Reyes 001 (MICCAI (2), 2019)

Dual-Stream Pyramid Registration Network. - Xiaojun Hu; Miao Kang; Weilin Huang; Matthew R. Scott; Roland Wiest; Mauricio Reyes 001 (MICCAI (2), 2019)

Assessing Reliability and Challenges of Uncertainty Estimations for Medical Image Segmentation. - Alain Jungo; Mauricio Reyes 001 (MICCAI (2), 2019)

Surface-Based Brain Morphometry for the Prediction of Fluid Intelligence in the Neurocognitive Prediction Challenge 2019. - Michael Rebsamen; Christian Rummel; Ines Mürner-Lavanchy; Mauricio Reyes 001; Roland Wiest; Richard McKinley (ABCD-NP@MICCAI, 2019)

On the Spatial and Temporal Influence for the Reconstruction of Magnetic Resonance Fingerprinting. - Fabian Balsiger; Olivier Scheidegger; Pierre G. Carlier; Benjamin Marty; Mauricio Reyes 001 (MIDL, 2019)

Simultaneous lesion and neuroanatomy segmentation in Multiple Sclerosis using deep neural networks. - Richard McKinley; Rik Wepfer; Fabian Aschwanden; Lorenz Grunder; Raphaela Muri; Christian Rummel; Rajeev Verma; Christian Weisstanner; Mauricio Reyes 001; Anke Salmen; Andrew Chan; Franca Wagner; et al. (CoRR, 2019)

Few-shot brain segmentation from weakly labeled data with deep heteroscedastic multi-task networks. - Richard McKinley; Michael Rebsamen; Raphael Meier; Mauricio Reyes 001; Christian Rummel; Roland Wiest (CoRR, 2019)

Automatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence. - Richard McKinley; Lorenz Grunder; Rik Wepfer; Fabian Aschwanden; Tim Fischer 005; Christoph Friedli; Raphaela Muri; Christian Rummel; Rajeev Verma; Christian Weisstanner; Mauricio Reyes 001; Anke Salmen; et al. (CoRR, 2019)

Informative sample generation using class aware generative adversarial networks for classification of chest Xrays. - Behzad Bozorgtabar; Dwarikanath Mahapatra; Hendrik von Teng; Alexander Pollinger; Lukas Ebner; Jean-Philippe Thiran; Mauricio Reyes 001 (Comput. Vis. Image Underst., 2019)

Supervised learning for bone shape and cortical thickness estimation from CT images for finite element analysis. - Vimal Chandran; Ghislain Maquer; Thomas Gerig; Philippe Zysset; Mauricio Reyes 001 (Medical Image Anal., 2019)

Overall Survival Prediction for Glioblastoma on Pre-treatment MRI Using Robust Radiomics and Priors. - Yannick Suter; Urspeter Knecht; Roland Wiest; Mauricio Reyes 001 (BrainLes@MICCAI (1), 2020)

Deep Learning-based Type Identification of Volumetric MRI Sequences. - Jean Pablo Vieira de Mello; Thiago M. Paixão; Rodrigo Ferreira Berriel; Mauricio Reyes 001; Claudine Badue; Alberto F. De Souza; Thiago Oliveira-Santos (ICPR, 2020)

Interpretability vs. Complexity: The Friction in Deep Neural Networks. - José Pereira Amorim; Pedro H. Abreu; Mauricio Reyes 001; João A. M. Santos (IJCNN, 2020)

Learning Bloch Simulations for MR Fingerprinting by Invertible Neural Networks. - Fabian Balsiger; Alain Jungo; Olivier Scheidegger; Benjamin Marty; Mauricio Reyes 001 (MLMIR@MICCAI, 2020)

Interpretability-Guided Content-Based Medical Image Retrieval. - Wilson Silva; Alexander Pollinger; Jaime S. Cardoso 001; Mauricio Reyes 001 (MICCAI (1), 2020)

Towards MRI Progression Features for Glioblastoma Patients: From Automated Volumetry and Classical Radiomics to Deep Feature Learning. - Yannick Suter; Urspeter Knecht; Roland Wiest; Ekkehard Hewer; Philippe Schucht; Mauricio Reyes 001 (MLCN/RNO-AI@MICCAI, 2020)

Brain SegNet: 3D local refinement network for brain lesion segmentation. - Xiaojun Hu; Weijian Luo; Jiliang Hu; Sheng Guo 005; Weilin Huang; Matthew R. Scott; Roland Wiest; Michael Dahlweid; Mauricio Reyes 001 (BMC Medical Imaging, 2020)

Spatially regularized parametric map reconstruction for fast magnetic resonance fingerprinting. - Fabian Balsiger; Alain Jungo; Olivier Scheidegger; Pierre G. Carlier; Mauricio Reyes 001; Benjamin Marty (Medical Image Anal., 2020)

Comparison of MR Preprocessing Strategies and Sequences for Radiomics-Based MGMT Prediction. - Daniel Abler; Vincent Andrearczyk; Valentin Oreiller; Javier Barranco Garcia; Diem Vuong; Stephanie Tanadini-Lang; Matthias Guckenberger; Mauricio Reyes 001; Adrien Depeursinge (BrainLes@MICCAI (2), 2021)

Prediction of Stroke Lesion at 90-Day Follow-Up by Fusing Raw DSC-MRI With Parametric Maps Using Deep Learning. - Adriano Pinto; Joana Amorim; Arsany Hakim; Victor Alves; Mauricio Reyes 001; Carlos A. Silva 002 (IEEE Access, 2021)

Analyzing magnetic resonance imaging data from glioma patients using deep learning. - Bjoern H. Menze; Fabian Isensee; Roland Wiest; Benedikt Wiestler; Klaus H. Maier-Hein; Mauricio Reyes 001; Spyridon Bakas (Comput. Medical Imaging Graph., 2021)

pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis. - Alain Jungo; Olivier Scheidegger; Mauricio Reyes 001; Fabian Balsiger (Comput. Methods Programs Biomed., 2021)

Common Limitations of Image Processing Metrics: A Picture Story. - Annika Reinke; Matthias Eisenmann; Minu Dietlinde Tizabi; Carole H. Sudre; Tim Rädsch; Michela Antonelli; Tal Arbel; Spyridon Bakas; M. Jorge Cardoso; Veronika Cheplygina; Keyvan Farahani; Ben Glocker; et al. (CoRR, 2021)

Combining unsupervised and supervised learning for predicting the final stroke lesion. - Adriano Pinto; Sérgio Pereira; Raphael Meier; Roland Wiest; Victor Alves; Mauricio Reyes 001; Carlos A. Silva 002 (Medical Image Anal., 2021)

The predictive value of segmentation metrics on dosimetry in organs at risk of the brain. - Robert Poel; Elias Rüfenacht; Evelyn Hermann; Stefan Scheib; Peter Manser; Daniel M. Aebersold; Mauricio Reyes 001 (Medical Image Anal., 2021)

Interpretability-Driven Sample Selection Using Self Supervised Learning for Disease Classification and Segmentation. - Dwarikanath Mahapatra; Alexander Pollinger; Ling Shao 001; Mauricio Reyes 001 (IEEE Trans. Medical Imaging, 2021)

Medical Image Super Resolution by Preserving Interpretable and Disentangled Features. - Dwarikanath Mahapatra; Behzad Bozorgtabar; Mauricio Reyes 001 (ECCV Workshops (7), 2022)

Multi-label Attention Map Assisted Deep Feature Learning for Medical Image Classification. - Dwarikanath Mahapatra; Mauricio Reyes 001 (ECCV Workshops (7), 2022)

Reliability of Quantification Estimates in MR Spectroscopy: CNNs vs Traditional Model Fitting. - Rudy Rizzo; Martyna Dziadosz; Sreenath P. Kyathanahally; Mauricio Reyes 001; Roland Kreis (MICCAI (8), 2022)

Metrics reloaded: Pitfalls and recommendations for image analysis validation. - Lena Maier-Hein; Annika Reinke; Evangelia Christodoulou; Ben Glocker; Patrick Godau; Fabian Isensee; Jens Kleesiek; Michal Kozubek 001; Mauricio Reyes 001; Michael A. Riegler; Manuel Wiesenfarth; Michael Baumgartner 001; et al. (CoRR, 2022)

ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset. - Moritz Roman Hernandez Petzsche; Ezequiel de la Rosa; Uta Hanning; Roland Wiest; Waldo Enrique Valenzuela Pinilla; Mauricio Reyes 001; Maria Inês Meyer; Sook-Lei Liew; Florian Kofler; Ivan Ezhov; David Robben; Alexandre Hutton; et al. (CoRR, 2022)

Dual-stream pyramid registration network. - Miao Kang; Xiaojun Hu; Weilin Huang; Matthew R. Scott; Mauricio Reyes 001 (Medical Image Anal., 2022)

Interpretability-Guided Inductive Bias For Deep Learning Based Medical Image. - Dwarikanath Mahapatra; Alexander Poellinger; Mauricio Reyes 001 (Medical Image Anal., 2022)

Self-Supervised Generalized Zero Shot Learning for Medical Image Classification Using Novel Interpretable Saliency Maps. - Dwarikanath Mahapatra; Zongyuan Ge; Mauricio Reyes 001 (IEEE Trans. Medical Imaging, 2022)

Towards Radiomics-Based Automated Disease Progression Assessment for Glioblastoma Patients. - Yannick Suter; Flurina Schuhmacher; Ekin Ermis; Urspeter Knecht; Philippe Schucht; Roland Wiest; Mauricio Reyes 001 (BrainLes/SWITCH@MICCAI, 2023)

ASTRA: Atomic Surface Transformations for Radiotherapy Quality Assurance. - Amith Kamath; Robert Poel; Jonas Willmann; Ekin Ermis; Nicolaus Andratschke; Mauricio Reyes 001 (EMBC, 2023)

How Sensitive Are Deep Learning Based Radiotherapy Dose Prediction Models To Variability In Organs At Risk Segmentation? - Amith Kamath; Robert Poel; Jonas Willmann; Nicolaus Andratschke; Mauricio Reyes 001 (ISBI, 2023)

SaGTTA: Saliency Guided Test Time Augmentation for Medical Image Segmentation Across Vendor Domain Shift. - Suhang You; Devavrat Tomar; Behzad Bozorgtabar; Mauricio Reyes 001 (ISBI, 2023)

Do We Really Need that Skip-Connection? Understanding Its Interplay with Task Complexity. - Amith Kamath; Jonas Willmann; Nicolaus Andratschke; Mauricio Reyes 001 (MICCAI (4), 2023)

Class Specific Feature Disentanglement and Text Embeddings for Multi-label Generalized Zero Shot CXR Classification. - Dwarikanath Mahapatra; Antonio José Jimeno-Yepes; Shiba Kuanar; Sudipta Roy 002; Behzad Bozorgtabar; Mauricio Reyes 001; Zongyuan Ge (MICCAI (2), 2023)

Dose Guidance for Radiotherapy-Oriented Deep Learning Segmentation. - Elias Rüfenacht; Robert Poel; Amith Kamath; Ekin Ermis; Stefan Scheib; Michael K. Fix; Mauricio Reyes 001 (MICCAI (9), 2023)

Understanding metric-related pitfalls in image analysis validation. - Annika Reinke; Minu Tizabi; Michael Baumgartner 001; Matthias Eisenmann; Doreen Heckmann-Nötzel; A. Emre Kavur; Tim Rädsch; Carole H. Sudre; Laura Ación; Michela Antonelli; Tal Arbel; Spyridon Bakas; et al. (CoRR, 2023)

Graph Node Based Interpretability Guided Sample Selection for Active Learning. - Dwarikanath Mahapatra; Alexander Poellinger; Mauricio Reyes 001 (IEEE Trans. Medical Imaging, 2023)

PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion. - Elias Rüfenacht; Amith Kamath; Yannick Suter; Robert Poel; Ekin Ermis; Stefan Scheib; Mauricio Reyes 001 (Comput. Methods Programs Biomed., 2023)

Combining Graph Transformers Based Multi-Label Active Learning and Informative Data Augmentation for Chest Xray Classification. - Dwarikanath Mahapatra; Behzad Bozorgtabar; Zongyuan Ge; Mauricio Reyes 001; Jean-Philippe Thiran (AAAI, 2024)

DWARF: Disease-Weighted Network for Attention Map Refinement. - Haozhe Luo; Aurélie Pahud de Mortanges; Oana Inel; Mauricio Reyes 001 (ISIC/iMIMIC/EARTH/DeCaF@MICCAI, 2024)

AutoDoseRank: Automated Dosimetry-Informed Segmentation Ranking for Radiotherapy. - Zahira Mercado; Amith Kamath; Robert Poel; Jonas Willmann; Ekin Ermis; Elena Riggenbach; Lucas Mose; Nicolaus Andratschke; Mauricio Reyes 001 (CaPTion@MICCAI, 2024)

INFORMER- Interpretability Founded Monitoring of Medical Image Deep Learning Models. - Shelley Zixin Shu; Aurélie Pahud de Mortanges; Alexander Poellinger; Dwarikanath Mahapatra; Mauricio Reyes 001 (UNSURE@MICCAI, 2024)

Comparing the Performance of Radiation Oncologists versus a Deep Learning Dose Predictor to Estimate Dosimetric Impact of Segmentation Variations for Radiotherapy. - Amith Kamath; Zahira Maur; Robert Poel; Jonas Willmann; Ekin Ermis; Elena Riggenbach; Nicolaus Andratschke; Mauricio Reyes 001 (MIDL, 2024)

Prior knowledge-guided vision-transformer-based unsupervised domain adaptation for intubation prediction in lung disease at one week. - Junlin Yang; John Anderson Garcia Henao; Nicha C. Dvornek; Jianchun He; Danielle V. Bower; Arno Depotter; Herkus Bajercius; Aurélie Pahud de Mortanges; Chenyu You; Christopher Gange; Roberta Eufrasia Ledda; Mario Silva; et al. (Comput. Medical Imaging Graph., 2024)

A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge. - Ezequiel de la Rosa; Mauricio Reyes 001; Sook-Lei Liew; Alexandre Hutton; Roland Wiest; Johannes Kaesmacher; Uta Hanning; Arsany Hakim; Richard Zubal; Waldo Valenzuela; David Robben; Diana Maria Sima; et al. (CoRR, 2024)

DWARF: Disease-weighted network for attention map refinement. - Haozhe Luo; Aurélie Pahud de Mortanges; Oana Inel; Abraham Bernstein; Mauricio Reyes 001 (CoRR, 2024)

ISLES'24: Improving final infarct prediction in ischemic stroke using multimodal imaging and clinical data. - Ezequiel de la Rosa; Ruisheng Su; Mauricio Reyes 001; Roland Wiest; Evamaria Olga Riedel; Florian Kofler; Kaiyuan Yang 003; Hakim Baazaoui; David Robben; Susanne Wegener; Jan S. Kirschke; Benedikt Wiestler; et al. (CoRR, 2024)

ISLES 2024: The first longitudinal multimodal multi-center real-world dataset in (sub-)acute stroke. - Evamaria Olga Riedel; Ezequiel de la Rosa; The Anh Baran; Moritz Roman Hernandez Petzsche; Hakim Baazaoui; Kaiyuan Yang 003; David Robben; Joaquin Oscar Seia; Roland Wiest; Mauricio Reyes 001; Ruisheng Su; Claus Zimmer; et al. (CoRR, 2024)

GANDALF: Graph-based transformer and Data Augmentation Active Learning Framework with interpretable features for multi-label chest Xray classification. - Dwarikanath Mahapatra; Behzad Bozorgtabar; Zongyuan Ge; Mauricio Reyes 001 (Medical Image Anal., 2024)

ALFREDO: Active Learning with FeatuRe disEntangelement and DOmain adaptation for medical image classification. - Dwarikanath Mahapatra; Ruwan B. Tennakoon; Yasmeen George; Sudipta Roy 002; Behzad Bozorgtabar; Zongyuan Ge; Mauricio Reyes 001 (Medical Image Anal., 2024)

Orchestrating explainable artificial intelligence for multimodal and longitudinal data in medical imaging. - Aurélie Pahud de Mortanges; Haozhe Luo; Shelley Zixin Shu; Amith Kamath; Yannick Suter; Mohamed Shelan; Alexander Poellinger; Mauricio Reyes 001 (npj Digit. Medicine, 2024)

SaRF: Saliency regularized feature learning improves MRI sequence classification. - Suhang You; Roland Wiest; Mauricio Reyes 001 (Comput. Methods Programs Biomed., 2024)

In the Picture: Medical Imaging Datasets, Artifacts, and their Living Review. - Amelia Jiménez-Sánchez; Natalia Rozalia Avlona; Sarah de Boer; Víctor M. Campello; Aasa Feragen; Enzo Ferrante; Melanie Ganz; Judy Wawira Gichoya; Camila González; Steff Groefsema; Alessa Hering; Adam Hulman; et al. (FAccT, 2025)

AUDIT: An open-source Python library for AI model evaluation with use cases in MRI brain tumor segmentation. - Carlos Aumente-Maestro; Michael Müller; Beatriz Remeseiro; Jorge Díez 001; Mauricio Reyes 001 (Comput. Methods Programs Biomed., 2025)

Multi-Label Generalized Zero Shot Chest X-Ray Classification by Combining Image-Text Information With Feature Disentanglement. - Dwarikanath Mahapatra; Antonio Jimeno-Yepes; Behzad Bozorgtabar; Sudipta Roy 002; Zongyuan Ge; Mauricio Reyes 001 (IEEE Trans. Medical Imaging, 2025)

From Claims to Evidence: A Unified Framework and Critical Analysis of CNN vs. Transformer vs. Mamba in Medical Image Segmentation. - Pooya Mohammadi Kazaj; Giovanni Baj; Yazdan Salimi; Anselm W. Stark; Waldo Valenzuela; George CM. Siontis; Habib Zaidi; Mauricio Reyes 001; Christoph Graeni; Isaac Shiri (CoRR, 2025)

ROXSI: Robust Cross-Sequence Semantic Interaction for Brain Tumor Segmentation on Multi-Sequence MR Images. - Zhuo Kuang; Zengqiang Yan; Aly Abayazeed; Franca Wagner; Li Yu 003; Mauricio Reyes 001 (IEEE J. Biomed. Health Informatics, 2025)

Corrections to "Multi-Label Generalized Zero Shot Chest X-Ray Classification By Combining Image-Text Information With Feature Disentanglement". - Dwarikanath Mahapatra; Antonio Jimeno-Yepes; Behzad Bozorgtabar; Sudipta Roy 002; Zongyuan Ge; Mauricio Reyes 001 (IEEE Trans. Medical Imaging, 2025)

On the Interplay of Human-AI Alignment,Fairness, and Performance Trade-offs in Medical Imaging. - Haozhe Luo; Ziyu Zhou; Shelley Zixin Shu; Aurélie Pahud de Mortanges; Robert Berke; Mauricio Reyes 001 (CoRR, 2025)

The added value for MRI radiomics and deep-learning for glioblastoma prognostication compared to clinical and molecular information. - Daniel Abler; O. Pusterla; A. Joye-Kühnis; Nicolaus Andratschke; Meritxell Bach; A. Bink; S. M. Christ; Patric Hagmann; B. Pouymayou; E. Pravatà; Piotr Radojewski; Mauricio Reyes 001; et al. (CoRR, 2025)