PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding. - Minghao Xu; Zuobai Zhang; Jiarui Lu; Zhaocheng Zhu; Yangtian Zhang; Chang Ma; Runcheng Liu; Jian Tang 005 (NeurIPS, 2022)

TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery. - Zhaocheng Zhu; Chence Shi; Zuobai Zhang; Shengchao Liu; Minghao Xu; Xinyu Yuan; Yangtian Zhang; Jun-Kun Chen; Huiyu Cai; Jiarui Lu; Chang Ma; Runcheng Liu; et al. (CoRR, 2022)

E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking. - Yangtian Zhang; Huiyu Cai; Chence Shi; Bozitao Zhong; Jian Tang 005 (CoRR, 2022)

E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking. - Yangtian Zhang; Huiyu Cai; Chence Shi; Jian Tang 005 (ICLR, 2023)

DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing. - Yangtian Zhang; Zuobai Zhang; Bozitao Zhong; Sanchit Misra; Jian Tang 005 (NeurIPS, 2023)

A Survey on Diffusion Models for Recommender Systems. - Jianghao Lin; Jiaqi Liu; Jiachen Zhu 001; Yunjia Xi; Chengkai Liu; Yangtian Zhang; Yong Yu 001; Weinan Zhang 001 (CoRR, 2024)

CaLMFlow: Volterra Flow Matching using Causal Language Models. - Sizhuang He; Daniel LeVine; Ivan Vrkic; Marco Francesco Bressana; David Zhang; Syed Asad Rizvi; Yangtian Zhang; Emanuele Zappala; David van Dijk (CoRR, 2024)

Flow Matching for Collaborative Filtering. - Chengkai Liu; Yangtian Zhang; Jianling Wang; Rex Ying; James Caverlee (CoRR, 2025)

Non-Markovian Discrete Diffusion with Causal Language Models. - Yangtian Zhang; Sizhuang He; Daniel LeVine; Lawrence Zhao; David Zhang; Syed Asad Rizvi; Emanuele Zappala; Rex Ying; David van Dijk (CoRR, 2025)