Dakai Jin  

Staff Scientist
@ PAII Inc.
Email: dakai.jin at gmail dot com
GoogleScholar, LinkedIn

Brief Bio

Since 2018, I have been working at PAII Inc, which is directed by Dr. Le Lu. My primary role is as a team lead for projects related to the radiotherapy target contouring (GTV/CTV/OAR/LN). I work with extraordinarily talented colleagues and physicians! Our team has developed the state-of-the-art segmentation and parsing models for esophageal gross tumor volume (GTV), clinical target volume (CTV), and > 60 comprehensive head & neck & chest organs at risk (OARs). These models are currently under two large-scale multi-center clinical evaluation studies, and methods have been presented in MICCAI 2019 (invited to MedIA MICCAI-2019 selected papers special issue) and CVPR 2020. We are also working on the challenging metastasis lymph node detection problem. Some initial works have been presented in MICCAI 2020.

Before that, I was a visiting research fellow at National Institutes of Health (NIH) worked on pulmonary image analysis, including the lung, lobe and airway tree segmentation and the interstitial lung disease detection. I received my Ph.D. at University of Iowa in 2016 under the supervision of Prof. Punam Saha and Prof. Eric Hoffman. In my Ph.D., I developed two 3D skeletonization (surface and curve) algorithms that can accurately and robustly extract the medial surfaces or centerlines of the 3D structures while keeping their topology. These algorithms have also been successfully applied in the topological and geometrical quantifications of trabecular bones and tubular anatomies, such as airway and coronary artery.


[02/2021] Co-editing a special issue "Machine Learning for Quantitative Neuroimaging Analysis" in Frontiers in Neuroscience (IF:3.7, h5-index 80). Welcome to contribute!

[12/2020] Invited to serve as Associate Editor for the journal of Visual Computer.

[09/2020] One paper titled "DeepTarget" is accepted by Medical Image Analysis. (Special Issue of MICCAI-2019 Best Papers)

[08/2020] Three abstracts are accepted by RSNA 2020. (Two oral presentation)

[06/2020] Invited talk at the Medical Computer Vision Workshop @ CVPR 2020.

[05/2020] Three papers are accepted by MICCAI 2020. (All early accepts, one won MICCAI-2020 NIH Award)

[02/2020] One paper on 42 head & neck organs at risk segmentation is accepted by CVPR 2020.

[06/2019] Three papers are accepted by MICCAI 2019. (All early accepts, one for oral presentation)

[06/2019] One paper collaborated with NIAID is accepted by Science Translational Medicine. (IF:16.3; Highlighted on cover)



[Medical Image Analysis] DeepTarget: Gross Tumor and Clinical Target Volume Segmentation in Esophageal Cancer Radiotherapy. Dakai Jin*, Dazhou Guo*, Tsung-Ying Ho, Adam P Harrison, Jing Xiao, Chen-kan Tseng, Le Lu. [pdf] (MICCAI-2019 Best Papers Special Issue)

[Artificial Intelligence in Medicine: Technical Basis and Clinical Applications] Chapter 14: Artificial Intelligence in Radiology. Dakai Jin, Adam P. Harrison, Ling Zhang, Ke Yan, Yirui Wang, Jinzheng Cai, Shun Miao, Le Lu. [pdf]

[IEEE TMI] Learning from Multiple Datasets with Heterogeneous and Partial Labels for Universal Lesion Detection in CT. Ke Yan, Jinzheng Cai, Youjing Zheng, Adam P. Harrison, Dakai Jin, You-Bao Tang, Yu-Xing Tang, Lingyun Huang, Jing Xiao, Le Lu. [pdf]

[European Radiology] From Community Acquired Pneumonia to COVID-19: A Deep Learning Based Method for Quantitative Analysis of COVID-19 on thick-section CT Scans. Zhang Li*, Zheng Zhong*, Yang Li, Tianyu Zhang, Liangxin Gao, Dakai Jin, Yue Sun, Xianghua Ye, Li Yu, Zheyu Hu, Jing Xiao, Lingyun Huang, Yuling Tang. [pdf]

[MICCAI] Lymph Node Gross Tumor Volume Detection and Segmentation via Distance-Based Gating Using 3D CT/PET Imaging in Radiotherapy. Zhuotun Zhu, Dakai Jin, Ke Yan, Tsung-Ying Ho, Xianghua Ye, Dazhou Guo, Chun-Hung Chao, Jing Xiao, Alan Yuille, Le Lu. [pdf] (Early accept, MICCAI-2020 NIH Award)

[MICCAI] Lymph Node Gross Tumor Volume Detection in Oncology Imaging via Relationship Learning Using Graph Neural Network. Chun-Hung Chao, Zhuotun Zhu*, Dazhou Guo*, Ke Yan*, Tsung-Ying Ho, Jinzheng Cai, Adam P Harrison, Xianghua Ye, Jing Xiao, Alan Yuille, Min Sun, Le Lu, Dakai Jin. [pdf] (Early accept)

[MICCAI] Robust Pancreatic Ductal Adenocarcinoma Segmentation with Multi-institutional Multi-phase Partially-Annotated CT Scans. Ling Zhang, Yu Shi, Jiawen Yao, Yun Bian, Kai Cao, Dakai Jin, Jing Xiao, Le Lu. [pdf] (Early accept)

[ECCV] JSSR: A Joint Synthesis, Segmentation, and Registration System for 3D Multi-Modal Image Alignment of Large-scale Pathological CT Scans. Fengze Liu, Jinzheng Cai, Yuankai Huo, Chi-Tung Cheng, Ashwin Raju, Dakai Jin, Jing Xiao, Alan Yuille, Le Lu, ChienHung Liao, Adam P Harrison. [pdf]

[CVPR] Organ at Risk Segmentation for Head and Neck Cancer using Stratified Learning and Neural Architecture Search. Dazhou Guo, Dakai Jin, Zhuotun Zhu, Tsung-Ying Ho, Adam P Harrison, Chun-Hung Chao, Jing Xiao, Le Lu. [pdf]


[MICCAI] Accurate Esophageal Gross Tumor Volume Segmentation in PET/CT Using Two-Stream Chained 3D Deep Network Fusion. Dakai Jin, Dazhou Guo, Tsung-Ying Ho, Adam P Harrison, Jing Xiao, Chen-kan Tseng, Le Lu. [pdf] (Early accept and oral presentation)

[MICCAI] Deep Esophageal Clinical Target Volume Delineation Using Encoded 3D Spatial Context of Tumors, Lymph Nodes, and Organs At Risk. Dakai Jin, Dazhou Guo, Tsung-Ying Ho, Adam P Harrison, Jing Xiao, Chen-kan Tseng, Le Lu. [pdf] (Early accept)

[MICCAI] Weakly Supervised Universal Fracture Detection in Pelvic X-Rays. Yirui Wang, Le Lu, Chi-Tung Cheng, Dakai Jin, Adam P Harrison, Jing Xiao, Chien-Hung Liao, Shun Miao. [pdf] (Early accept)

[IEEE TMI] Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge. Hugo J. Kuijf, J. Matthijs Biesbroek, Jeroen de Bresser, Rutger Heinen, Simon Andermatt, Mariana Bento, Matt Berseth, Mikhail Belyaev, M. Jorge Cardoso, Adrià Casamitjana, D. Louis Collins, Mahsa Dadar, Achilleas Georgiou, Mohsen Ghafoorian, Dakai Jin, April Khademi, Jesse Knight, Hongwei Li, Xavier Lladó, Miguel Luna, Qaiser Mahmood, Richard McKinley, Alireza Mehrtash, Sébastien Ourselin, Bo-yong Park, Hyunjin Park, Sang Hyun Park, Simon Pezold, Elodie Puybareau, Leticia Rittner, Carole H. Sudre, Sergi Valverde, Verónica Vilaplana, Roland Wiest, Yongchao Xu, Ziyue Xu, Guodong Zeng, Jianguo Zhang, Guoyan Zheng, Christopher Chen, Wiesje van der Flier, Frederik Barkhof, Max A. Viergever, Geert Jan Biessels. [pdf]

[JMI] Fully automated prostate whole gland and central gland segmentation on MRI using holistically nested networks with short connections . Ruida Cheng, Nathan Lay, Holger R Roth, Baris Turkbey, Dakai Jin, William Gandler, Evan S McCreedy, Tom Pohida, Peter Pinto, Peter Choyke, Matthew J McAuliffe, Ronald M Summers. [pdf]

[Science Translational Medicine] Lymphocyte-driven regional immunopathology in pneumonitis caused by impaired central immune tolerance. Elise MN Ferré, Timothy J Break, Peter D Burbelo, Michael Allgäuer, David E Kleiner, Dakai Jin, Ziyue Xu, Les R Folio, Daniel J Mollura, Muthulekha Swamydas, Wenjuan Gu, Sally Hunsberger, Chyi-Chia R Lee, Anamaria Bondici, Kevin W Hoffman, Jean K Lim, Kerry Dobbs, Julie E Niemela, Thomas A Fleisher, Amy P Hsu, Laquita N Snow, Dirk N Darnell, Samar Ojaimi, Megan A Cooper, Martin Bozzola, Gary I Kleiner, Juan C Martinez, Robin R Deterding, Douglas B Kuhns, Theo Heller, Karen K Winer, Arun Rajan, Steven M Holland, Luigi D Notarangelo, Kevin P Fennelly, Kenneth N Olivier, Michail S Lionakis. [pdf] (IF:16.3; Highlighted on cover)


[MICCAI] CT-Realistic Lung Nodule Simulation from 3D Conditional Generative Adversarial Networks for Robust Lung Segmentation. Dakai Jin, Ziyue Xu, Youbao Tang, Adam P Harrison, Daniel J Mollura. [pdf] (MICCAI 2018 top 10 highly cited paper)

[ISBI] White matter hyperintensity segmentation from T1 and FLAIR images using fully convolutional neural networks enhanced with residual connections. Dakai Jin, Ziyue Xu, Adam P Harrison, Daniel J Mollura. [pdf]

[IEEE TVCG] Fuzzy Object Skeletonization: Theory, Algorithms, and Applications. Punam K Saha (PhD advisor), Dakai Jin, Yinxiao Liu, Gary E Christensen, Cheng Chen. (One of the two major skeletonization algorithms I developed in my PhD. The top journal in the field of visualization and computer graphics)

[Medical Physics] Quantitative imaging of peripheral trabecular bone microarchitecture using MDCT. Cheng Chen, Xiaoliu Zhang, Junfeng Guo, Dakai Jin, Elena M Letuchy, Trudy L Burns, Steven M Levy, Eric A Hoffman, Punam K Saha. [pdf]


[MLMI] 3D Convolutional Neural Networks with Graph Refinement for Airway Segmentation Using Incomplete Data Labels. Dakai Jin, Ziyue Xu, Adam P. Harrison, Kevin George, Daniel J. Mollura. [pdf] (The first 3D deep learning algorithm on airway tree segmentation, and without the need of manual annotation)

[DLMIA] Pathological Pulmonary Lobe Segmentation from CT Images using Progressive Holistically Nested Neural Networks and Random Walker. Kevin George, Adam P. Harrison, Dakai Jin, Ziyue Xu, Daniel J Mollura. [pdf] (The first deep learning algorithm on the challenging lung lobe segmentation problem)

[Skeletonization: Theory, Methods and Applications] Chapter 6: Curve skeletonization using minimum-cost path. Dakai Jin, Cheng Chen, Eric A Hoffman, Punam K Saha. [pdf]


[Pattern Recognition Letters] A robust and efficient curve skeletonization algorithm for tree-like objects using minimum cost paths. Dakai Jin, Krishna S Iyer, Cheng Chen, Eric A Hoffman, Punam K Saha. [pdf] (A very accurate and robust algorithm to extract the centerline/curve skeleton in 3D elongated structures!)

[American Journal of Respiratory and Critical Care Medicine] Quantitative Dual-Energy Computed Tomography Supports a Vascular Etiology of Smoking-induced Inflammatory Lung Disease . Krishna S Iyer, John D Newell, Dakai Jin, Matthew K Fuld, Punam K Saha, Sif Hansdottir, Eric A Hoffman. [pdf] (Top journal in Pulmonology, IF:17.5; Highlighted on cover)

[Physics in Medicine & Biology] Trabecular bone characterization on the continuum of plates and rods using in vivo MR imaging and volumetric topological analysis. Cheng Chen, Dakai Jin, Yinxiao Liu , Felix W Wehrli, Gregory Chang, Peter J Snyder, Ravinder R Regatte, Punam K Saha. [pdf]

[Medical Physics] A controlled statistical study to assess measurement variability as a function of test object position and configuration for automated surveillance in a multicenter longitudinal COPD study (SPIROMICS). Junfeng Guo, Chao Wang, Kung‐Sik Chan, Dakai Jin, Punam K Saha, Jered P Sieren, R Graham Barr, MeiLan K Han, Ella Kazerooni, Christopher B Cooper, David Couper, John D Newell Jr, Eric A Hoffman, SPIROMICS Research Group. [pdf]


[Medical Physics] Automated cortical bone segmentation for multirow detector CT imaging with validation and application to human studies. Cheng Li, Dakai Jin, Cheng Chen, Elena M Letuchy, Kathleen F Janz, Trudy L Burns, James C Torner, Steven M Levy, Punam K Saha. [pdf]

[Medical Physics] Characterization of trabecular bone plate‐rod microarchitecture using multirow detector CT and the tensor scale: Algorithms, validation, and applications to pilot human studies. Punam K Saha, Yinxiao Liu, Cheng Chen, Dakai Jin, Elena M Letuchy, Ziyue Xu, Ryan E Amelon, Trudy L Burns, James C Torner, Steven M Levy, Chadi A Calarge. [pdf]

[ICIAP] Filtering Non-Significant Quench Points Using Collision Impact in Grassfire Propagation. Dakai Jin, Cheng Chen, Punam K Saha. [pdf]

[ISVC] Fuzzy Skeletonization Improves the Performance of Characterizing Trabecular Bone Micro-architecture. Cheng Chen, Dakai Jin, Punam K Saha.


[IEEE TBME] A Robust Algorithm for Thickness Computation at Low Resolution and Its Application to In Vivo Trabecular Bone CT Imaging. Yinxiao Liu, Dakai Jin, Cheng Li, Kathleen F Janz, Trudy L Burns, James C Torner, Steven M Levy, Punam K Saha. [pdf]

[ICPR] A new approach of arc skeletonization for tree-like objects using minimum cost path. Dakai Jin, Krishna S Iyer, Eric A Hoffman, Punam K Saha. [pdf]

[International Symposium on Visual Computing (ISVC)] Automated Assessment of Pulmonary Arterial Morphology in Multi-row Detector CT Imaging Using Correspondence with Anatomic Airway Branches. Dakai Jin, Krishna S Iyer, Eric A Hoffman, Punam K Saha. [pdf] (Oral presentation)


[International Conference on Image Analysis and Processing (ICIAP)] A New Fuzzy Skeletonization Algorithm and Its Applications to Medical Imaging. Dakai Jin and Punam K. Saha. [pdf]

[ICIAP] A New Algorithm for Cortical Bone Segmentation with Its Validation and Applications to In Vivo Imaging. Cheng Li, Dakai Jin, Trudy L Burns, James C Torner, Steven M Levy, Punam K Saha. [pdf]

[ISBI] A new algorithm for trabecular bone thickness computation at low resolution achieved under in vivo condition. Yinxiao Liu, Dakai Jin, Punam K Saha. [pdf]

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