Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks. - Shuangjia Zheng; Jiahua Rao; Zhongyue Zhang; Jun Xu 017; Yuedong Yang (CoRR, 2019)

Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network. - Yuansong Zeng; Xiang Zhou; Jiahua Rao; Yutong Lu; Yuedong Yang (BIBM, 2020)

Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting. - Yaobin Ke; Jiahua Rao; Huiying Zhao; Yutong Lu; Nong Xiao 001; Yuedong Yang (Bioinform., 2020)

Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. - Shuangjia Zheng; Jiahua Rao; Zhongyue Zhang; Jun Xu 017; Yuedong Yang (J. Chem. Inf. Model., 2020)

Learning Attributed Graph Representation with Communicative Message Passing Transformer. - Jianwen Chen; Shuangjia Zheng; Ying Song; Jiahua Rao; Yuedong Yang (IJCAI, 2021)

Integrating multi-omics data through deep learning for accurate cancer prognosis prediction. - Hua Chai; Xiang Zhou; Zhongyue Zhang; Jiahua Rao; Huiying Zhao; Yuedong Yang (Comput. Biol. Medicine, 2021)

Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction. - Jiahua Rao; Shuangjia Zheng; Yuedong Yang (CoRR, 2021)

Learning Attributed Graph Representations with Communicative Message Passing Transformer. - Jianwen Chen; Shuangjia Zheng; Ying Song; Jiahua Rao; Yuedong Yang (CoRR, 2021)

PharmKG: a dedicated knowledge graph benchmark for bomedical data mining. - Shuangjia Zheng; Jiahua Rao; Ying Song; Jixian Zhang; Xianglu Xiao; Evandro Fei Fang; Yuedong Yang; Zhangming Niu (Briefings Bioinform., 2021)

Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. - Jiahua Rao; Shuangjia Zheng; Sijie Mai; Yuedong Yang (IJCAI, 2022)

TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction. - Wei Lu; Qifeng Wu; Jixian Zhang; Jiahua Rao; Chengtao Li; Shuangjia Zheng (NeurIPS, 2022)

AlphaFold2-aware protein-DNA binding site prediction using graph transformer. - Qianmu Yuan; Sheng Chen; Jiahua Rao; Shuangjia Zheng; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2022)

Imputing DNA Methylation by Transferred Learning Based Neural Network. - Xinfeng Wang; Xiang Zhou; Jiahua Rao; Zhu-Jin Zhang; Yue-Dong Yang (J. Comput. Sci. Technol., 2022)

Quantitative evaluation of explainable graph neural networks for molecular property prediction. - Jiahua Rao; Shuangjia Zheng; Yutong Lu; Yuedong Yang (Patterns, 2022)

Integrating supercomputing and artificial intelligence for life science. - Jiahua Rao; Shuangjia Zheng; Yuedong Yang (Patterns, 2022)

Retrieval-based Knowledge Augmented Vision Language Pre-training. - Jiahua Rao; Zifei Shan; Longpo Liu; Yao Zhou; Yuedong Yang (ACM Multimedia, 2023)

Interpretable Drug Response Prediction through Molecule Structure-aware and Knowledge-Guided Visible Neural Network. - Jiancong Xie; Zhe Zhang; Youyou Li; Jiahua Rao; Yuedong Yang (BIBM, 2024)

Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks. - Jiahua Rao; Jiancong Xie; Hanjing Lin; Shuangjia Zheng; Zhen Wang 036; Yuedong Yang (CoRR, 2024)

Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. - Jiancong Xie; Yi Wang; Jiahua Rao; Shuangjia Zheng; Yuedong Yang (J. Chem. Inf. Model., 2024)

Predicting disease-gene associations through self-supervised mutual infomax graph convolution network. - Jiancong Xie; Jiahua Rao; Junjie Xie; Huiying Zhao; Yuedong Yang (Comput. Biol. Medicine, 2024)

Deep generative design of RNA aptamers using structural predictions. - Felix Wong; Dongchen He; Aarti Krishnan; Liang Hong; Alexander Z. Wang; Jiuming Wang; Zhihang Hu; Satotaka Omori; Alicia Li; Jiahua Rao; Qinze Yu; Wengong Jin; et al. (Nat. Comput. Sci., 2024)

Advancing Retrosynthesis with Retrieval-Augmented Graph Generation. - Anjie Qiao; Zhen Wang 036; Jiahua Rao; Yuedong Yang; Zhewei Wei (AAAI, 2025)

Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery. - Jiahua Rao; Hanjing Lin; Leyu Chen; Jiancong Xie; Shuangjia Zheng; Yuedong Yang (CVPR, 2025)

A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors. - Anjie Qiao; Yuting Chen; Junjie Xie; Weifeng Huang; Hao Zhang; Qirui Deng; Jiahua Rao; Ji Deng; Fanbo Meng; Zhen Wang 004; Mingyuan Xu; Hongming Chen 001; et al. (Briefings Bioinform., 2025)

A 3D pocket-aware and affinity-guided diffusion model for lead optimization. - Anjie Qiao; Junjie Xie; Weifeng Huang; Hao Zhang; Jiahua Rao; Shuangjia Zheng; Yuedong Yang; Zhen Wang 036; Guo-Bo Li; Jinping Lei (CoRR, 2025)

Fitness aligned structural modeling enables scalable virtual screening with AuroBind. - Zhongyue Zhang; Jiahua Rao; Jie Zhong; Weiqiang Bai; Dongxue Wang; Shaobo Ning; Lifeng Qiao; Sheng Xu; Runze Ma; Will Hua; Jack Xiaoyu Chen; Odin Zhang; et al. (CoRR, 2025)