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Yiqing Shen 0003
Person information
- affiliation: Johns Hopkins University, MD, USA
- affiliation (former): Beijing Infervision Technology Co., Ltd., Beijing, China
- affiliation (former): Shanghai Jiao Tong University, Shanghai, China
Other persons with the same name
- Yiqing Shen 0001 — Xi'an Jiaotong University, Xi'an, China
- Yiqing Shen 0002 — Chinese Academy of Sciences, Institute of Mechanics, LHD, Beijing, China (and 1 more)
- Yiqing Shen 0004 — Chongqing Medical University, Chongqing, China
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2020 – today
- 2025
- [e2]Zhongying Deng
, Yiqing Shen
Foundation Models for General Medical AI - Second International Workshop, MedAGI 2024, Held in Conjunction with MICCAI 2024, Marrakesh, Morocco, October 6, 2024, Proceedings. Lecture Notes in Computer Science 15184, Springer 2025, ISBN 978-3-031-73470-0 [contents] - 2024
- [j11]Dongsong Zhang, Changjian Wang
Scalable Swin Transformer network for brain tumor segmentation from incomplete MRI modalities. Artif. Intell. Medicine 149: 102788 (2024) - [j10]Erfan Darzi
Tackling heterogeneity in medical federated learning via aligning vision transformers. Artif. Intell. Medicine 155: 102936 (2024) - [j9]Jingpu Wu, Qianqi Huang, Yiqing Shen, Pengfei Guo, Jinyuan Zhou, Shanshan Jiang
Radiomic feature reliability of amide proton transfer-weighted MR images acquired with compressed sensing at 3 T. Int. J. Imaging Syst. Technol. 34(2) (2024) - [j8]Chong Wang
RandStainNA++: Enhance Random Stain Augmentation and Normalization Through Foreground and Background Differentiation. IEEE J. Biomed. Health Informatics 28(6): 3660-3671 (2024) - [c43]Chong Wang, Zhenqi He, Junjun He, Jin Ye, Yiqing Shen:
Histology Image Artifact Restoration with Lightweight Transformer Based Diffusion Model. AIME (2) 2024: 81-89 - [c42]Shiling Luo
Learning to Predict the Optimal Template in Stain Normalization for Histology Image Analysis. AIME (2) 2024: 95-103 - [c41]Tianyuan Song
TinySAM-Med3D: A Lightweight Segment Anything Model for Volumetric Medical Imaging with Mixture of Experts. AIME (2) 2024: 131-139 - [c40]Yiqing Shen
ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering. AIME (1) 2024: 373-383 - [c39]Yizhu Wen, Yiwei Wang, Kai Yi, Jing Ke, Yiqing Shen:
Diffimpute: Tabular Data Imputation with Denoising Diffusion Probabilistic Model. ICME 2024: 1-6 - [c38]Miao Zhang, Yiqing Shen, Zhuowei Li, Guofeng Pan, Shuai Lu:
A Retinex Structure-based Low-light Enhancement Model Guided by Spatial Consistency. ICRA 2024: 2154-2161 - [c37]Yiqing Shen:
KnowledgeIE: Unifying Online-Offline Distillation based on Knowledge Inheritance and Evolution. IJCNN 2024: 1-8 - [c36]Yiqing Shen, Xinyuan Shao, Blanca Inigo Romillo, David Dreizin, Mathias Unberath:
FastSAM-3DSlicer: A 3D-Slicer Extension for 3D Volumetric Segment Anything Model with Uncertainty Quantification. MedAGI@MICCAI 2024: 1-9 - [c35]Yiqing Shen, Guannan He, Mathias Unberath:
Promptable Counterfactual Diffusion Model for Unified Brain Tumor Segmentation and Generation with MRIs. MedAGI@MICCAI 2024: 81-90 - [c34]Yiqing Shen, Jingxing Li, Xinyuan Shao, Blanca Inigo Romillo, Ankush Jindal, David Dreizin, Mathias Unberath:
FastSAM3D: An Efficient Segment Anything Model for 3D Volumetric Medical Images. MICCAI (12) 2024: 542-552 - [c33]Yongtai Zhuo, Yiqing Shen
DiffuseReg: Denoising Diffusion Model for Obtaining Deformation Fields in Unsupervised Deformable Image Registration. MICCAI (2) 2024: 597-607 - [c32]Yufeng Jiang, Yiqing Shen
M4oE: A Foundation Model for Medical Multimodal Image Segmentation with Mixture of Experts. MICCAI (12) 2024: 621-631 - [c31]Daqin Luo
AutoM3L: An Automated Multimodal Machine Learning Framework with Large Language Models. ACM Multimedia 2024: 8586-8594 - [i24]Haoxiang Gao, Yaqian Li, Kaiwen Long, Ming Yang, Yiqing Shen:
A Survey for Foundation Models in Autonomous Driving. CoRR abs/2402.01105 (2024) - [i23]Yanfei Song, Bangzheng Pu, Peng Wang, Hongxu Jiang, Dong Dong, Yongxiang Cao, Yiqing Shen:
SAM-Lightening: A Lightweight Segment Anything Model with Dilated Flash Attention to Achieve 30 times Acceleration. CoRR abs/2403.09195 (2024) - [i22]Yiqing Shen, Jingxing Li, Xinyuan Shao, Blanca Inigo Romillo, Ankush Jindal, David Dreizin, Mathias Unberath:
FastSAM3D: An Efficient Segment Anything Model for 3D Volumetric Medical Images. CoRR abs/2403.09827 (2024) - [i21]Yizhu Wen, Kai Yi, Jing Ke, Yiqing Shen:
DiffImpute: Tabular Data Imputation With Denoising Diffusion Probabilistic Model. CoRR abs/2403.13863 (2024) - [i20]Yiqing Shen, Outongyi Lv, Houying Zhu, Yu Guang Wang:
ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering. CoRR abs/2405.06658 (2024) - [i19]Yiqing Shen, Zan Chen, Michail Mamalakis, Luhan He, Haiyang Xia, Tianbin Li, Yanzhou Su, Junjun He, Yu Guang Wang:
A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding. CoRR abs/2406.05540 (2024) - [i18]Daqin Luo, Chengjian Feng, Yuxuan Nong, Yiqing Shen:
AutoM3L: An Automated Multimodal Machine Learning Framework with Large Language Models. CoRR abs/2408.00665 (2024) - [i17]Yiqing Shen, Zan Chen, Michail Mamalakis, Yungeng Liu, Tianbin Li, Yanzhou Su, Junjun He, Pietro Liò, Yu Guang Wang:
TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering. CoRR abs/2408.15299 (2024) - [i16]Chong Wang, Mengyao Li, Junjun He, Zhongruo Wang, Erfan Darzi, Zan Chen, Jin Ye, Tianbin Li, Yanzhou Su, Jing Ke, Kaili Qu, Shuxin Li, Yi Yu, Pietro Liò, Tianyun Wang, Yu Guang Wang, Yiqing Shen:
A Survey for Large Language Models in Biomedicine. CoRR abs/2409.00133 (2024) - 2023
- [j7]Jing Ke, Yiqing Shen
Mine local homogeneous representation by interaction information clustering with unsupervised learning in histopathology images. Comput. Methods Programs Biomed. 235: 107520 (2023) - [j6]Jing Ke, Yizhou Lu, Yiqing Shen
ClusterSeg: A crowd cluster pinpointed nucleus segmentation framework with cross-modality datasets. Medical Image Anal. 85: 102758 (2023) - [j5]Yiqing Shen
A Federated Learning System for Histopathology Image Analysis With an Orchestral Stain-Normalization GAN. IEEE Trans. Medical Imaging 42(7): 1969-1981 (2023) - [j4]Jing Ke
Artifact Detection and Restoration in Histology Images With Stain-Style and Structural Preservation. IEEE Trans. Medical Imaging 42(12): 3487-3500 (2023) - [j3]Yonghao Li
A Hierarchical Graph V-Net With Semi-Supervised Pre-Training for Histological Image Based Breast Cancer Classification. IEEE Trans. Medical Imaging 42(12): 3907-3918 (2023) - [c30]Yingfan Li, Huaiji Zhou, Na Liu, Yiqing Shen:
Stain Normalization and Augmentation in Frequency Space for Histology Analysis. BIBM 2023: 2031-2035 - [c29]Yiqing Shen, Bingxin Zhou, Xinye Xiong, Ruitian Gao, Yu Guang Wang:
How GNNs Facilitate CNNs in Mining Geometric Information from Large-Scale Medical Images. BIBM 2023: 2227-2230 - [c28]Yuxiang Sun, Kai Liu, Yiqing Shen, Xiaodan Han, Jing Ke:
HistDeblur: A Pyramid Trustworthy Framework for Blurry Histologic Artifacts Quality Control. BIBM 2023: 2255-2258 - [c27]Yiqing Shen
Mixed Sample Augmentation for Online Distillation. ICASSP 2023: 1-5 - [c26]Qingyang Wu
A General Computationally-Efficient 3D Reconstruction Pipeline for Multiple Images with Point Clouds. ISIC/Care-AI/MedAGI/DeCaF@MICCAI 2023: 193-202 - [c25]Zhenqi He
TransNuSeg: A Lightweight Multi-task Transformer for Nuclei Segmentation. MICCAI (4) 2023: 206-215 - [c24]Eduard Lloret Carbonell
COVID-19 Pneumonia Classification with Transformer from Incomplete Modalities. MICCAI (5) 2023: 379-388 - [c23]Zhenqi He
Artifact Restoration in Histology Images with Diffusion Probabilistic Models. MICCAI (6) 2023: 518-527 - [c22]Yiqing Shen
StainDiff: Transfer Stain Styles of Histology Images with Denoising Diffusion Probabilistic Models and Self-ensemble. MICCAI (6) 2023: 549-559 - [c21]Junchao Zhu
An Anti-biased TBSRTC-Category Aware Nuclei Segmentation Framework with a Multi-label Thyroid Cytology Benchmark. MICCAI (6) 2023: 580-590 - [c20]Yanzhou Su, Yiqing Shen
Revisiting Feature Propagation and Aggregation in Polyp Segmentation. MICCAI (5) 2023: 632-641 - [c19]Yiqing Shen, Pengfei Guo, Jingpu Wu, Qianqi Huang, Nhat Le, Jinyuan Zhou, Shanshan Jiang, Mathias Unberath:
MoViT: Memorizing Vision Transformers for Medical Image Analysis. MLMI@MICCAI (2) 2023: 205-213 - [c18]Kai Yi, Bingxin Zhou, Yiqing Shen, Pietro Lió, Yuguang Wang:
Graph Denoising Diffusion for Inverse Protein Folding. NeurIPS 2023 - [e1]M. Emre Celebi
Medical Image Computing and Computer Assisted Intervention - MICCAI 2023 Workshops - ISIC 2023, Care-AI 2023, MedAGI 2023, DeCaF 2023, Held in Conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8-12, 2023, Proceedings. Lecture Notes in Computer Science 14393, Springer 2023, ISBN 978-3-031-47400-2 [contents] - [i15]Yiqing Shen, Pengfei Guo, Jingpu Wu, Qianqi Huang, Jinyuan Zhou, Shanshan Jiang, Mathias Unberath:
MoViT: Memorizing Vision Transformers for Medical Image Analysis. CoRR abs/2303.15553 (2023) - [i14]Miao Zhang, Yiqing Shen, Shenghui Zhong:
SCRNet: a Retinex Structure-based Low-light Enhancement Model Guided by Spatial Consistency. CoRR abs/2305.08053 (2023) - [i13]Kai Yi, Bingxin Zhou, Yiqing Shen, Pietro Liò, Yu Guang Wang:
Graph Denoising Diffusion for Inverse Protein Folding. CoRR abs/2306.16819 (2023) - [i12]Zhenqi He, Mathias Unberath, Jing Ke, Yiqing Shen:
TransNuSeg: A Lightweight Multi-Task Transformer for Nuclei Segmentation. CoRR abs/2307.08051 (2023) - [i11]Zhenqi He, Junjun He, Jin Ye, Yiqing Shen:
Artifact Restoration in Histology Images with Diffusion Probabilistic Models. CoRR abs/2307.14262 (2023) - [i10]Erfan Darzi, Yiqing Shen, Nanna Maria Sijtsema, Peter M. A. van Ooijen:
Tackling Heterogeneity in Medical Federated learning via Vision Transformers. CoRR abs/2310.09444 (2023) - [i9]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:
SAM-Med3D. CoRR abs/2310.15161 (2023) - [i8]Xu Liu, Tong Zhou, Yuanxin Wang
Towards the Unification of Generative and Discriminative Visual Foundation Model: A Survey. CoRR abs/2312.10163 (2023) - 2022
- [j2]Yiqing Shen
Sampling Based Tumor Recognition in Whole-Slide Histology Image With Deep Learning Approaches. IEEE ACM Trans. Comput. Biol. Bioinform. 19(4): 2431-2441 (2022) - [j1]Yiqing Shen
Identify Representative Samples by Conditional Random Field of Cancer Histology Images. IEEE Trans. Medical Imaging 41(12): 3835-3848 (2022) - [c17]Yibo Feng
MFA-DSLNet: Multi-scale Fusion Attention Mechanism with Dual-threshold Self-paced Learning for Pediatric Pneumonia Diagnosis. BIBM 2022: 1530-1533 - [c16]Yiqing Shen
Federated Learning for Chronic Obstructive Pulmonary Disease Classification with Partial Personalized Attention Mechanism. BIBM 2022: 1706-1709 - [c15]Yiqing Shen
CD2-pFed: Cyclic Distillation-guided Channel Decoupling for Model Personalization in Federated Learning. CVPR 2022: 10031-10040 - [c14]Yiqing Shen
Self-Distillation from the Last Mini-Batch for Consistency Regularization. CVPR 2022: 11933-11942 - [c13]Yiqing Shen
RandStainNA: Learning Stain-Agnostic Features from Histology Slides by Bridging Stain Augmentation and Normalization. MICCAI (2) 2022: 212-221 - [i7]Yiqing Shen, Liwu Xu, Yuzhe Yang, Yaqian Li, Yandong Guo:
Self-Distillation from the Last Mini-Batch for Consistency Regularization. CoRR abs/2203.16172 (2022) - [i6]Yiqing Shen, Yuyin Zhou, Lequan Yu:
CD2-pFed: Cyclic Distillation-guided Channel Decoupling for Model Personalization in Federated Learning. CoRR abs/2204.03880 (2022) - [i5]Yiqing Shen, Bingxin Zhou
How GNNs Facilitate CNNs in Mining Geometric Information from Large-Scale Medical Images. CoRR abs/2206.07599 (2022) - [i4]Yiqing Shen, Liwu Xu, Yuzhe Yang, Yaqian Li, Yandong Guo:
Online Distillation with Mixed Sample Augmentation. CoRR abs/2206.12370 (2022) - [i3]Yiqing Shen, Yulin Luo, Dinggang Shen, Jing Ke:
RandStainNA: Learning Stain-Agnostic Features from Histology Slides by Bridging Stain Augmentation and Normalization. CoRR abs/2206.12694 (2022) - [i2]Yiqing Shen, Baiyun Liu, Ruize Yu, Yudong Wang, Shaokang Wang, Jiangfen Wu, Weidao Chen:
Federated Learning for Chronic Obstructive Pulmonary Disease Classification with Partial Personalized Attention Mechanism. CoRR abs/2210.16142 (2022) - 2021
- [c12]Yiqing Shen
Cluster Image Patches with Multiple Mutual Information in Unlabelled Whole-Slide Image. BIBM 2021: 1509-1512 - [c11]Yiqing Shen
Su-Sampling Based Active Learning For Large-Scale Histopathology Image. ICIP 2021: 116-120 - [c10]Jing Ke, Yiqing Shen
Style Normalization In Histology With Federated Learning. ISBI 2021: 953-956 - [c9]Yiqing Shen
Representative Region Based Active Learning For Histological Classification Of Colorectal Cancer. ISBI 2021: 1730-1733 - [c8]Jinghan Huang, Yiqing Shen
CA2.5-Net Nuclei Segmentation Framework with a Microscopy Cell Benchmark Collection. MICCAI (8) 2021: 445-454 - [c7]Jing Ke
Contrastive Learning Based Stain Normalization Across Multiple Tumor in Histopathology. MICCAI (8) 2021: 571-580 - [c6]Jing Ke, Yiqing Shen
Multiple-datasets and multiple-label based color normalization in histopathology with cGAN. Medical Imaging: Digital Pathology 2021 - [i1]Yufei Wang, Yiqing Shen, Meng Yuan, Jing Xu, Bin Yang, Chi Liu, Wenjia Cai, Weijing Cheng, Wei Wang:
A Deep Learning-based Quality Assessment and Segmentation System with a Large-scale Benchmark Dataset for Optical Coherence Tomographic Angiography Image. CoRR abs/2107.10476 (2021) - 2020
- [c5]Jing Ke
A High-Throughput Tumor Location System with Deep Learning for Colorectal Cancer Histopathology Image. AIME 2020: 260-269 - [c4]Jing Ke, Yiqing Shen
Identifying patch-level MSI from histological images of Colorectal Cancer by a Knowledge Distillation Model. BIBM 2020: 1043-1046 - [c3]Jing Ke, Yiqing Shen
A Prediction Model of Microsatellite Status from Histology Images. ICBET 2020: 334-338 - [c2]Jing Ke, Yiqing Shen
Fast Tumor Detector in Whole-Slide Image With Dynamic Programing Based Monte Carlo Sampling. ICIP 2020: 2471-2475 - [c1]Yiqing Shen
A Deformable CRF Model for Histopathology Whole-Slide Image Classification. MICCAI (5) 2020: 500-508
Coauthor Index
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