I am currently a data analyst at the Bloomberg School of Public Health, Johns Hopkins University, advised by Gregory D. Kirk and Jing Sun. I received my M.S. degree in Biomedical Engineering from Whiting School of Engineering, Johns Hopkins University, advised by Hongkai Ji and Weiqiang Zhou. Prior to that, I obtained my B.S. degree in Computer Science from Nanjing Normal University, advised by Yanhui Gu.
My research interests lie in AI for Science, particularly in biology and medicine. Currently, I mainly focus on deep learning for large-scale genomic data representation. I also develop computational models to tackle biomedical challenges and drive progress in human healthcare. In the past, I have collaborated with Richen Liu at NJNU, Weihua Pan at CAAS, Robert Stevens, Junyu Chen at Johns Hopkins Medical Institutes.
π₯ News
I am applying for Fall 2025 PhD programs. If there are opportunities in your research group, please feel free to reach out!
Email: xchen279 [at] jhu [dot] com | Phone: (667) 434-8060
π Publications 
scMBERT: a Pre-trained Deep Learning Model based on Single-Cell Multiomic Data Representation and Prediction
Xiaojian Chen, Kuai Yu, Minzhi Jiang, Cihan Xiao, Ziqi Fu, Weiqiang Zhou.
Project | 
Correlation Ratio for Unsupervised Learning of Multi-modal Deformable Registration
Xiaojian Chen, Yihao Liu, Shuwen Wei, Aaron Carass, Yong Du, Junyu Chen.
Project | 
GFAP: Ultra-fast and Accurate Gene Functional Annotation Software for Plants
Dong Xu, Yingxue Yang, Desheng Gong, Xiaojian Chen, Kangming Jin, Heling Jiang, Wenjuan Yu, Jihong Li, Jin Zhang, Weihua Pan.
Project | 
π Journals
AI+medRisk Prediction for Non-cardiac Surgery Using the 12-Lead Electrocardiogram: An Explainable Deep Learning Approach Carl Harris, Anway Pimpalkar, Ataes Aggarwal, Jiyuan Yang, Xiaojian Chen, Samuel Schmidgall, Sampath Rapuri, Joseph L. Greenstein, Casey Overby Taylor, Robert D. Stevens. medRxiv 2024.11.19.24317577; Submitted to Circulation.
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comp+bioGFAP: Ultra-fast and Accurate Gene Functional Annotation Software for Plants Dong Xu, Yingxue Yang, Desheng Gong, Xiaojian Chen, Kangming Jin, Heling Jiang, Wenjuan Yu, Jihong Li, Jin Zhang, Weihua Pan. Plant Physiology, 193(3): 1745-1748, 2023. -
SciVISInteractive Geological Data Visualization in an Immersive Environment Xiaojian Chen, Hailong Wang, Yu Zhu, Hansheng Wang, Mingjun Su, Shuyu Bao, Yiping Wu. International Journal of Geo-Information, 11(3):176, 2022. -
SciVISNarrative Scientific Data Visualization in an Immersive Environment Richen Liu, Hailong Wang, Chuyu Zhang, Xiaojian Chen, Lijun Wang, Genlin Ji, Bin Zhao, Zhiwei Mao, Dan Yang. Bioinformatics, 37(14):2033-2041, 2021. -
SciVISMultiuser Collaborative Illustration and Visualization for Volumetric Scientific Data Richen Liu, Xiaodong Wen, Meng Jiang, Guang Yang, Chuyu Zhang, Xiaojian Chen. Software: Practice and Experience, 51(5):1080-1096, 2021.
π Conferences
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comp+bioscMBERT: a Pre-trained Deep Learning Model based on Single-Cell Multiomic Data Representation and Prediction Xiaojian Chen, Kuai Yu, Minzhi Jiang, Cihan Xiao, Ziqi Fu, Weiqiang Zhou. AAAI, 2025. -
AI+medCorrelation Ratio for Unsupervised Learning of Multi-modal Deformable Registration Xiaojian Chen, Yihao Liu, Shuwen Wei, Aaron Carass, Yong Du, Junyu Chen. SPIE Medical Imaging 2025. -
comp+bioMapLE: Matching Molecular Analogues Promptly with Low Computational Resources by Multi-metrics Evaluation Xiaojian Chen, Chuyue Liao, Yanhui Gu, Yafei Li, Jinlan Wang, Yi Chen, Masaru Kitsuregawa. AAAI, 2024. -
SciVISiTDW: Immersive Tiled Display Wall with Clustering-Driven Layout Hansheng Wang, Xiaojian Chen, Zeyu Xia, Hailong Wang, Xiaohan Wang, Richen Liu. ISMAR, 2022. -
SciVISVisualization Transfer from 2D Image to 3D Volume Dan Yang, Zhiwei Mao, Xiaojian Chen, Siru Chen, Xiaodong Wen, Meng Jiang, Yiping Wu. IEEE PacificVIS, 2021. -
SciVISMulti-user Collaborative Volume Data Illustration and Visualization Chuyu Zhang, Xiaojian Chen, Yu Zhu, Xiaohan Wang, Siru Chen, Xiaodong Wen, Richen Liu. VIS, 2020.
π Patents
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comp+bioLigand docking gesture virtual screening method based on quick retrieval Xiaojian Chen, Yanhui Gu, Chang Liu, Xianfeng Zhang, Haohui Xia, Yang Li, Yafei Li, Jinlan Wang. CN116246696A, 2023. -
comp+bioPrediction method of docking posture between protein and ligand based on graphic neural network Yanhui Gu, Xiaojian Chen, Xianfeng Zhang, Yuansu Hao, Yuxin Wen, Chuyue Liao. CN116343910A, 2023. -
SciVISImmersive virtual large screen construction method based on cluster driving Xiaojian Chen, Richen Liu, Hansheng Wang, Hailong Wang, Zeyu Xia, Yu Zhu, Jiaqi Xu, Xiaohan Wang, Siyu Yan, Xiaojun Qian. CN115934014A, 2023. -
SciVISMedical data visualization method based on histogram and nonlinear embedded transfer function Yu Zhu, Richen Liu, Xinru Li, Shuyu Bao, Xiaojian Chen, Guodong Chen, Rongxin Cang, Xiaohan Wang, Siyu Yan, Xiaojun Qian. CN116206735A, 2023.
π Honors and Awards
- 2024.02 AAAI-24 Student Scholarship and Volunteer Award
- 2022.10 National Scholarship (Undergraduate) (Top 1%)
- 2021.04 Best Poster Award at PacificVIS 2021
π Educations
- 2023.08 - 2024.08, Master, Johns Hopkins University, Baltimore.
- 2019.09 - 2023.06, Undergraduate, Nanjing Normal Univeristy, China.
π Teaching Assistant
- Fall, 2023, EN.580.487 Computational Medicine: Cardiology Laboratory, Johns Hopkins University (Instructor: Eileen B. Haase)
- Fall, 2022, C Programming Language Course, Nanjing Normal University
(Instructor: Yanhui Gu)
- Fall, 2022, Database Principle and Application Course, Nanjing Normal University
(Instructor: Yanhui Gu)
π» Experience
- 2024.06 - Now, Data Analyst, ALIVE, Johns Hopkins University. (Advisor: Jing Sun and Gregory D. Kirk)
- 2022.06 - 2023.06, Research Intern, AGIS, Chinese Academy of Agricultural Sciences. (Advisor: Weihua Pan)
- 2020.02 - 2022.06, Research Intern, DTXR, Nanjing Normal Unviersity. (Advisor: Richen Liu)
Last updated: 2025-05-14