Tianyuan Yao

According to our database, Tianyuan Yao authored at least 52 papers between 2021 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

Fine-grained Multi-class Nuclei Segmentation with Molecular-empowered All-in-SAM Model.

Xueyuan Li, Can Cui, Ruining Deng, Yucheng Tang, Quan Liu, Tianyuan Yao, Shunxing Bao, Naweed Chowdhury, Haichun Yang, Yuankai Huo

CoRR, August, 2025

Img2ST-Net: Efficient High-Resolution Spatial Omics Prediction from Whole Slide Histology Images via Fully Convolutional Image-to-Image Learning.

Junchao Zhu, Ruining Deng, Junlin Guo, Tianyuan Yao, Juming Xiong, Chongyu Qu, Mengmeng Yin, Yu Wang, Shilin Zhao, Haichun Yang, Daguang Xu, Yucheng Tang, Yuankai Huo

CoRR, August, 2025

ZeroReg3D: A Zero-shot Registration Pipeline for 3D Consecutive Histopathology Image Reconstruction.

Juming Xiong, Ruining Deng, Jialin Yue, Siqi Lu, Junlin Guo, Marilyn Lionts, Tianyuan Yao, Can Cui, Junchao Zhu, Chongyu Qu, Mengmeng Yin, Haichun Yang, Yuankai Huo

CoRR, June, 2025

Quantitative Benchmarking of Anomaly Detection Methods in Digital Pathology.

Can Cui, Xindong Zheng, Ruining Deng, Quan Liu, Tianyuan Yao, Keith T. Wilson, Lori A. Coburn, Bennett A. Landman, Haichun Yang, Yaohong Wang, Yuankai Huo

CoRR, June, 2025

IRS: Incremental Relationship-guided Segmentation for Digital Pathology.

Ruining Deng, Junchao Zhu, Juming Xiong, Can Cui, Tianyuan Yao, Junlin Guo, Siqi Lu, Marilyn Lionts, Mengmeng Yin, Yu Wang, Shilin Zhao, Yucheng Tang, Yihe Yang, Paul Dennis Simonson, Mert R. Sabuncu, Haichun Yang, Yuankai Huo

CoRR, May, 2025

DeepAndes: A Self-Supervised Vision Foundation Model for Multi-Spectral Remote Sensing Imagery of the Andes.

Junlin Guo, James 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, Yuankai Huo

CoRR, April, 2025

MagNet: Multi-Level Attention Graph Network for Predicting High-Resolution Spatial Transcriptomics.

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, Yuankai Huo

CoRR, February, 2025

KPIs 2024 Challenge: Advancing Glomerular Segmentation from Patch- to Slide-Level.

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, Noémie Moreau, Katarzyna Bozek, Shubham Innani, Ujjwal Baid, Kaura Solomon Kefas, Bennett A. Landman, Yu Wang, Shilin Zhao, Mengmeng Yin, Haichun Yang, Yuankai Huo

CoRR, February, 2025

Enhanced Feature-based Image Stitching for Endoscopic Videos in Pediatric Eosinophilic Esophagitis.

Juming Xiong, Muyang Li, Ruining Deng, Tianyuan Yao, Shunxing Bao, Regina N. Tyree, Girish Hiremath, Yuankai Huo

CoRR, February, 2025

Post-Training Quantization for 3D Medical Image Segmentation: A Practical Study on Real Inference Engines.

Chongyu Qu, Ritchie Zhao, Ye Yu, Bin Liu, Tianyuan Yao, Junchao Zhu, Bennett A. Landman, Yucheng Tang, Yuankai Huo

CoRR, January, 2025

Polyhedra Encoding Transformers: Enhancing Diffusion MRI Analysis Beyond Voxel and Volumetric Embedding.

Tianyuan Yao, Zhiyuan Li, Praitayini Kanakaraj, Derek B. Archer, Kurt Schilling, Lori L. Beason-Held, Susan M. Resnick, Bennett A. Landman, Yuankai Huo

CoRR, January, 2025

PySpatial: A High-Speed Whole Slide Image Pathomics Toolkit.

Yuechen Yang, Yu Wang, Tianyuan Yao, Ruining Deng, Mengmeng Yin, Shilin Zhao, Haichun Yang, Yuankai Huo

CoRR, January, 2025

ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics.

Junchao Zhu, Ruining Deng, Tianyuan Yao, Juming Xiong, Chongyu Qu, Junlin Guo, Siqi Lu, Mengmeng Yin, Yu Wang, Shilin Zhao, Haichun Yang, Yuankai Huo

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2025

2024

DeepN4: Learning N4ITK Bias Field Correction for T1-weighted Images.

Praitayini Kanakaraj, Tianyuan Yao, Leon Y. Cai, Ho Hin Lee, Nancy R. Newlin, Michael E. Kim, Chenyu Gao, Kimberly R. Pechman, Derek B. Archer, Timothy J. Hohman, Angela L. Jefferson, Lori L. Beason-Held, Susan M. Resnick, Eleftherios Garyfallidis, Adam W. Anderson, Kurt G. Schilling, Bennett A. Landman, Daniel Moyer

Neuroinformatics, April, 2024

GloFinder: AI-empowered QuPath Plugin for WSI-level Glomerular Detection, Visualization, and Curation.

Jialin Yue, Tianyuan Yao, Ruining Deng, Siqi Lu, Junlin Guo, Quan Liu, Mengmeng Yin, Juming Xiong, Haichun Yang, Yuankai Huo

CoRR, 2024

Glo-In-One-v2: Holistic Identification of Glomerular Cells, Tissues, and Lesions in Human and Mouse Histopathology.

Lining Yu, Mengmeng Yin, Ruining Deng, Quan Liu, Tianyuan Yao, Can Cui, Junlin Guo, Yu Wang, Yaohong Wang, Shilin Zhao, Haichun Yang, Yuankai Huo

CoRR, 2024

Cross-organ Deployment of EOS Detection AI without Retraining: Feasibility and Limitation.

Yifei Wu, Juming Xiong, Tianyuan Yao, Ruining Deng, Junlin Guo, Jialin Yue, Naweed Chowdhury, Yuankai Huo

CoRR, 2024

How Good Are We? Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment.

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, Yuankai Huo

CoRR, 2024

Automatic Image Unfolding and Stitching Framework for Esophageal Lining Video Based on Density-Weighted Feature Matching.

Muyang Li, Juming Xiong, Ruining Deng, Tianyuan Yao, Regina N. Tyree, Girish Hiremath, Yuankai Huo

CoRR, 2024

Multi-Modality Conditioned Variational U-Net for Field-of-View Extension in Brain Diffusion MRI.

Zhiyuan Li, Tianyuan Yao, Praitayini Kanakaraj, Chenyu Gao, Shunxing Bao, Lianrui Zuo, Michael E. Kim, Nancy R. Newlin, Gaurav Rudravaram, Nazirah Mohd Khairi, Yuankai Huo, Kurt G. Schilling, Walter Kukull, Arthur W. Toga, Derek B. Archer, Timothy J. Hohman, Bennett A. Landman

CoRR, 2024

Assessment of Cell Nuclei AI Foundation Models in Kidney Pathology.

Junlin Guo, Siqi Lu, Can Cui, Ruining Deng, Tianyuan Yao, Zhewen Tao, Yizhe Lin, Marilyn Lionts, Quan Liu, Juming Xiong, Catie Chang, Mitchell Wilkes, Mengmeng Yin, Haichun Yang, Yuankai Huo

CoRR, 2024

Adapting Mouse Pathological Model to Human Glomerular Lesion Segmentation.

Lining Yu, Mengmeng Yin, Ruining Deng, Quan Liu, Tianyuan Yao, Can Cui, Yu Wang, Yaohong Wang, Shilin Zhao, Haichun Yang, Yuankai Huo

CoRR, 2024

Dataset Distillation in Medical Imaging: A Feasibility Study.

Muyang Li, Can Cui, Quan Liu, Ruining Deng, Tianyuan Yao, Marilyn Lionts, Yuankai Huo

CoRR, 2024

PFPs: Prompt-guided Flexible Pathological Segmentation for Diverse Potential Outcomes Using Large Vision and Language Models.

Can Cui, Ruining Deng, Junlin Guo, Quan Liu, Tianyuan Yao, Haichun Yang, Yuankai Huo

CoRR, 2024

HoloHisto: End-to-end Gigapixel WSI Segmentation with 4K Resolution Sequential Tokenization.

Yucheng Tang, Yufan He, Vishwesh Nath, Pengfei Guo, Ruining Deng, Tianyuan Yao, Quan Liu, Can Cui, Mengmeng Yin, Ziyue Xu, Holger Roth, Daguang Xu, Haichun Yang, Yuankai Huo

CoRR, 2024

Weighted Circle Fusion: Ensembling Circle Representation from Different Object Detection Results.

Jialin Yue, Tianyuan Yao, Ruining Deng, Quan Liu, Juming Xiong, Haichun Yang, Yuankai Huo

CoRR, 2024

mTREE: Multi-Level Text-Guided Representation End-to-End Learning for Whole Slide Image Analysis.

Quan Liu, Ruining Deng, Can Cui, Tianyuan Yao, Vishwesh Nath, Yucheng Tang, Yuankai Huo

CoRR, 2024

Field-of-View Extension for Diffusion MRI via Deep Generative Models.

Chenyu Gao, Shunxing Bao, Michael E. Kim, Nancy Newlin, Praitayini Kanakaraj, Tianyuan Yao, Gaurav Rudravaram, Yuankai Huo, Daniel Moyer, Kurt Schilling, Walter Kukull, Arthur W. Toga, Derek B. Archer, Timothy J. Hohman, Bennett A. Landman, Zhiyuan Li

CoRR, 2024

Ts-FWE: Token-Aware Single-Shell Free Water Estimation for Brain Diffusion MRI.

Tianyuan Yao, Derek B. Archer, Zhiyuan Li, Leon Y. Cai, Praitayini Kanakaraj, Nancy Newlin, Quan Liu, Ruining Deng, Can Cui, Shunxing Bao, Kurt Schilling, Bennett A. Landman, Yuankai Huo

Proceedings of the Computational Diffusion MRI - 15th International Workshop, 2024

HATs: Hierarchical Adaptive Taxonomy Segmentation for Panoramic Pathology Image Analysis.

Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Juming Xiong, Shunxing Bao, Hao Li, Mengmeng Yin, Yu Wang, Shilin Zhao, Yucheng Tang, Haichun Yang, Yuankai Huo

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2024, 2024

PrPSeg: Universal Proposition Learning for Panoramic Renal Pathology Segmentation.

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, Yuankai Huo

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2024

Enhancing Physician Flexibility: Prompt-Guided Multi-class Pathological Segmentation for Diverse Outcomes.

Can Cui, Ruining Deng, Junlin Guo, Quan Liu, Tianyuan Yao, Haichun Yang, Yuankai Huo

Proceedings of the IEEE EMBS International Conference on Biomedical and Health Informatics, 2024

2023

Omni-Seg: A Scale-Aware Dynamic Network for Renal Pathological Image Segmentation.

Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jun Long, Zuhayr Asad, R. Michael Womick, Zheyu Zhu, Agnes B. Fogo, Shilin Zhao, Haichun Yang, Yuankai Huo

IEEE Trans. Biomed. Eng., September, 2023

Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access.

Mingquan Lin, Bo-Jian Hou, Swati Mishra, Tianyuan Yao, Yuankai Huo, Qian Yang, Fei Wang, George Shih, Yifan Peng

Comput. Biol. Medicine, June, 2023

Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology.

Jiayuan Chen, Yu Wang, Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Yilin Liu, Jianyong Zhong, Agnes B. Fogo, Haichun Yang, Shilin Zhao, Yuankai Huo

CoRR, 2023

All-in-SAM: from Weak Annotation to Pixel-wise Nuclei Segmentation with Prompt-based Finetuning.

Can Cui, Ruining Deng, Quan Liu, Tianyuan Yao, Shunxing Bao, Lucas W. Remedios, Yucheng Tang, Yuankai Huo

CoRR, 2023

Robust Fiber ODF Estimation Using Deep Constrained Spherical Deconvolution for Diffusion MRI.

Tianyuan Yao, Francois Rheault, Leon Y. Cai, Vishwesh Nath, Zuhayr Asad, Nancy Newlin, Can Cui, Ruining Deng, Karthik Ramadass, Andrea T. Shafer, Susan M. Resnick, Kurt Schilling, Bennett A. Landman, Yuankai Huo

CoRR, 2023

Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging.

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, Yuankai Huo

CoRR, 2023

A Unified Single-stage Learning Model for Estimating Fiber Orientation Distribution Functions on Heterogeneous Multi-shell Diffusion-weighted MRI.

Tianyuan Yao, Nancy Newlin, Praitayini Kanakaraj, Vishwesh Nath, Leon Y. Cai, Karthik Ramadass, Kurt Schilling, Bennett A. Landman, Yuankai Huo

CoRR, 2023

Deep constrained spherical deconvolution for robust harmonization.

Tianyuan Yao, Francois Rheault, Leon Y. Cai, Vishwesh Nath, Zuhayr Asad, Nancy Newlin, Can Cui, Ruining Deng, Karthik Ramadass, Kurt Schilling, Bennett A. Landman, Yuankai Huo

Proceedings of the Medical Imaging 2023: Image Processing, 2023

Comparing voxel- and feature-wise harmonization of complex graph measures from multiple sites for structural brain network investigation of aging.

Nancy R. Newlin, Leon Y. Cai, Tianyuan Yao, Derek B. Archer, Kurt G. Schilling, Timothy J. Hohman, Kimberly R. Pechman, Angela L. Jefferson, Andrea T. Shafer, Susan M. Resnick, Bennett A. Landman

Proceedings of the Medical Imaging 2023: Image Processing, 2023

A Unified Learning Model for Estimating Fiber Orientation Distribution Functions on Heterogeneous Multi-shell Diffusion-Weighted MRI.

Tianyuan Yao, Nancy Newlin, Praitayini Kanakaraj, Vishwesh Nath, Leon Y. Cai, Karthik Ramadass, Kurt Schilling, Bennett A. Landman, Yuankai Huo

Proceedings of the Computational Diffusion MRI - 14th International Workshop, 2023

2022

Compound Figure Separation of Biomedical Images: Mining Large Datasets for Self-supervised Learning.

Tianyuan Yao, Chang 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, Yuankai Huo

CoRR, 2022

Omni-Seg+: A Scale-aware Dynamic Network for Pathological Image Segmentation.

Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jun Long, Zuhayr Asad, R. Michael Womick, Zheyu Zhu, Agnes B. Fogo, Shilin Zhao, Haichun Yang, Yuankai Huo

CoRR, 2022

Glo-In-One: Holistic Glomerular Detection, Segmentation, and Lesion Characterization with Large-scale Web Image Mining.

Tianyuan Yao, Yuzhe Lu, Jun Long, Aadarsh Jha, Zheyu Zhu, Zuhayr Asad, Haichun Yang, Agnes B. Fogo, Yuankai Huo

CoRR, 2022

Holistic Fine-grained GGS Characterization: From Detection to Unbalanced Classification.

Yuzhe Lu, Haichun Yang, Zuhayr Asad, Zheyu Zhu, Tianyuan Yao, Jiachen Xu, Agnes B. Fogo, Yuankai Huo

CoRR, 2022

Large-Scale Patch-Wise Pathological Image Feature Dataset with a Hardware-agnostic Feature Extraction Tool.

Zheyu Zhu, Ruining Deng, Quan Liu, Zuhayr Asad, Can Cui, Tianyuan Yao, Yuankai Huo

Proceedings of the Medical Image Understanding and Analysis - 26th Annual Conference, 2022

Self-supervised learning with large-scale web image mining for characterizing glomerular lesions.

Tianyuan Yao, Yuzhe Lu, Ruining Deng, Zheyu Zhu, Zuhayr Asad, Haichun Yang, Lee E. Wheless, Agnes B. Fogo, Yuankai Huo

Proceedings of the Medical Imaging 2022: Digital and Computational Pathology, 2022

Leverage Supervised and Self-supervised Pretrain Models for Pathological Survival Analysis via a Simple and Low-cost Joint Representation Tuning.

Quan Liu, Can Cui, Ruining Deng, Zuhayr Asad, Tianyuan Yao, Zheyu Zhu, Yuankai Huo

Proceedings of the Resource-Efficient Medical Image Analysis - First MICCAI Workshop, 2022

2021

VoxelEmbed: 3D Instance Segmentation and Tracking with Voxel Embedding based Deep Learning.

Mengyang Zhao, Quan Liu, Aadarsh Jha, Ruining Deng, Tianyuan Yao, Anita Mahadevan-Jansen, Matthew J. Tyska, Bryan A. Millis, Yuankai Huo

Proceedings of the Machine Learning in Medical Imaging - 12th International Workshop, 2021

Compound Figure Separation of Biomedical Images with Side Loss.

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, Yuankai Huo

Proceedings of the Deep Generative Models, and Data Augmentation, Labelling, and Imperfections, 2021

SimTriplet: Simple Triplet Representation Learning with a Single GPU.

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

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 - 24th International Conference, Strasbourg, France, September 27, 2021