CogDL: An Extensive Toolkit for Deep Learning on Graphs. - Yukuo Cen; Zhenyu Hou; Yan Wang 120; Qibin Chen; Yizhen Luo; Xingcheng Yao; Aohan Zeng; Shiguang Guo; Peng Zhang 077; Guohao Dai; Yu Wang 002; Chang Zhou; et al. (CoRR, 2021)

DAIR-V2X: A Large-Scale Dataset for Vehicle-Infrastructure Cooperative 3D Object Detection. - Haibao Yu; Yizhen Luo; Mao Shu; Yiyi Huo; Zebang Yang; Yifeng Shi; Zhenglong Guo; Hanyu Li; Xing Hu; Jirui Yuan; Zaiqing Nie (CVPR, 2022)

CogDL: A Comprehensive Library for Graph Deep Learning. - Yukuo Cen; Zhenyu Hou; Yan Wang 120; Qibin Chen; Yizhen Luo; Zhongming Yu; Hengrui Zhang; Xingcheng Yao; Aohan Zeng; Shiguang Guo; Yuxiao Dong; Yang Yang 009; et al. (WWW, 2023)

Empowering AI drug discovery with explicit and implicit knowledge. - Yizhen Luo; Kui Huang; Massimo Hong; Kai Yang; Jiahuan Zhang; Yushuai Wu; Zaiqing Nie (CoRR, 2023)

MolFM: A Multimodal Molecular Foundation Model. - Yizhen Luo; Kai Yang; Massimo Hong; Xing Yi Liu; Zaiqing Nie (CoRR, 2023)

BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine. - Yizhen Luo; Jiahuan Zhang; Siqi Fan 002; Kai Yang; Yushuai Wu; Mu Qiao; Zaiqing Nie (CoRR, 2023)

LangCell: Language-Cell Pre-training for Cell Identity Understanding. - Suyuan Zhao; Jiahuan Zhang; Yushuai Wu; Yizhen Luo; Zaiqing Nie (ICML, 2024)

Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge. - Yizhen Luo; Kai Yang; Massimo Hong; Xing Yi Liu; Zikun Nie; Hao Zhou 012; Zaiqing Nie (KDD, 2024)

MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering. - Yizhen Luo; Zikun Nie; Massimo Hong; Suyuan Zhao; Hao Zhou 012; Zaiqing Nie (NeurIPS, 2024)

DeepCRE: Transforming Drug R&D via AI-Driven Cross-drug Response Evaluation. - Yushuai Wu; Ting Zhang; Hao Zhou 012; Hainan Wu; Hanwen Sunchu; Lei Hu; Xiaofang Chen; Suyuan Zhao; Gaochao Liu; Chao Sun; Jiahuan Zhang; Yizhen Luo; et al. (CoRR, 2024)

PharMolixFM: All-Atom Foundation Models for Molecular Modeling and Generation. - Yizhen Luo; Jiashuo Wang; Siqi Fan 002; Zaiqing Nie (CoRR, 2025)

SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics. - Suyuan Zhao; Yizhen Luo; Ganbo Yang; Yan Zhong; Hao Zhou 012; Zaiqing Nie (CoRR, 2025)