I am an incoming PhD student in Computer Science at the University of Washington, where I am fortunated advised by Su-In Lee. My research interests lie in AI for Science, particularly in biology and medicine. Currently, I mainly focus on deep learning for large-scale single cell data representation. I am also dedicated to developing applications for model interpretability in the biomedical field.

Previously, I was a data analyst at the Johns Hopkins Bloomberg School of Public Health, and received my MSE degree in Biomedical Engineering, advised by Hongkai Ji and Weiqiang Zhou. I obtained my Bachelor’s degree in Computer Science from Nanjing Normal University.

📚 Publications

Full publication list can be found in

AAAI 2025

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 |

SPIE Medical Imaging 2025

Correlation Ratio for Unsupervised Learning of Multi-modal Deformable Registration
Xiaojian Chen, Yihao Liu, Shuwen Wei, Aaron Carass, Yong Du, Junyu Chen.

Project |

Plant Physiology

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 |

📕 Journals

• AI+med Risk 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.

• comp+bio 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. Plant Physiology, 193(3): 1745-1748, 2023.

• SciVIS Interactive 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.

• SciVIS Narrative 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.

• SciVIS Multiuser 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.

📘 Conferences

• comp+bio 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. AAAI, 2025.

• AI+med Correlation 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+bio MapLE: 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.

• SciVIS iTDW: Immersive Tiled Display Wall with Clustering-Driven Layout Hansheng Wang, Xiaojian Chen, Zeyu Xia, Hailong Wang, Xiaohan Wang, Richen Liu. ISMAR, 2022.

• SciVIS Visualization Transfer from 2D Image to 3D Volume Dan Yang, Zhiwei Mao, Xiaojian Chen, Siru Chen, Xiaodong Wen, Meng Jiang, Yiping Wu. IEEE PacificVIS, 2021.

• SciVIS Multi-user Collaborative Volume Data Illustration and Visualization Chuyu Zhang, Xiaojian Chen, Yu Zhu, Xiaohan Wang, Siru Chen, Xiaodong Wen, Richen Liu. VIS, 2020.

📔 Patents

• comp+bio Ligand 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+bio Prediction 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.

• SciVIS Immersive 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. CN115934014B, 2023.

• SciVIS Medical 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.

🏆 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

🏫 Educations

• 2025.09 - Now, PhD, University of Washington, Seattle.
• 2023.08 - 2024.08, Master, Johns Hopkins University, Baltimore.
• 2019.09 - 2023.06, Undergraduate, Nanjing Normal Univeristy, China.

💻 Experience

• 2024.06 - 2025.05, 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)

📝 Academic Service

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)

Academic Reviewer

• AAAI Conference on Artificial Intelligence (AAAI), 2026
• International Conference on Learning Representations (ICLR) Workshop, 2025
• Conference on Neural Information Processing Systems (NeurIPS) Workshop, 2024

Last updated: 2025-09-04