[HTML][HTML] Joint masking and self-supervised strategies for inferring small molecule-miRNA associations

Z Zhou, L Zhuo, X Fu, J Lv, Q Zou, R Qi - Molecular Therapy-Nucleic Acids, 2024 - cell.com
Inferring small molecule-miRNA associations (MMAs) is crucial for revealing the intricacies
of biological processes and disease mechanisms. Deep learning, renowned for its …

StableDNAm: towards a stable and efficient model for predicting DNA methylation based on adaptive feature correction learning

L Zhuo, R Wang, X Fu, X Yao - BMC genomics, 2023 - Springer
Background DNA methylation, instrumental in numerous life processes, underscores the
paramount importance of its accurate prediction. Recent studies suggest that deep learning …

GAM-MDR: probing miRNA–drug resistance using a graph autoencoder based on random path masking

Z Zhou, Z Du, X Jiang, L Zhuo, Y Xu, X Fu… - Briefings in …, 2024 - academic.oup.com
MicroRNAs (miRNAs) are found ubiquitously in biological cells and play a pivotal role in
regulating the expression of numerous target genes. Therapies centered around miRNAs …

Predicting miRNA-drug interactions via dual-channel network based on TCN and BiLSTM

X Zhang, X Lei - Frontiers of Computer Science, 2025 - Springer
Discovering new drugs is a complicated, time-consuming, costly, risky and failure-prone
process. However, about 80% of the drugs that have been approved so far are targeted at …

A weighted integration method based on graph representation learning for drug repositioning

H Lian, P Ding, C Yu, X Zhang, G Liu, B Yu - Applied Soft Computing, 2024 - Elsevier
The time-consuming and expensive nature of traditional drug discovery necessitates a cost-
effective approach to facilitate disease treatment. Drug repositioning, discovering innovative …

ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction

L Cai, G Yue, Y Chen, L Wang, X Yao… - Briefings in …, 2025 - academic.oup.com
Motivation Accurately predicting the degradation capabilities of proteolysis-targeting
chimeras (PROTACs) for given target proteins and E3 ligases is important for PROTAC …

Enhancing drug–food interaction prediction with precision representations through multilevel self-supervised learning

J Wei, Z Li, L Zhuo, X Fu, M Wang, K Li… - Computers in Biology and …, 2024 - Elsevier
Drug–food interactions (DFIs) crucially impact patient safety and drug efficacy by modifying
absorption, distribution, metabolism, and excretion. The application of deep learning for …

HGGN: Prediction of microRNA-Mediated drug sensitivity based on interpretable heterogeneous graph global-attention network

J Liu, X Zhao, Y Jia, S Wang, T Zhao - Future Generation Computer …, 2024 - Elsevier
Drug sensitivity significantly influences therapeutic outcomes. Recent discoveries have
highlighted the pivotal role of miRNAs in regulating drug sensitivity by modulating genes …

ASGCL: Adaptive Sparse Map**-based graph contrastive learning network for cancer drug response prediction

Y Dong, Y Zhang, Y Qian, Y Zhao… - PLOS Computational …, 2025 - journals.plos.org
Personalized cancer drug treatment is emerging as a frontier issue in modern medical
research. Considering the genomic differences among cancer patients, determining the …

Accurate identification of snoRNA targets using variational graph autoencoder to advance the redevelopment of traditional medicines

Z Wang, Y Chen, H Ma, H Gao, Y Zhu… - Frontiers in …, 2025 - frontiersin.org
Existing studies indicate that dysregulation or abnormal expression of small nucleolar RNA
(snoRNA) is closely associated with various diseases, including lung cancer. Furthermore …