📄 For a full and up-to-date list, see Google Scholar. Following publications are updated using generative AI, so minor inconsistencies may occur.

Pre-print

  1. Chongyu Qu, Ritchie Zhao, Ye Yu, Bin Liu, Tianyuan Yao, Junchao Zhu, Bennett A. Landman, Yucheng Tang, and Yuankai Huo. “Post-Training Quantization for 3D Medical Image Segmentation: A Practical Study on Real Inference Engines.” arXiv

Journal

  1. Chongyu Qu, Ritchie Zhao, Ye Yu, Bin Liu, Tianyuan Yao, Junchao Zhu, Bennett A. Landman, Yucheng Tang, and Yuankai Huo. “MedPTQ: a practical pipeline for real post-training quantization in 3D medical image segmentation.” Journal of Medical Imaging (2026).
  2. Ruining Deng, Tianyuan Yao, Yucheng Tang, Junlin Guo, Siqi Lu, Juming Xiong, Lining Yu, Quan Huu Cap, Pengzhou Cai, Libin Lan, Ze Zhao, Adrian Galdran, Amit Kumar, Gunjan Deotale, Dev Kumar Das, Inyoung Paik, Joonho Lee, Geongyu Lee, Yujia Chen, Wangkai Li, Zhaoyang Li, Xuege Hou, Zeyuan Wu, Shengjin Wang, Maximilian Fischer, Lars Kramer, Anghong Du, Le Zhang, Maria Sanchez Sanchez, Helena Sanchez Ulloa, David Ribalta Heredia, Carlos Perez de Arenaza Garcia, Shuoyu Xu, Bingdou He, Xinping Cheng, Tao Wang, Noemie Moreau, Katarzyna Bozek, Shubham Innani, Ujjwal Baid, Kaura Solomon Kefas, Bennett A Landman, Yu Wang, Shilin Zhao, Mengmeng Yin, Haichun Yang, and Yuankai Huo. “Kpis 2024 challenge: Advancing glomerular segmentation from patch-to slide-level.” Medical Image Analysis (2026).
  3. Tianyuan Yao, Derek B Archer, Praitayini Kanakaraj, Nancy R Newlin, Shunxing Bao, Daniel Moyer, Kurt G. Schilling, Bennett A. Landman, and Yuankai Huo. “Deep learning-based free-water correction for single-shell diffusion MRI.” Magnetic Resonance Imaging (2025).
  4. Junlin Guo, James R Zimmer-Dauphinee, Jordan M Nieusma, Siqi Lu, Quan Liu, Ruining Deng, Can Cui, Jialin Yue, Yizhe Lin, Tianyuan Yao, Juming Xiong, Junchao Zhu, Chongyu Qu, Yuechen Yang, Mitchell Wilkes, Xiao Wang, Parker VanValkenburgh, Steven A Wernke, and Yuankai Huo. “DeepAndes: A Self-Supervised Vision Foundation Model for Multi-Spectral Remote Sensing Imagery of the Andes.” IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing (2025).
  5. Zhengyi Lu, H Liang, M Lu, Xiao Wang, X Yan, and Yuankai Huo. “Fast-RF-Shimming: Accelerate RF shimming in 7T MRI using deep learning.” Meta-Radiology (2025).
  6. Lining Yu, Mengmeng Yin, Ruining Deng, Quan Liu, Tianyuan Yao, Can Cui, Junlin Guo, Yu Wang, Yaohong Wang, Shilin Zhao, Haichun Yang, and Yuankai Huo. “Glo-In-One-v2: holistic identification of glomerular cells, tissues, and lesions in human and mouse histopathology.” Journal of Medical Imaging (2025).
  7. Jialin Yue, Tianyuan Yao, Ruining Deng, Siqi Lu, Junlin Guo, Q Liu, Juming Xiong, Mengmeng Yin, Haichun Yang, and Yuankai Huo. “GloFinder: AI-empowered QuPath plugin for WSI-level glomerular detection, visualization, and curation.” Journal of Pathology Informatics (2025).
  8. Junchao Zhu, Ruining Deng, Junlin Guo, Tianyuan Yao, Juming Xiong, Chongyu Qu, Mengmeng Yin, Yu Wang, Shilin Zhao, Haichun Yang, Daguang Xu, Yucheng Tang, and Yuankai Huo. “Img2ST-Net: efficient high-resolution spatial omics prediction from whole-slide histology images via fully convolutional image-to-image learning.” Journal of Medical Imaging (2025).
  9. Siqi Lu, Junlin Guo, James R Zimmer-Dauphinee, Jordan M Nieusma, Xiao Wang, Parker VanValkenburgh, Steven A Wernke, and Yuankai Huo. “Vision Foundation Models in Remote Sensing: A Survey.” IEEE Geoscience and Remote Sensing Magazine (2025).
  10. Junlin Guo, Siqi Lu, Can Cui, Ruining Deng, Tianyuan Yao, Zhewen Tao, Yizhe Lin, Marilyn Lionts, Quan Liu, Juming Xiong, Yu Wang, Shilin Zhao, Catie Chang, Mitchell Wilkes, Mengmeng Yin, Haichun Yang, and Yuankai Huo. “Evaluating Cell ai Foundation Models in Kidney Pathology With Human‐in‐the‐Loop Enrichment.” Communications Medicine (2025).
  11. Juming Xiong, Ethan H. Nguyen, Yilin Liu, Ruining Deng, Regina N Tyree, HernĂĄn Correa, Girish Hiremath, Yaohong Wang, Haichun Yang, Agnes B. Fogo, and Yuankai Huo. “Circle Representation for Medical Instance Object Segmentation.” The Journal of Machine Learning for Biomedical Imaging (2024).
  12. Ruining Deng, Can Cui, Lucas W Remedios, Shunxing Bao, R Michael Womick, Sophie Chiron, Jia Li, Joseph T Roland, Ken S Lau, Qi Liu, Keith T Wilson, Yaohong Wang, Lori A Coburn, Bennett A Landman, and Yuankai Huo. “Cross-scale multi-instance learning for pathological image diagnosis.” Medical Image Analysis (2024).
  13. Quan Liu, Brandon T Swartz, Ivan Kravchenko, Jason G Valentine, and Yuankai Huo. “ExtremeMETA: High-speed lightweight image segmentation model by remodeling multi-channel metamaterial imagers.” (2024).Journal of Imaging Science and Technology (2024).
  14. Tianyuan Yao, Francois Rheault, Leon Y Cai, Vishwesh Nath, Zuhayr Asad, Nancy Newlin, Can Cui, Ruining Deng, Karthik Ramadass, Andrea Shafer, Susan Resnick, Kurt Schilling, Bennett A Landman, and Yuankai Huo. “Robust fiber orientation distribution function estimation using deep constrained spherical deconvolution for diffusion-weighted magnetic resonance imaging.” Journal of Medical Imaging (2024).
  15. Can Cui, Haichun Yang, Yaohong Wang, Shilin Zhao, Zuhayr Asad, Lori A Coburn, Keith T Wilson, Bennett A Landman, and Yuankai Huo. “Deep multimodal fusion of image and non-image data in disease diagnosis and prognosis: a review.” Progress in Biomedical Engineering (2023).
  16. Quan Liu, Hanyu Zheng, Brandon T Swartz, Ho hin Lee, Zuhayr Asad, Ivan Kravchenko, Jason G Valentine, and Yuankai Huo. “Digital modeling on large kernel metamaterial neural network.” Journal of Imaging Science and Technology (2023).
  17. Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jun Long, Zuhayr Asad, R Michael Womick, Zheyu Zhu, Agnes B Fogo, Shilin Zhao, Haichun Yang, and Yuankai Huo. “Omni-seg: A scale-aware dynamic network for renal pathological image segmentation.” IEEE Transactions on Biomedical Engineering (2023).
  18. Ho Hin Lee, Yucheng Tang, Qi Yang, Xin Yu, Leon Y Cai, Lucas W Remedios, Shunxing Bao, Bennett A Landman, and Yuankai Huo. “Semantic-aware contrastive learning for multi-object medical image segmentation.” IEEE journal of biomedical and health informatics (2023).
  19. Tianyuan Yao, Changbing Qu, Jun Long, Quan Liu, Ruining Deng, Yuanhan Tian, Jiachen Xu, Aadarsh Jha, Zuhayr Asad, Shunxing Bao, Mengyang Zhao, Agnes B. Fogo, Bennett A.Landman, Haichun Yang, Catie Chang, and Yuankai Huo. “Compound Figure Separation of Biomedical Images: Mining Large Datasets for Self-supervised Learning.” The Journal of Machine Learning for Biomedical Imaging (2022).
  20. Tianyuan Yao, Yuzhe Lu, Jun Long, Aadarsh Jha, Zheyu Zhu, Zuhayr Asad, Haichun Yang, Agnes B. Fogo, and Yuankai Huo. “Glo-In-One: holistic glomerular detection, segmentation, and lesion characterization with large-scale web image mining.” Journal of Medical Imaging (2022).
  21. Yuzhe Lu, Haichun Yang, Zuhayr Asad, Zheyu Zhu, Tianyuan Yao, Jiachen Xu, Agnes B. Fogo, and Yuankai Huo. “Holistic fine-grained global glomerulosclerosis characterization: from detection to unbalanced classification.” Journal of Medical Imaging (2022).
  22. Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jun Long, Zuhayr Asad, R. M. Womick, Zheyu Zhu, Agnes B. Fogo, Shilin Zhao, Haichun Yang, and Yuankai Huo. “Omni-Seg: A Scale-aware Dynamic Network for Pathological Image Segmentation.” IEEE Transactions on Biomedical Engineering (2022).
  23. Quan Liu, Isabella M Gaeta, Mengyang Zhao, Ruining Deng, Aadarsh Jha, Bryan A Millis, Anita Mahadevan-Jansen, Matthew J Tyska, and Yuankai Huo. “ASIST: Annotation-free synthetic instance segmentation and tracking by adversarial simulations.” Computers in Biology and Medicine (2021).
  24. Ho Hin Lee, Yucheng Tang, Qi Yang, Xin Yu, Shunxing Bao, Bennett A. Landman, and Yuankai Huo. "" IEEE Journal of Biomedical and Health Informatics (2021).
  25. Ethan H Nguyen, Haichun Yang, Ruining Deng, Yuzhe Lu, Zheyu Zhu, Joseph T Roland, Le Lu, Bennett A Landman, Agnes B Fogo, and Yuankai Huo. “Circle representation for medical object detection.” IEEE Transactions on Medical Imaging (2021).
  26. Mengyang Zhao, Aadarsh Jha, Quan Liu, Bryan A Millis, Anita Mahadevan-Jansen, Le Lu, Bennett A Landman, Matthew J Tyska, and Yuankai Huo. “Faster Mean-shift: GPU-accelerated clustering for cosine embedding-based cell segmentation and tracking.” Medical Image Analysis (2021).
  27. Jiachen Xu, James Zimmer-Dauphinee, Quan Liu, Yuxuan Shi, Steven A. Wernke, and Yuankai Huo. “Semi-Supervised Contrastive Learning for Remote Sensing: Identifying Ancient Urbanization in the South-Central Andes.” International Journal of Remote Sensing (2021).
  28. Aadarsh Jha, Haichun Yang, Ruining Deng, Meghan E. Kapp, Agnes B. Fogo, and Yuankai Huo. “Instance segmentation for whole slide imaging: end-to-end or detect-then-segment.” Journal of Medical Imaging (2020).
  29. Ruining Deng, Haichun Yang, Aadarsh Jha, Yuzhe Lu, Peng Chu, Agnes B. Fogo, and Yuankai Huo. “Map3D: Registration Based Multi-Object Tracking on 3D Serial Whole Slide Images.” IEEE Transactions on Medical Imaging (2020).

Conference

  1. Xiao Li, Yanfan Zhu, Ruining Deng, WQ Wei, Yaohong Wang, Shilin Zhao, Yihan Wang, Haichun Yang, and Yuankai Huo. “MedFoundationHub: a lightweight and secure toolkit for deploying medical vision language foundation models.” SPIE Medical Imaging (2026).
  2. Xiaoyu Huang, LM Maxson, T Nguyen, CJ Song, and Yuankai Huo. “Organoid tracker: a SAM2‑powered platform for zero‑shot cyst analysis in human kidney organoid videos.” SPIE Medical Imaging (2026).
  3. Yucheng Tang, Yufan He, Vishwesh Nath, Pengfeig Guo, Ruining Deng, Tianyuan Yao, Quan Liu, Can Cui, Mengmeng Yin, Ziyue Xu, Holger Roth, Daguang Xu, Haichun Yang, and Yuankai Huo. “Holohisto: End-to-end gigapixel wsi segmentation with 4k resolution sequential tokenization.” IS&T International Symposium on Electronic Imaging (2024).
  4. Junchao Zhu, Ruining Deng, Tianyuan Yao, Juming Xiong, Chongyu Qu, Junlin Guo, Siqi Lu, Mengmeng Yin, Yu Wang, Shilin Zhao, Haichun Yang, and Yuankai Huo. “Asign: an anatomy-aware spatial imputation graphic network for 3d spatial transcriptomics.” Proceedings of the Computer Vision and Pattern Recognition Conference (CVPR) (2025).
  5. Junlin Guo, Siqi Lu, Can Cui, Ruining Deng, Tianyuan Yao, Zhewen Tao, Yizhe Lin, Marilyn Lionts, Quan Liu, Juming Xiong, Yu Wang, Shilin Zhao, Catie Chang, Mitchell Wilkes, Mengmeng Yin, Haichun Yang, and Yuankai Huo. “Assessment of cell nuclei ai foundation models in kidney pathology.” SPIE Medical Imaging (2025).
  6. Chongyu Qu, Allen J. Luna, Thomas Z. Li, Junchao Zhu, Junlin Guo, Juming Xiong, Kim L. Sandler, Bennett A. Landman, and Yuankai Huo. “Cohort-Aware Agents for Individualized Lung Cancer Risk Prediction Using a Retrieval-Augmented Model Selection Framework.” SPIE Medical Imaging (2025).
  7. Yifei Wu, Juming Xiong, Tianyuan Yao, Ruining Deng, Junlin Guo, Jialin Yue, N Chowdhury, and Yuankai Huo. “Cross-organ deployment of EOS detection AI without retraining: feasibility and limitation.” SPIE Medical Imaging (2025).
  8. Junchao Zhu, Mengmeng Yin, Ruining Deng, Y Long, Yaohong Wang, Yihan Wang, Shilin Zhao, Haichun Yang, and Yuankai Huo. “Cross-species data integration for enhanced layer segmentation in kidney pathology.” SPIE Medical Imaging (2025).
  9. Mengyang Li, Can Cui, Q Liu, Ruining Deng, Tianyuan Yao, Marilyn Lionts, and Yuankai Huo. “Dataset distillation in medical imaging: A feasibility study.” SPIE Medical Imaging (2025).
  10. Juming Xiong, Mingyao Li, Ruining Deng, Tianyuan Yao, Shunxing Bao, Regina N Tyree, Girish Hiremath, and Yuankai Huo. “Enhanced feature-based image stitching for endoscopic videos in pediatric eosinophilic esophagitis.” SPIE Medical Imaging 2025 (2025).
  11. Juming Xiong, H Xiong, Q Liu, Ruining Deng, Regina N Tyree, Girish Hiremath, and Yuankai Huo. “Expanding training data for endoscopic phenotyping of eosinophilic esophagitis.” SPIE Medical Imaging (2025).
  12. Junchao Zhu, Ruining Deng, Tianyuan Yao, Juming Xiong, Chongyu Qu, Junlin Guo, Siqi Lu, Yucheng Tang, Daguang Xu, Mengmeng Yin, Yu Wang, Shilin Zhao, Yaohong Wang, Haichun Yang, and Yuankai Huo. “Magnet: Multi-level attention graph network for predicting high-resolution spatial transcriptomics.” Medical Imaging with Deep Learning (MIDL) (2025).
  13. Zhengyi Lu, H Liang, Xiao Wang, X Yan, and Yuankai Huo. “Optimizing transmit field inhomogeneity of parallel RF transmit design in 7T MRI using deep learning.” SPIE Medical Imaging (2025).
  14. Tianyuan Yao, Zhiyuan Li, Praitayini Kanakaraj, Derek B Archer, Kurt G. Schilling, Lori L. Beason-Held, Susan M. Resnick, Bennett A. Landman, and Yuankai Huo. “Polyhedra Encoding Transformers: Enhancing Diffusion MRI Analysis Beyond Voxel and Volumetric Embedding.” SPIE Medical Imaging 2025 (2025).
  15. Yuechen Yang, Yaohong Wang, Tianyuan Yao, Ruining Deng, Mengmeng Yin, Shilin Zhao, Haichun Yang, and Yuankai Huo. “PySpatial: A high-speed whole slide image pathomics toolkit.” IS&T International Symposium on Electronic Imaging (2025).
  16. John Bohatch, and Yuankai Huo. “Realtime dual camera localization and orientation tracking for calibrating magnetically navigated capsule endoscopy.” SPIE Medical Imaging (2025).
  17. Ruining Deng, Can Cui, Quan Liu, Tianyuan Yao, Lucas W Remedios, Shunxing Bao, Bennett A Landman, Lee E Wheless, Lori A Coburn, Keith T Wilson, Yaohong Wang, Shilin Zhao, Agnes B Fogo, Haichun Yang, Yucheng Tang, and Yuankai Huo. “Segment anything model (sam) for digital pathology: Assess zero-shot segmentation on whole slide imaging.” IS&T International Symposium on Electronic Imaging (2025).
  18. Yitian Long, Zeyuan Wu, X Su, Lining Yu, Ruining Deng, Haichun Yang, and Yuankai Huo. “Towards fine-grained renal vasculature segmentation: full-scale hierarchical learning with fh-seg.” SPIE Medical Imaging (2025).
  19. Jialin Yue, Tianyuan Yao, Ruining Deng, Q Liu, Juming Xiong, Junlin Guo, Haichun Yang, and Yuankai Huo. “Weighted circle fusion: ensembling circle representation from different object detection results.” SPIE Medical Imaging (2025).
  20. Quan Liu, Can Cui, Ruining Deng, Tianyuan Yao, Y Yang, Yucheng Tang, and Yuankai Huo. “Write Sentence with Images: Revisit the Large Vision Model with Visual Sentence.” IS&T International Symposium on Electronic Imaging (2025).
  21. Quan Liu, Ruining Deng, Can Cui, Tianyuan Yao, Y Yang, Vishwesh Nath, B Li, Y Chen, Yucheng Tang, and Yuankai Huo. “mtree: Multi-level text-guided representation end-to-end learning for whole slide image analysis.” IS&T International Symposium on Electronic Imaging (2025).
  22. Can Cui, Ruining Deng, Quan Liu, Tianyuan Yao, Shunxing Bao, Lucas W Remedios, Bennett A Landman, Yucheng Tang, and Yuankai Huo. “All-in-sam: from weak annotation to pixel-wise nuclei segmentation with prompt-based finetuning.” Asia Conference on Computers and Communications (ACCC) (2024).
  23. Shunxing Bao, Ho Hin Lee, Qi Yang, Lucas W Remedios, Ruining Deng, Can Cui, Leon Y Cai, Kaiwen Xu, Xin Yu, Sophie Chiron, Yike Li, Nathan Heath Patterson, Yaohong Wang, Jia Li, Qi Liu, Ken S Lau, Joseph T Roland, Lori A Coburn, Keith T Wilson, Bennett A Landman, and Yuankai Huo. “Alleviating tiling effect by random walk sliding window in high-resolution histological whole slide image synthesis.” Medical Imaging with Deep Learning (MIDL) (2024).
  24. Muyang Li, Juming Xiong, Ruining Deng, Tianyuan Yao, Regina N Tyree, Girish Hiremath, and Yuankai Huo. “Automatic Image Unfolding and Stitching Framework for Esophageal Lining Video Based on Density-Weighted Feature Matching.” SPIE Medical Imaging (2024).
  25. Marilyn Lionts, E Haugen, Anita Mahadevan-Jansen, and Yuankai Huo. “Deep-learning-based acquisitional denoising for Raman spectroscopy using CNN and transformer.” SPIE Emerging Topics in Artificial Intelligence (2024).
  26. Can Cui, Ruining Deng, Junlin Guo, Q Liu, Tianyuan Yao, Haichun Yang, and Yuankai Huo. “Enhancing physician flexibility: Prompt-guided multi-class pathological segmentation for diverse outcomes.” IEEE EMBS International Conference on Biomedical and Health Informatics (BHI) (2024).
  27. Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Juming Xiong, Shunxing Bao, Hao Li, Mengmeng Yin, Yu Wang, Shilin Zhao, Yucheng Tang, Haichun Yang, and Yuankai Huo. “Hats: Hierarchical adaptive taxonomy segmentation for panoramic pathology image analysis.” International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) (2024).
  28. Tianyuan Yao, Derek B Archer, Praitayini Kanakaraj, Nancy R Newlin, Shunxing Bao, Daniel Moyer, Kurt G. Schilling, Bennett A. Landman, and Yuankai Huo. “Learning-based free-water correction using single-shell diffusion MRI.” SPIE Medical Imaging (2024).
  29. Xueyuan Li, Ruining Deng, Yucheng Tang, Shunxing Bao, Haichun Yang, and Yuankai Huo. “Leverage weekly annotation to pixel-wise annotation via zero-shot segment anything model for molecular-empowered learning.” SPIE Medical Imaging (2024).
  30. Yanfan Zhu, Yashbir Singh, Khaled Younis, Shunxing Bao, and Yuankai Huo. “Persistence Image from 3D Medical Image: Superpixel and Optimized Gaussian Coefficient.” SPIE Medical Imaging (2024).
  31. Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jialin Yue, Juming Xiong, Lining Yu, Yifei Wu, Mengmeng Yin, Yu Wang, Shilin Zhao, Yucheng Tang, Haichun Yang, and Yuankai Huo. “Prpseg: Universal proposition learning for panoramic renal pathology segmentation.” Proceedings of the IEEE/CVF conference on computer vision and pattern recognition (CVPR) (2024).
  32. Jiayuan Chen, Yu Wang, Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Yilin Liu, Jianyong Zhong, Agnes B Fogo, Haichun Yang, Shilin Zhao, and Yuankai Huo. “Spatial pathomics toolkit for quantitative analysis of podocyte nuclei with histology and spatial transcriptomics data in renal pathology.” SPIE Medical Imaging (2024).
  33. Tianyuan Yao, Nancy Newlin, Praitayini Kanakaraj, Vishwesh Nath, Leon Y Cai, Karthik Ramadass, Kurt Schilling, Bennett A Landman, and Yuankai Huo. “A unified learning model for estimating fiber orientation distribution functions on heterogeneous multi-shell diffusion-weighted MRI.” International Workshop on Computational Diffusion MRI (2023).
  34. Haoju Leng, Ruining Deng, Zuhayr Asad, R. M. Womick, Haichun Yang, Lipeng Wan, and Yuankai Huo. “An Accelerated Pipeline for Multi-label Renal Pathology Image Segmentation at the Whole Slide Image Level.” SPIE Medical Imaging (2023).
  35. Peize Li, Ruining Deng, and Yuankai Huo. “An End-to-end Pipeline for 3D Slide-wise Multi-stain Renal Pathology Registration.” SPIE Medical Imaging (2023).
  36. Shunxing Bao, Sichen Zhu, Vasantha L. Kolachala, Lucas W. Remedios, Y. Hwang, Yutong Sun, Ruining Deng, Can Cui, Yike Li, Jia Li, Joseph T. Roland, Qi Liu, Ken S. Lau, S. Kugathasan, Peng-Chao Qiu, Keith T. Wilson, Lori A. Coburn, Bennett A. Landman, and Yuankai Huo. “Cell Spatial Analysis in Crohn’s Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures.” SPIE Medical Imaging (2023).
  37. Chenxi Dong, Thomas Z Li, Kaiwen Xu, Zekun Wang, Fabien Maldonado, Kim Sandler, Bennett A Landman, and Yuankai Huo. “Characterizing browser-based medical imaging AI with serverless edge computing: towards addressing clinical data security constraints.” SPIE Medical Imaging (2023).
  38. Juming Xiong, Yilin Liu, Ruining Deng, Regina N Tyree, HernĂĄn Correa, Girish Hiremath, Yaohong Wang, and Yuankai Huo. “Deep Learning-Based Open Source Toolkit for Eosinophil Detection in Pediatric Eosinophilic Esophagitis.” SPIE Medical Imaging (2023).
  39. Tianyuan Yao, Francois Rheault, Leon Y Cai, Vishwesh Nath, Zuhayr Asad, Nancy Newlin, Can Cui, Ruining Deng, Karthik Ramadass, Kurt Schilling, Bennett A Landman, and Yuankai Huo. “Deep constrained spherical deconvolution for robust harmonization.” SPIE Medical Imaging (2023).
  40. Ruining Deng, Yanwei Li, Peize Li, Jiacheng Wang, Lucas W Remedios, Saydolimkhon Agzamkhodjaev, Zuhayr Asad, Quan Liu, Can Cui, Yaohong Wang, Yihan Wang, Yucheng Tang, Haichun Yang, and Yuankai Huo. “Democratizing pathological image segmentation with lay annotators via molecular-empowered learning.” International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) (2023).
  41. Yilin Liu, Ruining Deng, Juming Xiong, Regina N Tyree, HernĂĄn Correa, Girish Hiremath, Yaohong Wang, and Yuankai Huo. “Eosinophils Instance Object Segmentation on Whole Slide Imaging Using Multi-label Circle Representation.” SPIE Medical Imaging (2023).
  42. Muhao Liu, Chenyang Qi, Shunxing Bao, QUAN LIU, Ruining Deng, Yu Wang, Shilin Zhao, Haichun Yang, and Yuankai Huo. “Evaluation Kidney Layer Segmentation on Whole Slide Imaging using Convolutional Neural Networks and Transformers.” SPIE Medical Imaging (2023).
  43. Can Cui, Yaohong Wang, Shunxing Bao, Yucheng Tang, Ruining Deng, Lucas W. Remedios, Zuhayr Asad, Joseph T. Roland, Ken S. Lau, Qi Liu, Lori A. Coburn, Keith T. Wilson, Bennett A. Landman, and Yuankai Huo. “Feasibility of Universal Anomaly Detection without Knowing the Abnormality in Medical Images.” MICCAI Medical Image Learning with Limited and Noisy Data Workshop (2023).
  44. Q Liu, Jiawen Yao, L Yao, X Chen, J Zhou, Le Lu, L Zhang, Z Liu, and Yuankai Huo. “Fusion: Bayesian-Based Multimodal Multi-level Fusion on Colorectal Cancer Microsatellite Instability Prediction.” MICCAI Workshop (2023).
  45. Haoju Leng, Ruining Deng, Shunxing Bao, Dazheng Fang, Bryan A. Millis, Yucheng Tang, Haichun Yang, Xiao Wang, Yifan Peng, Lipeng Wan, and Yuankai Huo. “High-performance data management for whole slide image analysis in digital pathology.” SPIE Medical Imaging (2023).
  46. Can Cui, Shunxing Bao, Jia Li, Ruining Deng, Lucas W. Remedios, Zuhayr Asad, Sophie Chiron, Ken S. Lau, Yaohong Wang, Lori A. Coburn, Keith T. Wilson, Joseph T. Roland, Bennett A. Landman, Qi Liu, and Yuankai Huo. “Influence of Cell-type Ratio on Spatially Resolved Single-cell Transcriptomes using the Tangram Algorithm: Based on Implementation on Single-Cell and MxIF Data.” SPIE Medical Imaging (2023).
  47. Xueyuan Li, Ruining Deng, Yucheng Tang, Shunxing Bao, Haichun Yang, and Yuankai Huo. “Leverage Weakly Annotation to Pixel-wise Annotation via Zero-shot Segment Anything Model for Molecular-empowered Learning.” SPIE Medical Imaging (2023).
  48. Franklin Hu, Ruining Deng, Shunxing Bao, Haichun Yang, and Yuankai Huo. “Multi-scale Multi-site Renal Microvascular Structures Segmentation for Whole Slide Imaging in Renal Pathology.” SPIE Medical Imaging (2023).
  49. Shunxing Bao, Can Cui, Jia Li, Yucheng Tang, Ho Hin Lee, Ruining Deng, Lucas W. Remedios, Xin Yu, Qi Yang, Sophie Chiron, Nathan Heath Patterson, Ken S. Lau, Qi Liu, Joseph T. Roland, Lori A. Coburn, Keith T. Wilson, Bennett A. Landman, and Yuankai Huo. “Topological-Preserving Membrane Skeleton Segmentation in Multiplex Immunofluorescence Imaging.” SPIE Medical Imaging (2023).
  50. Ethan H. Nguyen, Haichun Yang, Zuhayr Asad, Ruining Deng, Agnes B. Fogo, and Yuankai Huo. “CircleSnake: Instance Segmentation with Circle Representation.” MICCAI Machine Learning in Medical Imaging Workshop (2022).
  51. Ruining Deng, Can Cui, Lucas W Remedios, Shunxing Bao, R Michael Womick, Sophie Chiron, Jia Li, Joseph T Roland, Ken S Lau, Qi Liu, Keith T Wilson, Yaohong Wang, Lori A Coburn, Bennett A Landman, and Yuankai Huo. “Cross-scale attention guided multi-instance learning for crohn’s disease diagnosis with pathological images.” International Workshop on Multiscale Multimodal Medical Imaging (2022).
  52. Ruining Deng, Haichun Yang, Zuhayr Asad, Zheyu Zhu, Shiru Wang, Lee E. Wheless, Agnes B. Fogo, and Yuankai Huo. “Dense Multi-Object 3D Glomerular Reconstruction and Quantification on 2D Serial Section Whole Slide Images.” SPIE Medical Imaging (2022).
  53. Yuxuan Shi, Quan Liu, Jiachen Xu, Zuhayr Asad, Can Cui, HernĂĄn Correa, Yash A Choksi, Girish Hiremath, and Yuankai Huo. “Eosinophilic esophagitis multi-label feature recognition on whole slide imaging using transfer learning.” SPIE Medical Imaging (2022).
  54. Shunxing Bao, Yucheng Tang, Ho Hin Lee, Riqiang Gao, Qi Yang, Xin Yu, Sophie Chiron, Lori A. Coburn, Keith T. Wilson, Joseph T. Roland, Bennett A. Landman, and Yuankai Huo. “Inpainting Missing Tissue in Multiplexed Immunofluorescence Imaging.” SPIE Medical Imaging (2022).
  55. Quan Liu, Bryan A. Millis, Zuhayr Asad, Can Cui, William F Dean, Isabelle T. Smith, Christopher Madden, Joseph T. Roland, Jeffrey P Zwerner, Shilin Zhao, Lee E. Wheless, and Yuankai Huo. “Integrate memory efficiency methods for self-supervised learning on pathological image analysis.” SPIE Medical Imaging (2022).
  56. Zheyu Zhu, Ruining Deng, Quan Liu, Zuhayr Asad, Can Cui, Tianyuan Yao, and Yuankai Huo. “Large-Scale Patch-Wise Pathological Image Feature Dataset with a Hardware-agnostic Feature Extraction Tool.” Annual Conference on Medical Image Understanding and Analysis (2022).
  57. Quan Liu, Can Cui, Ruining Deng, Zuhayr Asad, Tianyuan Yao, Zheyu Zhu, and Yuankai Huo. “Leverage Supervised and Self-supervised Pretrain Models for Pathological Survival Analysis via a Simple and Low-cost Joint Representation Tuning.” MICCAI REMIA Workshop (2022).
  58. Kai-Lin Pang, Zuhayr Asad, Shilin Zhao, and Yuankai Huo. “MAG: A Simple Learning-Based Patient-Level Aggregation Method for Detecting Microsatellite Instability from Whole-Slide Images.” IEEE International Symposium on Biomedical Imaging (ISBI) (2022).
  59. Can Cui, Zuhayr Asad, William F Dean, Isabelle T Smith, Christopher Madden, Shunxing Bao, Bennett A Landman, Joseph T Roland, Lori A Coburn, Keith T Wilson, Jeffrey P Zwerner, Shilin Zhao, Lee E Wheless, and Yuankai Huo. “Multi-modal learning with missing data for cancer diagnosis using histopathological and genomic data.” SPIE Medical Imaging (2022).
  60. Shunxing Bao, Jia Li, Can Cui, Yucheng Tang, Ruining Deng, Lucas W. Remedios, Ho Hin Lee, Sophie Chiron, Nathan Heath Patterson, Ken S. Lau, Lori A. Coburn, Keith T. Wilson, Joseph T. Roland, Bennett A. Landman, Qi Liu, and Yuankai Huo. “MxIF Q-score: Biology-Informed Quality Assurance for Multiplexed Immunofluorescence Imaging.” MICCAI MOVI Workshop (2022).
  61. Tianyuan Yao, Yuzhe Lu, Ruining Deng, Zheyu Zhu, Zuhayr Asad, Haichun Yang, Lee E. Wheless, Agnes B. Fogo, and Yuankai Huo. “Self-supervised learning with large-scale web image mining for characterizing glomerular lesions.” SPIE Medical Imaging (2022).
  62. Ruining Deng, QUAN LIU, Can Cui, Zuhayr Asad, Haichun Yang, and Yuankai Huo. “Single Dynamic Network for Multi-label Renal Pathology Image Segmentation.” International Conference on Medical Imaging with Deep Learning (MIDL) (2022).
  63. Can Cui, Han Liu, Quan Liu, Ruining Deng, Zuhayr Asad, Yaohong Wang, Shilin Zhao, Haichun Yang, Bennett A Landman, and Yuankai Huo. “Survival prediction of brain cancer with incomplete radiology, pathology, genomic, and demographic data.” International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) (2022).
  64. Xing Li, Haichun Yang, Jiaxing He, Aadarsh Jha, Agnes B. Fogo, Lee E. Wheless, Shilin Zhao, and Yuankai Huo. “Beds: Bagging Ensemble Deep Segmentation For Nucleus Segmentation With Testing Stage Stain Augmentation.” IEEE International Symposium on Biomedical Imaging (ISBI) (2021).
  65. Tianyuan Yao, Chang Qu, Quan Liu, Ruining Deng, Yuanhan Tian, Jiachen Xu, Aadarsh Jha, Shunxing Bao, Mengyang Zhao, Agnes B Fogo, Bennett A Landman, Catie Chang, Haichun Yang, and Yuankai Huo. “Compound figure separation of biomedical images with side loss.” MICCAI Workshop on Deep Generative Models (2021).
  66. Yuzhe Lu, Aadarsh Jha, and Yuankai Huo. “Contrastive learning meets transfer learning: a case study in medical image analysis.” SPIE Medical Imaging (2021).
  67. Cam-Ngoan Nguyen, Zuhayr Asad, and Yuankai Huo. “Evaluating transformer-based semantic segmentation networks for pathological image segmentation.” SPIE Medical Imaging (2021).
  68. Yuzhe Lu, Haichun Yang, Zheyu Zhu, Ruining Deng, Agnes B. Fogo, and Yuankai Huo. “Improve Global Glomerulosclerosis Classification with Imbalanced Data using CircleMix Augmentation.” SPIE Medical Imaging (2021).
  69. Can Luo, James G Terry, Yucheng Tang, Kaiwen Xu, Pierre P Massion, Bennett A. Landman, John Jeffrey Carr, and Yuankai Huo. “Measure Partial Liver Volumetric Variations from Paired Inspiratory-expiratory Chest CT Scans.” SPIE Medical Imaging (2021).
  70. Ruining Deng, Quan Liu, Can Cui, Zuhayr Asad, Haichun Yang, and Yuankai Huo. “Omni-Seg: A Single Dynamic Network for Multi-label Renal Pathology Image Segmentation using Partially Labeled Data.” International Conference on Medical Imaging with Deep Learning (MIDL) (2022).
  71. Shunxing Bao, Yucheng Tang, Ho Hin Lee, Riqiang Gao, Sophie Chiron, Ilwoo Lyu, Lori A Coburn, Keith T Wilson, Joseph T Roland, Bennett A Landman, and Yuankai Huo. “Random multi-channel image synthesis for multiplexed immunofluorescence imaging.” MICCAI Workshop on Computational Pathology (2021).
  72. Quan Liu, Peter C Louis, Yuzhe Lu, Aadarsh Jha, Mengyang Zhao, Ruining Deng, Tianyuan Yao, Joseph T Roland, Haichun Yang, Shilin Zhao, Lee E Wheless, and Yuankai Huo. “Simtriplet: Simple triplet representation learning with a single gpu.” International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) (2021).
  73. Mengyang Zhao, Quan Liu, Aadarsh Jha, Ruining Deng, Tianyuan Yao, Anita Mahadevan-Jansen, Matthew J Tyska, Bryan A Millis, and Yuankai Huo. “VoxelEmbed: 3D instance segmentation and tracking with voxel embedding based deep learning.” International Workshop on Machine Learning in Medical Imaging (2021).
  74. Zekun Wang, Peng Wang, Peter C. Louis, Lee E. Wheless, and Yuankai Huo. “WearMask: Fast In-browser Face Mask Detection with Serverless Edge Computing for COVID-19.” High Performance Computing for Imaging (2021).
  75. Ruining Deng, Quan Liu, Shunxing Bao, Aadarsh Jha, Catie Chang, Bryan A. Millis, Matthew J. Tyska, and Yuankai Huo. “CaCL: Class-aware Codebook Learning for Weakly Supervised Segmentation on Diffuse Image Patterns.” MICCAI DGM4MICCAI Workshop (2020).
  76. Haichun Yang, Ruining Deng, Yuzhe Lu, Zheyu Zhu, Ye Chen, Joseph T Roland, Le Lu, Bennett A Landman, Agnes B Fogo, and Yuankai Huo. “CircleNet: Anchor-free glomerulus detection with circle representation.” International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) (2020).
  77. Zheyu Zhu, Yuzhe Lu, Ruining Deng, Haichun Yang, Agnes B. Fogo, and Yuankai Huo. “EasierPath: An Open-source Tool for Human-in-the-loop Deep Learning of Renal Pathology.” MICCAI LABELS Workshop (2020).
  78. QUAN Liu, Isabella M. Gaeta, Bryan A. Millis, Matthew J. Tyska, and Yuankai Huo. “GAN based unsupervised segmentation: should we match the exact number of objects.” SPIE Medical Imaging (2020).
  79. Ye Chen, and Yuankai Huo. “Limitation of acyclic oriented graphs matching as cell tracking accuracy measure when evaluating mitosis.” SPIE Medical Imaging (2020).

Book Chapters

  1. Yucheng Tang, Jie Liu, Zongwei Zhou, Xin Yu, and Yuankai Huo. “Efficient 3D Representation Learning for Medical Image Analysis.” World Sci. Annu. Rev. Artif. Intell. (2024).
  2. Bennett A.Landman, Ilwoo Lyu, Yuankai Huo, and Andrew J. Asman. “Multiatlas segmentation.” In Handbook of Medical Image Computing and Computer Assisted Intervention, pp. 137-164. Academic Press, 2020.

Patents

  1. Adam P. Harrison, Yuankai Huo, Cai Jinzheng, Raju Ashwin, Yan Ke, and Le Lu. “Systems and methods for tumor characterization.” U.S. Patent 16/836,855 (2021)
  2. Adam P. Harrison, Raju Ashwin, Yuankai Huo, Cai Jinzheng, and Le Lu. “Co-heterogeneous and adaptive 3d pathological abdominal organ segmentation using multi-source and multi-phase clinical image datasets.” U.S. Patent 17/089,257 (2021).
  3. Cai Jinzheng, Adam P. Harrison, Yan Ke, Yuankai Huo, and Le Lu. “Method and system for harvesting lesion annotations.” U.S. Patent 16/984,727 (2021).
  4. Cai Jinzheng, Yuankai Huo, Le Lu, and Adam P. Harrison. “Device and method for alignment of multi-modal clinical images using joint synthesis, segmentation, and registration.” U.S. Patent 17/110,859, 2021.
  5. Xu Zhoubing, Yuankai Huo, Jin-hyeong Park, Sasa Grbic, and Shaohua Kevin Zhou. “Segmentation, landmark detection and view classification using multi-task learning.” U.S. Patent 10,910,099, (2021).