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*: Corresponding Author.
†: Equal Contribution.
ICLR 2025
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
Haitao Lin†, Guojiang Zhao†, Odin Zhang, Yufei Huang, Lirong Wu, Zicheng Liu, Cheng Tan, Zhifeng Gao, Stan Z. Li*→
MeToken: Uniform Microenvironment Token Boosts Post-Translational Modification Prediction
Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Lirong Wu, Siyuan Li, Yufei Huang, JunXia, Bozhen Hu, Stan Z. Li*
EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow
Yufei Huang , Yunshu Liu ,Lirong Wu , Haitao Lin , ChengTan , Odin Zhang , ZhangyangGao , Siyuan Li , Zicheng Liu ,Yunfan Liu , Tailin Wu , Stan Z.Li*
Bridging the Gap between Database Search and \emph{De Novo} Peptide Sequencing with SearchNovo
Jun Xia, Sizhe Liu, Jingbo Zhou, Shaorong Chen, hongxin xiang, Zicheng Liu, Yue Liu, Stan Z. Li*
A Simple yet Effective ΔΔ𝐺Predictor is An Unsupervised Antibody Optimizer and Explainer
Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Guojiang Zhao, Zhifeng Gao, Stan Z. Li*
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*
CVPR 2024 (CCF-A)
General Point Model Pretraining with Autoencoding and Autoregressive
Zhe Li†, Zhangyang Gao†, Cheng Tan†, Bocheng Ren, Laurence T.Yang*,Stan Z. Li*
NeurIPS 2024 (CCF-A)
Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptive Residual Module
Jingbo Zhou, Yixuan Du, Ruqiong Zhang, Jun Xia, Zhizhi Yu, Zelin Zang, Di Jin, Carl Yang, Rui Zhang, Stan Z. Li*
NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics
Jingbo Zhou, Shaorong Chen, Jun Xia, Sizhe Liu, Tianze Ling, Wenjie Du, Yue Liu, Jianwei Yin, Stan Z. Li*
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*
AdaNovo:Towards Robust 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*
ProtGO: Function-Guided Protein Modeling for Unified Representation Learning
Bozhen Hu, Cheng Tan, Yongjie Xu, Zhangyang Gao, Jun Xia, Lirong Wu, Stan Z. Li*
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*
PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation
ChenRui Duan, Zelin Zang, Siyuan Li, Yongjie Xu, Stan Z. Li*
UniIF: Unified molecule inverse folding
Zhangyang Gao, Jue Wang, Cheng Tan, Lirong Wu, Yufei Huang, Siyuan Li, Zhirui Ye, Stan Z. Li*
ICML 2024 (CCF-A)
DiffAug: Enhance Unsupervised Contrastive Learning with Domain-Knowledge-Free Diffusion-based Data Augmentation
Zelin Zang, Hao Luo, Kai Wang, Panpan Zhang, Fan Wang, Stan.Z Li*, Yang You
Short-Long Convolutions Help Hardware-Efficient Linear Attention to Focus on Long Sequences
Zicheng Liu, Siyuan Li, Li Wang, Zedong Wang, Yunfan Liu, Stan Z. Li*
A Graph is Worth K words: Euclideanizing Graph using Pure Transformer
Zhangyang Gao, Daize Dong, Cheng Tan, Jun Xia, Bozhen Hu, Stan Z. Li*
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*
PPFlow: Target-aware Peptide Design with Torsional Flow Matching
Haitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang, Lirong Wu, Zicheng Liu, Yufei Huang, Stan Z. Li*
GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation
Haitao Lin, Lirong Wu, Yufei Huang, Yunfan Liu, Odin Zhang, Yuanqing Zhou, Rui Sun, Stan Z. Li*
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*
Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning
Lirong Wu, Yijun Tian, Haitao Lin, Yufei Huang, Siyuan Li, Nitesh V Chawla, Stan Z. Li*
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*
VQMAE: Surface-VQMAE: Vector-quantized Masked Auto-encoders on Molecular Surfaces
Fang Wu, Stan Z. Li*
ICLR 2024 (CCF-A)
MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
Lirong Wu, Yijun Tian, Yufei Huang, Siyuan Li, Haitao Lin, Nitesh V Chawla, Stan Z. Li*
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*
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*
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*
SemiReward: A General Reward Model for Semi-supervised Learning
Siyuan Li, Weiyang Jin, Zedong Wang, Fang Wu, Zicheng Liu, Cheng Tan, Stan Z. Li*
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*
CVPR 2023 (CCF-A)
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*
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 (CCF-A)
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*
Why Deep Models Often cannot Beat Non-deep Counterparts on Molecular Property Prediction?
Jun Xia, Lecheng Zhang, Xiao Zhu, Stan Z.Li*
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration
Haitao Lin, Yufei Huang, Odin Zhang, Lirong Wu, Siyuan Li, Zhiyuan Chen, Stan Z. Li*
ProteinInvBench: Benchmarking Protein Inverse Folding on Diverse Tasks, Models, and Metrics
Zhangyang Gao, Cheng Tan, Yijie Zhang, Xingran Chen, Lirong Wu, Stan Z. Li*
Harnessing Hard Mixed Samples with Decoupled Regularizer
Zicheng Liu, Siyuan Li, Ge Wang, Cheng Tan, Lirong Wu, Stan Z. Li*
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design
Fang Wu, Stan Z. Li*
ICLR 2023 (CCF-A)
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*
PiFold: Toward effective and efficient protein inverse folding
Zhangyang Gao, Cheng Tan, Pablo Chacón, Stan Z. Li*
NSCL: Noise-Resistant Soft Contrastive Learning for Universal Domain Adaptation
Zelin Zang, Lei Shang, Senqiao Yang, Baigui Sun, Xuansong Xie, Stan Z. Li*
ICML 2023 (CCF-A)
NSCL: Noise-Resistant Soft Contrastive Learning for Universal Domain Adaptation
Fang Wu, Siyuan Li, Xurui Jin, Yinghui Jiang, Dragomir Radev, Zhangming Niu, Stan Z. Li*
Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs
Lirong Wu, Haitao Lin, Yufei Huang, Stan Z. Li*
Dink-Net: Neural Clustering on Large Graphs
Yue Liu, Ke Liang, Jun Xia, Sihang Zhou, Xihong Yang, Xinwang Liu, Stan Z. Li*
Architecture-Agnostic Masked Image Modeling -- From ViT back to CNN
Siyuan Li, Di Wu, Fang Wu, Zelin Zang, Stan.Z.Li*
ICCV 2023 (CCF-A)
Boosting Novel Category Discovery Over Domains with Soft Contrastive Learning and All-in-One Classifier
Zelin Zang, Lei Shang, Senqiao Yang, Fei Wang, Baigui Sun, Xuansong Xie, Stan Z. Li*
CVPR 2022 (CCF-A)
CVPR2022 | 不需要RNN结构就能做好视频预测的SimVP
Hyperspherical Consistency Regularization
Cheng Tan, Zhangyang Gao, Lirong Wu, Siyuan Li, Stan Z. Li*
SimVP: Simpler yet Better Video Prediction
Zhangyang Gao, Cheng Tan, Lirong Wu, Stan Z. Li*
NeurIPS 2022 (CCF-A)
Knowledge Distillation Improves Graph Structure Augmentation for Graph Neural Networks
Lirong Wu, Haitao Lin, Yufei Huang, Stan Z. Li*
Towards Reasonable Budget Allocation in Untargeted Graph Structure Attacks via Gradient Debias
Zihan Liu, Yun Luo, Lirong Wu, Zicheng Liu, Stan Z. Li*
ICML 2022 (CCF-A)
Pre-training Graph Neural Networks for Molecular Representations: Retrospect and Prospect
Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li*
专利
1.基于数据非依赖采集质谱的分子组学数据结构的实现方法：郭天南,栾钟治,李子青,张芳菲,禹韶阳,臧泽林。专利号：ZL 2020 10144110.0 授权日：2020.11.17
2.生物组学数据分析系统：臧泽林 夏翰宸 耿雨岚 徐永杰 李子青。专利号：ZL 2022 10730991.3 授权日：2023.4.14
3.一种可解释的神经网络高维数据降维分析系统：臧泽林 夏翰宸 李子青。专利号：ZL 2022 11110651.7 授权日： 2024.3.26
4.基于流形学习的数据嵌入方法：臧泽林;徐永杰;李子青。专利号：ZL 2021 1 1014241.8 授权日：2024.3.15
5.基于深度流形变换网络的高维数据处理方法：李子青,吴立荣,臧泽林。申请号：202110315106.0
6.一种基于图流形学习的文献关系发现方法及系统：臧泽林 李子青。申请号：202211570190.1
7.基于深度流形学习的生物数据可视化和批次矫正系统：徐永杰 臧泽林 耿雨岚 李子青。申请号：202211489015 .X
8.一种用于血液中心的用血量预测方法及预测系统：臧泽林 马思骐 潘凌凌 夏翰宸 李子青。申请号：202211534022.7
9.一种一体化域适应图像分类方法：臧泽林，杨森乔，商磊，李子青。申请号：202310335371.4
10.基于深度流形学习的多模态组学数据的多任务表征处理方法、装置及存储介质：臧泽林,李梁玉,徐永杰,李子青。申请号：2024101258989
11.基于功能驱动和预训练的宏基因功能预测方法、装置及存储介质：段晨瑞,臧泽林,徐永杰,贺航,李子青。申请号：202410678198.2
12.一种基于生物大语言模型的发育树推断方法、装置及介质：段晨瑞,臧泽林,李思远,徐永杰,李子青。申请号：2024115282998