Clustering Based on Graph of Density Topology. - Zhangyang Gao; Haitao Lin; Stan Z. Li (CoRR, 2020)

LookHops: light multi-order convolution and pooling for graph classification. - Zhangyang Gao; Haitao Lin; Stan Z. Li (CoRR, 2020)

Conditional Local Filters with Explainers for Spatio-Temporal Forecasting. - Haitao Lin; Zhangyang Gao; Lirong Wu; Stan Z. Li (CoRR, 2021)

Self-supervised on Graphs: Contrastive, Generative, or Predictive. - Lirong Wu; Haitao Lin; Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CoRR, 2021)

GraphMixup: Improving Class-Imbalanced Node Classification on Graphs by Self-supervised Context Prediction. - Lirong Wu; Haitao Lin; Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CoRR, 2021)

Git: Clustering Based on Graph of Intensity Topology. - Zhangyang Gao; Haitao Lin; Cheng Tan 012; Lirong Wu; Stan Z. Li (CoRR, 2021)

Extensive Deep Temporal Point Process. - Haitao Lin; Cheng Tan 012; Lirong Wu; Zhangyang Gao; Stan Z. Li (CoRR, 2021)

Conditional Local Convolution for Spatio-Temporal Meteorological Forecasting. - Haitao Lin; Zhangyang Gao; Yongjie Xu; Lirong Wu; Ling Li; Stan Z. Li (AAAI, 2022)

Hyperspherical Consistency Regularization. - Cheng Tan 012; Zhangyang Gao; Lirong Wu; Siyuan Li 002; Stan Z. Li (CVPR, 2022)

SimVP: Simpler yet Better Video Prediction. - Zhangyang Gao; Cheng Tan 012; Lirong Wu; Stan Z. Li (CVPR, 2022)

GraphMixup: Improving Class-Imbalanced Node Classification by Reinforcement Mixup and Self-supervised Context Prediction. - Lirong Wu; Jun Xia 001; Zhangyang Gao; Haitao Lin; Cheng Tan 012; Stan Z. Li (ECML/PKDD (4), 2022)

AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB. - Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CoRR, 2022)

SemiRetro: Semi-template framework boosts deep retrosynthesis prediction. - Zhangyang Gao; Cheng Tan 012; Lirong Wu; Stan Z. Li (CoRR, 2022)

Generative De Novo Protein Design with Global Context. - Cheng Tan 012; Zhangyang Gao; Jun Xia 001; Stan Z. Li (CoRR, 2022)

Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning. - Cheng Tan 012; Zhangyang Gao; Siyuan Li 002; Yongjie Xu; Stan Z. Li (CoRR, 2022)

CoSP: Co-supervised pretraining of pocket and ligand. - Zhangyang Gao; Cheng Tan 012; Lirong Wu; Stan Z. Li (CoRR, 2022)

A Survey on Generative Diffusion Model. - Hanqun Cao; Cheng Tan 012; Zhangyang Gao; Guangyong Chen; Pheng-Ann Heng; Stan Z. Li (CoRR, 2022)

Teaching Yourself: Graph Self-Distillation on Neighborhood for Node Classification. - Lirong Wu; Jun Xia 001; Haitao Lin; Zhangyang Gao; Zicheng Liu 006; Guojiang Zhao; Stan Z. Li (CoRR, 2022)

SimVP: Towards Simple yet Powerful Spatiotemporal Predictive Learning. - Cheng Tan 012; Zhangyang Gao; Stan Z. Li (CoRR, 2022)

RFold: Towards Simple yet Effective RNA Secondary Structure Prediction. - Cheng Tan 012; Zhangyang Gao; Stan Z. Li (CoRR, 2022)

Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning. - Cheng Tan 012; Zhangyang Gao; Lirong Wu; Yongjie Xu; Jun Xia 001; Siyuan Li 002; Stan Z. Li (CVPR, 2023)

Global-Context Aware Generative Protein Design. - Cheng Tan 012; Zhangyang Gao; Jun Xia 001; Bozhen Hu; Stan Z. Li (ICASSP, 2023)

PiFold: Toward effective and efficient protein inverse folding. - Zhangyang Gao; Cheng Tan 012; Stan Z. Li (ICLR, 2023)

Mole-BERT: Rethinking Pre-training Graph Neural Networks for Molecules. - Jun Xia 001; Chengshuai Zhao; Bozhen Hu; Zhangyang Gao; Cheng Tan 012; Yue Liu 008; Siyuan Li 002; Stan Z. Li (ICLR, 2023)

OpenSTL: A Comprehensive Benchmark of Spatio-Temporal Predictive Learning. - Cheng Tan 012; Siyuan Li 002; Zhangyang Gao; Wenfei Guan; Zedong Wang; Zicheng Liu 006; Lirong Wu; Stan Z. Li (NeurIPS, 2023)

ProteinInvBench: Benchmarking Protein Inverse Folding on Diverse Tasks, Models, and Metrics. - Zhangyang Gao; Cheng Tan 012; Yijie Zhang; Xingran Chen; Lirong Wu; Stan Z. Li (NeurIPS, 2023)

Understanding the Limitations of Deep Models for Molecular property prediction: Insights and Solutions. - Jun Xia 001; Lecheng Zhang; Xiao Zhu; Yue Liu 008; Zhangyang Gao; Bozhen Hu; Cheng Tan 012; Jiangbin Zheng 002; Siyuan Li 002; Stan Z. Li (NeurIPS, 2023)

Co-supervised Pre-training of Pocket and Ligand. - Zhangyang Gao; Cheng Tan 012; Jun Xia 001; Stan Z. Li (ECML/PKDD (1), 2023)

Target-Aware Molecular Graph Generation. - Cheng Tan 012; Zhangyang Gao; Stan Z. Li (ECML/PKDD (6), 2023)

Learning to Augment Graph Structure for both Homophily and Heterophily Graphs. - Lirong Wu; Cheng Tan 012; Zihan Liu; Zhangyang Gao; Haitao Lin; Stan Z. Li (ECML/PKDD (3), 2023)

DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints. - Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CoRR, 2023)

Generative Tertiary Structure-based RNA Design. - Cheng Tan 012; Zhangyang Gao; Stan Z. Li (CoRR, 2023)

PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding. - Zhangyang Gao; Yuqi Hu; Cheng Tan 012; Stan Z. Li (CoRR, 2023)

Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer. - Cheng Tan 012; Zhangyang Gao; Stan Z. Li (CoRR, 2023)

Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement. - Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CoRR, 2023)

MotifRetro: Exploring the Combinability-Consistency Trade-offs in retrosynthesis via Dynamic Motif Editing. - Zhangyang Gao; Xingran Chen; Cheng Tan 012; Stan Z. Li (CoRR, 2023)

Enhancing Human-like Multi-Modal Reasoning: A New Challenging Dataset and Comprehensive Framework. - Jingxuan Wei; Cheng Tan 012; Zhangyang Gao; Linzhuang Sun; Siyuan Li 002; Bihui Yu; Ruifeng Guo; Stan Z. Li (CoRR, 2023)

VQPL: Vector Quantized Protein Language. - Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CoRR, 2023)

Revisiting the Temporal Modeling in Spatio-Temporal Predictive Learning under A Unified View. - Cheng Tan 012; Jue Wang 004; Zhangyang Gao; Siyuan Li 002; Lirong Wu; Jun Xia 001; Stan Z. Li (CoRR, 2023)

Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction. - Yufei Huang 002; Siyuan Li 002; Jin Su; Lirong Wu; Odin Zhang; Haitao Lin; Jingqi Qi; Zihan Liu; Zhangyang Gao; Yuyang Liu; Jiangbin Zheng 002; Stan Z. Li (CoRR, 2023)

General Point Model with Autoencoding and Autoregressive. - Zhe Li; Zhangyang Gao; Cheng Tan 012; Stan Z. Li; Laurence T. Yang (CoRR, 2023)

Boosting the Power of Small Multimodal Reasoning Models to Match Larger Models with Self-Consistency Training. - Cheng Tan 012; Jingxuan Wei; Zhangyang Gao; Linzhuang Sun; Siyuan Li 002; Xihong Yang; Stan Z. Li (CoRR, 2023)

Efficiently Predicting Protein Stability Changes Upon Single-point Mutation with Large Language Models. - Yijie Zhang; Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CoRR, 2023)

MMDesign: Multi-Modality Transfer Learning for Generative Protein Design. - Jiangbin Zheng 002; Siyuan Li 002; Yufei Huang 002; Zhangyang Gao; Cheng Tan 012; Bozhen Hu; Jun Xia 001; Ge Wang; Stan Z. Li (CoRR, 2023)

Self-Supervised Learning on Graphs: Contrastive, Generative, or Predictive. - Lirong Wu; Haitao Lin; Cheng Tan 012; Zhangyang Gao; Stan Z. Li (IEEE Trans. Knowl. Data Eng., 2023)

Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody Designer. - Cheng Tan 012; Zhangyang Gao; Lirong Wu; Jun Xia 001; Jiangbin Zheng 002; Xihong Yang; Yue Liu 008; Bozhen Hu; Stan Z. Li (AAAI, 2024)

Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction. - Yufei Huang 002; Siyuan Li 002; Lirong Wu; Jin Su; Haitao Lin; Odin Zhang; Zihan Liu; Zhangyang Gao; Jiangbin Zheng 002; Stan Z. Li (AAAI, 2024)

PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction. - Lirong Wu; Yufei Huang 002; Cheng Tan 012; Zhangyang Gao; Bozhen Hu; Haitao Lin; Zicheng Liu 006; Stan Z. Li (AAAI, 2024)

Text-To-AMP: Antimicrobial Peptide Design Guided by Natural Text. - Yixuan Huang; Yang Xiao; Alexander Teng; Fei Ye; Yiyao Yu; Chenyi Lei; Ruihao Zhang; Zhangyang Gao; Cheng Tan 012; Xiao Liu (BIBM, 2024)

General Point Model Pretraining with Autoencoding and Autoregressive. - Zhe Li; Zhangyang Gao; Cheng Tan 012; Bocheng Ren; Laurence T. Yang; Stan Z. Li (CVPR, 2024)

MLIP: Enhancing Medical Visual Representation with Divergence Encoder and Knowledge-guided Contrastive Learning. - Zhe Li; Laurence T. Yang; Bocheng Ren; Xin Nie; Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CVPR, 2024)

Boosting the Power of Small Multimodal Reasoning Models to Match Larger Models with Self-consistency Training. - Cheng Tan 012; Jingxuan Wei; Zhangyang Gao; Linzhuang Sun; Siyuan Li 002; Ruifeng Guo; Bihui Yu; Stan Z. Li (ECCV (40), 2024)

DiscoGNN: A Sample-Efficient Framework for Self-Supervised Graph Representation Learning. - Jun Xia 001; Shaorong Chen; Yue Liu 008; Zhangyang Gao; Jiangbin Zheng 002; Xihong Yang; Stan Z. Li (ICDE, 2024)

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design. - Cheng Tan 012; Yijie Zhang; Zhangyang Gao; Bozhen Hu; Siyuan Li 002; Zicheng Liu 006; Stan Z. Li (ICLR, 2024)

Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks. - Tianyu Fan; Lirong Wu; Yufei Huang 002; Haitao Lin; Cheng Tan 012; Zhangyang Gao; Stan Z. Li (ICLR, 2024)

KW-Design: Pushing the Limit of Protein Design via Knowledge Refinement. - Zhangyang Gao; Cheng Tan 012; Xingran Chen; Yijie Zhang; Jun Xia 001; Siyuan Li 002; Stan Z. Li (ICLR, 2024)

Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge. - Yufei Huang 002; Odin Zhang; Lirong Wu; Cheng Tan 012; Haitao Lin; Zhangyang Gao; Siyuan Li 002; Stan Z. Li (ICML, 2024)

Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective. - Cheng Tan 012; Zhangyang Gao; Hanqun Cao; Xingran Chen; Ge Wang; Lirong Wu; Jun Xia 001; Jiangbin Zheng 002; Stan Z. Li (ICML, 2024)

A Graph is Worth K Words: Euclideanizing Graph using Pure Transformer. - Zhangyang Gao; Daize Dong; Cheng Tan 012; Jun Xia 001; Bozhen Hu; Stan Z. Li (ICML, 2024)

AdaNovo: Towards Robust emph{De Novo} Peptide Sequencing in Proteomics against Data Biases. - Jun Xia 001; Shaorong Chen; Jingbo Zhou; Xiaojun Shan; Wenjie Du 003; Zhangyang Gao; Cheng Tan 012; Bozhen Hu; Jiangbin Zheng 002; Stan Z. Li (NeurIPS, 2024)

UniIF: Unified Molecule Inverse Folding. - Zhangyang Gao; Jue Wang 004; Cheng Tan 012; Lirong Wu; Yufei Huang 002; Siyuan Li 002; Zhirui Ye; Stan Z. Li (NeurIPS, 2024)

ProtGO: Function-Guided Protein Modeling for Unified Representation Learning. - Bozhen Hu; Cheng Tan 012; Yongjie Xu; Zhangyang Gao; Jun Xia 001; Lirong Wu; Stan Z. Li (NeurIPS, 2024)

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning. - Sizhe Liu; Jun Xia 001; Lecheng Zhang; Yuchen Liu; Yue Liu 008; Wenjie Du 003; Zhangyang Gao; Bozhen Hu; Cheng Tan 012; Hongxin Xiang; Stan Z. Li (NeurIPS, 2024)

Interpretable and Generalizable Spatiotemporal Predictive Learning with Disentangled Consistency. - Jingxuan Wei; Cheng Tan 012; Zhangyang Gao; Linzhuang Sun; Bihui Yu; Ruifeng Guo; Stan Z. Li (ECML/PKDD (3), 2024)

R3Design: deep tertiary structure-based RNA sequence design and beyond. - Cheng Tan 012; Yijie Zhang; Zhangyang Gao; Hanqun Cao; Siyuan Li 002; Siqi Ma; Mathieu Blanchette; Stan Z. Li (Briefings Bioinform., 2024)

DCS-Net: Pioneering Leakage-Free Point Cloud Pretraining Framework with Global Insights. - Zhe Li; Zhangyang Gao; Cheng Tan 012; Stan Z. Li; Laurence T. Yang (CoRR, 2024)

Retrieval Meets Reasoning: Even High-school Textbook Knowledge Benefits Multimodal Reasoning. - Cheng Tan 012; Jingxuan Wei; Linzhuang Sun; Zhangyang Gao; Siyuan Li 002; Bihui Yu; Ruifeng Guo; Stan Z. Li (CoRR, 2024)

Peer Review as A Multi-Turn and Long-Context Dialogue with Role-Based Interactions. - Cheng Tan 012; Dongxin Lyu; Siyuan Li 002; Zhangyang Gao; Jingxuan Wei; Siqi Ma; Zicheng Liu 006; Stan Z. Li (CoRR, 2024)

FoldToken2: Learning compact, invariant and generative protein structure language. - Zhangyang Gao; Cheng Tan 012; Stan Z. Li (CoRR, 2024)

AQND: An asymmetric quorum-based neighbor discovery protocol for reducing delay in sensor based systems. - Ziqing Xia; Zhangyang Gao; Anfeng Liu; Neal N. Xiong (Inf. Sci., 2024)

Beyond Homophily and Homogeneity Assumption: Relation-Based Frequency Adaptive Graph Neural Networks. - Lirong Wu; Haitao Lin; Bozhen Hu; Cheng Tan 012; Zhangyang Gao; Zicheng Liu 006; Stan Z. Li (IEEE Trans. Neural Networks Learn. Syst., 2024)

A Survey on Generative Diffusion Models. - Hanqun Cao; Cheng Tan 012; Zhangyang Gao; Yilun Xu; Guangyong Chen; Pheng-Ann Heng; Stan Z. Li (IEEE Trans. Knowl. Data Eng., 2024)

A Teacher-Free Graph Knowledge Distillation Framework With Dual Self-Distillation. - Lirong Wu; Haitao Lin; Zhangyang Gao; Guojiang Zhao; Stan Z. Li (IEEE Trans. Knowl. Data Eng., 2024)

Enhancing human-like multimodal reasoning: a new challenging dataset and comprehensive framework. - Jingxuan Wei; Cheng Tan 012; Zhangyang Gao; Linzhuang Sun; Siyuan Li 002; Bihui Yu; Ruifeng Guo; Stan Z. Li (Neural Comput. Appl., 2024)

dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. - Cheng Tan 012; Yijie Zhang; Zhangyang Gao; Yufei Huang 002; Haitao Lin; Lirong Wu; Fandi Wu; Mathieu Blanchette; Stan Z. Li (AAAI, 2025)

FoldToken: Learning Protein Language via Vector Quantization and Beyond. - Zhangyang Gao; Cheng Tan 012; Jue Wang 004; Yufei Huang 002; Lirong Wu; Stan Z. Li (AAAI, 2025)

Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization. - Lirong Wu; Haitao Lin; Yufei Huang 002; Zhangyang Gao; Cheng Tan 012; Yunfan Liu 002; Tailin Wu; Stan Z. Li (AAAI, 2025)

From Words to Structured Visuals: A Benchmark and Framework for Text-to-Diagram Generation and Editing. - Jingxuan Wei; Cheng Tan 012; Qi Chen; Gaowei Wu; Siyuan Li 002; Zhangyang Gao; Linzhuang Sun; Bihui Yu; Ruifeng Guo (CVPR, 2025)

EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow. - Yufei Huang 002; Yunshu Liu; Lirong Wu; Haitao Lin; Cheng Tan 012; Odin Zhang; Zhangyang Gao; Siyuan Li 002; Zicheng Liu 006; Yunfan Liu 002; Tailin Wu; Stan Z. Li (ICLR, 2025)

MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction. - Cheng Tan 012; Zhenxiao Cao; Zhangyang Gao; Lirong Wu; Siyuan Li 002; Yufei Huang 002; Jun Xia 001; Bozhen Hu; Stan Z. Li (ICLR, 2025)

ReNovo: Retrieval-Based emph{De Novo} Mass Spectrometry Peptide Sequencing. - Shaorong Chen; Jun Xia 001; Jingbo Zhou; Lecheng Zhang; Zhangyang Gao; Bozhen Hu; Cheng Tan 012; Wenjie Du 003; Stan Z. Li (ICLR, 2025)

G2PDiffusion: Genotype-to-Phenotype Prediction with Diffusion Models. - Mengdi Liu; Zhangyang Gao; Hong Chang 001; Stan Z. Li; Shiguang Shan; Xilin Chen 001 (CoRR, 2025)

An Extensive Survey With Empirical Studies on Deep Temporal Point Process. - Haitao Lin; Cheng Tan 012; Lirong Wu; Zicheng Liu 006; Zhangyang Gao; Stan Z. Li (IEEE Trans. Knowl. Data Eng., 2025)

ProtInvTree: Deliberate Protein Inverse Folding with Reward-guided Tree Search. - Mengdi Liu; Xiaoxue Cheng; Zhangyang Gao; Hong Chang 001; Cheng Tan 012; Shiguang Shan; Xilin Chen 001 (CoRR, 2025)

AlphaFold Database Debiasing for Robust Inverse Folding. - Cheng Tan 012; Zhenxiao Cao; Zhangyang Gao; Siyuan Li 002; Yufei Huang 002; Stan Z. Li (CoRR, 2025)

PFMBench: Protein Foundation Model Benchmark. - Zhangyang Gao; Hao Wang 074; Cheng Tan 012; Chenrui Xu; Mengdi Liu; Bozhen Hu; Linlin Chao; Xiaoming Zhang; Stan Z. Li (CoRR, 2025)

Protein-SE(3): Benchmarking SE(3)-based Generative Models for Protein Structure Design. - Lang Yu; Zhangyang Gao; Cheng Tan; Qin Chen; Jie Zhou; Liang He (CoRR, 2025)

USTEP: Spatio-Temporal Predictive Learning Under a Unified View. - Cheng Tan 012; Jue Wang 004; Zhangyang Gao; Siyuan Li 002; Stan Z. Li (IEEE Trans. Pattern Anal. Mach. Intell., 2025)