ML Anthology

Tan, Cheng

52 publications

NeurIPS 2025 AlphaFold Database Debiasing for Robust Inverse Folding Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Siyuan Li, Yufei Huang, Stan Z. Li
ICLR 2025 CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Cheng Tan, Zicheng Liu, Zhifeng Gao, Stan Z. Li
CVPR 2025 DaCapo: Score Distillation as Stacked Bridge for Fast and High-Quality 3D Editing Yufei Huang, Bangyan Liao, Yuqi Hu, Haitao Lin, Lirong Wu, Siyuan Li, Cheng Tan, Zicheng Liu, Yunfan Liu, Zelin Zang, Chang Yu, Zhen Lei
ICLR 2025 EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow Yufei Huang, Yunshu Liu, Lirong Wu, Haitao Lin, Cheng Tan, Odin Zhang, Zhangyang Gao, Siyuan Li, Zicheng Liu, Yunfan Liu, Tailin Wu, Stan Z. Li
AAAI 2025 FoldToken: Learning Protein Language via Vector Quantization and Beyond Zhangyang Gao, Cheng Tan, Jue Wang, Yufei Huang, Lirong Wu, Stan Z. Li
CVPR 2025 From Words to Structured Visuals: A Benchmark and Framework for Text-to-Diagram Generation and Editing Jingxuan Wei, Cheng Tan, Qi Chen, Gaowei Wu, Siyuan Li, Zhangyang Gao, Linzhuang Sun, Bihui Yu, Ruifeng Guo
ICLR 2025 MeToken: Uniform Micro-Environment Token Boosts Post-Translational Modification Prediction Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Lirong Wu, Siyuan Li, Yufei Huang, Jun Xia, Bozhen Hu, Stan Z. Li
CVPR 2025 MergeVQ: A Unified Framework for Visual Generation and Representation with Disentangled Token Merging and Quantization Siyuan Li, Luyuan Zhang, Zedong Wang, Juanxi Tian, Cheng Tan, Zicheng Liu, Chang Yu, Qingsong Xie, Haonan Lu, Haoqian Wang, Zhen Lei
NeurIPS 2025 ProtInvTree: Deliberate Protein Inverse Folding with Reward-Guided Tree Search Mengdi Liu, Xiaoxue Cheng, Zhangyang Gao, Hong Chang, Cheng Tan, Shiguang Shan, Xilin Chen
ICLR 2025 ReNovo: Retrieval-Based \emph{De Novo} Mass Spectrometry Peptide Sequencing Shaorong Chen, Jun Xia, Jingbo Zhou, Lecheng Zhang, Zhangyang Gao, Bozhen Hu, Cheng Tan, Wenjie Du, Stan Z. Li
AAAI 2025 Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization Lirong Wu, Haitao Lin, Yufei Huang, Zhangyang Gao, Cheng Tan, Yunfan Liu, Tailin Wu, Stan Z. Li
IJCAI 2025 SketchAgent: Generating Structured Diagrams from Hand-Drawn Sketches Cheng Tan, Qi Chen, Jingxuan Wei, Gaowei Wu, Zhangyang Gao, Siyuan Li, Bihui Yu, Ruifeng Guo, Stan Z. Li
AAAI 2025 dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-Driven Pre-Binding Antigen Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li
ICML 2024 A Graph Is Worth $k$ Words: Euclideanizing Graph Using Pure Transformer Zhangyang Gao, Daize Dong, Cheng Tan, Jun Xia, Bozhen Hu, Stan Z. Li
NeurIPS 2024 AdaNovo: Towards Robust \emph{De Novo} Peptide Sequencing in Proteomics Against Data Biases Jun Xia, Shaorong Chen, Jingbo Zhou, Xiaojun Shan, Wenjie Du, Zhangyang Gao, Cheng Tan, Bozhen Hu, Jiangbin Zheng, Stan Z. Li
ECCV 2024 Boosting the Power of Small Multimodal Reasoning Models to Match Larger Models with Self-Consistency Training Cheng Tan, Jingxuan Wei, Zhangyang Gao, Linzhuang Sun, Siyuan Li, Ruifeng Guo, BiHui Yu, Stan Z. Li
AAAI 2024 Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody Designer Cheng Tan, Zhangyang Gao, Lirong Wu, Jun Xia, Jiangbin Zheng, Xihong Yang, Yue Liu, Bozhen Hu, Stan Z. Li
ICML 2024 Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective Cheng Tan, Zhangyang Gao, Hanqun Cao, Xingran Chen, Ge Wang, Lirong Wu, Jun Xia, Jiangbin Zheng, Stan Z. Li
ICLR 2024 Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-Training Tasks Tianyu Fan, Lirong Wu, Yufei Huang, Haitao Lin, Cheng Tan, Zhangyang Gao, Stan Z. Li
NeurIPS 2024 FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning Sizhe Liu, Jun Xia, Lecheng Zhang, Yuchen Liu, Yue Liu, Wenjie Du, Zhangyang Gao, Bozhen Hu, Cheng Tan, Hongxin Xiang, Stan Z. Li
NeurIPSW 2024 GeneGench: Systematic Evaluation of Genomic Foundation Models and Beyond Zicheng Liu, Jiahui Li, Lei Xin, Siyuan Li, Chang Yu, Zelin Zang, Cheng Tan, Yufei Huang, Yajingbai, Jun Xia, Stan Z. Li
CVPR 2024 General Point Model Pretraining with Autoencoding and Autoregressive Zhe Li, Zhangyang Gao, Cheng Tan, Bocheng Ren, Laurence T. Yang, Stan Z. Li
ECML-PKDD 2024 Interpretable and Generalizable Spatiotemporal Predictive Learning with Disentangled Consistency Jingxuan Wei, Cheng Tan, Zhangyang Gao, Linzhuang Sun, Bihui Yu, Ruifeng Guo, Stan Z. Li
ICLR 2024 KW-Design: Pushing the Limit of Protein Design via Knowledge Refinement Zhangyang Gao, Cheng Tan, Xingran Chen, Yijie Zhang, Jun Xia, Siyuan Li, Stan Z. Li
NeurIPS 2024 Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure Bozhen Hu, Cheng Tan, Jun Xia, Yue Liu, Lirong Wu, Jiangbin Zheng, Yongjie Xu, Yufei Huang, 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, Stan Z. Li
ICLR 2024 MogaNet: Multi-Order Gated Aggregation Network Siyuan Li, Zedong Wang, Zicheng Liu, Cheng Tan, Haitao Lin, Di Wu, Zhiyuan Chen, Jiangbin Zheng, Stan Z. Li
NeurIPS 2024 NN4SysBench: Characterizing Neural Network Verification for Computer Systems Shuyi Lin, Haoyu He, Tianhao Wei, Kaidi Xu, Huan Zhang, Gagandeep Singh, Changliu Liu, Cheng Tan
AAAI 2024 PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction Lirong Wu, Yufei Huang, Cheng Tan, Zhangyang Gao, Bozhen Hu, Haitao Lin, Zicheng Liu, Stan Z. Li
NeurIPS 2024 ProtGO: Function-Guided Protein Modeling for Unified Representation Learning Bozhen Hu, Cheng Tan, Yongjie Xu, Zhangyang Gao, Jun Xia, Lirong Wu, Stan Z. Li
ICLR 2024 RDesign: Hierarchical Data-Efficient Representation Learning for Tertiary Structure-Based RNA Design Cheng Tan, Yijie Zhang, Zhangyang Gao, Bozhen Hu, Siyuan Li, Zicheng Liu, Stan Z. Li
ICML 2024 Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge Yufei Huang, Odin Zhang, Lirong Wu, Cheng Tan, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan Z. Li
ICLR 2024 SemiReward: A General Reward Model for Semi-Supervised Learning Siyuan Li, Weiyang Jin, Zedong Wang, Fang Wu, Zicheng Liu, Cheng Tan, Stan Z. Li
NeurIPS 2024 UniIF: Unified Molecule Inverse Folding Zhangyang Gao, Jue Wang, Cheng Tan, Lirong Wu, Yufei Huang, Siyuan Li, Zhirui Ye, Stan Z. Li
ICML 2024 VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling Siyuan Li, Zedong Wang, Zicheng Liu, Di Wu, Cheng Tan, Jiangbin Zheng, Yufei Huang, Stan Z. Li
AAAI 2024 Wavelet-Driven Spatiotemporal Predictive Learning: Bridging Frequency and Time Variations Xuesong Nie, Yunfeng Yan, Siyuan Li, Cheng Tan, Xi Chen, Haoyuan Jin, Zhihang Zhu, Stan Z. Li, Donglian Qi
CVPR 2023 CVT-SLR: Contrastive Visual-Textual Transformation for Sign Language Recognition with Variational Alignment Jiangbin Zheng, Yile Wang, Cheng Tan, Siyuan Li, Ge Wang, Jun Xia, Yidong Chen, Stan Z. Li
ECML-PKDD 2023 Co-Supervised Pre-Training of Pocket and Ligand Zhangyang Gao, Cheng Tan, Jun Xia, Stan Z. Li
NeurIPS 2023 Harnessing Hard Mixed Samples with Decoupled Regularizer Zicheng Liu, Siyuan Li, Ge Wang, Lirong Wu, Cheng Tan, Stan Z. Li
ECML-PKDD 2023 Learning to Augment Graph Structure for Both Homophily and Heterophily Graphs Lirong Wu, Cheng Tan, Zihan Liu, Zhangyang Gao, Haitao Lin, Stan Z. Li
ICLR 2023 Mole-BERT: Rethinking Pre-Training Graph Neural Networks for Molecules Jun Xia, Chengshuai Zhao, Bozhen Hu, Zhangyang Gao, Cheng Tan, Yue Liu, Siyuan Li, Stan Z. Li
NeurIPS 2023 OpenSTL: A Comprehensive Benchmark of Spatio-Temporal Predictive Learning Cheng Tan, Siyuan Li, Zhangyang Gao, Wenfei Guan, Zedong Wang, Zicheng Liu, Lirong Wu, Stan Z. Li
ICLR 2023 Personalized Reward Learning with Interaction-Grounded Learning (IGL) Jessica Maghakian, Paul Mineiro, Kishan Panaganti, Mark Rucker, Akanksha Saran, Cheng Tan
ICLR 2023 PiFold: Toward Effective and Efficient Protein Inverse Folding Zhangyang Gao, Cheng Tan, Stan Z. Li
NeurIPS 2023 ProteinInvBench: Benchmarking Protein Inverse Folding on Diverse Tasks, Models, and Metrics Zhangyang Gao, Cheng Tan, Yijie Zhang, Xingran Chen, Lirong Wu, Stan Z. Li
ECML-PKDD 2023 Target-Aware Molecular Graph Generation Cheng Tan, Zhangyang Gao, Stan Z. Li
CVPR 2023 Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning Cheng Tan, Zhangyang Gao, Lirong Wu, Yongjie Xu, Jun Xia, Siyuan Li, Stan Z. Li
NeurIPS 2023 Understanding the Limitations of Deep Models for Molecular Property Prediction: Insights and Solutions Jun Xia, Lecheng Zhang, Xiao Zhu, Yue Liu, Zhangyang Gao, Bozhen Hu, Cheng Tan, Jiangbin Zheng, Siyuan Li, Stan Z. Li
ECML-PKDD 2022 GraphMixup: Improving Class-Imbalanced Node Classification by Reinforcement Mixup and Self-Supervised Context Prediction Lirong Wu, Jun Xia, Zhangyang Gao, Haitao Lin, Cheng Tan, Stan Z. Li
CVPR 2022 Hyperspherical Consistency Regularization Cheng Tan, Zhangyang Gao, Lirong Wu, Siyuan Li, Stan Z. Li
CVPR 2022 SimVP: Simpler yet Better Video Prediction Zhangyang Gao, Cheng Tan, Lirong Wu, Stan Z. Li
ICMLW 2022 Target-Aware Molecular Graph Generation Cheng Tan, Zhangyang Gao, Stan Z. Li