Broadbent, Charles, Tianci Song, and Rui Kuang. 2024. “Deciphering High-Order Structures in Spatial Transcriptomes With Graph-Guided Tucker Decomposition”. Bioinformatics 40 (Special Issue of The Proceedings of The 32nd International Conference on Intelligent Systems for Molecular Biology (ISMB). Oxford University Press: i529-i538.
High-order Graph Models
Song, Tianci, Quoc Nguyen, Charles Broadbent, and Rui Kuang. 2026. “CTFacTomo: Reconstructing 3D Spatial Structures of RNA Tomography Transcriptomes by Collapsed Tensor Factorization”. PLOS Computational Biology 22. Public Library of Science: e1013457.
Li, Zhuliu, Tianci Song, Jeongsik Yong, and Rui Kuang. 2021. “Imputation of Spatially-Resolved Transcriptomes by Graph-Regularized Tensor Completion”. PLoS Computational Biology 17. Public Library of Science San Francisco, CA USA: e1008218.
Song, Tianci, Charles Broadbent, and Rui Kuang. 2023. “GNTD: Reconstructing Spatial Transcriptomes With Graph-Guided Neural Tensor Decomposition Informed by Spatial and Functional Relations”. Nature Communications 14. Nature Publishing Group UK London: 8276.
Tian, Ze, Taehyun Hwang, and Rui Kuang. 2009. “A Hypergraph-Based Learning Algorithm for Classifying Gene Expression and ArrayCGH Data With Prior Knowledge”. Bioinformatics 25. Oxford University Press: 2831-38.
Zhang, Wei, Jeremy Chien, Jeongsik Yong, and Rui Kuang. 2017. “Network-Based Machine Learning and Graph Theory Algorithms for Precision Oncology”. NPJ Precision Oncology 1. Nature Publishing Group UK London: 25.
Li, Zhuliu, Wei Zhang, Stephanie Huang, and Rui Kuang. 2019. “Learning a Low-Rank Tensor of Pharmacogenomic Multi-Relations from Biomedical Networks”. In 2019 IEEE International Conference on Data Mining (ICDM), 409-18. IEEE.
Tian, Ze, Taehyun Hwang, and Rui Kuang. 2009. “A Hypergraph-Based Learning Algorithm for Classifying Arraycgh Data With Spatial Prior”. In 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, 1-4. IEEE.
Li, Zhuliu, Raphael Petegrosso, Shaden Smith, David Sterling, George Karypis, and Rui Kuang. 2021. “Scalable Label Propagation for Multi-Relational Learning on the Tensor Product of Graphs”. IEEE Transactions on Knowledge and Data Engineering 34. IEEE: 5964-78.
Hwang, Taehyun, Ze Tian, Rui Kuangy, and Jean-Pierre Kocher. 2008. “Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction”. In 2008 Eighth IEEE International Conference on Data Mining, 293-302. IEEE.