CV

Research interests

Exploring machine learning methods for understanding protein structures and advancing biological AI models

B.S. in Computer Science and Technology, Tsinghua University, 2022 (Beijing, China)
Ph.D. in Machine Learning, MBZUAI, 2026 (expected) (Abu Dhabi, UAE)
- Focus: Protein structural prediction with machine learning

Summer 2021: Research Assistant
- Wang Lab (Link)
- Supervisor: Shen Wang
- Duties: Processed biomedical text with language models; co-first authored “GraphPrompt: Graph-Based Prompt Templates for Biomedical Synonym Prediction,” published at AAAI 2023.
Summer 2022: Research Assistant
- MBZUAI SAILING LAB (Link)
- Supervisor: Eric Xing
- Duties: Worked on theories of standardized machine learning; performed code engineering for an NLP Python package.
Summer 2023: Intern
- BioMap R&D Department
- Supervisor: Le Song
- Duties: Developed diffusion models for antibody multi-conformation generation (Link); created a state-of-the-art template-based docking program for antibody-antigen docking.
Summer 2024: Visiting Researcher
- CMU SAILING LAB (Link)
- Supervisor: Eric Xing
- Duties: Worked on biological foundation models (AIDO series); developed a protein structure tokenizer, published as first author at NeurIPS 2024 MLSB Workshop (Paper Huggingface). In this work we trained a 16B structural-informed language model which has the SOTA performance on MSA-free structure prediction.
2024–Present: Intern
- GenBio AI (Link)
- Duties: Optimizing the structure prediction models with better data pipelines.

Zou, S., Zhang, J., Zhao, B., Li, H., Song, L.
Accurate RNA 3D Structure Prediction via Language Model-Augmented AlphaFold 3
ICLR 2026 (under review)
Hu, J., Zhang, J., Cui, S., Zhang, K., Chen, G.
MixAR: Mixture Autoregressive Image Generation
CVPR 2026 (under review)

Zhang, J., Shen, Y., Chen, G., Song, L., Xing, E. P.
Dimensional Collapse in VQVAEs: Evidence and Remedies
NeurIPS 2025
PDF coming soon

Zhang, J., Meynard-Piganeau, B., Gong, J., Cheng, X., Luo, Y., Ly, H., Song, L., Xing, E. P.
Balancing Locality and Reconstruction in Protein Structure Tokenizer
NeurIPS 2024 Workshop on Machine Learning in Structural Biology (MLSB)
[bioRxiv] • DOI: 10.1101/2024.12.02.626366
Wang, X., Li, C., Wang, Z., Bai, F., Luo, H., Zhang, J., Jojic, N., Xing, E. P., Hu, Z.
PromptAgent: Strategic Planning with Language Models Enables Expert-Level Prompt Optimization
ICLR 2024
[arXiv:2310.16427]

Xu, H., Zhang, J., Wang, Z., Zhang, S., Bhalerao, M., Liu, Y., Zhu, D., Wang, S.
GraphPrompt: Graph-Based Prompt Templates for Biomedical Synonym Prediction
AAAI Conference on Artificial Intelligence (AAAI 2023)
[AAAI]

Programming Languages: Python, C/C++
Machine Learning Frameworks: PyTorch, Hugging Face, Megatron-LM
Bioinformatics Tools: AlphaFold, MMSeqs2, Jackhmmer, HHBlits
Specialized Skills: Training Large Language Models, Protein Structure Prediction
DevOps: Docker