John A. Onofrey

64 papers A* 1A 1Misc 1Journal 31Unranked 30

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Equi-ViT: Rotational Equivariant Vision Transformer for Robust Histopathology Analysis. CoRR Fuyao Chen, Yuexi Du, Eléonore V. Lieffrig, Nicha C. Dvornek, John A. Onofrey
2026	J	`jnl`	PET Head Motion Estimation Using Supervised Deep Learning With Attention. IEEE Trans. Medical Imaging Zhuotong Cai, Tianyi Zeng, Jiazhen Zhang, Eléonore V. Lieffrig, Kathryn Fontaine, Chenyu You, Enette Mae Revilla, James S. Duncan, Jingmin Xin, Yihuan Lu, John A. Onofrey
2025	J	`jnl`	A Flow-based Truncated Denoising Diffusion Model for super-resolution Magnetic Resonance Spectroscopic Imaging. Medical Image Anal. Siyuan Dong, Zhuotong Cai, Gilbert Hangel, Wolfgang Bogner, Georg Widhalm, Yaqing Huang, Qinghao Liang, Chenyu You, Chathura Kumaragamage, Robert K. Fulbright, Amit Mahajan, Amin Karbasi, John A. Onofrey, Robin A. de Graaf, James S. Duncan
2025	J	`jnl`	CT-Less Whole-Body Bone Segmentation of PET Images Using a Multimodal Deep Learning Network. IEEE J. Biomed. Health Informatics Nan Bao, Jiaxin Zhang, Zhikun Li, Shiyu Wei, Jiazhen Zhang, Stephen E. Greenwald, John A. Onofrey, Yihuan Lu, Lisheng Xu
2025	—	`conf`	Conditional Convolution of Clinical Data Embeddings for Multimodal Prostate Cancer Classification. ISBI Jiayang Zhong, Fuyao Chen, Lihui Chen, Dennis Shung, John A. Onofrey
2025	—	`conf`	Enhancing Uncertainty Estimation in Semantic Segmentation via Monte-Carlo Frequency Dropout. ISBI Tal Zeevi, Lawrence H. Staib, John A. Onofrey
2025	J	`jnl`	Enhancing Uncertainty Estimation in Semantic Segmentation via Monte-Carlo Frequency Dropout. CoRR Tal Zeevi, Lawrence H. Staib, John A. Onofrey
2025	J	`jnl`	Equivariant Imaging Biomarkers for Robust Unsupervised Segmentation of Histopathology. CoRR Fuyao Chen, Yuexi Du, Tal Zeevi, Nicha C. Dvornek, John A. Onofrey
2025	J	`jnl`	GMR-Conv: An Efficient Rotation and Reflection Equivariant Convolution Kernel Using Gaussian Mixture Rings. CoRR Yuexi Du, Jiazhen Zhang, Nicha C. Dvornek, John A. Onofrey
2025	J	`jnl`	Head Motion Degrades Machine Learning Classification of Alzheimer's Disease from Positron Emission Tomography. CoRR Eléonore V. Lieffrig, Takuya Toyonaga, Jiazhen Zhang, John A. Onofrey
2025	—	`conf`	Improved Vessel Segmentation with Symmetric Rotation-Equivariant U-Net. ISBI Jiazhen Zhang, Yuexi Du, Nicha C. Dvornek, John A. Onofrey
2025	J	`jnl`	Improved Vessel Segmentation with Symmetric Rotation-Equivariant U-Net. CoRR Jiazhen Zhang, Yuexi Du, Nicha C. Dvornek, John A. Onofrey
2025	—	`conf`	Multi-view and Multi-scale Alignment for Contrastive Language-Image Pre-training in Mammography. IPMI (2) Yuexi Du, John A. Onofrey, Nicha C. Dvornek
2025	J	`jnl`	PET Head Motion Estimation Using Supervised Deep Learning with Attention. CoRR Zhuotong Cai, Tianyi Zeng, Jiazhen Zhang, Eléonore V. Lieffrig, Kathryn Fontaine, Chenyu You, Enette Mae Revilla, James S. Duncan, Jingmin Xin, Yihuan Lu, John A. Onofrey
2025	A*	`conf`	Rate-In: Information-Driven Adaptive Dropout Rates for Improved Inference-Time Uncertainty Estimation. CVPR Tal Zeevi, Ravid Shwartz-Ziv, Yann LeCun, Lawrence H. Staib, John A. Onofrey
2025	—	`conf`	SRE-CONV: Symmetric Rotation Equivariant Convolution for Biomedical Image Classification. ISBI Yuexi Du, Jiazhen Zhang, Tal Zeevi, Nicha C. Dvornek, John A. Onofrey
2025	J	`jnl`	SRE-Conv: Symmetric Rotation Equivariant Convolution for Biomedical Image Classification. CoRR Yuexi Du, Jiazhen Zhang, Tal Zeevi, Nicha C. Dvornek, John A. Onofrey
2025	J	`jnl`	Spatially-Aware Evaluation of Segmentation Uncertainty. CoRR Tal Zeevi, Eléonore V. Lieffrig, Lawrence H. Staib, John A. Onofrey
2024	J	`jnl`	A Flow-based Truncated Denoising Diffusion Model for Super-resolution Magnetic Resonance Spectroscopic Imaging. CoRR Siyuan Dong, Zhuotong Cai, Gilbert Hangel, Wolfgang Bogner, Georg Widhalm, Yaqing Huang, Qinghao Liang, Chenyu You, Chathura Kumaragamage, Robert K. Fulbright, Amit Mahajan, Amin Karbasi, John A. Onofrey, Robin A. de Graaf, James S. Duncan
2024	—	`conf`	Monte-Carlo Frequency Dropout for Predictive Uncertainty Estimation in Deep Learning. ISBI Tal Ze'evi, Rajesh Venkataraman, Lawrence H. Staib, John A. Onofrey
2024	J	`jnl`	Multi-View and Multi-Scale Alignment for Contrastive Language-Image Pre-training in Mammography. CoRR Yuexi Du, John A. Onofrey, Nicha C. Dvornek
2024	J	`jnl`	Patient-Specific Heart Geometry Modeling for Solid Biomechanics Using Deep Learning. IEEE Trans. Medical Imaging Daniel H. Pak, Minliang Liu, Theodore Kim, Liang Liang, Andrés Caballero, John A. Onofrey, Shawn S. Ahn, Yilin Xu, Raymond McKay, Wei Sun, Rudolph L. Gleason, James S. Duncan
2024	J	`jnl`	Rate-In: Information-Driven Adaptive Dropout Rates for Improved Inference-Time Uncertainty Estimation. CoRR Tal Zeevi, Ravid Shwartz-Ziv, Yann LeCun, Lawrence H. Staib, John A. Onofrey
2024	J	`jnl`	Reliable Prostate Cancer Risk Mapping From MRI Using Targeted and Systematic Core Needle Biopsy Histopathology. IEEE Trans. Biomed. Eng. Tal Ze'evi, Michael S. Leapman, Preston C. Sprenkle, Rajesh Venkataraman, Lawrence H. Staib, John A. Onofrey
2024	Misc	`conf`	Symmetric Consistency with Cross-Domain Mixup for Cross-Modality Cardiac Segmentation. ICASSP Zhuotong Cai, Jingmin Xin, Siyuan Dong, John A. Onofrey, Nanning Zheng, James S. Duncan
2023	J	`jnl`	Co-attention spatial transformer network for unsupervised motion tracking and cardiac strain analysis in 3D echocardiography. Medical Image Anal. Shawn S. Ahn, Kevinminh Ta, Stephanie Thorn, John A. Onofrey, Inga H. Melvinsdottir, Supum Lee, Jonathan Langdon, Albert J. Sinusas, James S. Duncan
2023	—	`conf`	Cross-Attention for Improved Motion Correction in Brain PET. MLCN@MICCAI Zhuotong Cai, Tianyi Zeng, Eléonore V. Lieffrig, Jiazhen Zhang, Fuyao Chen, Takuya Toyonaga, Chenyu You, Jingmin Xin, Nanning Zheng, Yihuan Lu, James S. Duncan, John A. Onofrey
2023	J	`jnl`	DuSFE: Dual-Channel Squeeze-Fusion-Excitation co-attention for cross-modality registration of cardiac SPECT and CT. Medical Image Anal. Xiongchao Chen, Bo Zhou, Huidong Xie, Xueqi Guo, Jiazhen Zhang, James S. Duncan, Edward J. Miller, Albert J. Sinusas, John A. Onofrey, Chi Liu
2023	—	`conf`	Fast Reconstruction for Deep Learning PET Head Motion Correction. MICCAI (10) Tianyi Zeng, Jiazhen Zhang, Eléonore V. Lieffrig, Zhuotong Cai, Fuyao Chen, Chenyu You, Mika Naganawa, Yihuan Lu, John A. Onofrey
2023	—	`conf`	Integrating Prostate Specific Antigen Density Biomarker Into Deep Learning Prostate MRI Lesion Segmentation Models. ISBI Jiayang Zhong, Lawrence H. Staib, Rajesh Venkataraman, John A. Onofrey
2023	—	`conf`	Multi-Task Deep Learning and Uncertainty Estimation for Pet Head Motion Correction. ISBI Eléonore V. Lieffrig, Tianyi Zeng, Jiazhen Zhang, Kathryn Fontaine, Xi Fang, Enette Mae Revilla, Yihuan Lu, John A. Onofrey
2023	—	`conf`	Unsupervised Domain Adaptation by Cross-Prototype Contrastive Learning for Medical Image Segmentation. BIBM Zhuotong Cai, Jingmin Xin, Siyuan Dong, Chenyu You, Peiwen Shi, Tianyi Zeng, Jiazhen Zhang, John A. Onofrey, Nanning Zheng, James S. Duncan
2022	J	`jnl`	Adaptive data-driven motion detection and optimized correction for brain PET. NeuroImage Enette Mae Revilla, Jean-Dominique Gallezot, Mika Naganawa, Takuya Toyonaga, Kathryn Fontaine, Tim Mulnix, John A. Onofrey, Richard E. Carson, Yihuan Lu
2022	J	`jnl`	An objective evaluation method for head motion estimation in PET - Motion corrected centroid-of-distribution. NeuroImage Chen Sun, Enette Mae Revilla, Jiazhen Zhang, Kathryn Fontaine, Takuya Toyonaga, Jean-Dominique Gallezot, Tim Mulnix, John A. Onofrey, Richard E. Carson, Yihuan Lu
2022	—	`conf`	Atlas-Based Semantic Segmentation of Prostate Zones. MICCAI (5) Jiazhen Zhang, Rajesh Venkataraman, Lawrence H. Staib, John A. Onofrey
2022	—	`conf`	Dual-Branch Squeeze-Fusion-Excitation Module for Cross-Modality Registration of Cardiac SPECT and CT. MICCAI (6) Xiongchao Chen, Bo Zhou, Huidong Xie, Xueqi Guo, Jiazhen Zhang, Albert J. Sinusas, John A. Onofrey, Chi Liu
2022	J	`jnl`	Dual-Branch Squeeze-Fusion-Excitation Module for Cross-Modality Registration of Cardiac SPECT and CT. CoRR Xiongchao Chen, Bo Zhou, Huidong Xie, Xueqi Guo, Jiazhen Zhang, Albert J. Sinusas, John A. Onofrey, Chi Liu
2022	—	`conf`	Flow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging. DGM4MICCAI@MICCAI Siyuan Dong, Gilbert Hangel, Eric Z. Chen, Shanhui Sun, Wolfgang Bogner, Georg Widhalm, Chenyu You, John A. Onofrey, Robin A. de Graaf, James S. Duncan
2022	J	`jnl`	Flow-based Visual Quality Enhancer for Super-resolution Magnetic Resonance Spectroscopic Imaging. CoRR Siyuan Dong, Gilbert Hangel, Eric Z. Chen, Shanhui Sun, Wolfgang Bogner, Georg Widhalm, Chenyu You, John A. Onofrey, Robin A. de Graaf, James S. Duncan
2022	—	`conf`	Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation. DeCaF/FAIR@MICCAI Chenyu You, Jinlin Xiang, Kun Su, Xiaoran Zhang, Siyuan Dong, John A. Onofrey, Lawrence H. Staib, James S. Duncan
2022	J	`jnl`	Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation. CoRR Chenyu You, Jinlin Xiang, Kun Su, Xiaoran Zhang, Siyuan Dong, John A. Onofrey, Lawrence H. Staib, James S. Duncan
2022	—	`conf`	Multi-scale Super-Resolution Magnetic Resonance Spectroscopic Imaging with Adjustable Sharpness. MICCAI (6) Siyuan Dong, Gilbert Hangel, Wolfgang Bogner, Georg Widhalm, Karl Rössler, Siegfried Trattnig, Chenyu You, Robin A. de Graaf, John A. Onofrey, James S. Duncan
2022	J	`jnl`	Multi-scale Super-resolution Magnetic Resonance Spectroscopic Imaging with Adjustable Sharpness. CoRR Siyuan Dong, Gilbert Hangel, Wolfgang Bogner, Georg Widhalm, Karl Rössler, Siegfried Trattnig, Chenyu You, Robin A. de Graaf, John A. Onofrey, James S. Duncan
2022	—	`conf`	Supervised Deep Learning for Head Motion Correction in PET. MICCAI (4) Tianyi Zeng, Jiazhen Zhang, Enette Mae Revilla, Eléonore V. Lieffrig, Xi Fang, Yihuan Lu, John A. Onofrey
2021	—	`conf`	TVnet: Automated Time-Resolved Tracking of the Tricuspid Valve Plane in MRI Long-Axis Cine Images with a Dual-Stage Deep Learning Pipeline. MICCAI (6) Ricardo A. Gonzales, Jérôme Lamy, Felicia Seemann, Einar Heiberg, John A. Onofrey, Dana C. Peters
2021	—	`conf`	Weakly Supervised Deep Learning for Aortic Valve Finite Element Mesh Generation from 3D CT Images. IPMI Daniel H. Pak, Minliang Liu, Shawn S. Ahn, Andrés Caballero, John A. Onofrey, Liang Liang, Wei Sun, James S. Duncan
2019	—	`conf`	A Novel Loss Function Incorporating Imaging Acquisition Physics for PET Attenuation Map Generation Using Deep Learning. MICCAI (4) Luyao Shi, John A. Onofrey, Enette Mae Revilla, Takuya Toyonaga, David Menard, Joseph Ankrah, Richard E. Carson, Chi Liu, Yihuan Lu
2019	J	`jnl`	A Novel Loss Function Incorporating Imaging Acquisition Physics for PET Attenuation Map Generation using Deep Learning. CoRR Luyao Shi, John A. Onofrey, Enette Mae Revilla, Takuya Toyonaga, David Menard, Joseph Ankrah, Richard E. Carson, Chi Liu, Yihuan Lu
2019	J	`jnl`	Deep-learned placental vessel segmentation for intraoperative video enhancement in fetoscopic surgery. Int. J. Comput. Assist. Radiol. Surg. Praneeth Sadda, Metehan Imamoglu, Michael Dombrowski, Xenophon Papademetris, Mert Ozan Bahtiyar, John A. Onofrey
2019	—	`conf`	Generalizable Multi-Site Training and Testing Of Deep Neural Networks Using Image Normalization. ISBI John A. Onofrey, Dana I. Casetti-Dinescu, Andreas D. Lauritzen, Saradwata Sarkar, Rajesh Venkataraman, Richard E. Fan, Geoffrey A. Sonn, Preston C. Sprenkle, Lawrence H. Staib, Xenophon Papademetris
2019	J	`jnl`	Segmenting the Brain Surface From CT Images With Artifacts Using Locally Oriented Appearance and Dictionary Learning. IEEE Trans. Medical Imaging John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris
2018	—	`conf`	A fetal fMRI specific motion correction algorithm using 2 ISBI Dustin Scheinost, John A. Onofrey, Soo Hyun Kwon, Sarah N. Cross, Gordon Sze, Laura R. Ment, Xenophon Papademetris
2018	—	`conf`	Better Feature Matching for Placental Panorama Construction. DATRA/PIPPI@MICCAI Praneeth Sadda, John A. Onofrey, Mert Ozan Bahtiyar, Xenophon Papademetris
2018	—	`conf`	Deep Learning Retinal Vessel Segmentation from a Single Annotated Example: An Application of Cyclic Generative Adversarial Neural Networks. CVII-STENT/LABELS@MICCAI Praneeth Sadda, John A. Onofrey, Xenophon Papademetris
2018	J	`jnl`	Non-Rigid Event-by-Event Continuous Respiratory Motion Compensated List-Mode Reconstruction for PET. IEEE Trans. Medical Imaging Chung Chan, John A. Onofrey, Yiqiang Jian, Mary Germino, Xenophon Papademetris, Richard E. Carson, Chi Liu
2017	J	`jnl`	Learning Non-rigid Deformations for Robust, Constrained Point-based Registration in Image-Guided MR-TRUS Prostate Intervention. Medical Image Anal. John A. Onofrey, Lawrence H. Staib, Saradwata Sarkar, Rajesh Venkataraman, Cayce B. Nawaf, Preston C. Sprenkle, Xenophon Papademetris
2016	—	`conf`	MRI-TRUS Image Synthesis with Application to Image-Guided Prostate Intervention. SASHIMI@MICCAI John A. Onofrey, Ilkay Öksüz, Saradwata Sarkar, Rajesh Venkataraman, Lawrence H. Staib, Xenophon Papademetris
2015	A	`conf`	A Scalable Algorithm for Structured Kernel Feature Selection. AISTATS Shaogang Ren, Shuai Huang, John A. Onofrey, Xenios Papademetris, Xiaoning Qian
2015	—	`conf`	Learning nonrigid deformations for constrained point-based registration for image-guided MR-TRUS prostate intervention. ISBI John A. Onofrey, Lawrence H. Staib, Saradwata Sarkar, Rajesh Venkataraman, Xenophon Papademetris
2015	J	`jnl`	Low-Dimensional Non-Rigid Image Registration Using Statistical Deformation Models From Semi-Supervised Training Data. IEEE Trans. Medical Imaging John A. Onofrey, Xenophon Papademetris, Lawrence H. Staib
2015	—	`conf`	Segmenting the Brain Surface from CT Images with Artifacts Using Dictionary Learning for Non-rigid MR-CT Registration. IPMI John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris
2013	—	`conf`	Fast nonrigid image registration using statistical deformation models learned from richly-annotated data. ISBI John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris
2013	—	`conf`	Learning Nonrigid Deformations for Constrained Multi-modal Image Registration. MICCAI (3) John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris
2013	—	`conf`	Semi-supervised Learning of Nonrigid Deformations for Image Registration. MCV John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris