A Semantics-Preserving Approach for Extracting OWL Ontologies from UML Class Diagrams. - Zhuoming Xu; Yuyan Ni; Lili Lin; Huajian Gu (FGIT-DTA, 2009)

Automatic extraction of OWL ontologies from UML class diagrams: a semantics-preserving approach. - Zhuoming Xu; Yuyan Ni; Wenjie He; Lili Lin; Qin Yan (World Wide Web, 2012)

R2RML Processor for Materializing RDF View of Relational Data: Algorithms and Experiments. - Shufeng Zhou; Zhuoming Xu; Yuyan Ni; Haifei Zhang (IEEE WISA, 2013)

Fractional Denoising for 3D Molecular Pre-training. - Shikun Feng; Yuyan Ni; Yanyan Lan; Zhi-Ming Ma; Wei-Ying Ma (ICML, 2023)

Unified Molecular Modeling via Modality Blending. - Qiying Yu; Yudi Zhang 008; Yuyan Ni; Shikun Feng; Yanyan Lan; Hao Zhou; Jingjing Liu (CoRR, 2023)

Elastic Information Bottleneck. - Yuyan Ni; Yanyan Lan; Ao Liu; Zhiming Ma (CoRR, 2023)

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 (ICLR, 2024)

Multimodal Molecular Pretraining via Modality Blending. - Qiying Yu; Yudi Zhang 008; Yuyan Ni; Shikun Feng; Yanyan Lan; Hao Zhou; Jingjing Liu (ICLR, 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 (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 (ICML, 2024)

Beyond Efficiency: Molecular Data Pruning for Enhanced Generalization. - Dingshuo Chen; Zhixun Li; Yuyan Ni; Guibin Zhang; Ding Wang; Qiang Liu 006; Shu Wu; Jeffrey Xu Yu; Liang Wang (NeurIPS, 2024)

Contextual Molecule Representation Learning from Chemical Reaction Knowledge. - Han Tang; Shikun Feng; Bicheng Lin; Yuyan Ni; Jingjing Liu; Wei-Ying Ma; Yanyan Lan (CoRR, 2024)

Pre-training with fractional denoising to enhance molecular property prediction. - Yuyan Ni; Shikun Feng; Xin Hong; Yuancheng Sun; Wei-Ying Ma; Zhi-Ming Ma; Qiwei Ye; Yanyan Lan (Nat. Mac. Intell., 2024)

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