Measuring phenotype semantic similarity using Human Phenotype Ontology. - Jiajie Peng; Hansheng Xue; Yukai Shao; Xuequn Shang 001; Yadong Wang 001; Jin Chen 004 (BIBM, 2016)

A novel method to measure the semantic similarity of HPO terms. - Jiajie Peng; Hansheng Xue; Yukai Shao; Xuequn Shang 001; Yadong Wang 001; Jin Chen 004 (Int. J. Data Min. Bioinform., 2017)

TSGOE: A web tool for tissue-specific gene ontology enrichment. - Jiajie Peng; Guilin Lu; Hansheng Xue; Tao Wang 082; Xuequn Shang 001 (BIBM, 2018)

Deep Feature Learning of Multi-Network Topology for Node Classification. - Hansheng Xue; Jiajie Peng; Xuequn Shang 001 (CoRR, 2018)

Towards Gene Function Prediction via Multi-Networks Representation Learning. - Hansheng Xue; Jiajie Peng; Xuequn Shang 001 (AAAI, 2019)

Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding. - Hansheng Xue; Jiajie Peng; Jiying Li; Xuequn Shang 001 (CIKM, 2019)

TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. - Jiajie Peng; Guilin Lu; Hansheng Xue; Tao Wang 082; Xuequn Shang 001 (BMC Bioinform., 2019)

Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. - Hansheng Xue; Jiajie Peng; Xuequn Shang 001 (BMC Syst. Biol., 2019)

Modeling Dynamic Heterogeneous Network for Link Prediction Using Hierarchical Attention with Temporal RNN. - Hansheng Xue; Luwei Yang; Wen Jiang; Yi Wei; Yi Hu; Yu Lin 001 (ECML/PKDD (1), 2020)

Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks. - Hansheng Xue; Luwei Yang; Vaibhav Rajan; Wen Jiang; Yi Wei; Yu Lin 001 (WWW, 2021)

Integrating multi-network topology for gene function prediction using deep neural networks. - Jiajie Peng; Hansheng Xue; Zhongyu Wei; Idil Tuncali; Jianye Hao; Xuequn Shang 001 (Briefings Bioinform., 2021)

RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning. - Hansheng Xue; Vijini Mallawaarachchi; Yujia Zhang; Vaibhav Rajan; Yu Lin 001 (AAAI, 2022)

Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction. - Hansheng Xue; Vaibhav Rajan; Yu Lin 001 (NeurIPS, 2022)

Modeling User Intent Beyond Trigger: Incorporating Uncertainty for Trigger-Induced Recommendation. - Jianxing Ma; Zhibo Xiao; Luwei Yang; Hansheng Xue; Xuanzhou Liu; Wen Jiang; Wei Ning; Guannan Zhang (CIKM, 2024)

Encoding Unitig-level Assembly Graphs with Heterophilous Constraints for Metagenomic Contigs Binning. - Hansheng Xue; Vijini Mallawaarachchi; Lexing Xie; Vaibhav Rajan (ICLR, 2024)

Personalised Drug Identifier for Cancer Treatment with Transformers using Auxiliary Information. - Aishwarya Jayagopal; Hansheng Xue; Ziyang He; Robert J. Walsh; Krishna Kumar Hariprasannan; David Shao Peng Tan; Tuan Zea Tan; Jason J. Pitt; Anand D. Jeyasekharan; Vaibhav Rajan (KDD, 2024)

Solving genomic puzzles: computational methods for metagenomic binning. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Hansheng Xue; Bhavya Nalagampalli Papudeshi; Susanna R. Grigson; George Bouras; Rosa E. Prahl; Anubhav Kaphle; Andrey Verich; Berenice Talamantes-Becerra; Elizabeth A. Dinsdale; Robert A. Edwards (Briefings Bioinform., 2024)

Improving CTR Prediction with Graph-Enhanced Interest Networks for Sparse Behavior Sequences. - Xuanzhou Liu; Zhibo Xiao; Luwei Yang; Hansheng Xue; Jianxing Ma; Yujiu Yang (WSDM, 2025)