I am currently a second year Computer Science PhD student at Tsinghua University. My advisor is professor Yang Liu and I am glad to be affiliated with both THUNLP and AIR. I am also in close cooperation with professor Wenbing Huang from Renmin University of China.

I am deeply passionate about exploring the fascinating and wondrous realms of science, particularly at the crossroads of chemistry and biology. My current research in AI is driven by the profound curiosity to unravel the mysteries within these disciplines, and the practical pursuit of developing innovative pharmaceutical solutions. I am committed to leveraging AI to decipher the intricate connections between chemical and biological processes, with the ultimate goal of advancing both our fundamental understanding of science and the development of impactful solutions in the field of pharmaceuticals. Despite the acknowledgement that these aspirations may be viewed as idealistic, I firmly believe that actively striving towards these goals is a more meaningful pursuit than passively waiting, making the endeavor a worthwhile and fulfilling journey.

Selected Publications (full list)

• Nat. Biomed. Eng.Peptide design through binding interface mimicry with PepMimic
  Xiangzhe Kong, Rui Jiao, Haowei Lin, Ruihan Guo, Wenbing Huang, Wei-Ying Ma, Zihua Wang, Yang Liu, Jianzhu Ma.
  Nature Biomedical Engineering, 2025.

        @article{Kong2025,
          title={Peptide design through binding interface mimicry with PepMimic},
          author={Kong, Xiangzhe and Jiao, Rui and Lin, Haowei and Guo, Ruihan and Huang, Wenbing and Ma, Wei-Ying and Wang, Zihua and Liu, Yang and Ma, Jianzhu},
          journal={Nature Biomedical Engineering},
          year={2025},
          month={Oct},
          day={01},
          issn={2157-846X},
          doi={10.1038/s41551-025-01507-4},
          url={https://doi.org/10.1038/s41551-025-01507-4}
        }
      

[bib] [paper] [github]



• ICML 2025UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design
  Xiangzhe Kong, Zishen Zhang, Ziting Zhang, Rui Jiao, Jianzhu Ma, Wenbing Huang, Kai Liu, Yang Liu.
  In Proceedings of the 42th International Conference on Machine Learning, 2025.
  Despite good ratings from reviewers from the beginning, still assigned as a poster paper. But I really like this work.

        @inproceedings{
          kong2025unimomo,
          title={UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design},
          author={Xiangzhe Kong and Zishen Zhang and Ziting Zhang and Rui Jiao and Jianzhu Ma and Wenbing Huang and Kai Liu and Yang Liu},
          booktitle={Forty-second International Conference on Machine Learning},
          year={2025},
          url={https://openreview.net/forum?id=KUN7A7Okb6}
        }
      

[bib] [paper] [github]



• NeurIPS 2024Full-Atom Peptide Design with Geometric Latent Diffusion
  Xiangzhe Kong, Yinjun Jia, Wenbing Huang, Yang Liu.
  Advances in Neural Information Processing Systems, 2024.

        @article{kong2025full,
          title={Full-atom peptide design with geometric latent diffusion},
          author={Kong, Xiangzhe and Jia, Yinjun and Huang, Wenbing and Liu, Yang},
          journal={Advances in Neural Information Processing Systems},
          volume={37},
          pages={74808--74839},
          year={2025}
        }
      

[bib] [paper] [github]



• Cell SystemsFlowDesign: Improved Design of Antibody CDRs Through Flow Matching and Better Prior Distributions
  Jun Wu, Xiangzhe Kong, Ningguan Sun, Jing Wei, Sisi Shan, Fuli Feng, Feng Wu, Jian Peng, Linqi Zhang, Yang Liu, Jianzhu Ma.
  Cell Systems, 2025, Featured Cover Article.

        @article{wu2025flowdesign,
          title={FlowDesign: Improved design of antibody CDRs through flow matching and better prior distributions},
          author={Wu, Jun and Kong, Xiangzhe and Sun, Ningguan and Wei, Jing and Shan, Sisi and Feng, Fuli and Wu, Feng and Peng, Jian and Zhang, Linqi and Liu, Yang and Ma, Jianzhu},
          journal = {Cell Systems},
          volume = {16},
          number = {6},
          pages = {101270},
          year = {2025},
          issn = {2405-4712},
          doi = {https://doi.org/10.1016/j.cels.2025.101270}
        }
      

[bib] [paper] [github]



• ICML 2023End-to-End Full-Atom Antibody Design
  Xiangzhe Kong, Wenbing Huang, Yang Liu.
  In Proceedings of the 40th International Conference on Machine Learning, 2023.

      @InProceedings{pmlr-v202-kong23c,
        title = {End-to-End Full-Atom Antibody Design},
        author = {Kong, Xiangzhe and Huang, Wenbing and Liu, Yang},
        booktitle = {Proceedings of the 40th International Conference on Machine Learning},
        pages = {17409--17429},
        year = {2023},
        editor = {Krause, Andreas and Brunskill, Emma and Cho, Kyunghyun and Engelhardt, Barbara and Sabato, Sivan and Scarlett, Jonathan},
        volume = {202},
        series = {Proceedings of Machine Learning Research},
        month = {23--29 Jul},
        publisher = {PMLR},
        pdf = {https://proceedings.mlr.press/v202/kong23c/kong23c.pdf},
        url = {https://proceedings.mlr.press/v202/kong23c.html}
      }
    

[bib] [paper] [github]



• ICLR 2023Conditional Antibody Design as 3D Equivariant Graph Translation
  Xiangzhe Kong, Wenbing Huang, Yang Liu.
  In Proceedings of the 11th International Conference on Learning Representations, 2023.
  Outstanding Paper Honorable Mention

      @inproceedings{
	kong2023conditional,
	title={Conditional Antibody Design as 3D Equivariant Graph Translation},
	author={Xiangzhe Kong and Wenbing Huang and Yang Liu},
	booktitle={The Eleventh International Conference on Learning Representations },
	year={2023},
	url={https://openreview.net/forum?id=LFHFQbjxIiP}
      }
    

[bib] [paper] [github]



• NeurIPS 2022Molecule Generation by Principal Subgraph Mining and Assembling
  Xiangzhe Kong, Wenbing Huang, Zhixing Tan, Yang Liu.
  Advances in Neural Information Processing Systems, 2022
  Oral Presentation

	@inproceedings{NEURIPS2022_1160792e,
	  author = {Kong, Xiangzhe and Huang, Wenbing and Tan, Zhixing and Liu, Yang},
	  booktitle = {Advances in Neural Information Processing Systems},
	  editor = {S. Koyejo and S. Mohamed and A. Agarwal and D. Belgrave and K. Cho and A. Oh},
	  pages = {2550--2563},
	  publisher = {Curran Associates, Inc.},
	  title = {Molecule Generation by Principal Subgraph Mining and Assembling},
	  url = {https://proceedings.neurips.cc/paper_files/paper/2022/file/1160792eab11de2bbaf9e71fce191e8c-Paper-Conference.pdf},
	  volume = {35},
	  year = {2022}
	}
      

[bib] [paper] [github]

Honors and Awards

• 2023.10 ByteDance Scholars Program (about 10 students in China each year)

Educations

• 2025.07 - present, visiting PhD in Bruno Correia's lab, EPFL, Lausane, Switzerland
• 2022.09 - present, PhD in Yang Liu's lab, Tsinghua University, Bejing, China
• 2018.09 - 2022.07, Undergraduate, Tsinghua University, Bejing, China
• 2015.09 - 2018.07, Hangzhou No.2 High School of Zhejiang Province, Zhejiang, China