Ma, Wei-Ying

60 publications

TMLR 2026 ACDiT: Interpolating Autoregressive Conditional Modeling and Diffusion Transformer Jinyi Hu, Shengding Hu, Yuxuan Song, Yufei Huang, Mingxuan Wang, Hao Zhou, Zhiyuan Liu, Wei-Ying Ma, Maosong Sun

ICLR 2025 A Periodic Bayesian Flow for Material Generation Hanlin Wu, Yuxuan Song, Jingjing Gong, Ziyao Cao, Yawen Ouyang, Jianbing Zhang, Hao Zhou, Wei-Ying Ma, Jingjing Liu

NeurIPS 2025 AANet: Virtual Screening Under Structural Uncertainty via Alignment and Aggregation Wenyu Zhu, Jianhui Wang, Bowen Gao, Yinjun Jia, Haichuan Tan, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan

ICLRW 2025 ACDiT: Interpolating Autoregressive Conditional Modeling and Diffusion Transformer Jinyi Hu, Shengding Hu, Yuxuan Song, Yufei Huang, Mingxuan Wang, Hao Zhou, Zhiyuan Liu, Wei-Ying Ma, Maosong Sun

NeurIPS 2025 Accelerating 3D Molecule Generative Models with Trajectory Diagnosis Zhilong Zhang, Yuxuan Song, Yichun Wang, Jingjing Gong, Hanlin Wu, Dongzhan Zhou, Hao Zhou, Wei-Ying Ma

NeurIPS 2025 CIDD: Collaborative Intelligence for Structure-Based Drug Design Empowered by LLMs Bowen Gao, Yanwen Huang, Yiqiao Liu, Wenxuan Xie, Bowei He, Haichuan Tan, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan

NeurIPS 2025 DAPO: An Open-Source LLM Reinforcement Learning System at Scale Qiying Yu, Zheng Zhang, Ruofei Zhu, Yufeng Yuan, Xiaochen Zuo, YuYue, Weinan Dai, Tiantian Fan, Gaohong Liu, Juncai Liu, LingJun Liu, Xin Liu, Haibin Lin, Zhiqi Lin, Bole Ma, Guangming Sheng, Yuxuan Tong, Chi Zhang, Mofan Zhang, Ru Zhang, Wang Zhang, Hang Zhu, Jinhua Zhu, Jiaze Chen, Jiangjie Chen, Chengyi Wang, Hongli Yu, Yuxuan Song, Xiangpeng Wei, Hao Zhou, Jingjing Liu, Wei-Ying Ma, Ya-Qin Zhang, Lin Yan, Yonghui Wu, Mingxuan Wang

ICML 2025 Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networks Keyue Qiu, Yuxuan Song, Jie Yu, Hongbo Ma, Ziyao Cao, Zhilong Zhang, Yushuai Wu, Mingyue Zheng, Hao Zhou, Wei-Ying Ma

NeurIPS 2025 FIGRDock: Fast Interaction-Guided Regression for Flexible Docking Shikun Feng, Bicheng Lin, Yuanhuan Mo, Yuyan Ni, Wenyu Zhu, Bowen Gao, Wei-Ying Ma, Haitao Li, Yanyan Lan

NeurIPS 2025 MOF-BFN: Metal-Organic Frameworks Structure Prediction via Bayesian Flow Networks Rui Jiao, Hanlin Wu, Wenbing Huang, Yuxuan Song, Yawen Ouyang, Yu Rong, Tingyang Xu, Pengju Wang, Hao Zhou, Wei-Ying Ma, Jingjing Liu, Yang Liu

NeurIPS 2025 Manipulating 3D Molecules in a Fixed-Dimensional E(3)-Equivariant Latent Space Zitao Chen, Yinjun Jia, Zitong Tian, Wei-Ying Ma, Yanyan Lan

ICLRW 2025 MoMa: A Modular Deep Learning Framework for Material Property Prediction Botian Wang, Yawen Ouyang, Yaohui Li, Yiqun Wang, Haorui Cui, Jianbing Zhang, Xiaonan Wang, Wei-Ying Ma, Hao Zhou

ICML 2025 Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule Keyue Qiu, Yuxuan Song, Zhehuan Fan, Peidong Liu, Zhe Zhang, Mingyue Zheng, Hao Zhou, Wei-Ying Ma

ICLRW 2025 Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule Keyue Qiu, Yuxuan Song, Zhehuan Fan, Peidong Liu, Zhe Zhang, Mingyue Zheng, Hao Zhou, Wei-Ying Ma

NeurIPS 2025 Rationalized All-Atom Protein Design with Unified Multi-Modal Bayesian Flow Hanlin Wu, Yuxuan Song, Zhe Zhang, Zhilong Zhang, Hao Zhou, Wei-Ying Ma, Jingjing Liu

ICLR 2025 Redefining the Task of Bioactivity Prediction Yanwen Huang, Bowen Gao, Yinjun Jia, Hongbo Ma, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan

ICLR 2025 Reframing Structure-Based Drug Design Model Evaluation via Metrics Correlated to Practical Needs Bowen Gao, Haichuan Tan, Yanwen Huang, Minsi Ren, Xiao Huang, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan

NeurIPS 2025 Retro-R1: LLM-Based Agentic Retrosynthesis Wei Liu, Jiangtao Feng, Hongli Yu, Yuxuan Song, Yuqiang Li, Shufei Zhang, Lei Bai, Wei-Ying Ma, Hao Zhou

AISTATS 2025 RetroDiff: Retrosynthesis as Multi-Stage Distribution Interpolation Yiming Wang, Yuxuan Song, Yiqun Wang, Minkai Xu, Rui Wang, Hao Zhou, Wei-Ying Ma

ICLRW 2025 ShortListing Model: A Streamlined Simplex Diffusion for Biological Sequence Generation Yuxuan Song, Zhe Zhang, Yu Pei, Jingjing Gong, Mingxuan Wang, Hao Zhou, Jingjing Liu, Wei-Ying Ma

NeurIPS 2025 ShortListing Model: A Streamlined Simplex Diffusion for Discrete Variable Generation Yuxuan Song, Zhe Zhang, Yu Pei, Jingjing Gong, Qiying Yu, Zheng Zhang, Mingxuan Wang, Hao Zhou, Jingjing Liu, Wei-Ying Ma

ICML 2025 Smooth Interpolation for Improved Discrete Graph Generative Models Yuxuan Song, Juntong Shi, Jingjing Gong, Minkai Xu, Stefano Ermon, Hao Zhou, Wei-Ying Ma

ICLR 2025 Steering Protein Family Design Through Profile Bayesian Flow Jingjing Gong, Yu Pei, Siyu Long, Yuxuan Song, Zhe Zhang, Wenhao Huang, Ziyao Cao, Shuyi Zhang, Hao Zhou, Wei-Ying Ma

NeurIPS 2025 Straight-Line Diffusion Model for Efficient 3D Molecular Generation Yuyan Ni, Shikun Feng, Haohan Chi, Bowen Zheng, Huan-ang Gao, Wei-Ying Ma, Zhi-Ming Ma, Yanyan Lan

ICLRW 2025 Towards Extrapolation in Deep Material Property Regression Mianzhi Pan, JianFei Li, Yawen Ouyang, Wei-Ying Ma, Jianbing Zhang, Hao Zhou

ICLR 2025 UniGEM: A Unified Approach to Generation and Property Prediction for Molecules Shikun Feng, Yuyan Ni, Lu Yan, Zhi-Ming Ma, Wei-Ying Ma, Yanyan Lan

ICML 2024 ESM All-Atom: Multi-Scale Protein Language Model for Unified Molecular Modeling Kangjie Zheng, Siyu Long, Tianyu Lu, Junwei Yang, Xinyu Dai, Ming Zhang, Zaiqing Nie, Wei-Ying Ma, Hao Zhou

ICML 2024 Mol-AE: Auto-Encoder Based Molecular Representation Learning with 3D Cloze Test Objective Junwei Yang, Kangjie Zheng, Siyu Long, Zaiqing Nie, Ming Zhang, Xinyu Dai, Wei-Ying Ma, Hao Zhou

ICML 2024 MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space Yanru Qu, Keyue Qiu, Yuxuan Song, Jingjing Gong, Jiawei Han, Mingyue Zheng, Hao Zhou, Wei-Ying Ma

ICLR 2024 Protein-Ligand Binding Representation Learning from Fine-Grained Interactions Shikun Feng, Minghao Li, Yinjun Jia, Wei-Ying Ma, Yanyan Lan

ICML 2024 Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion Bowen Gao, Minsi Ren, Yuyan Ni, Yanwen Huang, Bo Qiang, Zhi-Ming Ma, Wei-Ying Ma, Yanyan Lan

ICLR 2024 Self-Supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment Bowen Gao, Yinjun Jia, YuanLe Mo, Yuyan Ni, Wei-Ying Ma, Zhi-Ming Ma, Yanyan Lan

ICLR 2024 Sliced Denoising: A Physics-Informed Molecular Pre-Training Method Yuyan Ni, Shikun Feng, Wei-Ying Ma, Zhi-Ming Ma, Yanyan Lan

ICML 2024 UniCorn: A Unified Contrastive Learning Approach for Multi-View Molecular Representation Learning Shikun Feng, Yuyan Ni, Minghao Li, Yanwen Huang, Zhi-Ming Ma, Wei-Ying Ma, Yanyan Lan

ICLR 2024 Unified Generative Modeling of 3D Molecules with Bayesian Flow Networks Yuxuan Song, Jingjing Gong, Hao Zhou, Mingyue Zheng, Jingjing Liu, Wei-Ying Ma

ICMLW 2023 Annealed Biological Sequence Optimization Yuxuan Song, Botian Wang, Hao Zhou, Wei-Ying Ma

ICML 2023 Coarse-to-Fine: A Hierarchical Diffusion Model for Molecule Generation in 3D Bo Qiang, Yuxuan Song, Minkai Xu, Jingjing Gong, Bowen Gao, Hao Zhou, Wei-Ying Ma, Yanyan Lan

NeurIPS 2023 DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening Bowen Gao, Bo Qiang, Haichuan Tan, Yinjun Jia, Minsi Ren, Minsi Lu, Jingjing Liu, Wei-Ying Ma, Yanyan Lan

NeurIPS 2023 Equivariant Flow Matching with Hybrid Probability Transport for 3D Molecule Generation Yuxuan Song, Jingjing Gong, Minkai Xu, Ziyao Cao, Yanyan Lan, Stefano Ermon, Hao Zhou, Wei-Ying Ma

ICML 2023 Fractional Denoising for 3D Molecular Pre-Training Shikun Feng, Yuyan Ni, Yanyan Lan, Zhi-Ming Ma, Wei-Ying Ma

ICLR 2022 Energy-Inspired Molecular Conformation Optimization Jiaqi Guan, Wesley Wei Qian, Qiang Liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng

AAAI 2017 Topic Aware Neural Response Generation Chen Xing, Wei Wu, Yu Wu, Jie Liu, Yalou Huang, Ming Zhou, Wei-Ying Ma

NeurIPS 2016 Dual Learning for Machine Translation Di He, Yingce Xia, Tao Qin, Liwei Wang, Nenghai Yu, Tie-Yan Liu, Wei-Ying Ma

AAAI 2016 Hashtag-Based Sub-Event Discovery Using Mutually Generative LDA in Twitter Chen Xing, Yuan Wang, Jie Liu, Yalou Huang, Wei-Ying Ma

ICLR 2014 Learning High-Level Image Representation for Image Retrieval via Multi-Task DNN Using Clickthrough Data Yalong Bai, Kuiyuan Yang, Wei Yu, Wei-Ying Ma, Tiejun Zhao

CVPR 2010 ARISTA - Image Search to Annotation on Billions of Web Photos Xin-Jing Wang, Lei Zhang, Ming Liu, Yi Li, Wei-Ying Ma

ICCV 2009 Efficient Indexing for Large Scale Visual Search Xiao Zhang, Zhiwei Li, Lei Zhang, Wei-Ying Ma, Heung-Yeung Shum

CVPR 2009 Vocabulary Hierarchy Optimization for Effective and Transferable Retrieval Rongrong Ji, Xing Xie, Hongxun Yao, Wei-Ying Ma

CVPR 2008 What Are the High-Level Concepts with Small Semantic Gaps? Yijuan Lu, Lei Zhang, Qi Tian, Wei-Ying Ma

CVPR 2006 AnnoSearch: Image Auto-Annotation by Search Xin-Jing Wang, Lei Zhang, Feng Jing, Wei-Ying Ma

ECML-PKDD 2006 Fast Spectral Clustering of Data Using Sequential Matrix Compression Bo Chen, Bin Gao, Tie-Yan Liu, Yu-Fu Chen, Wei-Ying Ma

CVPR 2006 Learning Distance Metrics with Contextual Constraints for Image Retrieval Steven C. H. Hoi, Wei Liu, Michael R. Lyu, Wei-Ying Ma

ICML 2005 2D Conditional Random Fields for Web Information Extraction Jun Zhu, Zaiqing Nie, Ji-Rong Wen, Bo Zhang, Wei-Ying Ma

ICCV 2005 A Probabilistic Semantic Model for Image Annotation and Multi-Modal Image Retrieva Ruofei Zhang, Zhongfei (Mark) Zhang, Mingjing Li, Wei-Ying Ma, HongJiang Zhang

CVPR 2005 A Unified Optimization Based Learning Method for Image Retrieval Hanghang Tong, Jingrui He, Mingjing Li, Wei-Ying Ma, Changshui Zhang, HongJiang Zhang

ICML 2003 An Evaluation on Feature Selection for Text Clustering Tao Liu, Shengping Liu, Zheng Chen, Wei-Ying Ma

UAI 2003 Collaborative Ensemble Learning: Combining Collaborative and Content-Based Information Filtering via Hierarchical Bayes Kai Yu, Anton Schwaighofer, Volker Tresp, Wei-Ying Ma, HongJiang Zhang

CVPR 2001 Learning Similarity Measure for Natural Image Retrieval with Relevance Feedback Guodong Guo, Anil K. Jain, Wei-Ying Ma, HongJiang Zhang

CVPR 1997 Edge Flow: A Framework of Boundary Detection and Image Segmentation Wei-Ying Ma, B. S. Manjunath

CVPR 1996 Texture Features and Learning Similarity Wei-Ying Ma, B. S. Manjunath