Multi-modal Representation Learning for Short Video Understanding and Recommendation. - Daya Guo; Jiangshui Hong; Binli Luo; Qirui Yan; Zhangming Niu (ICME Workshops, 2019)

Communicative Representation Learning on Attributed Molecular Graphs. - Ying Song; Shuangjia Zheng; Zhangming Niu; Zhang-Hua Fu; Yutong Lu; Yuedong Yang (IJCAI, 2020)

Weakly Supervised Deep Learning for COVID-19 Infection Detection and Classification From CT Images. - Shaoping Hu; Yuan Gao 017; Zhangming Niu; Yinghui Jiang; Lao Li; Xianglu Xiao; Minhao Wang; Evandro Fei Fang; Wade Menpes-Smith; Jun Xia 002; Hui Ye; Guang Yang 006 (IEEE Access, 2020)

SARA-GAN: Self-Attention and Relative Average Discriminator Based Generative Adversarial Networks for Fast Compressed Sensing MRI Reconstruction. - Zhenmou Yuan; Mingfeng Jiang; Yaming Wang; Bo Wei 004; Yongming Li 003; Pin Wang; Wade Menpes-Smith; Zhangming Niu; Guang Yang 006 (Frontiers Neuroinformatics, 2020)

A spatial-temporal gated attention module for molecular property prediction based on molecular geometry. - Chunyan Li 002; Jianmin Wang 016; Zhangming Niu; Junfeng Yao; Xiangxiang Zeng (Briefings Bioinform., 2021)

HeTDR: Drug repositioning based on heterogeneous networks and text mining. - Shuting Jin; Zhangming Niu; Changzhi Jiang; Wei Huang; Feng Xia 007; Xurui Jin; Xiangrong Liu; Xiangxiang Zeng (Patterns, 2021)

PharmKG: a dedicated knowledge graph benchmark for bomedical data mining. - Shuangjia Zheng; Jiahua Rao; Ying Song; Jixian Zhang; Xianglu Xiao; Evandro Fei Fang; Yuedong Yang; Zhangming Niu (Briefings Bioinform., 2021)

Robust weakly supervised learning for COVID-19 recognition using multi-center CT images. - Qinghao Ye; Yuan Gao 017; Weiping Ding 001; Zhangming Niu; Chengjia Wang; Yinghui Jiang; Minhao Wang; Evandro Fei Fang; Wade Menpes-Smith; Jun Xia 002; Guang Yang 006 (Appl. Soft Comput., 2022)

Learning spatial structures of proteins improves protein-protein interaction prediction. - Bosheng Song; Xiaoyan Luo; Xiaoli Luo; Yuansheng Liu; Zhangming Niu; Xiangxiang Zeng (Briefings Bioinform., 2022)

Pre-training of Deep Protein Models with Molecular Dynamics Simulations for Drug Binding. - Fang Wu 002; Qiang Zhang 026; Dragomir R. Radev; Yuyang Wang; Xurui Jin; Yinghui Jiang; Zhangming Niu; Stan Z. Li (CoRR, 2022)

To Improve Prediction of Binding Residues With DNA, RNA, Carbohydrate, and Peptide Via Multi-Task Deep Neural Networks. - Zhe Sun; Shuangjia Zheng; Huiying Zhao; Zhangming Niu; Yutong Lu; Yi Pan 001; Yuedong Yang (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Rethinking Explaining Graph Neural Networks via Non-parametric Subgraph Matching. - Fang Wu 002; Siyuan Li 002; Xurui Jin; Yinghui Jiang; Dragomir Radev; Zhangming Niu; Stan Z. Li (ICML, 2023)

Explaining Graph Neural Networks via Non-parametric Subgraph Matching. - Fang Wu 002; Siyuan Li 002; Lirong Wu; Dragomir Radev; Yinghui Jiang; Xurui Jin; Zhangming Niu; Stan Z. Li (CoRR, 2023)

Modality-DTA: Multimodality Fusion Strategy for Drug-Target Affinity Prediction. - Xixi Yang; Zhangming Niu; Yuansheng Liu; Bosheng Song; Weiqiang Lu; Li Zeng; Xiangxiang Zeng (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

An extensive benchmark study on biomedical text generation and mining with ChatGPT. - Qijie Chen; Haotong Sun; Haoyang Liu; Yinghui Jiang; Ting Ran; Xurui Jin; Xianglu Xiao; Zhimin Lin; Hongming Chen 001; Zhangming Niu (Bioinform., 2023)

A Smart Strategy for Photoresponsive Molecules: Utilizing Generative Pre-trained Transformer and TDDFT Calculations in Drug Delivery. - Junjie Hu; Peng Wu; Qi Li; Shiyi Wang; Xianglu Xiao; Zhangming Niu; Binju Wang; Guang Yang 006 (EMBC, 2024)

How Good are Current Pocket-Based 3D Generative Models?: The Benchmark Set and Evaluation of Protein Pocket-Based 3D Molecular Generative Models. - Haoyang Liu; Yifei Qin; Zhangming Niu; Mingyuan Xu; Jiaqiang Wu; Xianglu Xiao; Jinping Lei; Ting Ran; Hongming Chen 001 (J. Chem. Inf. Model., 2024)

Geometry-Based Molecular Generation With Deep Constrained Variational Autoencoder. - Chunyan Li 002; Junfeng Yao; Wei Wei 006; Zhangming Niu; Xiangxiang Zeng; Jin Li 007; Jianmin Wang 016 (IEEE Trans. Neural Networks Learn. Syst., 2024)

Automated molecular structure segmentation from documents using ChemSAM. - Bowen Tang; Zhangming Niu; Xiaofeng Wang; Junjie Huang; Chao Ma; Jing Peng; Yinghui Jiang; Ruiquan Ge; Hongyu Hu; Luhao Lin; Guang Yang 006 (J. Cheminformatics, 2024)

Artificial immunofluorescence in a flash: Rapid synthetic imaging from brightfield through residual diffusion. - Xiaodan Xing; Chunling Tang; Siofra Murdoch; Giorgos Papanastasiou; Yunzhe Guo; Xianglu Xiao; Jan Oscar Cross-Zamirski; Carola-Bibiane Schönlieb; Kristina Xiao Liang; Zhangming Niu; Evandro Fei Fang; Yinhai Wang; et al. (Neurocomputing, 2025)

Adaptive symmetry-based adversarial perturbation augmentation for molecular graph representations with dual-fusion attention information. - Shuting Jin; Xiangrong Liu; Junlin Xu; Sisi Yuan; Hongxing Xiang; Lian Shen; Chunyan Li 002; Zhangming Niu; Yinhui Jiang (Inf. Fusion, 2025)