Publications

• 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 2025Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints
  Dapeng Jiang*, Xiangzhe Kong*, Jiaqi Han*, Mingyu Li, Rui Jiao, Wenbing Huang, Stefano Ermon, Jianzhu Ma, Yang Liu.
  In Proceedings of the 42th International Conference on Machine Learning, 2025.

        @inproceedings{
          jiang2025zeroshot,
          title={Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints},
          author={Dapeng Jiang and Xiangzhe Kong and Jiaqi Han and Mingyu Li and Rui Jiao and Wenbing Huang and Stefano Ermon and Jianzhu Ma and Yang Liu},
          booktitle={Forty-second International Conference on Machine Learning},
          year={2025},
          url={https://openreview.net/forum?id=Q0rJmpLat9}
        }
      

[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]



• 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]



• 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]



• NeurIPS 20243D Structure Prediction of Atomic Systems with Flow-Based Direct Preference Optimization
  Rui Jiao, Xiangzhe Kong, Wenbing Huang, Yang Liu.
  Advances in Neural Information Processing Systems, 2024.

        @article{jiao20253d,
          title={3D Structure Prediction of Atomic Systems with Flow-based Direct Preference Optimization},
          author={Jiao, Rui and Kong, Xiangzhe and Huang, Wenbing and Liu, Yang},
          journal={Advances in Neural Information Processing Systems},
          volume={37},
          pages={110197--110217},
          year={2025}
        }
      

[bib] [paper] [github]



• ICML 2024Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning
  Xiangzhe Kong, Wenbing Huang, Yang Liu.
  In Proceedings of the 41th International Conference on Machine Learning, 2024.

	@InProceedings{pmlr-v235-kong24b,
	  title = 	 {Generalist Equivariant Transformer Towards 3{D} Molecular Interaction Learning},
	  author =       {Kong, Xiangzhe and Huang, Wenbing and Liu, Yang},
	  booktitle = 	 {Proceedings of the 41st International Conference on Machine Learning},
	  pages = 	 {25149--25175},
	  year = 	 {2024},
	  editor = 	 {Salakhutdinov, Ruslan and Kolter, Zico and Heller, Katherine and Weller, Adrian and Oliver, Nuria and Scarlett, Jonathan and Berkenkamp, Felix},
	  volume = 	 {235},
	  series = 	 {Proceedings of Machine Learning Research},
	  month = 	 {21--27 Jul},
	  publisher =    {PMLR},
	  pdf = 	 {https://raw.githubusercontent.com/mlresearch/v235/main/assets/kong24b/kong24b.pdf},
	  url = 	 {https://proceedings.mlr.press/v235/kong24b.html},
	}
      

[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]