Spatial Information in Entropy-Based Image Registration. - Mert R. Sabuncu; Peter J. Ramadge (WBIR, 2003)

Fast alignment of digital images using a lower bound on an entropy metric. - Mert R. Sabuncu; Peter J. Ramadge (ICIP, 2004)

Graph-theoretic image registration using prior examples. - Mert Rory Sabuncu; Peter J. Ramadge (EUSIPCO, 2005)

Gradient Based Optimization of an EMST Image Registration Function. - Mert R. Sabuncu; Peter J. Ramadge (ICASSP (2), 2005)

What Data to Co-register for Computing Atlases. - B. T. Thomas Yeo; Mert R. Sabuncu; Hartmut Mohlberg; Katrin Amunts; Karl Zilles; Polina Golland; Bruce Fischl (ICCV, 2007)

A Robust Algorithm for Fiber-Bundle Atlas Construction. - Ulas Ziyan; Mert R. Sabuncu; W. Eric L. Grimson; Carl-Fredrik Westin (ICCV, 2007)

Nonlinear Registration of Diffusion MR Images Based on Fiber Bundles. - Ulas Ziyan; Mert R. Sabuncu; Lauren O'Donnell; Carl-Fredrik Westin (MICCAI (1), 2007)

Analysis of Surfaces Using Constrained Regression Models. - Sune Darkner; Mert R. Sabuncu; Polina Golland; Rasmus R. Paulsen; Rasmus Larsen 001 (MICCAI (1), 2008)

Discovering Modes of an Image Population through Mixture Modeling. - Mert R. Sabuncu; Serdar K. Balci; Polina Golland (MICCAI (2), 2008)

Spherical Demons: Fast Surface Registration. - B. T. Thomas Yeo; Mert R. Sabuncu; Tom Vercauteren; Nicholas Ayache; Bruce Fischl; Polina Golland (MICCAI (1), 2008)

Effects of registration regularization and atlas sharpness on segmentation accuracy. - B. T. Thomas Yeo; Mert R. Sabuncu; Rahul Desikan; Bruce Fischl; Polina Golland (Medical Image Anal., 2008)

Using Spanning Graphs for Efficient Image Registration. - Mert R. Sabuncu; Peter J. Ramadge (IEEE Trans. Image Process., 2008)

A Unified Framework for MR Based Disease Classification. - Kilian M. Pohl; Mert R. Sabuncu (IPMI, 2009)

Image-Driven Population Analysis Through Mixture Modeling. - Mert R. Sabuncu (ISBI, 2009)

Supervised Nonparametric Image Parcellation. - Mert R. Sabuncu; B. T. Thomas Yeo; Koen Van Leemput; Bruce Fischl; Polina Golland (MICCAI (1), 2009)

Asymmetric Image-Template Registration. - Mert R. Sabuncu; B. T. Thomas Yeo; Koen Van Leemput; Tom Vercauteren; Polina Golland (MICCAI (1), 2009)

Task-Optimal Registration Cost Functions. - B. T. Thomas Yeo; Mert R. Sabuncu; Polina Golland; Bruce Fischl (MICCAI (1), 2009)

Consistency Clustering: A Robust Algorithm for Group-wise Registration, Segmentation and Automatic Atlas Construction in Diffusion MRI. - Ulas Ziyan; Mert R. Sabuncu; W. Eric L. Grimson; Carl-Fredrik Westin (Int. J. Comput. Vis., 2009)

Image-Driven Population Analysis Through Mixture Modeling. - Mert R. Sabuncu; Serdar K. Balci; Martha Elizabeth Shenton; Polina Golland (IEEE Trans. Medical Imaging, 2009)

Robust Atlas-Based Segmentation of Highly Variable Anatomy: Left Atrium Segmentation. - Michal Depa; Mert R. Sabuncu; Godtfred Holmvang; Reza Nezafat; Ehud J. Schmidt; Polina Golland (STACOM/CESC, 2010)

A Generative Model for Image Segmentation Based on Label Fusion. - Mert R. Sabuncu; B. T. Thomas Yeo; Koenraad Van Leemput; Bruce Fischl; Polina Golland (IEEE Trans. Medical Imaging, 2010)

Spherical Demons: Fast Diffeomorphic Landmark-Free Surface Registration. - B. T. Thomas Yeo; Mert R. Sabuncu; Tom Vercauteren; Nicholas Ayache; Bruce Fischl; Polina Golland (IEEE Trans. Medical Imaging, 2010)

Learning Task-Optimal Registration Cost Functions for Localizing Cytoarchitecture and Function in the Cerebral Cortex. - B. T. Thomas Yeo; Mert R. Sabuncu; Tom Vercauteren; Daphne J. Holt; Katrin Amunts; Karl Zilles; Polina Golland; Bruce Fischl (IEEE Trans. Medical Imaging, 2010)

Modeling anatomical heterogeneity in populations. - Polina Golland; Mert R. Sabuncu (ICASSP, 2011)

The Relevance Voxel Machine (RVoxM): A Bayesian Method for Image-Based Prediction. - Mert R. Sabuncu; Koen Van Leemput (MICCAI (3), 2011)

A generative model for multi-atlas segmentation across modalities. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (ISBI, 2012)

A Generative Model for Probabilistic Label Fusion of Multimodal Data. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (MBIA, 2012)

Incorporating Parameter Uncertainty in Bayesian Segmentation Models: Application to Hippocampal Subfield Volumetry. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (MICCAI (3), 2012)

The influence of head motion on intrinsic functional connectivity MRI. - Koene R. A. Van Dijk; Mert R. Sabuncu; Randy L. Buckner (NeuroImage, 2012)

Measuring and comparing brain cortical surface area and other areal quantities. - Anderson M. Winkler; Mert R. Sabuncu; B. T. Thomas Yeo; Bruce Fischl; Douglas N. Greve; Peter V. Kochunov; Thomas E. Nichols; John Blangero; David C. Glahn (NeuroImage, 2012)

The Relevance Voxel Machine (RVoxM): A Self-Tuning Bayesian Model for Informative Image-Based Prediction. - Mert R. Sabuncu; Koen Van Leemput (IEEE Trans. Medical Imaging, 2012)

Joint Modeling of Imaging and Genetics. - Nematollah Batmanghelich; Adrian V. Dalca; Mert R. Sabuncu; Polina Golland (IPMI, 2013)

Symmetric non-rigid image registration via an adaptive quasi-volume-preserving constraint. - Iman Aganj; Martin Reuter 001; Mert R. Sabuncu; Bruce Fischl (ISBI, 2013)

An Improved Optimization Method for the Relevance Voxel Machine. - Melanie Ganz; Mert R. Sabuncu; Koen Van Leemput (MLMI, 2013)

A Probabilistic, Non-parametric Framework for Inter-modality Label Fusion. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (MICCAI (3), 2013)

On Feature Relevance in Image-Based Prediction Models: An Empirical Study. - Ender Konukoglu; Melanie Ganz; Koen Van Leemput; Mert R. Sabuncu (MLMI, 2013)

Example-Based Restoration of High-Resolution Magnetic Resonance Image Acquisitions. - Ender Konukoglu; André J. W. van der Kouwe; Mert Rory Sabuncu; Bruce Fischl (MICCAI (1), 2013)

A Bayesian Algorithm for Image-Based Time-to-Event Prediction. - Mert R. Sabuncu (MLMI, 2013)

A Surface-based Analysis of Language Lateralization and Cortical Asymmetry. - Douglas N. Greve; Lise Van der Haegen; Qing Cai; Steven M. Stufflebeam; Mert R. Sabuncu; Bruce Fischl; Marc Brysbaert (J. Cogn. Neurosci., 2013)

Improved inference in Bayesian segmentation using Monte Carlo sampling: Application to hippocampal subfield volumetry. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (Medical Image Anal., 2013)

A unified framework for cross-modality multi-atlas segmentation of brain MRI. - Juan Eugenio Iglesias; Mert Rory Sabuncu; Koen Van Leemput (Medical Image Anal., 2013)

Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models. - Jorge L. Bernal-Rusiel; Douglas N. Greve; Martin Reuter 001; Bruce Fischl; Mert R. Sabuncu (NeuroImage, 2013)

Spatiotemporal linear mixed effects modeling for the mass-univariate analysis of longitudinal neuroimage data. - Jorge L. Bernal-Rusiel; Martin Reuter 001; Douglas N. Greve; Bruce Fischl; Mert R. Sabuncu (NeuroImage, 2013)

On Removing Interpolation and Resampling Artifacts in Rigid Image Registration. - Iman Aganj; B. T. Thomas Yeo; Mert R. Sabuncu; Bruce Fischl (IEEE Trans. Image Process., 2013)

Segmentation of Cerebrovascular Pathologies in Stroke Patients with Spatial and Shape Priors. - Adrian Vasile Dalca; Ramesh Sridharan; Lisa Cloonan; Kaitlin M. Fitzpatrick; Allison Kanakis; Karen L. Furie; Jonathan Rosand; Ona Wu; Mert R. Sabuncu; Natalia S. Rost; Polina Golland (MICCAI (2), 2014)

A Cautionary Analysis of STAPLE Using Direct Inference of Segmentation Truth. - Koenraad Van Leemput; Mert R. Sabuncu (MICCAI (1), 2014)

A Universal and Efficient Method to Compute Maps from Image-Based Prediction Models. - Mert R. Sabuncu (MICCAI (3), 2014)

Event time analysis of longitudinal neuroimage data. - Mert R. Sabuncu; Jorge L. Bernal-Rusiel; Martin Reuter 001; Douglas N. Greve; Bruce Fischl (NeuroImage, 2014)

Mid-Space-Independent Symmetric Data Term for Pairwise Deformable Image Registration. - Iman Aganj; Juan Eugenio Iglesias; Martin Reuter 001; Mert R. Sabuncu; Bruce Fischl (MICCAI (2), 2015)

Predictive Modeling of Anatomy with Genetic and Clinical Data. - Adrian V. Dalca; Ramesh Sridharan; Mert R. Sabuncu; Polina Golland (MICCAI (3), 2015)

A Sparse Bayesian Learning Algorithm for Longitudinal Image Data. - Mert R. Sabuncu (MICCAI (3), 2015)

Multi-atlas segmentation of biomedical images: A survey. - Juan Eugenio Iglesias; Mert R. Sabuncu (Medical Image Anal., 2015)

Avoiding symmetry-breaking spatial non-uniformity in deformable image registration via a quasi-volume-preserving constraint. - Iman Aganj; Martin Reuter 001; Mert R. Sabuncu; Bruce Fischl (NeuroImage, 2015)

Corrigendum to "Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models" [NeuroImage 66 (1 February 2013) 249-260]. - Jorge L. Bernal-Rusiel; Douglas N. Greve; Martin Reuter 001; Bruce Fischl; Mert R. Sabuncu (NeuroImage, 2015)

Corrigendum to "Spatiotemporal linear mixed effects modeling for the mass-univariate analysis of longitudinal neuroimage data" [NeuroImage 81 (1 November 2013) 358-370]. - Jorge L. Bernal-Rusiel; Martin Reuter 001; Douglas N. Greve; Bruce Fischl; Mert R. Sabuncu (NeuroImage, 2015)

A kernel machine method for detecting effects of interaction between multidimensional variable sets: An imaging genetics application. - Tian Ge; Thomas E. Nichols; Debashis Ghosh; Elizabeth C. Mormino; Jordan W. Smoller; Mert R. Sabuncu (NeuroImage, 2015)

An algorithm for optimal fusion of atlases with different labeling protocols. - Juan Eugenio Iglesias; Mert Rory Sabuncu; Iman Aganj; Priyanka Bhatt; Christen Casillas; David H. Salat; Adam L. Boxer; Bruce Fischl; Koen Van Leemput (NeuroImage, 2015)

Corrigendum to "Event time analysis of longitudinal neuroimage data" [NeuroImage 97 (15 August 2014) 9-18]. - Mert R. Sabuncu; Jorge L. Bernal-Rusiel; Martin Reuter 001; Douglas N. Greve; Bruce Fischl (NeuroImage, 2015)

Clinical Prediction from Structural Brain MRI Scans: A Large-Scale Empirical Study. - Mert R. Sabuncu; Ender Konukoglu (Neuroinformatics, 2015)

Population Based Image Imputation. - Adrian V. Dalca; Katherine L. Bouman; William T. Freeman; Natalia S. Rost; Mert R. Sabuncu; Polina Golland (IPMI, 2017)

Guest editorial of the IJCARS MICCAI 2016 special issue. - Sébastien Ourselin; Mert R. Sabuncu; William M. Wells III; Leo Joskowicz; Gözde B. Ünal; Andreas K. Maier (Int. J. Comput. Assist. Radiol. Surg., 2017)

The 19th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2016). - Sébastien Ourselin; Mert R. Sabuncu; William M. Wells III; Leo Joskowicz; Gözde B. Ünal; Andreas K. Maier (Medical Image Anal., 2017)

Mid-space-independent deformable image registration. - Iman Aganj; Juan Eugenio Iglesias; Martin Reuter 001; Mert Rory Sabuncu; Bruce Fischl (NeuroImage, 2017)

Diffeomorphic functional brain surface alignment: Functional demons. - Karl-Heinz Nenning; Hesheng Liu; Satrajit S. Ghosh; Mert R. Sabuncu; Ernst Schwartz; Georg Langs (NeuroImage, 2017)

An Unsupervised Learning Model for Deformable Medical Image Registration. - Guha Balakrishnan; Amy Zhao; Mert R. Sabuncu; John V. Guttag; Adrian V. Dalca (CVPR, 2018)

Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation. - Adrian V. Dalca; John V. Guttag; Mert R. Sabuncu (CVPR, 2018)

Unsupervised Learning for Fast Probabilistic Diffeomorphic Registration. - Adrian V. Dalca; Guha Balakrishnan; John V. Guttag; Mert R. Sabuncu (MICCAI (1), 2018)

3D Convolutional Neural Networks for Classification of Functional Connectomes. - Meenakshi Khosla; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (DLMIA/ML-CDS@MICCAI, 2018)

A Bayesian Disease Progression Model for Clinical Trajectories. - Yingying Zhu 004; Mert R. Sabuncu (GRAIL/Beyond-MIC@MICCAI, 2018)

Generalized Cross Entropy Loss for Training Deep Neural Networks with Noisy Labels. - Zhilu Zhang 004; Mert R. Sabuncu (NeurIPS, 2018)

Is deep learning better than kernel regression for functional connectivity prediction of fluid intelligence? - Tong He; Ru Kong; Avram J. Holmes; Mert R. Sabuncu; Simon B. Eickhoff; Danilo Bzdok; Jiashi Feng; B. T. Thomas Yeo (PRNI, 2018)

Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models. - Mohammad Haft-Javaherian; Linjing Fang; Victorine P. Muse; Chris B. Schaffer; Nozomi Nishimura; Mert R. Sabuncu (CoRR, 2018)

A Probabilistic Disease Progression Model for Predicting Future Clinical Outcome. - Yingying Zhu 004; Mert R. Sabuncu (CoRR, 2018)

Ensemble learning with 3D convolutional neural networks for connectome-based prediction. - Meenakshi Khosla; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (CoRR, 2018)

Machine learning in resting-state fMRI analysis. - Meenakshi Khosla; Keith Jamison; Gia H. Ngo; Amy Kuceyeski; Mert R. Sabuncu (CoRR, 2018)

Learning-Based Optimization of the Under-Sampling Pattern in MRI. - Cagla Deniz Bahadir; Adrian V. Dalca; Mert R. Sabuncu (IPMI, 2019)

A Convolutional Autoencoder Approach To Learn Volumetric Shape Representations For Brain Structures. - Evan M. Yu; Mert R. Sabuncu (ISBI, 2019)

Unsupervised Deep Learning for Bayesian Brain MRI Segmentation. - Adrian V. Dalca; Evan M. Yu; Polina Golland; Bruce Fischl; Mert R. Sabuncu; Juan Eugenio Iglesias (MICCAI (3), 2019)

Detecting Abnormalities in Resting-State Dynamics: An Unsupervised Learning Approach. - Meenakshi Khosla; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (MLMI@MICCAI, 2019)

RSANet: Recurrent Slice-Wise Attention Network for Multiple Sclerosis Lesion Segmentation. - Hang Zhang 010; Jinwei Zhang; Qihao Zhang; Jeremy Kim; Shun Zhang; Susan A. Gauthier; Pascal Spincemaille; Thanh D. Nguyen; Mert R. Sabuncu; Yi Wang 028 (MICCAI (3), 2019)

Detecting Cannabis-Associated Cognitive Impairment Using Resting-State fNIRS. - Yingying Zhu 004; Jodi M. Gilman; Anne Eden Evins; Mert R. Sabuncu (MICCAI (5), 2019)

Learning Conditional Deformable Templates with Convolutional Networks. - Adrian V. Dalca; Marianne Rakic; John V. Guttag; Mert R. Sabuncu (NeurIPS, 2019)

Image Registration in Medical Robotics and Intelligent Systems: Fundamentals and Applications. - Jun Liu 007; Gurpreet Singh; Subhi Al'Aref; Benjamin C. Lee; Olachi Oleru; James K. Min; Simon Dunham; Mert R. Sabuncu; Bobak Mosadegh (Adv. Intell. Syst., 2019)

Unsupervised Data Imputation via Variational Inference of Deep Subspaces. - Adrian V. Dalca; John V. Guttag; Mert R. Sabuncu (CoRR, 2019)

Confidence Calibration for Convolutional Neural Networks Using Structured Dropout. - Zhilu Zhang 004; Adrian V. Dalca; Mert R. Sabuncu (CoRR, 2019)

Adaptive Compressed Sensing MRI with Unsupervised Learning. - Cagla Deniz Bahadir; Adrian V. Dalca; Mert R. Sabuncu (CoRR, 2019)

Few Labeled Atlases are Necessary for Deep-Learning-Based Segmentation. - Hyeon Woo Lee; Mert R. Sabuncu; Adrian V. Dalca (CoRR, 2019)

Unsupervised learning of probabilistic diffeomorphic registration for images and surfaces. - Adrian V. Dalca; Guha Balakrishnan; John V. Guttag; Mert R. Sabuncu (Medical Image Anal., 2019)

Ensemble learning with 3D convolutional neural networks for functional connectome-based prediction. - Meenakshi Khosla; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (NeuroImage, 2019)

Global signal regression strengthens association between resting-state functional connectivity and behavior. - Jingwei Li 003; Ru Kong; Raphaël Liégeois; Csaba Orban; Yanrui Tan; Nanbo Sun; Avram J. Holmes; Mert R. Sabuncu; Tian Ge; B. T. Thomas Yeo (NeuroImage, 2019)

Multi-modal latent factor exploration of atrophy, cognitive and tau heterogeneity in Alzheimer's disease. - Nanbo Sun; Elizabeth C. Mormino; Jianzhong Chen; Mert R. Sabuncu; B. T. Thomas Yeo; Alzheimer's Disease Neuroimaging Initiative (NeuroImage, 2019)

VoxelMorph: A Learning Framework for Deformable Medical Image Registration. - Guha Balakrishnan; Amy Zhao; Mert R. Sabuncu; John V. Guttag; Adrian V. Dalca (IEEE Trans. Medical Imaging, 2019)

Medical Image Imputation From Image Collections. - Adrian V. Dalca; Katherine L. Bouman; William T. Freeman; Natalia S. Rost; Mert R. Sabuncu; Polina Golland (IEEE Trans. Medical Imaging, 2019)

Synthetic Learning: Learn From Distributed Asynchronized Discriminator GAN Without Sharing Medical Image Data. - Qi Chang; Hui Qu; Yikai Zhang 003; Mert R. Sabuncu; Chao Chen 012; Tong Zhang 001; Dimitris N. Metaxas (CVPR, 2020)

Volumetric Landmark Detection with a Multi-Scale Shift Equivariant Neural Network. - Tianyu Ma; Ajay Gupta; Mert R. Sabuncu (ISBI, 2020)

A Shared Neural Encoding Model for the Prediction of Subject-Specific fMRI Response. - Meenakshi Khosla; Gia H. Ngo; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (MICCAI (7), 2020)

From Connectomic to Task-Evoked Fingerprints: Individualized Prediction of Task Contrasts from Resting-State Functional Connectivity. - Gia H. Ngo; Meenakshi Khosla; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (MICCAI (7), 2020)

Neural Network-Based Reconstruction in Compressed Sensing MRI Without Fully-Sampled Training Data. - Alan Q. Wang 003; Adrian V. Dalca; Mert R. Sabuncu (MLMIR@MICCAI, 2020)

Learning Conditional Deformable Shape Templates for Brain Anatomy. - Evan M. Yu; Adrian V. Dalca; Mert R. Sabuncu (MLMI@MICCAI, 2020)

Extending LOUPE for K-Space Under-Sampling Pattern Optimization in Multi-coil MRI. - Jinwei Zhang; Hang Zhang 010; Alan Wang 003; Qihao Zhang; Mert R. Sabuncu; Pascal Spincemaille; Thanh D. Nguyen; Yi Wang 028 (MLMIR@MICCAI, 2020)

An Auto-Encoder Strategy for Adaptive Image Segmentation. - Evan M. Yu; Juan Eugenio Iglesias; Adrian V. Dalca; Mert R. Sabuncu (MIDL, 2020)

Bayesian Learning of Probabilistic Dipole Inversion for Quantitative Susceptibility Mapping. - Jinwei Zhang; Hang Zhang 010; Mert R. Sabuncu; Pascal Spincemaille; Thanh D. Nguyen; Yi Wang 028 (MIDL, 2020)

Neural encoding with visual attention. - Meenakshi Khosla; Gia H. Ngo; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (NeurIPS, 2020)

Self-Distillation as Instance-Specific Label Smoothing. - Zhilu Zhang 004; Mert R. Sabuncu (NeurIPS, 2020)

Learning the Distribution: A Unified Distillation Paradigm for Fast Uncertainty Estimation in Computer Vision. - Yichen Shen 003; Zhilu Zhang 004; Mert R. Sabuncu; Lin Sun (CoRR, 2020)

Intelligence plays dice: Stochasticity is essential for machine learning. - Mert R. Sabuncu (CoRR, 2020)

Deep neural networks and kernel regression achieve comparable accuracies for functional connectivity prediction of behavior and demographics. - Tong He; Ru Kong; Avram J. Holmes; Minh Nguyen 002; Mert R. Sabuncu; Simon B. Eickhoff; Danilo Bzdok; Jiashi Feng; B. T. Thomas Yeo (NeuroImage, 2020)

Fidelity imposed network edit (FINE) for solving ill-posed image reconstruction. - Jinwei Zhang; Zhe Liu 042; Shun Zhang; Hang Zhang 010; Pascal Spincemaille; Thanh D. Nguyen; Mert R. Sabuncu; Yi Wang 028 (NeuroImage, 2020)

Deep-Learning-Based Optimization of the Under-Sampling Pattern in MRI. - Cagla Deniz Bahadir; Alan Q. Wang 003; Adrian V. Dalca; Mert R. Sabuncu (IEEE Trans. Computational Imaging, 2020)

Text2Brain: Synthesis of Brain Activation Maps from Free-Form Text Query. - Gia H. Ngo; Minh Nguyen 002; Nancy F. Chen; Mert R. Sabuncu (MICCAI (7), 2021)

HyperRecon: Regularization-Agnostic CS-MRI Reconstruction with Hypernetworks. - Alan Q. Wang 003; Adrian V. Dalca; Mert R. Sabuncu (MLMIR@MICCAI, 2021)

Joint Optimization of Hadamard Sensing and Reconstruction in Compressed Sensing Fluorescence Microscopy. - Alan Q. Wang 003; Aaron K. LaViolette; Leo Moon; Chris Xu; Mert R. Sabuncu (MICCAI (6), 2021)

Temporal Feature Fusion with Sampling Pattern Optimization for Multi-echo Gradient Echo Acquisition and Image Reconstruction. - Jinwei Zhang; Hang Zhang 010; Chao Li; Pascal Spincemaille; Mert R. Sabuncu; Thanh D. Nguyen; Yi Wang 028 (MICCAI (6), 2021)

Hybrid optimization between iterative and network fine-tuning reconstructions for fast quantitative susceptibility mapping. - Jinwei Zhang; Hang Zhang 010; Pascal Spincemaille; Thanh D. Nguyen; Mert R. Sabuncu; Yi Wang 028 (MIDL, 2021)

Ensembling Low Precision Models for Binary Biomedical Image Segmentation. - Tianyu Ma; Hang Zhang 010; Hanley Ong; Amar Vora; Thanh D. Nguyen; Ajay Gupta; Yi Wang 028; Mert R. Sabuncu (WACV, 2021)

Real-Time Uncertainty Estimation in Computer Vision via Uncertainty-Aware Distribution Distillation. - Yichen Shen 003; Zhilu Zhang 004; Mert R. Sabuncu; Lin Sun (WACV, 2021)

Regularization-Agnostic Compressed Sensing MRI Reconstruction with Hypernetworks. - Alan Q. Wang 003; Adrian V. Dalca; Mert R. Sabuncu (CoRR, 2021)

NeuroGen: activation optimized image synthesis for discovery neuroscience. - Zijin Gu; Keith Jamison; Meenakshi Khosla; Emily J. Allen; Yihan Wu; Thomas Naselaris; Kendrick N. Kay; Mert R. Sabuncu; Amy Kuceyeski (CoRR, 2021)

Ex uno plures: Splitting One Model into an Ensemble of Subnetworks. - Zhilu Zhang 004; Vianne R. Gao; Mert R. Sabuncu (CoRR, 2021)

Label conditioned segmentation. - Tianyu Ma; Benjamin C. Lee; Mert R. Sabuncu (MIDL, 2022)

KeyMorph: Robust Multi-modal Affine Registration via Unsupervised Keypoint Detection. - Evan M. Yu; Alan Q. Wang 003; Adrian V. Dalca; Mert R. Sabuncu (MIDL, 2022)

Characterizing the Ventral Visual Stream with Response-Optimized Neural Encoding Models. - Meenakshi Khosla; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (NeurIPS, 2022)

Hyper-Convolution Networks for Biomedical Image Segmentation. - Tianyu Ma; Adrian V. Dalca; Mert R. Sabuncu (WACV, 2022)

Personalized visual encoding model construction with small data. - Zijin Gu; Keith Jamison; Mert R. Sabuncu; Amy Kuceyeski (CoRR, 2022)

Hyper-Convolutions via Implicit Kernels for Medical Imaging. - Tianyu Ma; Alan Q. Wang 003; Adrian V. Dalca; Mert R. Sabuncu (CoRR, 2022)

Computing Multiple Image Reconstructions with a Single Hypernetwork. - Alan Q. Wang 003; Adrian V. Dalca; Mert R. Sabuncu (CoRR, 2022)

Semi-Parametric Deep Neural Networks in Linear Time and Memory. - Richa Rastogi; Yuntian Deng; Ian Lee; Mert R. Sabuncu; Volodymyr Kuleshov (CoRR, 2022)

GLACIAL: Granger and Learning-based Causality Analysis for Longitudinal Studies. - Minh Nguyen 002; Gia H. Ngo; Mert R. Sabuncu (CoRR, 2022)

A Simple Nadaraya-Watson Head can offer Explainable and Calibrated Classification. - Alan Q. Wang 003; Mert R. Sabuncu (CoRR, 2022)

A transformer-Based neural language model that synthesizes brain activation maps from free-form text queries. - Gia H. Ngo; Minh Nguyen 002; Nancy F. Chen; Mert R. Sabuncu (Medical Image Anal., 2022)

NeuroGen: Activation optimized image synthesis for discovery neuroscience. - Zijin Gu; Keith Jamison; Meenakshi Khosla; Emily J. Allen; Yihan Wu; Ghislain St-Yves; Thomas Naselaris; Kendrick N. Kay; Mert R. Sabuncu; Amy Kuceyeski (NeuroImage, 2022)

Predicting individual task contrasts from resting-state functional connectivity using a surface-based convolutional network. - Gia H. Ngo; Meenakshi Khosla; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (NeuroImage, 2022)

UniverSeg: Universal Medical Image Segmentation. - Victor Ion Butoi; Jose Javier Gonzalez Ortiz; Tianyu Ma; Mert R. Sabuncu; John V. Guttag; Adrian V. Dalca (ICCV, 2023)

Semi-Parametric Inducing Point Networks and Neural Processes. - Richa Rastogi; Yair Schiff; Alon Hacohen; Zhaozhi Li; Ian Lee; Yuntian Deng; Mert R. Sabuncu; Volodymyr Kuleshov (ICLR, 2023)

Characterizing the Features of Mitotic Figures Using a Conditional Diffusion Probabilistic Model. - Cagla Deniz Bahadir; Benjamin Liechty; David J. Pisapia; Mert R. Sabuncu (DGM4MICCAI, 2023)

Neural Pre-processing: A Learning Framework for End-to-End Brain MRI Pre-processing. - Xinzi He; Alan Q. Wang 003; Mert R. Sabuncu (MICCAI (8), 2023)

Empirical Analysis of a Segmentation Foundation Model in Prostate Imaging. - Heejong Kim; Victor Ion Butoi; Adrian V. Dalca; Mert R. Sabuncu (ISIC/Care-AI/MedAGI/DeCaF@MICCAI, 2023)

Zero-Shot Learning of Individualized Task Contrast Prediction from Resting-State Functional Connectomes. - Minh Nguyen 002; Gia H. Ngo; Mert R. Sabuncu (DALI@MICCAI, 2023)

Decoding natural image stimuli from fMRI data with a surface-based convolutional network. - Zijin Gu; Keith Jamison; Amy Kuceyeski; Mert R. Sabuncu (MIDL, 2023)

Learning to Compare Longitudinal Images. - Heejong Kim; Mert R. Sabuncu (MIDL, 2023)

Learning Invariant Representations with a Nonparametric Nadaraya-Watson Head. - Alan Q. Wang 003; Minh Nguyen 002; Mert R. Sabuncu (NeurIPS, 2023)

Patchwork Learning: A Paradigm Towards Integrative Analysis across Diverse Biomedical Data Sources. - Suraj Rajendran; Weishen Pan; Mert R. Sabuncu; Yong Chen 016; Jiayu Zhou; Fei Wang 001 (CoRR, 2023)

Deep learning analysis of blood flow sounds to detect arteriovenous fistula stenosis. - George Zhou; Yunchan Chen; Candace Chien; Leslie Revatta; Jannatul Ferdous; Michelle Chen; Shourov Deb; Sol De Leon Cruz; Alan Wang 003; Benjamin Lee; Mert R. Sabuncu; William Browne; et al. (npj Digit. Medicine, 2023)

A Flexible Nadaraya-Watson Head Can Offer Explainable and Calibrated Classification. - Alan Q. Wang 003; Mert R. Sabuncu (Trans. Mach. Learn. Res., 2023)

LARO: Learned acquisition and reconstruction optimization to accelerate quantitative susceptibility mapping. - Jinwei Zhang; Pascal Spincemaille; Hang Zhang 010; Thanh D. Nguyen; Chao Li; Jiahao Li 006; Ilhami Kovanlikaya; Mert R. Sabuncu; Yi Wang 028 (NeuroImage, 2023)

Hyper-convolutions via implicit kernels for medical image analysis. - Tianyu Ma; Alan Q. Wang 003; Adrian V. Dalca; Mert R. Sabuncu (Medical Image Anal., 2023)

A robust and interpretable deep learning framework for multi-modal registration via keypoints. - Alan Q. Wang 003; Evan M. Yu; Adrian V. Dalca; Mert R. Sabuncu (Medical Image Anal., 2023)

Assessing the Significance of Longitudinal Data in Alzheimer's Disease Forecasting. - Batuhan K. Karaman; Mert R. Sabuncu (AIiH (1), 2024)

Adapting to Shifting Correlations with Unlabeled Data Calibration. - Minh Nguyen 002; Alan Q. Wang 003; Heejong Kim; Mert R. Sabuncu (ECCV (87), 2024)

Longitudinal Mammogram Risk Prediction. - Batuhan K. Karaman; Katerina Dodelzon; Gözde Bozdagi Akar; Mert R. Sabuncu (MICCAI (5), 2024)

Robust Learning via Conditional Prevalence Adjustment. - Minh Nguyen 002; Alan Q. Wang 003; Heejong Kim; Mert R. Sabuncu (WACV, 2024)

A Framework for Interpretability in Machine Learning for Medical Imaging. - Alan Q. Wang 003; Batuhan K. Karaman; Heejong Kim; Jacob Rosenthal; Rachit Saluja; Sean I. Young; Mert R. Sabuncu (IEEE Access, 2024)

BrainMorph: A Foundational Keypoint Model for Robust and Flexible Brain MRI Registration. - Alan Q. Wang 003; Rachit Saluja; Heejong Kim; Xinzi He; Adrian V. Dalca; Mert R. Sabuncu (CoRR, 2024)

The 2024 Brain Tumor Segmentation (BraTS) Challenge: Glioma Segmentation on Post-treatment MRI. - Maria Correia de Verdier; Rachit Saluja; Louis Gagnon; Dominic LaBella; Ujjwal Baid; Nourel Hoda Tahon; Martha Foltyn-Dumitru; Jikai Zhang; Maram Alafif; Saif Baig; Ken Chang; Gennaro D'Anna; et al. (CoRR, 2024)

Effective Segmentation of Post-Treatment Gliomas Using Simple Approaches: Artificial Sequence Generation and Ensemble Models. - Heejong Kim; Léo Milecki; Mina C. Moghadam; Fengbei Liu; Minh Nguyen 002; Eric Qiu; Abhishek Thanki; Mert R. Sabuncu (CoRR, 2024)

POROver: Improving Safety and Reducing Overrefusal in Large Language Models with Overgeneration and Preference Optimization. - Batuhan K. Karaman; Ishmam Zabir; Alon Benhaim; Vishrav Chaudhary; Mert R. Sabuncu; Xia Song (CoRR, 2024)

Learning across diverse biomedical data modalities and cohorts: Challenges and opportunities for innovation. - Suraj Rajendran; Weishen Pan; Mert R. Sabuncu; Yong Chen 016; Jiayu Zhou; Fei Wang 001 (Patterns, 2024)

Efficient Identification of Direct Causal Parents via Invariance and Minimum Error Testing. - Minh Nguyen 002; Mert R. Sabuncu (Trans. Mach. Learn. Res., 2024)

LLM-Generated Rewrite and Context Modulation for Enhanced Vision Language Models in Digital Pathology. - Cagla Deniz Bahadir; Gozde Bozdagi Akar; Mert R. Sabuncu (WACV, 2025)

Rethinking clinical trials for medical AI with dynamic deployments of adaptive systems. - Jacob Rosenthal; Ashley Beecy; Mert R. Sabuncu (npj Digit. Medicine, 2025)

Knockout: A simple way to handle missing inputs. - Minh Nguyen 002; Batuhan K. Karaman; Heejong Kim; Alan Q. Wang 003; Fengbei Liu; Mert R. Sabuncu (Trans. Mach. Learn. Res., 2025)

CASC-AI: Consensus-aware Self-corrective AI Agents for Noise Cell Segmentation. - Ruining Deng; Yihe Yang; David J. Pisapia; Benjamin Liechty; Junchao Zhu; Juming Xiong; Junlin Guo; Zhengyi Lu; Jiacheng Wang; Xing Yao; Runxuan Yu; Rendong Zhang; et al. (CoRR, 2025)

Cancer Type, Stage and Prognosis Assessment from Pathology Reports using LLMs. - Rachit Saluja; Jacob Rosenthal; Yoav Artzi; David J. Pisapia; Benjamin Liechty; Mert R. Sabuncu (CoRR, 2025)

Fine-tuning Vision Language Models with Graph-based Knowledge for Explainable Medical Image Analysis. - Chenjun Li; Laurin Lux; Alexander H. Berger; Martin J. Menten; Mert R. Sabuncu; Johannes C. Paetzold (CoRR, 2025)

IRS: Incremental Relationship-guided Segmentation for Digital Pathology. - Ruining Deng; Junchao Zhu; Juming Xiong; Can Cui 006; Tianyuan Yao; Junlin Guo; Siqi Lu; Marilyn Lionts; Mengmeng Yin; Yu Wang; Shilin Zhao; Yucheng Tang; et al. (CoRR, 2025)

RealKeyMorph: Keypoints in Real-world Coordinates for Resolution-agnostic Image Registration. - Mina C. Moghadam; Alan Q. Wang 001; Omer Taub; Martin R. Prince; Mert R. Sabuncu (CoRR, 2025)

BPD-Neo: An MRI Dataset for Lung-Trachea Segmentation with Clinical Data for Neonatal Bronchopulmonary Dysplasia. - Rachit Saluja; Arzu Kovanlikaya; Candace Chien; Lauren Kathryn Blatt; Jeffrey M. Perlman; Stefan Worgall; Mert R. Sabuncu; Jonathan P. Dyke (CoRR, 2025)

Modality-agnostic, patient-specific digital twins modeling temporally varying digestive motion. - Jorge Tapias Gomez; Nishant Nadkarni; Lando S. Bosma; Jue Jiang; Ergys D. Subashi; William P. Segars; James M. Balter; Mert R. Sabuncu; Neelam Tyagi; Harini Veeraraghavan (CoRR, 2025)

CoFi: A Fast Coarse-to-Fine Few-Shot Pipeline for Glomerular Basement Membrane Segmentation. - Hongjin Fang; Daniel Reisenbüchler; Kenji Ikemura; Mert R. Sabuncu; Yihe Yang; Ruining Deng (CoRR, 2025)

DyMorph-B2I: Dynamic and Morphology-Guided Binary-to-Instance Segmentation for Renal Pathology. - Leiyue Zhao; Yuechen Yang; Yanfan Zhu; Haichun Yang; Yuankai Huo; Paul Dennis Simonson; Kenji Ikemura; Mert R. Sabuncu; Yihe Yang; Ruining Deng (CoRR, 2025)