Xuefei (Julie) Wang

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. I’m interested in the fundamental principles of building AI agents — how to make them efficient, diverse, and genuinely useful in real-world applications — and how they can be developed in service of equality and openness. I am also drawn to applying agents to scientific domains, particularly biology, for example, building on my earlier work developing deep learning models for spatial proteomics and spatial transcriptomics.

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

News

Publications

See Google Scholar for a full list.

  1. Knowledge-Centric Self-Improvement

    X. Wang, L. H. Yoon, C. Qu, A. Z. Wang, A. Sehgal, E. Mazumdar, and Y. Yue

    In submission 2026

  2. 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

    CVPR 2026

    Paper Code Project

  3. Idea Search: Discovering Performant Scientific Methods with Idea Bank-Augmented Tree Search

    X. Wang, H. Cui, M. P. Brenner, and S. Venugopalan

    In submission 2026

  4. 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 2025 · Under review at Science Advances

    Paper Code Project

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

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

    Nature 2026

    Paper Code Project Blog ERA Blog Nature News

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Revealing the temporal dynamics in non-invasive electrophysiological recordings with topography-based analyses

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

    bioRxiv 2019

    Paper Code

  13. 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

Beyond Research

My name 雪飞 means "flying snow" ❄️ — given to me on the morning I was born, when the world outside was quiet and white.

Outside the lab you'll probably find me climbing rocks 🧗‍♀️ (or trees 🌳), chasing snow 🏂 (or waves 🏄‍♀️), wandering up mountains ⛰️, sleeping in the dirt 🏕️, or parkour-ing off anything that looks jumpable 🤸‍♀️. On rest days I crochet 🧶 and read 📖.

I recently adopted a dog named Effy — she is the most wonderful thing in the world 🐾.

Words I Keep

Words I return to — from poets, thinkers, and lived experience.

  • “Be my own primary partner.”
  • “Live free, Run wild.”
  • “Help people (including myself) to become ourselves.”
  • “因上努力, 果上随缘”

    “Tend the seed with all your strength; let the fruit ripen as it will.”

  • “You can cut all the flowers but you cannot keep spring from coming.”
    — Pablo Neruda
  • “杨树: 我失去了一只臂膀, 就睁开了一只眼睛.”

    “Poplar: where my arm was lost, an eye has opened.”

    — 顾城 (Gu Cheng)
  • “Live the questions now. Perhaps you will then gradually, without noticing it, live along some distant day into the answer.”
    — Rainer Maria Rilke
  • “过去是无法改变的. 未来是充满希望的. 每一个当下都是全新的.”

    “The past is written in stone; the future, open sky; each present moment, the world begun again.”

  • “Expose enough surface area for new experiences to happen.”
  • “这条道路有一颗心吗?”

    “Is this a path with heart?”

  • “Chase your vision but allow it to change.”
  • “Yes, I am imperfect and vulnerable and sometimes afraid, but that doesn’t change the truth that I am also brave and worthy of love and belonging.”
    — Brené Brown
  • “万古是非浑短梦”

    “Ten thousand ages of right and wrong — all a passing dream.”

  • “我还能用谁的心去体会?”

    “Whose heart, if not my own, could ever feel this world?”

  • “除了这个身与这个心, 还有什么呢?”

    “Apart from this body, apart from this mind — what else could there ever be?”

Reading

Books I've enjoyed — in no particular order.

  • And Then There Were None Agatha Christie
  • Confessions Kanae Minato
  • Demian Hermann Hesse
  • Either/Or Søren Kierkegaard
  • Essays in Love Alain de Botton
  • Exhalation Ted Chiang
  • Fevre Dream George R.R. Martin
  • Golden Slumber Kotaro Isaka
  • 华莱士人鱼 岩井俊二
  • 饺子 李碧华
  • Literally Anything He Wrote Stefan Zweig
  • Mating in Captivity Esther Perel
  • On Becoming a Person Carl Rogers
  • Philosophy of Science Samir Okasha
  • Siddhartha Hermann Hesse
  • Stories of Your Life and Others Ted Chiang
  • The Human Chair Edogawa Rampo
  • The Power of Now Eckhart Tolle
  • The State of Affairs Esther Perel
  • The Stranger Albert Camus
  • When Breath Becomes Air Paul Kalanithi
  • 这些人, 那些事 吴念真