| 2026 | AAAI | Mitigating Hallucinations in Large Language Models via Causal Reasoning. | Yuangang Li, Yiqing Shen, Yi Nian, Jiechao Gao, Ziyi Wang, Chenxiao Yu, Li Li, Jie Wang, Xiyang Hu, Yue Zhao |
| 2026 | WACV | Multimodal Medical Image Binding via Shared Text Embeddings. | Yunhao Liu, Suyang Xi, Shiqi Liu, Hong Ding, Chicheng Jin, Chong Zhong, Junjun He, Catherine C. Liu, Yiqing Shen |
| 2026 | WACV | A Unified Diffusion-Based Framework for Multi-Agent Trajectory Prediction Integrating Structured Multi-Modal Representations. | Chenxi Yang, Suyang Xi, Hong Ding, Yiqing Shen, Yunhao Liu |
| 2025 | COLING | AutoProteinEngine: A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering. | Yungeng Liu, Zan Chen, Yuguang Wang, Yiqing Shen |
| 2025 | ICANN | Feature-Aware Sequence Models for Tabular Data Processing with Missing Values. | Yan Qian, Yiqing Shen |
| 2025 | ICCV | Online Reasoning Video Segmentation with Just-in-Time Digital Twins. | Yiqing Shen, Bohan Liu, Chenjia Li, Lalithkumar Seenivasan, Mathias Unberath |
| 2025 | MICCAI | Temporally-Constrained Video Reasoning Segmentation and Automated Benchmark Construction. | Yiqing Shen, Chenjia Li, Chenxiao Fan, Mathias Unberath |
| 2025 | MICCAI | Operating Room Workflow Analysis via Reasoning Segmentation over Digital Twins. | Yiqing Shen, Chenjia Li, Bohan Liu, Cheng-Yi Li, Tito Porras, Mathias Unberath |
| 2025 | MICCAI | Multi-scale Spatial Context with Learnable High-Frequency Augmentation for Polyp Segmentation. | Min Wang, Yanzhou Su, Yiqing Shen, Wen Wang |
| 2025 | PRICAI | SAM-Lightning: Segment Anything Model for Efficient Inference and Reduced Memory Footprint. | Yanfei Song, Hongxu Jiang, Bangzheng Pu, Peng Wang, Dong Dong, Yongxiang Cao, Runhua Zhang, Yiqing Shen |
| 2024 | AIME | Learning to Predict the Optimal Template in Stain Normalization for Histology Image Analysis. | Shiling Luo, Junxin Feng, Yiqing Shen, Qiongxiong Ma |
| 2024 | AIME | ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering. | Yiqing Shen, Outongyi Lv, Houying Zhu, Yu Guang Wang |
| 2024 | AIME | TinySAM-Med3D: A Lightweight Segment Anything Model for Volumetric Medical Imaging with Mixture of Experts. | Tianyuan Song, Guixia Kang, Yiqing Shen |
| 2024 | AIME | Histology Image Artifact Restoration with Lightweight Transformer Based Diffusion Model. | Chong Wang, Zhenqi He, Junjun He, Jin Ye, Yiqing Shen |
| 2024 | ECCV | SAM-Med3D: Towards General-Purpose Segmentation Models for Volumetric Medical Images. | Haoyu Wang, Sizheng Guo, Jin Ye, Zhongying Deng, Junlong Cheng, Tianbin Li, Jianpin Chen, Yanzhou Su, Ziyan Huang, Yiqing Shen, Bin Fu, Shaoting Zhang, Junjun He, Yu Qiao |
| 2024 | ICPR | TotalCT-SAM: A Whole-Body CT Segment Anything Model with Memorizing Transformer. | Zhiwei Zhang, Yiqing Shen |
| 2024 | IJCNN | KnowledgeIE: Unifying Online-Offline Distillation based on Knowledge Inheritance and Evolution. | Yiqing Shen |
| 2024 | ICRA | A Retinex Structure-based Low-light Enhancement Model Guided by Spatial Consistency. | Miao Zhang, Yiqing Shen, Zhuowei Li, Guofeng Pan, Shuai Lu |
| 2024 | MICCAI | M | Yufeng Jiang, Yiqing Shen |
| 2024 | MICCAI | Promptable Counterfactual Diffusion Model for Unified Brain Tumor Segmentation and Generation with MRIs. | Yiqing Shen, Guannan He, Mathias Unberath |
| 2024 | MICCAI | FastSAM3D: An Efficient Segment Anything Model for 3D Volumetric Medical Images. | Yiqing Shen, Jingxing Li, Xinyuan Shao, Blanca Inigo Romillo, Ankush Jindal, David Dreizin, Mathias Unberath |
| 2024 | MICCAI | FastSAM-3DSlicer: A 3D-Slicer Extension for 3D Volumetric Segment Anything Model with Uncertainty Quantification. | Yiqing Shen, Xinyuan Shao, Blanca Inigo Romillo, David Dreizin, Mathias Unberath |
| 2024 | MICCAI | DiffuseReg: Denoising Diffusion Model for Obtaining Deformation Fields in Unsupervised Deformable Image Registration. | Yongtai Zhuo, Yiqing Shen |
| 2023 | ICASSP | Mixed Sample Augmentation for Online Distillation. | Yiqing Shen, Liwu Xu, Yuzhe Yang, Yaqian Li, Yandong Guo |
| 2023 | MICCAI | COVID-19 Pneumonia Classification with Transformer from Incomplete Modalities. | Eduard Lloret Carbonell, Yiqing Shen, Xin Yang, Jing Ke |
| 2023 | MICCAI | Artifact Restoration in Histology Images with Diffusion Probabilistic Models. | Zhenqi He, Junjun He, Jin Ye, Yiqing Shen |
| 2023 | MICCAI | TransNuSeg: A Lightweight Multi-task Transformer for Nuclei Segmentation. | Zhenqi He, Mathias Unberath, Jing Ke, Yiqing Shen |
| 2023 | MICCAI | Evaluating STU-Net for Brain Tumor Segmentation. | Ziyan Huang, Jin Ye, Haoyu Wang, Zhongying Deng, Yanzhou Su, Tianbin Li, Junlong Cheng, Jianpin Chen, Sizheng Guo, Yiqing Shen, Junjun He |
| 2023 | MICCAI | StainDiff: Transfer Stain Styles of Histology Images with Denoising Diffusion Probabilistic Models and Self-ensemble. | Yiqing Shen, Jing Ke |
| 2023 | MICCAI | Revisiting Feature Propagation and Aggregation in Polyp Segmentation. | Yanzhou Su, Yiqing Shen, Jin Ye, Junjun He, Jian Cheng |
| 2023 | MICCAI | A General Computationally-Efficient 3D Reconstruction Pipeline for Multiple Images with Point Clouds. | Qingyang Wu, Yiqing Shen, Jing Ke |
| 2023 | MICCAI | An Anti-biased TBSRTC-Category Aware Nuclei Segmentation Framework with a Multi-label Thyroid Cytology Benchmark. | Junchao Zhu, Yiqing Shen, Haolin Zhang, Jing Ke |
| 2022 | CVPR | Self-Distillation from the Last Mini-Batch for Consistency Regularization. | Yiqing Shen, Liwu Xu, Yuzhe Yang, Yaqian Li, Yandong Guo |
| 2022 | CVPR | CD | Yiqing Shen, Yuyin Zhou, Lequan Yu |
| 2022 | MICCAI | RandStainNA: Learning Stain-Agnostic Features from Histology Slides by Bridging Stain Augmentation and Normalization. | Yiqing Shen, Yulin Luo, Dinggang Shen, Jing Ke |
| 2021 | ICIP | Su-Sampling Based Active Learning For Large-Scale Histopathology Image. | Yiqing Shen, Jing Ke |
| 2021 | MICCAI | CA | Jinghan Huang, Yiqing Shen, Dinggang Shen, Jing Ke |
| 2021 | MICCAI | Contrastive Learning Based Stain Normalization Across Multiple Tumor in Histopathology. | Jing Ke, Yiqing Shen, Xiaoyao Liang, Dinggang Shen |
| 2020 | AIME | A High-Throughput Tumor Location System with Deep Learning for Colorectal Cancer Histopathology Image. | Jing Ke, Yiqing Shen, Yi Guo, Jason D. Wright, Naifeng Jing, Xiaoyao Liang |
| 2020 | ICIP | Fast Tumor Detector in Whole-Slide Image With Dynamic Programing Based Monte Carlo Sampling. | Jing Ke, Yiqing Shen, Yi Guo, Xiaoyao Liang |
| 2020 | MICCAI | A Deformable CRF Model for Histopathology Whole-Slide Image Classification. | Yiqing Shen, Jing Ke |