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李子青
Person information
- unicode name: 李子青
- affiliation: Chinese Academy of Sciences, Institute of Automation, Beijing, China
- affiliation (2000 - 2004): Microsoft Research Asia, Beijing, China
- affiliation (former): Nanyang Technological University, Singapore
- affiliation (PhD): University of Surrey, Guilford, UK
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2020 – today
- 2025
[j142]Cheng Tan, Yijie Zhang
, Zhangyang Gao, Hanqun Cao, Siyuan Li, Siqi Ma, Mathieu Blanchette, Stan Z. Li:
R3Design: deep tertiary structure-based RNA sequence design and beyond. Briefings Bioinform. 26(1) (2025)- [j141]Yongjie Xu, Zelin Zang, Bozhen Hu, Yue Yuan, Cheng Tan, Jun Xia, Stan Z. Li:
Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation. Briefings Bioinform. 26(1) (2025) - [j140]Chenrui Duan, Zelin Zang, Yongjie Xu, Hang He, Siyuan Li, Zihan Liu, Zhen Lei, Ju-Sheng Zheng, Stan Z. Li:
FGeneBERT: function-driven pre-trained gene language model for metagenomics. Briefings Bioinform. 26(6) (2025) - [j139]Zelin Zang, Yongjie Xu, Chenrui Duan, Yue Yuan, Yue Shen, Jinlin Wu, Zhen Lei, Stan Z. Li:
A Review of BioTree Construction in the Context of Information Fusion: Priors, Methods, Applications and Trends. Inf. Fusion 121: 103108 (2025) - [j138]Tianyi Huang, Zhengjun Zhang, Xin Yuan, Stan Z. Li, Neal Naixue Xiong, Shenghui Cheng:
X-clustering beyond contextual representations. Inf. Sci. 717: 122291 (2025) - [j137]Cheng Tan, Jue Wang, Zhangyang Gao, Siyuan Li, Stan Z. Li:
USTEP: Spatio-Temporal Predictive Learning Under a Unified View. IEEE Trans. Pattern Anal. Mach. Intell. 47(8): 7064-7080 (2025) - [j136]Haitao Lin, Cheng Tan, Lirong Wu, Zicheng Liu, Zhangyang Gao, Stan Z. Li:
An Extensive Survey With Empirical Studies on Deep Temporal Point Process. IEEE Trans. Knowl. Data Eng. 37(4): 1599-1619 (2025) - [j135]Fang Wu, Stan Z. Li:
Dynamics-inspired Structure Hallucination for Protein-protein Interaction Modeling. Trans. Mach. Learn. Res. 2025 (2025) - [j134]Zelin Zang, Chenrui Duan, Siyuan Li, Jinlin Wu, BingoWing-Kuen Ling, Fuji Yang, Jiebo Luo, Zhen Lei, Stan Z. Li:
MDTree: A Masked Dynamic Autoregressive Model for Phylogenetic Inference. Trans. Mach. Learn. Res. 2025 (2025) - [j133]Hao Tan, Zichang Tan, Dunfang Weng, Ajian Liu, Jun Wan, Zhen Lei, Stan Z. Li:
Vision Transformer With Relation Exploration for Pedestrian Attribute Recognition. IEEE Trans. Multim. 27: 198-208 (2025) - [j132]Cheng Tan, Zhangyang Gao, Siyuan Li, Stan Z. Li:
SimVPv2: Towards Simple Yet Powerful Spatiotemporal Predictive Learning. IEEE Trans. Multim. 27: 5170-5184 (2025) - [j131]Siyuan Li, Zicheng Liu, Zelin Zang, Di Wu, Zhiyuan Chen, Stan Z. Li:
GenURL: A General Framework for Unsupervised Representation Learning. IEEE Trans. Neural Networks Learn. Syst. 36(1): 286-298 (2025) - [j130]Lirong Wu, Haitao Lin, Guojiang Zhao, Cheng Tan, Stan Z. Li:
Learning to Model Graph Structural Information on MLPs via Graph Structure Self-Contrasting. IEEE Trans. Neural Networks Learn. Syst. 36(7): 12772-12783 (2025) - [c378]Zhangyang Gao, Cheng Tan, Jue Wang, Yufei Huang, Lirong Wu, Stan Z. Li:
FoldToken: Learning Protein Language via Vector Quantization and Beyond. AAAI 2025: 219-227 - [c377]Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li:
dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. AAAI 2025: 782-790 - [c376]Fang Wu, Bozhen Hu, Stan Z. Li:
Generalized Implicit Neural Representations for Dynamic Molecular Surface Modeling. AAAI 2025: 877-885 - [c375]Lirong Wu, Haitao Lin, Yufei Huang, Zhangyang Gao, Cheng Tan, Yunfan Liu, Tailin Wu, Stan Z. Li:
Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization. AAAI 2025: 895-904 - [c374]Jiangbin Zheng, Ge Wang, Han Zhang, Stan Z. Li:
Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design. ICASSP 2025: 1-5 - [c373]Jiangbin Zheng, Qianhui Xu, Ruichen Xia, Stan Z. Li:
DapPep: Domain Adaptive Peptide-agnostic Learning for Universal T-cell Receptor-antigen Binding Affinity Prediction. ICASSP 2025: 1-5 - [c372]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:
EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow. ICLR 2025 - [c371]Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Lirong Wu, Siyuan Li, Yufei Huang, Jun Xia, Bozhen Hu, Stan Z. Li:
MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction. ICLR 2025 - [c370]Shaorong Chen, Jun Xia, Jingbo Zhou, Lecheng Zhang, Zhangyang Gao, Bozhen Hu, Cheng Tan, Wenjie Du, Stan Z. Li:
ReNovo: Retrieval-Based \emph{De Novo} Mass Spectrometry Peptide Sequencing. ICLR 2025 - [c369]Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Cheng Tan, Zicheng Liu, Zhifeng Gao, Stan Z. Li:
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. ICLR 2025 - [c368]Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Guojiang Zhao, Zhifeng Gao, Stan Z. Li:
A Simple yet Effective ΔΔG Predictor is An Unsupervised Antibody Optimizer and Explainer. ICLR 2025 - [c367]Jun Xia, Sizhe Liu, Jingbo Zhou, Shaorong Chen, Hongxin Xiang, Zicheng Liu, Yue Liu, Stan Z. Li:
Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo. ICLR 2025 - [c366]Cheng Tan, Qi Chen, Jingxuan Wei, Gaowei Wu, Zhangyang Gao, Siyuan Li, Bihui Yu, Ruifeng Guo, Stan Z. Li:
SketchAgent: Generating Structured Diagrams from Hand-Drawn Sketches. IJCAI 2025: 1918-1926 - [c365]Changxi Chi, Jun Xia, Jingbo Zhou, Jiabei Cheng, Chang Yu, Stan Z. Li:
GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype. IJCAI 2025: 4949-4957 - [c364]Jun Xia, Jingbo Zhou, Shaorong Chen, Tianze Ling, Stan Z. Li:
A Comprehensive and Systematic Review for Deep Learning-Based De Novo Peptide Sequencing. IJCAI 2025: 10733-10741 - [i224]Lirong Wu, Haitao Lin, Yufei Huang, Zhangyang Gao, Cheng Tan, Yunfan Liu, Tailin Wu, Stan Z. Li:
Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization. CoRR abs/2501.00013 (2025) - [i223]Mengdi Liu, Zhangyang Gao, Hong Chang, Stan Z. Li, Shiguang Shan, Xilin Chen:
G2PDiffusion: Genotype-to-Phenotype Prediction with Diffusion Models. CoRR abs/2502.04684 (2025) - [i222]Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Guojiang Zhao, Zhifeng Gao, Stan Z. Li:
A Simple yet Effective DDG Predictor is An Unsupervised Antibody Optimizer and Explainer. CoRR abs/2502.06913 (2025) - [i221]Zicheng Liu, Siyuan Li, Zhiyuan Chen, Lei Xin, Fang Wu, Chang Yu, Qirong Yang, Yucheng Guo, Yujie Yang, Stan Z. Li:
Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification. CoRR abs/2502.07299 (2025) - [i220]Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li:
dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. CoRR abs/2503.01910 (2025) - [i219]Yuang Jia, Xiaojuan Shan, Jun Xia, Guancheng Wan, Yuchen Zhang, Wenke Huang, Mang Ye, Stan Z. Li:
Adversarial Curriculum Graph-Free Knowledge Distillation for Graph Neural Networks. CoRR abs/2504.00540 (2025) - [i218]Changxi Chi, Jun Xia, Jingbo Zhou, Jiabei Cheng, Chang Yu, Stan Z. Li:
GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype. CoRR abs/2505.03853 (2025) - [i217]Haitao Lin, Odin Zhang, Jia Xu, Yunfan Liu, Zheng Chen, Lirong Wu, Yufei Huang, Zhifeng Gao, Stan Z. Li:
Tokenizing Electron Cloud in Protein-Ligand Interaction Learning. CoRR abs/2505.19014 (2025) - [i216]Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Siyuan Li, Yufei Huang, Stan Z. Li:
AlphaFold Database Debiasing for Robust Inverse Folding. CoRR abs/2506.08365 (2025) - [i215]Zhangyang Gao, Hao Wang, Cheng Tan, Chenrui Xu, Mengdi Liu, Bozhen Hu, Linlin Chao, Xiaoming Zhang, Stan Z. Li:
PFMBench: Protein Foundation Model Benchmark. CoRR abs/2506.14796 (2025) - [i214]Changxi Chi, Jun Xia, Yufei Huang, Jingbo Zhou, Siyuan Li, Yunfan Liu, Chang Yu, Stan Z. Li:
Unlasting: Unpaired Single-Cell Multi-Perturbation Estimation by Dual Conditional Diffusion Implicit Bridges. CoRR abs/2506.21107 (2025) - [i213]Zelin Zang, WenZhe Li, Fei Chen, Yongjie Xu, Chang Yu, Zhen Lei, Stan Z. Li:
Hierarchical Quantized Diffusion Based Tree Generation Method for Hierarchical Representation and Lineage Analysis. CoRR abs/2506.23287 (2025) - [i212]Xinzhe Zheng, Hao Du, Fanding Xu, Jinzhe Li, Zhiyuan Liu, Wenkang Wang, Tao Chen, Wanli Ouyang, Stan Z. Li, Yan Lu, Nanqing Dong, Yang Zhang:
PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs. CoRR abs/2507.05101 (2025) - [i211]Qirong Yang, Yucheng Guo, Zicheng Liu, Yujie Yang, Qijin Yin, Siyuan Li, Shaomin Ji, Linlin Chao, Xiaoming Zhang, Stan Z. Li:
TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling. CoRR abs/2507.19229 (2025) - [i210]Cheng Tan, Qi Chen, Jingxuan Wei, Gaowei Wu, Zhangyang Gao, Siyuan Li, Bihui Yu, Ruifeng Guo, Stan Z. Li:
SketchAgent: Generating Structured Diagrams from Hand-Drawn Sketches. CoRR abs/2508.01237 (2025) - [i209]Bozhen Hu, Cheng Tan, Siyuan Li, Jiangbin Zheng, Sizhe Qiu, Jun Xia, Stan Z. Li:
Multimodal Regression for Enzyme Turnover Rates Prediction. CoRR abs/2509.11782 (2025) - [i208]Changxi Chi, Yufei Huang, Jun Xia, Jiangbin Zheng, Yunfan Liu, Zelin Zang, Stan Z. Li:
Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges. CoRR abs/2511.13124 (2025) - [i207]Siyuan Li, Kai Yu, Anna Wang, Zicheng Liu, Chang Yu, Jingbo Zhou, Qirong Yang, Yucheng Guo, Xiaoming Zhang, Stan Z. Li:
MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging. CoRR abs/2511.14806 (2025) - [i206]Mengran Li, Zelin Zang, Wenbin Xing, Junzhou Chen, Ronghui Zhang, Jiebo Luo, Stan Z. Li:
Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling. CoRR abs/2511.21120 (2025) - [i205]Haitao Lin, Peiyan Hu, Minsi Ren, Zhifeng Gao, Zhi-Ming Ma, Guolin ke, Tailin Wu, Stan Z. Li:
On the Design of One-step Diffusion via Shortcutting Flow Paths. CoRR abs/2512.11831 (2025) - 2024
- [j129]Jingxuan Wei, Cheng Tan, Zhangyang Gao, Linzhuang Sun, Siyuan Li, Bihui Yu, Ruifeng Guo, Stan Z. Li:
Enhancing human-like multimodal reasoning: a new challenging dataset and comprehensive framework. Neural Comput. Appl. 36(33): 20849-20861 (2024) - [j128]Hao Fang, Ajian Liu, Jun Wan, Sergio Escalera, Chenxu Zhao, Xu Zhang, Stan Z. Li, Zhen Lei:
Surveillance Face Anti-Spoofing. IEEE Trans. Inf. Forensics Secur. 19: 1535-1546 (2024) - [j127]Jun Xia, Haitao Lin, Yongjie Xu, Cheng Tan, Lirong Wu, Siyuan Li, Stan Z. Li:
GNN Cleaner: Label Cleaner for Graph Structured Data. IEEE Trans. Knowl. Data Eng. 36(2): 640-651 (2024) - [j126]Hanqun Cao, Cheng Tan, Zhangyang Gao, Yilun Xu, Guangyong Chen, Pheng-Ann Heng, Stan Z. Li:
A Survey on Generative Diffusion Models. IEEE Trans. Knowl. Data Eng. 36(7): 2814-2830 (2024) - [j125]Lirong Wu, Haitao Lin, Zhangyang Gao, Guojiang Zhao, Stan Z. Li:
A Teacher-Free Graph Knowledge Distillation Framework With Dual Self-Distillation. IEEE Trans. Knowl. Data Eng. 36(9): 4375-4385 (2024) - [j124]Fang Wu, Siyuan Li, Stan Z. Li:
Discovering the Representation Bottleneck of Graph Neural Networks. IEEE Trans. Knowl. Data Eng. 36(12): 7998-8008 (2024) - [j123]Lirong Wu, Haitao Lin, Bozhen Hu, Cheng Tan, Zhangyang Gao, Zicheng Liu, Stan Z. Li:
Beyond Homophily and Homogeneity Assumption: Relation-Based Frequency Adaptive Graph Neural Networks. IEEE Trans. Neural Networks Learn. Syst. 35(6): 8497-8509 (2024) - [j122]Lirong Wu, Haitao Lin, Zihan Liu, Zicheng Liu, Yufei Huang, Stan Z. Li:
Homophily-Enhanced Self-Supervision for Graph Structure Learning: Insights and Directions. IEEE Trans. Neural Networks Learn. Syst. 35(9): 12358-12372 (2024) - [j121]Zelin Zang, Shenghui Cheng, Hanchen Xia, Liangyu Li, Yaoting Sun, Yongjie Xu, Lei Shang, Baigui Sun, Stan Z. Li:
DMT-EV: An Explainable Deep Network for Dimension Reduction. IEEE Trans. Vis. Comput. Graph. 30(3): 1710-1727 (2024) - [c363]Lirong Wu, Yufei Huang, Cheng Tan, Zhangyang Gao, Bozhen Hu, Haitao Lin, Zicheng Liu, Stan Z. Li:
PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction. AAAI 2024: 310-319 - [c362]Xuesong Nie, Yunfeng Yan, Siyuan Li, Cheng Tan, Xi Chen, Haoyuan Jin, Zhihang Zhu, Stan Z. Li, Donglian Qi:
Wavelet-Driven Spatiotemporal Predictive Learning: Bridging Frequency and Time Variations. AAAI 2024: 4334-4342 - [c361]Yufei Huang, Siyuan Li, Lirong Wu, Jin Su, Haitao Lin, Odin Zhang, Zihan Liu, Zhangyang Gao, Jiangbin Zheng, Stan Z. Li:
Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction. AAAI 2024: 12662-12670 - [c360]Cheng Tan, Zhangyang Gao, Lirong Wu, Jun Xia, Jiangbin Zheng, Xihong Yang, Yue Liu, Bozhen Hu, Stan Z. Li:
Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody Designer. AAAI 2024: 15222-15230 - [c359]Zelin Zang, Liangyu Li, Yongjie Xu, Jiahao Li, Chenrui Duan, Yi Sun, Zhen Lei, Stan Z. Li:
MuST: Maximizing the Latent Capacity of Spatial Transcriptomics Data with Multi-modality Structure Transformation. BIBM 2024: 1321-1326 - [c358]Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Stan Z. Li:
Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation. CIKM 2024: 2554-2563 - [c357]Zhe Li, Laurence T. Yang, Bocheng Ren, Xin Nie, Zhangyang Gao, Cheng Tan, Stan Z. Li:
MLIP: Enhancing Medical Visual Representation with Divergence Encoder and Knowledge-guided Contrastive Learning. CVPR 2024: 11704-11714 - [c356]Zhe Li, Zhangyang Gao, Cheng Tan, Bocheng Ren, Laurence T. Yang, Stan Z. Li:
General Point Model Pretraining with Autoencoding and Autoregressive. CVPR 2024: 20954-20964 - [c355]Cheng Tan, Jingxuan Wei, Zhangyang Gao, Linzhuang Sun, Siyuan Li, Ruifeng Guo, Bihui Yu, Stan Z. Li:
Boosting the Power of Small Multimodal Reasoning Models to Match Larger Models with Self-consistency Training. ECCV (40) 2024: 305-322 - [c354]Fang Wu, Stan Z. Li:
InsertGNN: A Hierarchical Graph Neural Network for the TOEFL Sentence Insertion Problem. EMNLP (Findings) 2024: 173-180 - [c353]Bozhen Hu, Zelin Zang, Cheng Tan, Stan Z. Li:
Deep Manifold Transformation for Protein Representation Learning. ICASSP 2024: 1801-1805 - [c352]Jun Xia, Shaorong Chen, Yue Liu, Zhangyang Gao, Jiangbin Zheng, Xihong Yang, Stan Z. Li:
DiscoGNN: A Sample-Efficient Framework for Self-Supervised Graph Representation Learning. ICDE 2024: 2876-2888 - [c351]Cheng Tan, Yijie Zhang, Zhangyang Gao, Bozhen Hu, Siyuan Li, Zicheng Liu, Stan Z. Li:
RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design. ICLR 2024 - [c350]Tianyu Fan, Lirong Wu, Yufei Huang, Haitao Lin, Cheng Tan, Zhangyang Gao, Stan Z. Li:
Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks. ICLR 2024 - [c349]Zhangyang Gao, Cheng Tan, Xingran Chen, Yijie Zhang, Jun Xia, Siyuan Li, Stan Z. Li:
KW-Design: Pushing the Limit of Protein Design via Knowledge Refinement. ICLR 2024 - [c348]Siyuan Li, Weiyang Jin, Zedong Wang, Fang Wu, Zicheng Liu, Cheng Tan, Stan Z. Li:
SemiReward: A General Reward Model for Semi-supervised Learning. ICLR 2024 - [c347]Siyuan Li, Zedong Wang, Zicheng Liu, Cheng Tan, Haitao Lin, Di Wu, Zhiyuan Chen, Jiangbin Zheng, Stan Z. Li:
MogaNet: Multi-order Gated Aggregation Network. ICLR 2024 - [c346]Lirong Wu, Yijun Tian, Yufei Huang, Siyuan Li, Haitao Lin, Nitesh V. Chawla, Stan Z. Li:
MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding. ICLR 2024 - [c345]Jiangbin Zheng, Stan Z. Li:
Progressive Multi-Modality Learning for Inverse Protein Folding. ICME 2024: 1-6 - [c344]Yufei Huang, Odin Zhang, Lirong Wu, Cheng Tan, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan Z. Li:
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge. ICML 2024 - [c343]Zicheng Liu, Siyuan Li, Li Wang, Zedong Wang, Yunfan Liu, Stan Z. Li:
Short-Long Convolutions Help Hardware-Efficient Linear Attention to Focus on Long Sequences. ICML 2024 - [c342]Cheng Tan, Zhangyang Gao, Hanqun Cao, Xingran Chen, Ge Wang, Lirong Wu, Jun Xia, Jiangbin Zheng, Stan Z. Li:
Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective. ICML 2024 - [c341]Zhangyang Gao, Daize Dong, Cheng Tan, Jun Xia, Bozhen Hu, Stan Z. Li:
A Graph is Worth K Words: Euclideanizing Graph using Pure Transformer. ICML 2024 - [c340]Siyuan Li, Zedong Wang, Zicheng Liu, Di Wu, Cheng Tan, Jiangbin Zheng, Yufei Huang, Stan Z. Li:
VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling. ICML 2024 - [c339]Haitao Lin, Lirong Wu, Yufei Huang, Yunfan Liu, Odin Zhang, Yuanqing Zhou, Rui Sun, Stan Z. Li:
GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation. ICML 2024 - [c338]Haitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang, Lirong Wu, Zicheng Liu, Yufei Huang, Stan Z. Li:
PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching. ICML 2024 - [c337]Lirong Wu, Yijun Tian, Haitao Lin, Yufei Huang, Siyuan Li, Nitesh V. Chawla, Stan Z. Li:
Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning. ICML 2024 - [c336]Fang Wu, Stan Z. Li:
Surface-VQMAE: Vector-quantized Masked Auto-encoders on Molecular Surfaces. ICML 2024 - [c335]Zelin Zang, Hao Luo, Kai Wang, Panpan Zhang, Fan Wang, Stan Z. Li, Yang You:
DiffAug: Enhance Unsupervised Contrastive Learning with Domain-Knowledge-Free Diffusion-based Data Augmentation. ICML 2024 - [c334]Jiangbin Zheng, Stan Z. Li:
CCPL: Cross-Modal Contrastive Protein Learning. ICPR (27) 2024: 22-38 - [c333]Zicheng Liu, Li Wang, Siyuan Li, Zedong Wang, Haitao Lin, Stan Z. Li:
LongVQ: Long Sequence Modeling with Vector Quantization on Structured Memory. IJCAI 2024: 4614-4622 - [c332]Jiangbin Zheng, Han Zhang, Qianqing Xu, An-Ping Zeng, Stan Z. Li:
MetaEnzyme: Meta Pan-Enzyme Learning for Task-Adaptive Redesign. ACM Multimedia 2024: 1721-1730 - [c331]Jun Xia, Shaorong Chen, Jingbo Zhou, Xiaojun Shan, Wenjie Du, Zhangyang Gao, Cheng Tan, Bozhen Hu, Jiangbin Zheng, Stan Z. Li:
AdaNovo: Towards Robust \emph{De Novo} Peptide Sequencing in Proteomics against Data Biases. NeurIPS 2024 - [c330]Fang Wu, Shuting Jin, Siyuan Li, Stan Z. Li:
Instructor-inspired Machine Learning for Robust Molecular Property Prediction. NeurIPS 2024 - [c329]Chenrui Duan, Zelin Zang, Siyuan Li, Yongjie Xu, Stan Z. Li:
PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation. NeurIPS 2024 - [c328]Zhangyang Gao, Jue Wang, Cheng Tan, Lirong Wu, Yufei Huang, Siyuan Li, Zhirui Ye, Stan Z. Li:
UniIF: Unified Molecule Inverse Folding. NeurIPS 2024 - [c327]Bozhen Hu, Cheng Tan, Jun Xia, Yue Liu, Lirong Wu, Jiangbin Zheng, Yongjie Xu, Yufei Huang, Stan Z. Li:
Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure. NeurIPS 2024 - [c326]Bozhen Hu, Cheng Tan, Yongjie Xu, Zhangyang Gao, Jun Xia, Lirong Wu, Stan Z. Li:
ProtGO: Function-Guided Protein Modeling for Unified Representation Learning. NeurIPS 2024 - [c325]Sizhe Liu, Jun Xia, Lecheng Zhang, Yuchen Liu, Yue Liu, Wenjie Du, Zhangyang Gao, Bozhen Hu, Cheng Tan, Hongxin Xiang, Stan Z. Li:
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning. NeurIPS 2024 - [c324]Jingbo Zhou, Shaorong Chen, Jun Xia, Sizhe Liu, Tianze Ling, Wenjie Du, Yue Liu, Jianwei Yin, Stan Z. Li:
NovoBench: Benchmarking Deep Learning-based \emph{De Novo} Sequencing Methods in Proteomics. NeurIPS 2024 - [c323]Jingbo Zhou, Yixuan Du, Ruqiong Zhang, Jun Xia, Zhizhi Yu, Zelin Zang, Di Jin, Carl Yang, Rui Zhang, Stan Z. Li:
Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptative Residual Module. NeurIPS 2024 - [c322]Jingxuan Wei, Cheng Tan, Zhangyang Gao, Linzhuang Sun, Bihui Yu, Ruifeng Guo, Stan Z. Li:
Interpretable and Generalizable Spatiotemporal Predictive Learning with Disentangled Consistency. ECML/PKDD (3) 2024: 3-20 - [i204]Siyuan Li, Luyuan Zhang, Zedong Wang, Di Wu, Lirong Wu, Zicheng Liu, Jun Xia, Cheng Tan, Yang Liu, Baigui Sun, Stan Z. Li:
Masked Modeling for Self-supervised Representation Learning on Vision and Beyond. CoRR abs/2401.00897 (2024) - [i203]Ge Wang, Zelin Zang, Jiangbin Zheng, Jun Xia, Stan Z. Li:
Graph-level Protein Representation Learning by Structure Knowledge Refinement. CoRR abs/2401.02713 (2024) - [i202]Bozhen Hu, Zelin Zang, Jun Xia, Lirong Wu, Cheng Tan, Stan Z. Li:
Deep Manifold Graph Auto-Encoder for Attributed Graph Embedding. CoRR abs/2401.06727 (2024) - [i201]Zelin Zang, Liangyu Li, Yongjie Xu, Chenrui Duan, Kai Wang, Yang You, Yi Sun, Stan Z. Li:
Must: Maximizing Latent Capacity of Spatial Transcriptomics Data. CoRR abs/2401.07543 (2024) - [i200]Zhe Li, Laurence T. Yang, Bocheng Ren, Xin Nie, Zhangyang Gao, Cheng Tan, Stan Z. Li:
MLIP: Enhancing Medical Visual Representation with Divergence Encoder and Knowledge-guided Contrastive Learning. CoRR abs/2402.02045 (2024) - [i199]Zhe Li, Zhangyang Gao, Cheng Tan, Stan Z. Li, Laurence T. Yang:
DCS-Net: Pioneering Leakage-Free Point Cloud Pretraining Framework with Global Insights. CoRR abs/2402.02088 (2024) - [i198]Zhangyang Gao, Daize Dong, Cheng Tan, Jun Xia, Bozhen Hu, Stan Z. Li:
A Graph is Worth K Words: Euclideanizing Graph using Pure Transformer. CoRR abs/2402.02464 (2024) - [i197]Lirong Wu, Yufei Huang, Cheng Tan, Zhangyang Gao, Bozhen Hu, Haitao Lin, Zicheng Liu, Stan Z. Li:
PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction. CoRR abs/2402.08198 (2024) - [i196]Siyuan Li, Zicheng Liu, Juanxi Tian, Ge Wang, Zedong Wang, Weiyang Jin, Di Wu, Cheng Tan, Tao Lin, Yang Liu, Baigui Sun, Stan Z. Li:
Switch EMA: A Free Lunch for Better Flatness and Sharpness. CoRR abs/2402.09240 (2024) - [i195]Bozhen Hu, Zelin Zang, Cheng Tan, Stan Z. Li:
Deep Manifold Transformation for Protein Representation Learning. CoRR abs/2402.09416 (2024) - [i194]Yufei Huang, Odin Zhang, Lirong Wu, Cheng Tan, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan Z. Li:
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge. CoRR abs/2402.11459 (2024) - [i193]Lirong Wu, Yijun Tian, Yufei Huang, Siyuan Li, Haitao Lin, Nitesh V. Chawla, Stan Z. Li:
MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding. CoRR abs/2402.14391 (2024) - [i192]Chenrui Duan, Zelin Zang, Yongjie Xu, Hang He, Zihan Liu, Zijia Song, Ju-Sheng Zheng, Stan Z. Li:
FGBERT: Function-Driven Pre-trained Gene Language Model for Metagenomics. CoRR abs/2402.16901 (2024) - [i191]Rui Sun, Lirong Wu, Haitao Lin, Yufei Huang, Stan Z. Li:
Enhancing Protein Predictive Models via Proteins Data Augmentation: A Benchmark and New Directions. CoRR abs/2403.00875 (2024) - [i190]Tianyu Fan, Lirong Wu, Yufei Huang, Haitao Lin, Cheng Tan, Zhangyang Gao, Stan Z. Li:
Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks. CoRR abs/2403.01400 (2024) - [i189]Lirong Wu, Haitao Lin, Zhangyang Gao, Guojiang Zhao, Stan Z. Li:
A Teacher-Free Graph Knowledge Distillation Framework with Dual Self-Distillation. CoRR abs/2403.03483 (2024) - [i188]Jun Xia, Shaorong Chen, Jingbo Zhou, Tianze Ling, Wenjie Du, Sizhe Liu, Stan Z. Li:
AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information. CoRR abs/2403.07013 (2024) - [i187]Zhangyang Gao, Cheng Tan, Jue Wang, Yufei Huang, Lirong Wu, Stan Z. Li:
FoldToken: Learning Protein Language via Vector Quantization and Beyond. CoRR abs/2403.09673 (2024) - [i186]Zicheng Liu, Li Wang, Siyuan Li, Zedong Wang, Haitao Lin, Stan Z. Li:
LongVQ: Long Sequence Modeling with Vector Quantization on Structured Memory. CoRR abs/2404.11163 (2024) - [i185]Haitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang, Lirong Wu, Zicheng Liu, Yufei Huang, Stan Z. Li:
PPFlow: Target-aware Peptide Design with Torsional Flow Matching. CoRR abs/2405.06642 (2024) - [i184]Lirong Wu, Yijun Tian, Haitao Lin, Yufei Huang, Siyuan Li, Nitesh V. Chawla, Stan Z. Li:
Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning. CoRR abs/2405.10348 (2024) - [i183]Siyuan Li, Zedong Wang, Zicheng Liu, Di Wu, Cheng Tan, Jiangbin Zheng, Yufei Huang, Stan Z. Li:
VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling. CoRR abs/2405.10812 (2024) - [i182]Zhangyang Gao, Jue Wang, Cheng Tan, Lirong Wu, Yufei Huang, Siyuan Li, Zhirui Ye, Stan Z. Li:
UniIF: Unified Molecule Inverse Folding. CoRR abs/2405.18968 (2024) - [i181]Cheng Tan, Jingxuan Wei, Linzhuang Sun, Zhangyang Gao, Siyuan Li, Bihui Yu, Ruifeng Guo, Stan Z. Li:
Retrieval Meets Reasoning: Even High-school Textbook Knowledge Benefits Multimodal Reasoning. CoRR abs/2405.20834 (2024) - [i180]Zicheng Liu, Jiahui Li, Siyuan Li, Zelin Zang, Cheng Tan, Yufei Huang, Yajing Bai, Stan Z. Li:
GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models. CoRR abs/2406.01627 (2024) - [i179]Cheng Tan, Dongxin Lyu, Siyuan Li, Zhangyang Gao, Jingxuan Wei, Siqi Ma, Zicheng Liu, Stan Z. Li:
Peer Review as A Multi-Turn and Long-Context Dialogue with Role-Based Interactions. CoRR abs/2406.05688 (2024) - [i178]Zijia Song, Zelin Zang, Yelin Wang, Guozheng Yang, Jiangbin Zheng, Kaicheng yu, Wanyu Chen, Stan Z. Li:
Gentle-CLIP: Exploring Aligned Semantic In Low-Quality Multimodal Data With Soft Alignment. CoRR abs/2406.05766 (2024) - [i177]Zicheng Liu, Siyuan Li, Li Wang, Zedong Wang, Yunfan Liu, Stan Z. Li:
Short-Long Convolutions Help Hardware-Efficient Linear Attention to Focus on Long Sequences. CoRR abs/2406.08128 (2024) - [i176]Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Zicheng Liu, Siyuan Li, Cheng Tan, Zhifeng Gao, Stan Z. Li:
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. CoRR abs/2406.10840 (2024) - [i175]Jingbo Zhou, Shaorong Chen, Jun Xia, Sizhe Liu, Tianze Ling, Wenjie Du, Yue Liu, Jianwei Yin, Stan Z. Li:
NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics. CoRR abs/2406.11906 (2024) - [i174]Zhangyang Gao, Cheng Tan, Stan Z. Li:
FoldToken2: Learning compact, invariant and generative protein structure language. CoRR abs/2407.00050 (2024) - [i173]Xinna Lin, Siqi Ma, Junjie Shan, Xiaojing Zhang, Shell Xu Hu, Tiannan Guo, Stan Z. Li, Kaicheng Yu:
BioKGBench: A Knowledge Graph Checking Benchmark of AI Agent for Biomedical Science. CoRR abs/2407.00466 (2024) - [i172]Sitao Luan, Chenqing Hua, Qincheng Lu, Liheng Ma, Lirong Wu, Xinyu Wang, Minkai Xu, Xiao-Wen Chang, Doina Precup, Rex Ying, Stan Z. Li, Jian Tang, Guy Wolf, Stefanie Jegelka:
The Heterophilic Graph Learning Handbook: Benchmarks, Models, Theoretical Analysis, Applications and Challenges. CoRR abs/2407.09618 (2024) - [i171]Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Stan Z. Li:
Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation. CoRR abs/2407.14768 (2024) - [i170]Hao Tan, Zichang Tan, Jun Li, Jun Wan, Zhen Lei, Stan Z. Li:
SSPA: Split-and-Synthesize Prompting with Gated Alignments for Multi-Label Image Recognition. CoRR abs/2407.20920 (2024) - [i169]Jiangbin Zheng, Han Zhang, Qianqing Xu, An-Ping Zeng, Stan Z. Li:
MetaEnzyme: Meta Pan-Enzyme Learning for Task-Adaptive Redesign. CoRR abs/2408.10247 (2024) - [i168]Xin Jin, Hongyu Zhu, Siyuan Li, Zedong Wang, Zicheng Liu, Chang Yu, Huafeng Qin, Stan Z. Li:
A Survey on Mixup Augmentations and Beyond. CoRR abs/2409.05202 (2024) - [i167]Lirong Wu, Haitao Lin, Guojiang Zhao, Cheng Tan, Stan Z. Li:
Learning to Model Graph Structural Information on MLPs via Graph Structure Self-Contrasting. CoRR abs/2409.05573 (2024) - [i166]Zelin Zang, Yongjie Xu, Chenrui Duan, Jinlin Wu, Stan Z. Li, Zhen Lei:
A Review of Artificial Intelligence based Biological-Tree Construction: Priorities, Methods, Applications and Trends. CoRR abs/2410.04815 (2024) - [i165]Siyuan Li, Juanxi Tian, Zedong Wang, Luyuan Zhang, Zicheng Liu, Weiyang Jin, Yang Liu, Baigui Sun, Stan Z. Li:
Unveiling the Backbone-Optimizer Coupling Bias in Visual Representation Learning. CoRR abs/2410.06373 (2024) - [i164]Sizhe Liu, Jun Xia, Lecheng Zhang, Yuchen Liu, Yue Liu, Wenjie Du, Zhangyang Gao, Bozhen Hu, Cheng Tan, Hongxin Xiang, Stan Z. Li:
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning. CoRR abs/2410.15010 (2024) - [i163]Zelin Zang, Yuhao Wang, Jinlin Wu, Hong Liu, Yue Shen, Stan Z. Li, Zhen Lei:
DMT-HI: MOE-based Hyperbolic Interpretable Deep Manifold Transformation for Unspervised Dimensionality Reduction. CoRR abs/2410.19504 (2024) - [i162]Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Lirong Wu, Siyuan Li, Yufei Huang, Jun Xia, Bozhen Hu, Stan Z. Li:
MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction. CoRR abs/2411.01856 (2024) - [i161]Yang Hu, Xiao Wang, Lirong Wu, Huatian Zhang, Stan Z. Li, Sheng Wang, Tianlong Chen:
FM-TS: Flow Matching for Time Series Generation. CoRR abs/2411.07506 (2024) - [i160]Xiangyu Zhu, Chang Yu, Jiankuo Zhao, Zhaoxiang Zhang, Stan Z. Li, Zhen Lei:
Revisiting Marr in Face: The Building of 2D-2.5D-3D Representations in Deep Neural Networks. CoRR abs/2411.16148 (2024) - [i159]Jiangbin Zheng, Ge Wang, Han Zhang, Stan Z. Li:
Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design. CoRR abs/2411.17795 (2024) - [i158]Jiangbin Zheng, Qianhui Xu, Ruichen Xia, Stan Z. Li:
DapPep: Domain Adaptive Peptide-agnostic Learning for Universal T-cell Receptor-antigen Binding Affinity Prediction. CoRR abs/2411.17798 (2024) - [i157]