| Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion Q Yuan, J Xie, J Xie, H Zhao, Y Yang Briefings in bioinformatics 24 (3), bbad117, 2023 | 47 | 2023 |
| From intuition to AI: evolution of small molecule representations in drug discovery M McGibbon, S Shave, J Dong, Y Gao, DR Houston, J Xie, Y Yang, ... Briefings in bioinformatics 25 (1), bbad422, 2024 | 23 | 2024 |
| Selective functionalization of hindered meta-C–H bond of o-alkylaryl ketones promoted by automation and deep learning J Qiu, J Xie, S Su, Y Gao, H Meng, Y Yang, K Liao Chem 8 (12), 3275-3287, 2022 | 20 | 2022 |
| Cross‐Modal Graph Contrastive Learning with Cellular Images S Zheng, J Rao, J Zhang, L Zhou, J Xie, E Cohen, W Lu, C Li, Y Yang Advanced Science 11 (32), 2404845, 2024 | 10 | 2024 |
| A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions J Rao, J Xie, Q Yuan, D Liu, Z Wang, Y Lu, S Zheng, Y Yang Nature Communications 15 (1), 4476, 2024 | 9 | 2024 |
| MolRep: A deep representation learning library for molecular property prediction J Rao, S Zheng, Y Song, J Chen, C Li, J Xie, H Yang, H Chen, Y Yang bioRxiv, 2021.01. 13.426489, 2021 | 5 | 2021 |
| Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph J Xie, Y Wang, J Rao, S Zheng, Y Yang Journal of Chemical Information and Modeling 64 (6), 1945-1954, 2024 | 3 | 2024 |
| Predicting disease-gene associations through self-supervised mutual infomax graph convolution network J Xie, J Rao, J Xie, H Zhao, Y Yang Computers in Biology and Medicine 170, 108048, 2024 | 2 | 2024 |
| Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks J Rao, J Xie, H Lin, S Zheng, Z Wang, Y Yang arXiv preprint arXiv:2402.04710, 2024 | 1 | 2024 |
| An interpretable survival model for diffuse large B-cell lymphoma patients using a biologically informed visible neural network J Tan, J Xie, J Huang, W Deng, H Chai, Y Yang Computational and Structural Biotechnology Journal 24, 523-532, 2024 | | 2024 |
| CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells Y Zeng, J Xie, Z Wei, Y Su, N Shangguan, S Yang, C Zhang, W Li, ... bioRxiv, 2024.06. 04.597369, 2024 | | 2024 |
| Interpretable Drug Response Prediction through Molecule Structure-aware and Knowledge-Guided Visible Neural Network J Xie, Z Zhang, Y Li, J Rao, Y Yang bioRxiv, 2024.02. 07.579280, 2024 | | 2024 |
