| Benchmarking spatial clustering methods with spatially resolved transcriptomics data Z Yuan, F Zhao, S Lin, Y Zhao, J Yao, Y Cui, XY Zhang, Y Zhao Nature Methods 21 (4), 712-722, 2024 | 48 | 2024 |
| SMG: self-supervised masked graph learning for cancer gene identification Y Cui, Z Wang, X Wang, Y Zhang, Y Zhang, T Pan, Z Zhang, S Li, Y Guo, ... Briefings in Bioinformatics 24 (6), bbad406, 2023 | 8 | 2023 |
| Ceir: Concept-based explainable image representation learning Y Cui, S Liu, L Li, Z Yuan arXiv preprint arXiv:2312.10747, 2023 | 5 | 2023 |
| Complete spatially resolved gene expression is not necessary for identifying spatial domains S Lin, Y Cui, F Zhao, Z Yang, J Song, J Yao, Y Zhao, BZ Qian, Y Zhao, ... Cell Genomics 4 (6), 2024 | 3 | 2024 |
| Better Explain Transformers by Illuminating Important Information L Song, Y Cui, A Luo, F Lecue, I Li arXiv preprint arXiv:2401.09972, 2024 | 1 | 2024 |
| Scalable individual treatment effect estimator for large graphs X Lin, H Bao, Y Cui, K Takeuchi, H Kashima Machine Learning 114 (1), 1-19, 2025 | | 2025 |
| Bridging the Dimensional Gap from Planar Spatial Transcriptomics to 3D Cell Atlases S Lin, Z Wang, Y CUI, Q Zou, C Han, R Yan, Z Yang, W Zhang, R Gao, ... bioRxiv, 2024.12. 06.627127, 2024 | | 2024 |
| NicheTrans: Spatial-aware Cross-omics Translation Z Wang, S Lin, Q Zou, Y Cui, C Han, Y Li, J Li, Y Zhao, R Gao, J Song, ... bioRxiv, 2024 | | 2024 |
| MARVEL: Microenvironment Annotation by Supervised Graph Contrastive Learning Y Cui, H Wen, R Yang, X Luo, H Liu, Y Xie bioRxiv, 2024.10. 29.620828, 2024 | | 2024 |
| Identifying Differential Spatial Expression Patterns across Different Slices, Conditions and Developmental Stages with Interpretable Deep Learning Y Cui, Z Yuan bioRxiv, 2024.08. 04.606512, 2024 | | 2024 |
| SOFisher: Reinforcement Learning-Guided Experiment Designs for Spatial Omics Z Li, W Wu, Y Cui, S Jian, Z Yuan bioRxiv, 2024.07. 05.602236, 2024 | | 2024 |
| Scalable Condition-relevant Cell Niche Analysis of Spatial Omics Data with Taichi Y Cui, Z Yuan bioRxiv, 2024.05. 30.596656, 2024 | | 2024 |