HNGRNMF: Heterogeneous Network-based Graph Regularized Nonnegative Matrix Factorization for predicting events of microbe-disease associations. - Wen Zhang 008; Xiaoting Lu; Weitai Yang; Feng Huang 004; Binlu Wang; Alan Wang; Qi Zhao (BIBM, 2018)

Prediction of Drug-Disease Associations and Their Effects by Signed Network-Based Nonnegative Matrix Factorization. - Wen Zhang 008; Feng Huang 004; Xiang Yue; Xiaoting Lu; Weitai Yang; Zhishuai Li; Feng Liu (BIBM, 2018)

The Bi-Direction Similarity Integration Method for Predicting Microbe-Disease Associations. - Wen Zhang 008; Weitai Yang; Xiaoting Lu; Feng Huang 004; Fei Luo 004 (IEEE Access, 2018)

Predicting drug-disease associations by using similarity constrained matrix factorization. - Wen Zhang 008; Xiang Yue; Weiran Lin; Wenjian Wu; Ruoqi Liu; Feng Huang 004; Feng Liu (BMC Bioinform., 2018)

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions. - Wen Zhang 008; Xiang Yue; Guifeng Tang; Wenjian Wu; Feng Huang 004; Xining Zhang (PLoS Comput. Biol., 2018)

Predicting microRNA-disease associations from knowledge graph using tensor decomposition with relational constraints. - Feng Huang 004; Zhankun Xiong; Guan Zhang; Zhouxin Yu; Xinran Xu; Wen Zhang 008 (CoRR, 2019)

SFLLN: A sparse feature learning ensemble method with linear neighborhood regularization for predicting drug-drug interactions. - Wen Zhang 008; Kanghong Jing; Feng Huang 004; Yanlin Chen 002; Bolin Li; Jinghao Li; Jing Gong (Inf. Sci., 2019)

CSGNN: Contrastive Self-Supervised Graph Neural Network for Molecular Interaction Prediction. - Chengshuai Zhao; Shuai Liu 017; Feng Huang 004; Shichao Liu 002; Wen Zhang 008 (IJCAI, 2021)

Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations. - Feng Huang 004; Xiang Yue; Zhankun Xiong; Zhouxin Yu; Shichao Liu 002; Wen Zhang 008 (Briefings Bioinform., 2021)

Predicting drug-disease associations through layer attention graph convolutional network. - Zhouxin Yu; Feng Huang 004; Xiaohan Zhao; Wenjie Xiao; Wen Zhang 008 (Briefings Bioinform., 2021)

HampDTI: a heterogeneous graph automatic meta-path learning method for drug-target interaction prediction. - Hongzhun Wang; Feng Huang 004; Wen Zhang 008 (CoRR, 2021)

A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations. - Wen Zhang 008; Zhishuai Li; Wenzheng Guo; Weitai Yang; Feng Huang 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

GraphCDR: a graph neural network method with contrastive learning for cancer drug response prediction. - Xuan Liu; Congzhi Song; Feng Huang 004; Haitao Fu; Wenjie Xiao; Wen Zhang 008 (Briefings Bioinform., 2022)

A heterogeneous network-based method with attentive meta-path extraction for predicting drug-target interactions. - Hongzhun Wang; Feng Huang 004; Zhankun Xiong; Wen Zhang 008 (Briefings Bioinform., 2022)

MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks. - Haitao Fu; Feng Huang 004; Xuan Liu; Yang Qiu; Wen Zhang 008 (Bioinform., 2022)

Hierarchical graph representation learning for the prediction of drug-target binding affinity. - Zhaoyang Chu; Feng Huang 004; Haitao Fu; Yuan Quan; Xionghui Zhou; Shichao Liu 002; Wen Zhang 008 (Inf. Sci., 2022)

A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs. - Zhankun Xiong; Feng Huang 004; Ziyan Wang; Shichao Liu 002; Wen Zhang 008 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Multi-Relational Contrastive Learning Graph Neural Network for Drug-Drug Interaction Event Prediction. - Zhankun Xiong; Shichao Liu 002; Feng Huang 004; Ziyan Wang; Xuan Liu; Zhongfei Zhang; Wen Zhang 008 (AAAI, 2023)

Multi-view Contrastive Learning Hypergraph Neural Network for Drug-Microbe-Disease Association Prediction. - Luotao Liu; Feng Huang 004; Xuan Liu; Zhankun Xiong; Menglu Li; Congzhi Song; Wen Zhang 008 (IJCAI, 2023)

HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction. - Shen Han; Haitao Fu; Yuyang Wu; Ganglan Zhao; Zhenyu Song; Feng Huang 004; Zhongfei Zhang; Shichao Liu 002; Wen Zhang 008 (Briefings Bioinform., 2023)

A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation. - Yongkang Wang; Xuan Liu; Feng Huang 004; Zhankun Xiong; Wen Zhang 008 (AAAI, 2024)

ZeroDDI: A Zero-Shot Drug-Drug Interaction Event Prediction Method with Semantic Enhanced Learning and Dual-modal Uniform Alignment. - Ziyan Wang; Zhankun Xiong; Feng Huang 004; Xuan Liu; Wen Zhang 008 (IJCAI, 2024)

Heterogeneous Causal Metapath Graph Neural Network for Gene-Microbe-Disease Association Prediction. - Kexin Zhang; Feng Huang 004; Luotao Liu; Zhankun Xiong; Hongyu Zhang; Yuan Quan; Wen Zhang 008 (IJCAI, 2024)

Coefficient Decomposition for Spectral Graph Convolution. - Feng Huang 004; Wen Zhang 008 (CoRR, 2024)

PKAG-DDI: Pairwise Knowledge-Augmented Language Model for Drug-Drug Interaction Event Text Generation. - Ziyan Wang; Zhankun Xiong; Feng Huang 004; Wen Zhang 008 (ACL (1), 2025)