Spatial-temporal Transformer Network with Self-supervised Learning for Traffic Flow Prediction. - Zhangzhi Peng; Xiaohui Huang (STRL@IJCAI, 2022)

E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction. - Tao Shen; Zhihang Hu; Zhangzhi Peng; Jiayang Chen; Peng Xiong; Liang Hong; Liangzhen Zheng; Yixuan Wang; Irwin King; Sheng Wang; Siqi Sun; Yu Li 006 (CoRR, 2022)

PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks. - Zhangzhi Peng (CIKM, 2024)

Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency. - Chentong Wang; Yannan Qu; Zhangzhi Peng; Yukai Wang; Hongli Zhu; Dachuan Chen; Longxing Cao (ICML, 2024)

Accurate prediction of antibody function and structure using bio-inspired antibody language model. - Hongtai Jing; Zhengtao Gao; Sheng Xu; Tao Shen; Zhangzhi Peng; Shwai He; Tao You; Shuang Ye; Wei Lin; Siqi Sun (Briefings Bioinform., 2024)

Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction. - Jarrid Rector-Brooks; Mohsin Hasan; Zhangzhi Peng; Zachary Quinn; Cheng-Hao Liu; Sarthak Mittal; Nouha Dziri; Michael M. Bronstein; Yoshua Bengio; Pranam Chatterjee; Alexander Tong 001; Avishek Joey Bose (CoRR, 2024)

Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction. - Jarrid Rector-Brooks; Mohsin Hasan; Zhangzhi Peng; Cheng-Hao Liu; Sarthak Mittal; Nouha Dziri; Michael M. Bronstein; Pranam Chatterjee; Alexander Tong 001; Joey Bose (ICLR, 2025)

Path Planning for Masked Diffusion Model Sampling. - Zhangzhi Peng; Zachary Bezemek; Sawan Patel; Jarrid Rector-Brooks; Sherwood Yao; Alexander Tong 001; Pranam Chatterjee (CoRR, 2025)