Prediction of LncRNA-Disease Associations Based on Network Representation Learning. - Xiao-Rui Su 001; Zhuhong You; Hai-Cheng Yi (BIBM, 2020)

A Novel Computational Approach for Predicting Drug-Target Interactions via Network Representation Learning. - Xiao-Rui Su 001; Zhu-Hong You; Ji-Ren Zhou; Hai-Cheng Yi; Xiao Li 007 (ICIC (2), 2020)

A Unified Deep Biological Sequence Representation Learning with Pretrained Encoder-Decoder Model. - Hai-Cheng Yi; Zhu-Hong You; Xiao-Rui Su 001; De-Shuang Huang; Zhen-Hao Guo (ICIC (2), 2020)

Predicting miRNA-Disease Associations via a New MeSH Headings Representation of Diseases and eXtreme Gradient Boosting. - Bo-Ya Ji; Zhu-Hong You; Lei Wang 121; Leon Wong; Xiao-Rui Su 001; Bo-Wei Zhao (ICIC (3), 2021)

Protein-Protein Interaction Prediction by Integrating Sequence Information and Heterogeneous Network Representation. - Xiao-Rui Su 001; Zhu-Hong You; Zhan-Heng Chen; Hai-Cheng Yi; Zhen-Hao Guo (ICIC (3), 2021)

Detection of Drug-Drug Interactions Through Knowledge Graph Integrating Multi-attention with Capsule Network. - Xiao-Rui Su 001; Zhu-Hong You; Hai-Cheng Yi; Bo-Wei Zhao (ICIC (3), 2021)

SANE: A sequence combined attentive network embedding model for COVID-19 drug repositioning. - Xiao-Rui Su 001; Zhuhong You; Lei Wang 121; Lun Hu; Leon Wong; Boya Ji; Bo-Wei Zhao (Appl. Soft Comput., 2021)

In silico drug repositioning using deep learning and comprehensive similarity measures. - Hai-Cheng Yi; Zhu-Hong You; Lei Wang 065; Xiao-Rui Su 001; Xi Zhou; Tong-Hai Jiang (BMC Bioinform., 2021)

MRLDTI: A Meta-path-Based Representation Learning Model for Drug-Target Interaction Prediction. - Bo-Wei Zhao; Lun Hu; Pengwei Hu 001; Zhu-Hong You; Xiao-Rui Su 001; Dong-Xu Li; Zhan-Heng Chen; Ping Zhang 027 (ICIC (2), 2022)

A Novel Fuzzy-Based MOPSO Algorithm for Identifying Clusters From Complex Networks. - Yue Yang; Xiaorui Su 001; Bowei Zhao; Yizhou He; Lun Hu (ICTAI, 2022)

A deep learning method for repurposing antiviral drugs against new viruses via multi-view nonnegative matrix factorization and its application to SARS-CoV-2. - Xiao-Rui Su 001; Lun Hu; Zhuhong You; Pengwei Hu 001; Lei Wang 121; Bo-Wei Zhao (Briefings Bioinform., 2022)

Attention-based Knowledge Graph Representation Learning for Predicting Drug-drug Interactions. - Xiao-Rui Su 001; Lun Hu; Zhuhong You; Pengwei Hu 001; Bo-Wei Zhao (Briefings Bioinform., 2022)

A machine learning framework based on multi-source feature fusion for circRNA-disease association prediction. - Lei Wang 121; Leon Wong; Zheng-Wei Li 001; Yuan Huang; Xiao-Rui Su 001; Bo-Wei Zhao; Zhuhong You (Briefings Bioinform., 2022)

HINGRL: predicting drug-disease associations with graph representation learning on heterogeneous information networks. - Bo-Wei Zhao; Lun Hu; Zhu-Hong You; Lei Wang 121; Xiao-Rui Su 001 (Briefings Bioinform., 2022)

A geometric deep learning framework for drug repositioning over heterogeneous information networks. - Bo-Wei Zhao; Xiao-Rui Su 001; Peng-Wei Hu 001; Yu-Peng Ma; Xi Zhou; Lun Hu (Briefings Bioinform., 2022)

Multi-view heterogeneous molecular network representation learning for protein-protein interaction prediction. - Xiao-Rui Su 001; Lun Hu; Zhu-Hong You; Pengwei Hu 001; Bo-Wei Zhao (BMC Bioinform., 2022)

RLFDDA: a meta-path based graph representation learning model for drug-disease association prediction. - Menglong Zhang; Bo-Wei Zhao; Xiao-Rui Su 001; Yi-Zhou He; Yue Yang; Lun Hu (BMC Bioinform., 2022)

NSECDA: Natural Semantic Enhancement for CircRNA-Disease Association Prediction. - Lei Wang 121; Leon Wong; Zhu-Hong You; De-Shuang Huang; Xiao-Rui Su 001; Bo-Wei Zhao (IEEE J. Biomed. Health Informatics, 2022)

Learning RNA sequence patterns to interpretably identify m6A modification sites. - Guodong Li; Bowei Zhao; Xiaorui Su 001; Yue Yang; Pengwei Hu 001; Lun Hu (BIBM, 2023)

Drug Repositioning Method Based on Pre-trained Large Model and Network Embedding Representation. - Dongxu Li; Bowei Zhao; Xiaorui Su 001; Guodong Li; Yue Yang; Pengwei Hu 001; Lun Hu (ICDM (Workshops), 2023)

A Novel Graph Representation Learning Model for Drug Repositioning Using Graph Transition Probability Matrix Over Heterogenous Information Networks. - Dong-Xu Li; Xun Deng; Bo-Wei Zhao; Xiao-Rui Su 001; Guo-Dong Li; Zhu-Hong You; Peng-Wei Hu 001; Lun Hu (ICIC (3), 2023)

A Deep Learning Approach Incorporating Data Missing Mechanism in Predicting Acute Kidney Injury in ICU. - Yuan Zhang; Zhengbo Zhang; Xiaoli Liu; Lei Zha; Fengcong; Xiaorui Su 001; Bowei Zhao; Lun Hu; Pengwei Hu 001 (ICIC (3), 2023)

Multi-level Subgraph Representation Learning for Drug-Disease Association Prediction Over Heterogeneous Biological Information Network. - Bo-Wei Zhao; Xiao-Rui Su 001; Yue Yang; Dong-Xu Li; Peng-Wei Hu 001; Zhu-Hong You; Lun Hu (ICIC (3), 2023)

Predicting Drug-Target Interactions Over Heterogeneous Information Network. - Xiao-Rui Su 001; Pengwei Hu 001; Hai-Cheng Yi; Zhuhong You; Lun Hu (IEEE J. Biomed. Health Informatics, 2023)

Incorporating higher order network structures to improve miRNA-disease association prediction based on functional modularity. - Yi-Zhou He; Yue Yang; Xiao-Rui Su 001; Bo-Wei Zhao; Shengwu Xiong 001; Lun Hu (Briefings Bioinform., 2023)

Biomedical Knowledge Graph Embedding With Capsule Network for Multi-Label Drug-Drug Interaction Prediction. - Xiaorui Su 001; Zhuhong You; Deshuang Huang; Lei Wang 121; Leon Wong; Boya Ji; Bowei Zhao (IEEE Trans. Knowl. Data Eng., 2023)

iGRLDTI: an improved graph representation learning method for predicting drug-target interactions over heterogeneous biological information network. - Bo-Wei Zhao; Xiao-Rui Su 001; Peng-Wei Hu 001; Yu-An Huang; Zhu-Hong You; Lun Hu (Bioinform., 2023)

Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks. - Dong-Xu Li; Peng Zhou; Bo-Wei Zhao; Xiao-Rui Su 001; Guo-Dong Li; Jun Zhang 003; Peng-Wei Hu 001; Lun Hu (BMC Bioinform., 2023)

Dual-Channel Learning Framework for Drug-Drug Interaction Prediction via Relation-Aware Heterogeneous Graph Transformer. - Xiaorui Su 001; Pengwei Hu 001; Zhu-Hong You; Philip S. Yu; Lun Hu (AAAI, 2024)

BioKG-CMI: a multi-source feature fusion model based on biological knowledge graph for predicting circRNA-miRNA interactions. - Mengmeng Wei; Lei Wang 121; Yang Li; Zhengwei Li; Bowei Zhao; Xiao-Rui Su 001; Yu Wei; Zhuhong You (Sci. China Inf. Sci., 2024)

Knowledge Graph Based Agent for Complex, Knowledge-Intensive QA in Medicine. - Xiaorui Su 001; Yibo Wang 001; Shanghua Gao; Xiaolong Liu; Valentina Giunchiglia; Djork-Arné Clevert; Marinka Zitnik (CoRR, 2024)

Fusing Higher and Lower-Order Biological Information for Drug Repositioning via Graph Representation Learning. - Bo-Wei Zhao; Lei Wang 121; Pengwei Hu 001; Leon Wong; Xiao-Rui Su 001; Bao-Quan Wang; Zhu-Hong You; Lun Hu (IEEE Trans. Emerg. Top. Comput., 2024)

Fuzzy-Based Deep Attributed Graph Clustering. - Yue Yang; Xiaorui Su 001; Bowei Zhao; GuoDong Li; Pengwei Hu 001; Jun Zhang 003; Lun Hu (IEEE Trans. Fuzzy Syst., 2024)

Discovering Consensus Regions for Interpretable Identification of RNA N6-Methyladenosine Modification Sites via Graph Contrastive Clustering. - Guodong Li; Bowei Zhao; Xiaorui Su 001; Yue Yang; Pengwei Hu 001; Xi Zhou; Lun Hu (IEEE J. Biomed. Health Informatics, 2024)

Motif-Aware miRNA-Disease Association Prediction via Hierarchical Attention Network. - Bo-Wei Zhao; Yi-Zhou He; Xiao-Rui Su 001; Yue Yang; Guo-Dong Li; Yu-An Huang; Peng-Wei Hu 001; Zhu-Hong You; Lun Hu (IEEE J. Biomed. Health Informatics, 2024)

Learning Sequential and Structural Dependencies Between Nucleotides for RNA N6-Methyladenosine Site Identification. - Guodong Li; Bowei Zhao; Xiaorui Su 001; Dong-Xu Li; Yue Yang; Zhi Zeng; Lun Hu (IEEE CAA J. Autom. Sinica, 2024)

KGARevion: An AI Agent for Knowledge-Intensive Biomedical QA. - Xiaorui Su 001; Yibo Wang 001; Shanghua Gao; Xiaolong Liu; Valentina Giunchiglia; Djork-Arné Clevert; Marinka Zitnik (ICLR, 2025)

Capturing short-range and long-range dependencies of nucleotides for identifying RNA N6-methyladenosine modification sites. - Guodong Li; Bowei Zhao; Xiao-Rui Su 001; Yue Yang; Zhi Zeng; Pengwei Hu 001; Lun Hu (Comput. Biol. Medicine, 2025)

Regulation-aware graph learning for drug repositioning over heterogeneous biological network. - Bo-Wei Zhao; Xiao-Rui Su 001; Yue Yang; Dong-Xu Li; Guo-Dong Li; Peng-Wei Hu 001; Zhu-Hong You; Xin Luo 001; Lun Hu (Inf. Sci., 2025)

A bijective inference network for interpretable identification of RNA N6-methyladenosine modification sites. - Guodong Li; Yue Yang; Dongxu Li; Xiao-Rui Su 001; Zhi Zeng; Pengwei Hu 001; Lun Hu (Pattern Recognit., 2025)

Multimodal Medical Code Tokenizer. - Xiao-Rui Su 001; Shvat Messica; Yepeng Huang; Ruth Johnson; Lukas Fesser; Shanghua Gao; Faryad Sahneh; Marinka Zitnik (CoRR, 2025)

Multimodal AI predicts clinical outcomes of drug combinations from preclinical data. - Yepeng Huang; Xiao-Rui Su 001; Varun Ullanat; Ivy Liang; Lindsay Clegg; Damilola Olabode; Nicholas Ho; Bino John; Megan Gibbs; Marinka Zitnik (CoRR, 2025)

TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools. - Shanghua Gao; Richard Zhu; Zhenglun Kong; Ayush Noori; Xiao-Rui Su 001; Curtis Ginder; Theodoros Tsiligkaridis; Marinka Zitnik (CoRR, 2025)

Knowledge Graph Neural Network With Spatial-Aware Capsule for Drug-Drug Interaction Prediction. - Xiao-Rui Su 001; Bowei Zhao; Guodong Li; Jun Zhang 003; Pengwei Hu 001; Zhuhong You; Lun Hu (IEEE J. Biomed. Health Informatics, 2025)

Integrating Transformer and Graph Attention Network for circRNA-miRNA Interaction Prediction. - Mengmeng Wei; Lei Wang 121; Bo-Wei Zhao; Xiao-Rui Su 001; Zhu-Hong You; De-Shuang Huang (IEEE J. Biomed. Health Informatics, 2025)

Multi-hop graph structural modeling for cancer-related circRNA-miRNA interaction prediction. - Mengmeng Wei; Lei Wang 121; Xiao-Rui Su 001; Bowei Zhao; Zhuhong You (Pattern Recognit., 2026)