Publications

• A multimodal approach for few-shot biomedical named entity recognition in low-resource languages
  Jian Chen, Leilei Su, Yihong Li, Mingquan Lin, Yifan Peng, Cong Sun. (Journal of Biomedical Informatics) [arXiv]

• Prediction of late stage AMD based on deep learning models using multimodal AREDS data
  Qiang Zhang, Qi Yan, Yifan Peng, Mingquan Lin, Joel S Schuman, Julia A Haller, Emily Y Chew. (Investigative Ophthalmology & Visual Science) [arXiv]

• Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge
  Gregory Holste, Yiliang Zhou, Song Wang, Ajay Jaiswal, Mingquan Lin et al. (Medical Image Analysis) [arXiv]

• Deep learning with noisy labels in medical prediction problems: a scoping review
  Yishu Wei, Yu Deng, Cong Sun, Mingquan Lin, Hongmei Jiang, Yifan Peng. (Journal of the American Medical Informatics Association) [arXiv]

• Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling
  Gregory Holste,Mingquan Lin, Ruiwen Zhou, Fei Wang, Lei Liu, Qi Yan, Sarah H. Van Tassel, Kyle Kovacs, Emily Y. Chew, Zhiyong Lu, Zhangyang Wang, Yifan Peng. NPJ Digital Medicine. [arXiv]

• A survey of recent methods for addressing AI fairness and bias in biomedicine
  Yifan Yang, Mingquan Lin, Han Zhao, Yifan Peng, Furong Huang, Zhiyong Lu. Journal of Biomedical Informatics. [arXiv]

• A New Classification Method for Diagnosing COVID-19 Pneumonia via Joint Parallel Deformable MLP Modules and Bi-LSTM With Multi-Source Generated Data of CXR Images
  Yiwen Liu, Wenyu Xing, Mingquan Lin, Yuping Liu, Tommy WS Chow. IEEE Transactions on Consumer Electronics. [arXiv]

• Improving Fairness of Automated Chest X-ray Diagnosis by Contrastive Learning
  Mingquan Lin, Tianhao Li, Zhaoyi Sun, Gregory Holste, Ying Ding, Fei Wang, George Shih, Yifan Peng (Radiology: Artificial Intelligence). [arXiv]

• An end-to-end framework for diagnosing COVID-19 pneumonia via Parallel Recursive MLP module and Bi-LTSM correlation
  Yiwen Liu, Wenyu Xing, Mingbo Zhao,Mingquan Lin (corresponding author). Medical Imaging with Deep Learning. [arXiv]

• Deep learning models to predict primary open-angle glaucoma
  Ruiwen Zhou, J Philip Miller, Mae Gordon, Michael Kass, Mingquan Lin, Yifan Peng, Fuhai Li, Jiarui Feng, Lei Liu. Stat. [paper]

• Multiclass and Multilabel Classifications by Consensus and Complementarity-Based Multiview Latent Space Projection
  Jianghong Ma, Weixuan Kou, Mingquan Lin, Carmen CM Cho, Bernard Chiu. IEEE Transactions on Systems, Man, and Cybernetics: Systems. [arXiv]

• Deep Learning Detection of Chest Compression Location Using Transesophageal Echocardiography
  Felipe Teran, ..., Mingquan Lin, Benjamin S Abella. Circulation. [arXiv]

• Improving model fairness in image-based computer-aided diagnosis
  Mingquan Lin, Tianhao Li, Yifan Yang, Gregory Holste, Ying Ding, Sarah H Van Tassel, Kyle Kovacs, George Shih, Zhangyang Wang, Zhiyong Lu, Fei Wang, Yifan Peng. Nature Communications. [arXiv]

• A scoping review on multimodal deep learning in biomedical images and texts
  Zhaoyi Sun,Mingquan Lin, Qingqing Zhu, Qianqian Xie, Fei Wang, Zhiyong Lu, Yifan Peng. (Journal of Biomedical Informatics). [arXiv]

• A new classification method for diagnosing COVID-19 pneumonia based on joint CNN features of chest X-ray images and parallel pyramid MLP-mixer module
  Yiwen Liu, Wenyu Xing, Mingbo Zhao, Mingquan Lin (corresponding author). (Neural Computing and Applications). [arXiv]

• Optimizing Embedding Space with Sub-categorical Supervised Pre-training: A Theoretical Approach Towards Improving Sepsis Prediction
  Tingyi Wanyan, Mingquan Lin, Ying Ding, Benjamin Glicksberg, Fei Wang, Yifan Peng. (J2023 IEEE 11th International Conference on Healthcare Informatics (ICHI)). [arXiv]

• Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access
  Mingquan Lin, Bojian Hou, Swati Mishra, Tianyuan Yao, Yuankai Huo, Qian Yang, Fei Wang, George Shih, Yifan Peng. (Computers in Biology and Medicine). [arXiv]

• Person re-identification via semi-supervised adaptive graph embedding
  Jiao Liu, Mingquan Lin (co-first author), Mingbo Zhao, Choujun Zhan, Bing Li, John Kwok Tai Chui. (Applied Intelligence). [arXiv]

• CXR-LT: Multi-Label Long-Tailed Classification on Chest X-Rays
  Gregory Holste, Song Wang, Ajay Jaiswal, Yuzhe Yang, Mingquan Lin, Yifan Peng, Atlas Wang. (PhysioNet). [arXiv]

• Evaluate underdiagnosis and overdiagnosis bias of deep learning model on primary open-angle glaucoma diagnosis in under-served populations
  Mingquan Lin, Yunyu Xiao, Bojian Hou, Tingyi Wanyan, Mohit Manoj Sharma, Zhangyang Wang, Fei Wang, Sarah Van Tassel, Yifan Peng. (AMIA Summits on Translational Science Proceedings). [arXiv]

• Multimodal Image Classification by Multiview Latent Pattern Extraction, Selection, and Correlation
  Jianghong Ma, Weixuan Kou,Mingquan Lin, Carmen CM Cho, Bernard Chiu. (IEEE Transactions on Neural Networks and Learning Systems). [arXiv]

• Primary Open-Angle Glaucoma Diagnosis From Optic Disc Photographs Using a Siamese Network
  Mingquan Lin, Lei Liu, Mae Gordon, Michael Kass, Fei Wang, Sarah H Van Tassel, Yifan Peng. (Ophthalmology Science). [arXiv]

• Multi-scale Multi-structure Siamese Network (MMSNet) for Primary Open-Angle Glaucoma Prediction
  Mingquan Lin, Lei Liu, Mae Gorden, Michael Kass, Sarah Van Tassel, Fei Wang, Yifan Peng. (International Workshop on Machine Learning in Medical Imaging). [arXiv]

• Automated diagnosing primary open-angle glaucoma from fundus image by simulating human’s grading with deep learning
  Mingquan Lin, Bojian Hou, Lei Liu, Mae Gordon, Michael Kass, Fei Wang, Sarah H Van Tassel, Yifan Peng. (Scientific reports). [arXiv]

• Supervised pretraining through contrastive categorical positive samplings to improve COVID-19 mortality prediction
  Tingyi Wanyan, Mingquan Lin, Eyal Klang, Kartikeya M Menon, Faris F Gulamali, Ariful Azad, Yiye Zhang, Ying Ding, Zhangyang Wang, Fei Wang, Benjamin Glicksberg, Yifan Peng. (ACM BCB). [arXiv]

• Knowledge Graph Applications in Medical Imaging Analysis: A Scoping Review
  Song Wang, Mingquan Lin (co-first author), Tirthankar Ghosal, Ying Ding, Yifan Peng. (Health data science). [arXiv]

• Radiology text analysis system (RadText): architecture and evaluation
  Song Wang, Mingquan Lin, Ying Ding, George Shih, Zhiyong Lu, Yifan Peng. (IEEE ICHI 2022). [arXiv]

• Cascaded Triplanar Autoencoder M-Net for Fully Automatic Segmentation of Left Ventricle Myocardial Scar From Three-Dimensional Late Gadolinium-Enhanced MR Images
  Mingquan Lin, Mingjie Jiang, Mingbo Zhao, Eranga Ukwatta, James A White, Bernard Chiu. (IEEE JBHI). [arXiv]

• Prior knowledge enhances radiology report generation
  Song Wang, Liyan Tang, Mingquan Lin, George Shih, Ying Ding, Yifan Peng. (AMIA Summits on Translational Science Proceedings). [arXiv]

• An empirical study of using radiology reports and images to improve ICU-mortality prediction
  Mingquan Lin, Song Wang, Ying Ding, Lihui Zhao, Fei Wang, Yifan Peng. (2021 IEEE 9th International Conference on Healthcare Informatics (ICHI)). [arXiv]

• An empirical study of using radiology reports and images to improve ICU-mortality prediction
  Mingquan Lin, Song Wang, Ying Ding, Lihui Zhao, Fei Wang, Yifan Peng. (2021 IEEE 9th International Conference on Healthcare Informatics (ICHI)). [arXiv]

• Fully automated segmentation of brain tumor from multiparametric MRI using 3D context deep supervised U‐Net
  Mingquan Lin, Shadab Momin, Yang Lei, Hesheng Wang, Walter J Curran, Tian Liu, Xiaofeng Yang. (Medical Physics). [arXiv]

• Artificial intelligence in tumor subregion analysis based on medical imaging: A review
  Mingquan Lin, Jacob F Wynne, Boran Zhou, Tonghe Wang, Yang Lei, Walter J Curran, Tian Liu, Xiaofeng Yang. (Journal of Applied Clinical Medical Physics). [arXiv]

• Fully automated segmentation of brain tumor from multiparametric MRI using 3D context U-Net with deep supervision
  Mingquan Lin, Shadab Momin, Boran Zhou, Katherine Tang, Yang Lei, Walter J Curran, Tian Liu, Xiaofeng Yang. (Medical Imaging 2021: Computer-Aided Diagnosis). [arXiv]

• Ultrasound GLCM texture analysis of radiation-induced acute toxicity following breast cancer radiotherapy
  Boran Zhou, Mingquan Lin, Xiaofeng Yang, Simone Henry, Jolinta Lin, Karen Godette, Shannon T Kahn, Walter J Curran, Mylin A Torres, Tian Liu. (Medical Imaging 2021: Ultrasonic Imaging and Tomography). [arXiv]

• Region of interest discovery using discriminative concrete autoencoder for COVID-19 lung CT images
  Yupei Zhang, Yang Lei, Mingquan Lin, Walter Curran, Tian Liu, Xiaofeng Yang. (Medical Imaging 2021: Computer-Aided Diagnosis). [arXiv]

• Using radiomics as prior knowledge for thorax disease classification and localization in chest x-rays
  Yan Han, Chongyan Chen, Liyan Tang, Mingquan Lin, Ajay Jaiswal, Song Wang, Ahmed Tewfik, George Shih, Ying Ding, Yifan Peng. (AMIA Annual Symposium Proceedings). [arXiv]

• Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS
  Gregory Ghahramani, Matthew Brendel, Mingquan Lin, Qingyu Chen, Tiarnan Keenan, Kun Chen, Emily Chew, Zhiyong Lu, Yifan Peng, Fei Wang. (AMIA Annual Symposium Proceedings). [arXiv]

• Deep-recursive residual network for image semantic segmentation
  Yue Zhang, Xianrui Li, Mingquan Lin, Bernard Chiu, Mingbo Zhao. (Neural computing and applications). [arXiv]

• Vessel wall segmentation of common carotid artery via multi-branch light network
  Haochen Tan, Huimin Shi, Mingquan Lin, J David Spence, Kwok-Leung Chan, Bernard Chiu. (Medical Imaging 2020: Image Processing). [arXiv]

• Three-dimensional ultrasound evaluation of the effects of pomegranate therapy on carotid plaque texture using locality preserving projection
  Xueli Chen, Mingquan Lin, He Cui, Yimin Chen, Arna van Engelen, Marleen de Bruijne, M Reza Azarpazhooh, Seyed Mojtaba Sohrevardi, Tommy WS Chow, J David Spence, Bernard Chiu. (Computer Methods and Programs in Biomedicine). [arXiv]

• Longitudinal assessment of carotid plaque texture in three-dimensional ultrasound images based on semi-supervised graph-based dimensionality reduction and feature selection
  Mingquan Lin, He Cui, Weifu Chen, Arna van Engelen, Marleen de Bruijne, M Reza Azarpazhooh, Seyed Mojtaba Sohrevardi, J David Spence, Bernard Chiu. (Computers in Biology and Medicine). [arXiv]

• Plaque components segmentation in carotid artery on simultaneous non-contrast angiography and intraplaque hemorrhage imaging using machine learning
  Qiang Zhang, Huiyu Qiao, Jiaqi Dou, Binbin Sui, Xihai Zhao, Zhensen Chen, Yishi Wang, Shuo Chen, Mingquan Lin, Bernard Chiu, Chun Yuan, Rui Li, Huijun Chen. (Magnetic Resonance Imaging). [arXiv]

• Trace ratio criterion based discriminative feature selection via l2, p-norm regularization for supervised learning
  Mingbo Zhao, Mingquan Lin, Bernard Chiu, Zhao Zhang, Xue-song Tang. (Neurocomputing). [arXiv]

• Prostate lesion delineation from multiparametric magnetic resonance imaging based on locality alignment discriminant analysis
  Mingquan Lin, Weifu Chen, Mingbo Zhao, Eli Gibson, Matthew Bastian‐Jordan, Derek W Cool, Zahra Kassam, Huageng Liang, Tommy WS Chow, Aaron D Ward, Bernard Chiu. (Medical physics). [arXiv]

• A self-tuned graph-based framework for localization and grading prostate cancer lesions: An initial evaluation based on multiparametric magnetic resonance imaging
  Weifu Chen, Mingquan Lin, Eli Gibson, Matthew Bastian-Jordan, Derek W Cool, Zahra Kassam, Huageng Liang, Guocan Feng, Aaron D Ward, Bernard Chiu. (Computers in Biology and Medicine). [arXiv]

• Prostate lesion detection and localization based on locality alignment discriminant analysis
  Mingquan Lin, Weifu Chen, Mingbo Zhao, Eli Gibson, Matthew Bastian-Jordan, Derek W Cool, Zahra Kassam, Tommy WS Chow, Aaron Ward, Bernard Chiu. (Medical Imaging 2017: Computer-Aided Diagnosis). [arXiv]

• AWM: Adaptive Weight Matting for medical image segmentation
  Jieyu Cheng, Mingbo Zhao, Mingquan Lin, Bernard Chiu. (Medical Imaging 2017: Image Processing). [arXiv]

Preprints

• Interpretable Differential Diagnosis with Dual-Inference Large Language Models
  Shuang Zhou, Sirui Ding, Jiashuo Wang, Mingquan Lin, Genevieve B. Melton, Rui Zhang. [arXiv]

• Large Language Models for Disease Diagnosis: A Scoping Review
  Shuang Zhou, Zidu Xu, Mian Zhang, Chunpu Xu, Yawen Guo, Zaifu Zhan, Sirui Ding, Jiashuo Wang, Kaishuai Xu, Yi Fang, Liqiao Xia, Jeremy Yeung, Daochen Zha, Mingquan Lin, Rui Zhang. [arXiv]