Selected Publications

1. 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).
2. 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, Yaohong Wang, Yihan Wang, Haichun Yang, and Yuankai Huo “Democratizing Pathological Image Segmentation with Lay Annotators via Molecular-empowered Learning.” MICCAI (2023).
3. Ho Hin Lee, Yucheng Tang, Qi Yang, Xin Yu, Shunxing Bao, Leon Y. Cai, Lucas W. Remedios, Bennett A. Landman, and Yuankai Huo “Semantic-Aware Contrastive Learning for Multi-object Medical Image Segmentation.” Journal of Biomedical and Health Informatics (2023).
4. Jiachen Xu, Junlin Guo, James Zimmer-Dauphinee, Quan Liu, Yuxuan Shi, Zuhayr Asad, D. Mitchell Wilkes, Parker VanValkenburgh, 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 (2023).
5. Tianyuan Yao, Chang Qu, Jun Long, Quan Liu, Ruining Deng, Yuanhan Tian, Jiachen Xu, Aadarsh Jha, Zuhayr Asad, Shunxing Bao, Mengyang Zhao, Agnes Fogo, Bennett Landman, Haichun Yang, Catie Chang, and Yuankai Huo. “Compound Figure Separation of Biomedical Images: Mining Large Datasets for Self-supervised Learning” Machine Learning for Biomedical Imaging (2022).
6. 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” MICCAI (2022).
7. Can Cui, Haichun Yang, Yaohong Wang, Shilin Zhao, Zuhayr Asad, Lori A. Coburn, Keith T. Wilson, Bennett Landman, and Yuankai Huo. “Deep Multi-modal Fusion of Image and Non-image Data in Disease Diagnosis and Prognosis: a Review.” Progress in Biomedical Engineering (2022).
8. Hanyu Zheng, Quan Liu, You Zhou, Ivan I Kravchenko, Yuankai Huo, and Jason Valentine. “Meta-optic Accelerators for Object Classifiers” Science Advances (2022)
9. 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)
10. 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)
11. 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, Yuankai Huo. “SimTriplet: Simple Triplet Representation Learning with a Single GPU.” MICCAI (2021).
12. Roza G. Bayrak, Colin B. Hansen, Jorge A. Salas, Nafis Ahmed, Ilwoo Lyu, Yuankai Huo, and Catie Chang. “From Brain to Body: Learning Low-Frequency Respiration and Cardiac Signals from fMRI Dynamics.” MICCAI (2021).
13. 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).
14. Ruining Deng, Haichun Yang, Aadarsh Jha, Yuzhe Lu, Peng Chu, Agnes Fogo, and Yuankai Huo. “Map3D: Registration Based Multi-Object Tracking on 3D Serial Whole Slide Images.” IEEE Transactions on Medical Imaging (2021).
15. Mengyang Zhao, Aadarsh Jha, Quan Liu, Bryan A. Millis, Anita Mahadevan-Jansen, Le Lu, Bennett A. Landman, Matthew J. Tyskac, and Yuankai Huo. “Faster Mean-shift: GPU-accelerated Embedding-clustering for Cell Segmentation and Tracking.” Medical Image Analysis (2021).
16. 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).
17. Yuankai Huo, Ruining Deng, Quan Liu, Agnes B. Fogo, and Haichun Yang. “AI applications in renal pathology.” Kidney International (2021).
18. Jorge A. Salas, Roza G. Bayrak, Yuankai Huo, and Catie Chang. “Reconstruction of respiratory variation signals from fMRI data.” NeuroImage (2020).
19. 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).
20. Jinzheng Cai, Adam P. Harrison, Youjing Zheng, Ke Yan, Yuankai Huo, Jing Xiao, Lin Yang, and Le Lu. “Lesion Harvester: Iteratively Mining Unlabeled Lesions and Hard-Negative Examples at Scale.” IEEE transactions on medical imaging (2020).
21. 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.” MICCAI (2020).
22. Roza G. Bayrak, Jorge A. Salas, Yuankai Huo, and Catie Chang. “A Deep Pattern Recognition Approach for Inferring Respiratory Volume Fluctuations from fMRI Data.” MICCAI (2020).
23. Bowen Li, Ke Yan, Dar-In Tai, Yuankai Huo, Le Lu, Jing Xiao, and Adam P. Harrison. “Reliable Liver Fibrosis Assessment from Ultrasound Using Global Hetero-Image Fusion and View-Specific Parameterization.” MICCAI (2020).
24. Ashwin Raju, Chi-Tung Cheng, Yunakai Huo, Jinzheng Cai, Junzhou Huang, Jing Xiao, Le Lu, ChienHuang Liao, and Adam P. Harrison. “Co-Heterogeneous and Adaptive Segmentation from Multi-Source and Multi-Phase CT Imaging Data: A Study on Pathological Liver and Lesion Segmentation.” ECCV (2020).
25. Fengze Liu, Jingzheng Cai, Yuankai Huo, Le Lu, and Adam P. Harrison. “JSSR: A Joint Synthesis, Segmentation, and Registration System for 3D Multi-Modal Image Alignment of Large-scale Pathological CT Scans.” ECCV (2020).
26. Yuankai Huo, Yucheng Tang, Yunqiang Chen, Dashan Gao, Shizhong Han, Shunxing Bao, Smita De, James G. Terry; Jeffrey J. Carr; Richard G. Abramson; and Bennett A. Landman. “Stochastic Tissue Window Normalization of Deep Learning on Computed Tomography.” Journal of Medical Imaging (2019).
27. Yuankai Huo, James G. Terry, Jiachen Wang, Sangeeta Nair, Thomas A. Lasko, Barry I. Freedman, Jeffery J. Carr, and Bennett A. Landman. “Fully Automatic Liver Attenuation Estimation Combing CNN Segmentation and Morphological Operations.” Medical physics (2019).
28. Yuankai Huo, Zhoubing Xu, Yunxi Xiong, Katherine Aboud, Prasanna Parvathaneni, Shunxing Bao, Camilo Bermudez, Susan M Resnick, Laurie E Cutting, Bennett A Landman. “3D whole Brain Segmentation using Spatially Localized Atlas Network Tiles.” NeuroImage (2019).
29. Yuankai Huo, Zhoubing Xu, Katherine Aboud, Prasanna Parvathaneni, Shunxing Bao, Camilo Bermudez, Susan M. Resnick, Laurie E. Cutting, and Bennett A. Landman. “Spatially Localized Atlas Network Tiles Enables 3D Whole Brain Segmentation from Limited Data.” MICCAI (2018).
30. Yuankai Huo, Zhoubing Xu, Shunxing Bao, Camilo Bermudez, Hyeonsoo Moon, Prasanna Parvathaneni, Tamara K. Moyo et al. “Splenomegaly Segmentation on Multi-modal MRI using Deep Convolutional Networks.” IEEE transactions on medical imaging (2018).
31. Yuankai Huo, Zhoubing Xu, Hyeonsoo Moon, Shunxing Bao, Albert Assad, Tamara K. Moyo, Michael R. Savona, Richard G. Abramson, and Bennett A. Landman. “SynSeg-Net: Synthetic Segmentation Without Target Modality Ground Truth.” IEEE transactions on medical imaging (2018).
32. Yuankai Huo, Justin Blaber, Stephen M. Damon, Brian D. Boyd, Shunxing Bao, Prasanna Parvathaneni, Camilo Bermudez Noguera et al. “Towards Portable Large-scale Image Processing with High-performance Computing.” Journal of digital imaging (2018).
33. Yuankai Huo, Jiaqi Liu, Zhoubing Xu, Robert L. Harrigan, Albert Assad, Richard G. Abramson, and Bennett A. Landman. “Robust Multicontrast MRI Spleen Segmentation for Splenomegaly Using Multi-Atlas Segmentation.” IEEE Transactions on Biomedical Engineering (2018).
34. Yuankai Huo, Andrew J. Asman, Andrew J. Plassard, and Bennett A. Landman. “Simultaneous total Intracranial Volume and Posterior Fossa Volume Estimation using Multi‐atlas Label Fusion.” Human brain mapping (2017).
35. Yuankai Huo, Andrew J. Plassard, Aaron Carass, Susan M. Resnick, Dzung L. Pham, Jerry L. Prince, and Bennett A. Landman. “Consistent Cortical Reconstruction and Multi-atlas Brain Segmentation.” NeuroImage (2016).
36. Yuankai Huo, Katherine Aboud, Hakmook Kang, Laurie E. Cutting, and Bennett A. Landman. “Mapping Lifetime Brain Volumetry with Covariate-adjusted Restricted Cubic Spline Regression from Cross-sectional Multi-site MRI.” MICCAI (2016).