Xuefei (Julie) Wang

PhD Student, Computation & Neural Systems

California Institute of Technology

I am a PhD student at Caltech, advised by David Van Valen and Yisong Yue. My research focuses on AI agents for scientific discovery and deep learning methods for biology, with applications in spatial proteomics and spatial transcriptomics.

During my PhD, I was also a student researcher at Google Research. I received my B.S. in Computer Science from Fudan University.

News

Oct 2025 Co-organized the LM4Sci Workshop at COLM.
Sep 2025 Contributed to a Google Research paper on AI for scientific software, now on arXiv.
Jun 2025 Joined Google Research as a Student Researcher on the Science AI Team.
Mar 2025 Organized a Foundation Models Workshop at Caltech.
Feb 2025 Presented a poster at the Winter Q-Bio Conference.
Jan 2025 Invited talk at the NYU Single-Cell Analysis Club.
Nov 2024 Posted my preprint on generalized cell phenotyping for spatial proteomics to bioRxiv.
Oct 2024 Talk at the EMBO Workshop on Spatial Omics and Human Diseases.
May 2024 Our paper on spot detection for spatial transcriptomics published in Cell Systems.
Mar 2024 Talk at the HuBMAP Demo Day.

Publications

See Google Scholar for a full list.

An AI system to help scientists write expert-level empirical software

E. Aygün, A. Belyaeva, G. Comanici, ..., X. Wang, ..., M. P. Brenner

arXiv 2025

Paper Code Project Blog Nature News
Simple Agents Outperform Experts in Biomedical Imaging Workflow Optimization

X. Wang, K. A. Horstmann, E. Lin, J. Chen, A. R. Farhang, S. Stiles, A. Sehgal, J. Light, D. Van Valen, Y. Yue, and J. J. Sun

arXiv 2025

Paper Code Project
Human biomolecular atlas program (HuBMAP): 3D human reference atlas construction and usage

K. Börner, P. D. Blood, J. C. Silverstein, et al. (incl. X. Wang as part of the HRA Team)

Nature Methods 22, 845–860, 2025

Paper Project
Automated classification of cellular expression in multiplexed imaging data with Nimbus

J. L. Rumberger, N. F. Greenwald, J. S. Ranek, ..., X. Wang, ..., M. Angelo

Nature Methods 22, 2161–2170, 2025

Paper Code
Generalized cell phenotyping for spatial proteomics with language-informed vision models

X. Wang, R. Dilip, A. R. Iqbal, Y. Bussi, C. Brown, E. Pradhan, Y. Jain, K. Yu, S. Li, M. Abt, K. Börner, L. Keren, Y. Yue, R. Barnowski, and D. Van Valen

bioRxiv 2024

Paper Code Project
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning

E. Laubscher, X. Wang, N. Razin, T. Dougherty, R. J. Xu, L. Ombelets, E. Pao, W. Graf, J. R. Moffitt, Y. Yue, and D. Van Valen

Cell Systems 15.5, 475–482.e6, 2024

Paper Code
Scaling biological discovery at the interface of deep learning and cellular imaging

M. Schwartz, U. Israel, X. Wang, E. Laubscher, C. Yu, R. Dilip, Q. Li, J. Mari, J. Soro, K. Yu, E. Pradhan, A. Ates, D. Gallandt, R. Barnowski, E. Pao, and D. Van Valen

Nature Methods 20.7, 956–957, 2023

Paper
Complementary Maps for Location and Environmental Structure in CA1 and Subiculum

J. M. Olson, A. B. Johnson, L. Chang, E. L. Tao, X. Wang, and D. A. Nitz

bioRxiv 2021

Paper
The dynamic and task-dependent representational transformation between the motor and sensory systems during speech production

W. Zhang, Y. Liu, X. Wang, and X. Tian

Cognitive Neuroscience 11.4, 194–204, 2020

Paper Code
Revealing the temporal dynamics in non-invasive electrophysiological recordings with topography-based analyses

X. Wang, H. Zhu, and X. Tian

bioRxiv 2019

Paper Code
Can computers understand word meanings like the human brain does? Comparable semantic representation in neural and computer systems

L. Zhang, L. Wang, J. Yang, P. Qian, X. Wang, X. Qiu, Z. Zhang, and X. Tian

bioRxiv 2019

Paper

Teaching

TA Artificial Intelligence for Microscopy Image Analysis Summer School MBL Aug 2025
TA EE/CS149: Large Language and Vision Models Caltech Spring 2024
TA Deep Learning for Microscopy Image Analysis Summer School MBL Aug 2023
TA Computational Neuroscience Summer School NeuroMatch Academy Jul 2021

Beyond Research

When I'm not doing research, I'm usually outside — rock climbing, tree climbing, snowboarding, surfing, hiking, camping, or finding things to parkour off of. I also crochet. My name 雪飞 means "flying snow" — given to me on the morning I was born, when the world outside was quiet and white.