Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model. - Shiwei Liu; Tian Zhu; Milong Ren; Chungong Yu; Dongbo Bu; Haicang Zhang (NeurIPS, 2023)

CarbonNovo: Joint Design of Protein Structure and Sequence Using a Unified Energy-based Model. - Milong Ren; Tian Zhu; Haicang Zhang (ICML, 2024)

Antibody Design Using a Score-based Diffusion Model Guided by Evolutionary, Physical and Geometric Constraints. - Tian Zhu; Milong Ren; Haicang Zhang (ICML, 2024)

Improving Molecular Graph Generation with Flow Matching and Optimal Transport. - Xiaoyang Hou; Tian Zhu; Milong Ren; Dongbo Bu; Xin Gao 001; Chunming Zhang; Shiwei Sun (CoRR, 2024)

Accurate and robust protein sequence design with CarbonDesign. - Milong Ren; Chungong Yu; Dongbo Bu; Haicang Zhang (Nat. Mac. Intell., 2024)

NIERT: Accurate Numerical Interpolation Through Unifying Scattered Data Representations Using Transformer Encoder. - Shizhe Ding; Boyang Xia; Milong Ren; Dongbo Bu (IEEE Trans. Knowl. Data Eng., 2024)

Multi-objective antibody design with constrained preference optimization. - Milong Ren; ZaiKai He; Haicang Zhang (ICLR, 2025)