PPaperPicks

Stan Z. Li

Chinese Academy of Sciences, Institute of Automation, Beijing, China

58 papers at tracked venues · 50 at CORE A* · active 2024–2026

DBLP profile ↗ORCID 0000-0002-2961-8096 ↗Google Scholar ↗Homepage ↗

Venues

ICLR ×12AAAI ×11NeurIPS ×11ICML ×10IJCAI ×4CVPR ×2ACM MM ×1CIKM ×1ECCV ×1ECML-PKDD ×1EMNLP ×1ICCV ×1ICDE ×1WWW ×1

Frequent coauthors

Cheng Tan
×30
Zhangyang Gao
×27
Yufei Huang
×22
Siyuan Li
×22
Lirong Wu
×21
Jun Xia
×18
Haitao Lin
×16
Zicheng Liu
×12
Bozhen Hu
×11
Jiangbin Zheng
×10
Jingbo Zhou
×9
Yunfan Liu
×8

Papers

  1. Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges
    AAAI 2026 ·
    Changxi Chi
    ,
    Yufei Huang
    ,
    Jun Xia
    ,
    Jiangbin Zheng
    ,
    Yunfan Liu
    ,
    Zelin Zang
    , Stan Z. Li
  2. Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling
    AAAI 2026 ·
    Mengran Li
    ,
    Zelin Zang
    ,
    Wenbin Xing
    ,
    Junzhou Chen
    ,
    Ronghui Zhang
    ,
    Jiebo Luo
    , Stan Z. Li
  3. MergeDNA: Context-Aware Genome Modeling with Dynamic Tokenization Through Token Merging
    AAAI 2026 ·
    Siyuan Li
    ,
    Kai Yu
    ,
    Anna Wang
    ,
    Zicheng Liu
    ,
    Chang Yu
    ,
    Jingbo Zhou
    ,
    Qirong Yang
    ,
    Yucheng Guo
    ,
    Xiaoming Zhang
    , Stan Z. Li
  4. VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention
    WWW 2026 ·
    Jingbo Zhou
    ,
    Jun Xia
    ,
    Siyuan Li
    ,
    Yunfan Liu
    ,
    Wenjun Wang
    ,
    Yufei Huang
    ,
    Changxi Chi
    ,
    Mutian Hong
    ,
    Zhuoli Ouyang
    ,
    Shu Wang
    ,
    Zhongqi Wang
    ,
    Xingyu Wu
    ,
    Chang Yu
    , Stan Z. Li
  5. A Comprehensive and Systematic Review for Deep Learning-Based De Novo Peptide Sequencing
    IJCAI 2025 ·
    Jun Xia
    ,
    Jingbo Zhou
    ,
    Shaorong Chen
    ,
    Tianze Ling
    , Stan Z. Li
  6. A Simple yet Effective ΔΔG Predictor is An Unsupervised Antibody Optimizer and Explainer
    ICLR 2025 ·
    Lirong Wu
    ,
    Yunfan Liu
    ,
    Haitao Lin
    ,
    Yufei Huang
    ,
    Guojiang Zhao
    ,
    Zhifeng Gao
    , Stan Z. Li
  7. AlphaFold Database Debiasing for Robust Inverse Folding
    NeurIPS 2025 ·
    Cheng Tan
    ,
    Zhenxiao Cao
    ,
    Zhangyang Gao
    ,
    Siyuan Li
    ,
    Yufei Huang
    , Stan Z. Li
  8. Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo
    ICLR 2025 ·
    Jun Xia
    ,
    Sizhe Liu
    ,
    Jingbo Zhou
    ,
    Shaorong Chen
    ,
    Hongxin Xiang
    ,
    Zicheng Liu
    ,
    Yue Liu
    , Stan Z. Li
  9. CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
    ICLR 2025 ·
    Haitao Lin
    ,
    Guojiang Zhao
    ,
    Odin Zhang
    ,
    Yufei Huang
    ,
    Lirong Wu
    ,
    Cheng Tan
    ,
    Zicheng Liu
    ,
    Zhifeng Gao
    , Stan Z. Li
  10. EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow
    ICLR 2025 ·
    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
  11. FoldToken: Learning Protein Language via Vector Quantization and Beyond
    AAAI 2025 ·
    Zhangyang Gao
    ,
    Cheng Tan
    ,
    Jue Wang
    ,
    Yufei Huang
    ,
    Lirong Wu
    , Stan Z. Li
  12. G2PDiffusion: Cross-Species Genotype-to-Phenotype Prediction Via Evolutionary Diffusion
    ICCV 2025 ·
    Mengdi Liu
    ,
    Zhangyang Gao
    ,
    Hong Chang
    , Stan Z. Li,
    Shiguang Shan
    ,
    Xilin Chen
  13. GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype
    IJCAI 2025 ·
    Changxi Chi
    ,
    Jun Xia
    ,
    Jingbo Zhou
    ,
    Jiabei Cheng
    ,
    Chang Yu
    , Stan Z. Li
  14. Generalized Implicit Neural Representations for Dynamic Molecular Surface Modeling
    AAAI 2025 ·
    Fang Wu
    ,
    Bozhen Hu
    , Stan Z. Li
  15. MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction
    ICLR 2025 ·
    Cheng Tan
    ,
    Zhenxiao Cao
    ,
    Zhangyang Gao
    ,
    Lirong Wu
    ,
    Siyuan Li
    ,
    Yufei Huang
    ,
    Jun Xia
    ,
    Bozhen Hu
    , Stan Z. Li
  16. PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs
    NeurIPS 2025 ·
    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
  17. ReNovo: Retrieval-Based \emph{De Novo} Mass Spectrometry Peptide Sequencing
    ICLR 2025 ·
    Shaorong Chen
    ,
    Jun Xia
    ,
    Jingbo Zhou
    ,
    Lecheng Zhang
    ,
    Zhangyang Gao
    ,
    Bozhen Hu
    ,
    Cheng Tan
    ,
    Wenjie Du
    , Stan Z. Li
  18. Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization
    AAAI 2025 ·
    Lirong Wu
    ,
    Haitao Lin
    ,
    Yufei Huang
    ,
    Zhangyang Gao
    ,
    Cheng Tan
    ,
    Yunfan Liu
    ,
    Tailin Wu
    , Stan Z. Li
  19. SketchAgent: Generating Structured Diagrams from Hand-Drawn Sketches
    IJCAI 2025 ·
    Cheng Tan
    ,
    Qi Chen
    ,
    Jingxuan Wei
    ,
    Gaowei Wu
    ,
    Zhangyang Gao
    ,
    Siyuan Li
    ,
    Bihui Yu
    ,
    Ruifeng Guo
    , Stan Z. Li
  20. dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen
    AAAI 2025 ·
    Cheng Tan
    ,
    Yijie Zhang
    ,
    Zhangyang Gao
    ,
    Yufei Huang
    ,
    Haitao Lin
    ,
    Lirong Wu
    ,
    Fandi Wu
    ,
    Mathieu Blanchette
    , Stan Z. Li
  21. A Graph is Worth K Words: Euclideanizing Graph using Pure Transformer
    ICML 2024 ·
    Zhangyang Gao
    ,
    Daize Dong
    ,
    Cheng Tan
    ,
    Jun Xia
    ,
    Bozhen Hu
    , Stan Z. Li
  22. AdaNovo: Towards Robust \emph{De Novo} Peptide Sequencing in Proteomics against Data Biases
    NeurIPS 2024 ·
    Jun Xia
    ,
    Shaorong Chen
    ,
    Jingbo Zhou
    ,
    Xiaojun Shan
    ,
    Wenjie Du
    ,
    Zhangyang Gao
    ,
    Cheng Tan
    ,
    Bozhen Hu
    ,
    Jiangbin Zheng
    , Stan Z. Li
  23. Boosting the Power of Small Multimodal Reasoning Models to Match Larger Models with Self-consistency Training
    ECCV 2024 ·
    Cheng Tan
    ,
    Jingxuan Wei
    ,
    Zhangyang Gao
    ,
    Linzhuang Sun
    ,
    Siyuan Li
    ,
    Ruifeng Guo
    ,
    Bihui Yu
    , Stan Z. Li
  24. Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody Designer
    AAAI 2024 ·
    Cheng Tan
    ,
    Zhangyang Gao
    ,
    Lirong Wu
    ,
    Jun Xia
    ,
    Jiangbin Zheng
    ,
    Xihong Yang
    ,
    Yue Liu
    ,
    Bozhen Hu
    , Stan Z. Li
  25. Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective
    ICML 2024 ·
    Cheng Tan
    ,
    Zhangyang Gao
    ,
    Hanqun Cao
    ,
    Xingran Chen
    ,
    Ge Wang
    ,
    Lirong Wu
    ,
    Jun Xia
    ,
    Jiangbin Zheng
    , Stan Z. Li
  26. Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks
    ICLR 2024 ·
    Tianyu Fan
    ,
    Lirong Wu
    ,
    Yufei Huang
    ,
    Haitao Lin
    ,
    Cheng Tan
    ,
    Zhangyang Gao
    , Stan Z. Li
  27. Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptative Residual Module
    NeurIPS 2024 ·
    Jingbo Zhou
    ,
    Yixuan Du
    ,
    Ruqiong Zhang
    ,
    Jun Xia
    ,
    Zhizhi Yu
    ,
    Zelin Zang
    ,
    Di Jin
    ,
    Carl Yang
    ,
    Rui Zhang
    , Stan Z. Li
  28. DiffAug: Enhance Unsupervised Contrastive Learning with Domain-Knowledge-Free Diffusion-based Data Augmentation
    ICML 2024 ·
    Zelin Zang
    ,
    Hao Luo
    ,
    Kai Wang
    ,
    Panpan Zhang
    ,
    Fan Wang
    , Stan Z. Li,
    Yang You
  29. DiscoGNN: A Sample-Efficient Framework for Self-Supervised Graph Representation Learning
    ICDE 2024 ·
    Jun Xia
    ,
    Shaorong Chen
    ,
    Yue Liu
    ,
    Zhangyang Gao
    ,
    Jiangbin Zheng
    ,
    Xihong Yang
    , Stan Z. Li
  30. FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning
    NeurIPS 2024 ·
    Sizhe Liu
    ,
    Jun Xia
    ,
    Lecheng Zhang
    ,
    Yuchen Liu
    ,
    Yue Liu
    ,
    Wenjie Du
    ,
    Zhangyang Gao
    ,
    Bozhen Hu
    ,
    Cheng Tan
    ,
    Hongxin Xiang
    , Stan Z. Li
  31. General Point Model Pretraining with Autoencoding and Autoregressive
    CVPR 2024 ·
    Zhe Li
    ,
    Zhangyang Gao
    ,
    Cheng Tan
    ,
    Bocheng Ren
    ,
    Laurence T. Yang
    , Stan Z. Li
  32. GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation
    ICML 2024 ·
    Haitao Lin
    ,
    Lirong Wu
    ,
    Yufei Huang
    ,
    Yunfan Liu
    ,
    Odin Zhang
    ,
    Yuanqing Zhou
    ,
    Rui Sun
    , Stan Z. Li
  33. InsertGNN: A Hierarchical Graph Neural Network for the TOEFL Sentence Insertion Problem
    EMNLP 2024 ·
    Fang Wu
    , Stan Z. Li
  34. Instructor-inspired Machine Learning for Robust Molecular Property Prediction
    NeurIPS 2024 ·
    Fang Wu
    ,
    Shuting Jin
    ,
    Siyuan Li
    , Stan Z. Li
  35. Interpretable and Generalizable Spatiotemporal Predictive Learning with Disentangled Consistency
    ECML-PKDD 2024 ·
    Jingxuan Wei
    ,
    Cheng Tan
    ,
    Zhangyang Gao
    ,
    Linzhuang Sun
    ,
    Bihui Yu
    ,
    Ruifeng Guo
    , Stan Z. Li
  36. KW-Design: Pushing the Limit of Protein Design via Knowledge Refinement
    ICLR 2024 ·
    Zhangyang Gao
    ,
    Cheng Tan
    ,
    Xingran Chen
    ,
    Yijie Zhang
    ,
    Jun Xia
    ,
    Siyuan Li
    , Stan Z. Li
  37. Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure
    NeurIPS 2024 ·
    Bozhen Hu
    ,
    Cheng Tan
    ,
    Jun Xia
    ,
    Yue Liu
    ,
    Lirong Wu
    ,
    Jiangbin Zheng
    ,
    Yongjie Xu
    ,
    Yufei Huang
    , Stan Z. Li
  38. Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning
    ICML 2024 ·
    Lirong Wu
    ,
    Yijun Tian
    ,
    Haitao Lin
    ,
    Yufei Huang
    ,
    Siyuan Li
    ,
    Nitesh V. Chawla
    , Stan Z. Li
  39. LongVQ: Long Sequence Modeling with Vector Quantization on Structured Memory
    IJCAI 2024 ·
    Zicheng Liu
    ,
    Li Wang
    ,
    Siyuan Li
    ,
    Zedong Wang
    ,
    Haitao Lin
    , Stan Z. Li
  40. MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
    ICLR 2024 ·
    Lirong Wu
    ,
    Yijun Tian
    ,
    Yufei Huang
    ,
    Siyuan Li
    ,
    Haitao Lin
    ,
    Nitesh V. Chawla
    , Stan Z. Li
  41. MLIP: Enhancing Medical Visual Representation with Divergence Encoder and Knowledge-guided Contrastive Learning
    CVPR 2024 ·
    Zhe Li
    ,
    Laurence T. Yang
    ,
    Bocheng Ren
    ,
    Xin Nie
    ,
    Zhangyang Gao
    ,
    Cheng Tan
    , Stan Z. Li
  42. MetaEnzyme: Meta Pan-Enzyme Learning for Task-Adaptive Redesign
    ACM MM 2024 ·
    Jiangbin Zheng
    ,
    Han Zhang
    ,
    Qianqing Xu
    ,
    An-Ping Zeng
    , Stan Z. Li
  43. MogaNet: Multi-order Gated Aggregation Network
    ICLR 2024 ·
    Siyuan Li
    ,
    Zedong Wang
    ,
    Zicheng Liu
    ,
    Cheng Tan
    ,
    Haitao Lin
    ,
    Di Wu
    ,
    Zhiyuan Chen
    ,
    Jiangbin Zheng
    , Stan Z. Li
  44. NovoBench: Benchmarking Deep Learning-based \emph{De Novo} Sequencing Methods in Proteomics
    NeurIPS 2024 ·
    Jingbo Zhou
    ,
    Shaorong Chen
    ,
    Jun Xia
    ,
    Sizhe Liu
    ,
    Tianze Ling
    ,
    Wenjie Du
    ,
    Yue Liu
    ,
    Jianwei Yin
    , Stan Z. Li
  45. PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching
    ICML 2024 ·
    Haitao Lin
    ,
    Odin Zhang
    ,
    Huifeng Zhao
    ,
    Dejun Jiang
    ,
    Lirong Wu
    ,
    Zicheng Liu
    ,
    Yufei Huang
    , Stan Z. Li
  46. PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction
    AAAI 2024 ·
    Lirong Wu
    ,
    Yufei Huang
    ,
    Cheng Tan
    ,
    Zhangyang Gao
    ,
    Bozhen Hu
    ,
    Haitao Lin
    ,
    Zicheng Liu
    , Stan Z. Li
  47. PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation
    NeurIPS 2024 ·
    Chenrui Duan
    ,
    Zelin Zang
    ,
    Siyuan Li
    ,
    Yongjie Xu
    , Stan Z. Li
  48. ProtGO: Function-Guided Protein Modeling for Unified Representation Learning
    NeurIPS 2024 ·
    Bozhen Hu
    ,
    Cheng Tan
    ,
    Yongjie Xu
    ,
    Zhangyang Gao
    ,
    Jun Xia
    ,
    Lirong Wu
    , Stan Z. Li
  49. Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction
    AAAI 2024 ·
    Yufei Huang
    ,
    Siyuan Li
    ,
    Lirong Wu
    ,
    Jin Su
    ,
    Haitao Lin
    ,
    Odin Zhang
    ,
    Zihan Liu
    ,
    Zhangyang Gao
    ,
    Jiangbin Zheng
    , Stan Z. Li
  50. RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design
    ICLR 2024 ·
    Cheng Tan
    ,
    Yijie Zhang
    ,
    Zhangyang Gao
    ,
    Bozhen Hu
    ,
    Siyuan Li
    ,
    Zicheng Liu
    , Stan Z. Li
  51. Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge
    ICML 2024 ·
    Yufei Huang
    ,
    Odin Zhang
    ,
    Lirong Wu
    ,
    Cheng Tan
    ,
    Haitao Lin
    ,
    Zhangyang Gao
    ,
    Siyuan Li
    , Stan Z. Li
  52. SemiReward: A General Reward Model for Semi-supervised Learning
    ICLR 2024 ·
    Siyuan Li
    ,
    Weiyang Jin
    ,
    Zedong Wang
    ,
    Fang Wu
    ,
    Zicheng Liu
    ,
    Cheng Tan
    , Stan Z. Li
  53. Short-Long Convolutions Help Hardware-Efficient Linear Attention to Focus on Long Sequences
    ICML 2024 ·
    Zicheng Liu
    ,
    Siyuan Li
    ,
    Li Wang
    ,
    Zedong Wang
    ,
    Yunfan Liu
    , Stan Z. Li
  54. Surface-VQMAE: Vector-quantized Masked Auto-encoders on Molecular Surfaces
    ICML 2024 ·
    Fang Wu
    , Stan Z. Li
  55. Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation
    CIKM 2024 ·
    Lirong Wu
    ,
    Yunfan Liu
    ,
    Haitao Lin
    ,
    Yufei Huang
    , Stan Z. Li
  56. UniIF: Unified Molecule Inverse Folding
    NeurIPS 2024 ·
    Zhangyang Gao
    ,
    Jue Wang
    ,
    Cheng Tan
    ,
    Lirong Wu
    ,
    Yufei Huang
    ,
    Siyuan Li
    ,
    Zhirui Ye
    , Stan Z. Li
  57. VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling
    ICML 2024 ·
    Siyuan Li
    ,
    Zedong Wang
    ,
    Zicheng Liu
    ,
    Di Wu
    ,
    Cheng Tan
    ,
    Jiangbin Zheng
    ,
    Yufei Huang
    , Stan Z. Li
  58. Wavelet-Driven Spatiotemporal Predictive Learning: Bridging Frequency and Time Variations
    AAAI 2024 ·
    Xuesong Nie
    ,
    Yunfeng Yan
    ,
    Siyuan Li
    ,
    Cheng Tan
    ,
    Xi Chen
    ,
    Haoyuan Jin
    ,
    Zhihang Zhu
    , Stan Z. Li,
    Donglian Qi