publications

(*) indicates equal contribution

2026

  1. bioRxiv
    AtlasFold: Protein structure prediction with metagenomic-scale language models
    Seonghwan Seo, Hyeongwoo Kim, Seokhyun Moon, Woo Youn Kim, and  Team KAIST
    bioRxiv, 2026
    HTML Code
  2. arXiv
    Atom-level Protein Representation Learning Improves Protein Structure Prediction
    Taewon Kim, Hyosoon Jang, Hyunjin Seo, Seonghwan Seo, Hyeongwoo Kim, Wonho Zhung, Mingyeong Shin, Wooyoun Kim, and Sungsoo Ahn
    arXiv preprint arXiv:2605.22133, 2026
    arXiv
  3. ICML Workshop
    Boltz2ESI: Accurate Enzyme Specificity Prediction with Co-folding Foundation Model
    Xiwei Cheng*, Seonghwan Seo*, Jihang Chen, Songlin Jiang, Pengkang Guo, and Wengong Jin
    In ICML Workshop on Generative and Experimental Perspectives for Biomolecular Design, 2026
    Awarded HTML
  4. ICML Workshop
    Generalized Multi-State Protein Design with AlphaFold3
    Xiwei Cheng, Pengkang Guo, Seonghwan Seo, and Wengong Jin
    In ICML Workshop on Generative and Experimental Perspectives for Biomolecular Design, 2026
    HTML

2025

  1. ICML
    Compositional Flows for 3D Molecule and Synthesis Pathway Co-design
    Tony Shen*, Seonghwan Seo*, Ross Irwin, Kieran Didi, Simon Olsson, Woo Youn Kim, and Martin Ester
    In International Conference on Machine Learning, 2025
    * Previously presented at ICLR AI4Mat and GEM Workshop 2025
    Award arXiv
  2. ICLR
    Generative Flows on Synthetic Pathway for Drug Design
    Seonghwan Seo, Minsu Kim, Tony Shen, Martin Ester, Jinkyoo Park, Sungsoo Ahn, and Woo Youn Kim
    In International Conference on Learning Representations, 2025
    * Previously presented at NeurIPS AIDrugX Workshop 2024
    arXiv Blog Code

2024

  1. Chem. Sci.
    PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening
    Seonghwan Seo, and Woo Youn Kim
    Chemical Science, 2024
    IF: 7.6, * Previously presented at NeurIPS AI4D3 Workshop 2023
    arXiv HTML Code
  2. TMLR
    TacoGFN: Target-conditioned GFlowNet for Structure-based Drug Design
    Tony Shen, Seonghwan Seo, Grayson Lee, Mohit Pandey, Jason R Smith, Artem Cherkasov, Woo Youn Kim, and Martin Ester
    Transactions on Machine Learning Research, 2024
    arXiv Code

2023

  1. Adv. Sci.
    Molecular generative model via retrosynthetically prepared chemical building block assembly
    Seonghwan Seo, Jaechang Lim, and Woo Youn Kim
    Advanced Science, 2023
    IF: 15.1
    Selected arXiv HTML Code

2022

  1. Chem. Sci.
    Drug-likeness scoring based on unsupervised learning
    Kyunghoon Lee*, Jinho Jang*, Seonghwan Seo*, Jaechang Lim, and Woo Youn Kim
    Chemical Science, 2022
    IF: 10.0
    HTML Code