Publications

Ziheng Duan, Siwei Xu, Shushrruth Sai Srinivasan, Ahyeon Hwang, Che Yu Lee, Feng Yue, Mark Gerstein, Yu Luan, Matthew Girgenti, Jing Zhang (2024). scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings in Bioinformatics.

PDF Cite Code DOI

Ziheng Duan, CheYu Lee, Jing Zhang (2023). ExAD-GNN: explainable graph neural network for Alzheimer’s disease state prediction from single-cell data. APSIPA Transactions on Signal and Information Processing.

PDF Cite Code DOI

Ziheng Duan, Yi Dai, Ahyeon Hwang, CheYu Lee, Kaichi Xie, Chutong Xiao, Min Xu, Matthew J. Girgenti, Jing Zhang (2023). iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease. Plos Computational Biology.

PDF Cite Code DOI

Ruiyi Zhang, Ziheng Duan, CheYu Lee, Dylan Riffle, Martin Renqiang Min, Jing Zhang (2023). Turtling: A Time-aware Neural Topic Model on NIH Grant Data. Bioinformatics Advances.

PDF Cite Code DOI

Che Yu Lee, Yuhang Chen, Ziheng Duan, Min Xu, Matthew J. Girgenti, Ke Xu, Mark Gerstein, Jing Zhang (2022). Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data. Plos Computational Biology.

PDF Cite Code DOI

Ziheng Duan, Haoyan Xu, Yueyang Wang, Yida Huang, Anni Ren, Yizhou Sun, Wei Wang (2022). Multivariate Time Series Classification with Hierarchical Variational Graph Pooling. Neural Networks.

PDF Cite Code DOI

Ziheng Duan, Haoyan Xu, Yida Huang, Jie Feng, Yueyang Wang (2022). Multivariate Time Series Forecasting with Transfer Entropy Graph. Tsinghua Science and Technology.

PDF Cite Code DOI

Ziheng Duan, Yueyang Wang, Weihao Ye, Qilin Fan, Xiuhua Li (2022). Connecting Latent ReLationships over Heterogeneous Attributed Network for Recommendation. Applied Intelligence.

PDF Cite Code DOI

Yueyang Wang, Ziheng Duan, Yida Huang, Haoyan Xu, Jie Feng, Anni Ren (2021). MTHetGNN: a heterogeneous graph embedding framework for multivariate time series forecasting. Pattern Recognition Letter.

PDF Cite Code DOI

Haoyan Xu, Ziheng Duan, Yueyan Wang, Jie Feng, Runjian Chen, Qianru Zhang, Zhongbin Xu (2021). Graph Partitioning and Graph Neural Network based Hierarchical Graph Matching for Graph Similarity Computation. Neurocomputing.

PDF Cite Code DOI

Zhehan Liao, Yizhang Yang, Chengfeng Sun, Ruiqi Wu, Ziheng Duan, Yueyang Wang, Xipeng Li, Jian Xu (2021). Image-based prediction of granular flow behaviors in a wedge-shaped hopper by combing DEM and deep learning methods. Powder Technology.

Dufan Wu, Daniel Montes, Ziheng Duan, Yangsibo Huang, Javier M. Romero, Ramon Gilberto Gonzalez, Quanzheng Li (2021). Deep Learning Based Detection and Localization of Cerebal Aneurysms in Computed Tomography Angiography.

Li Liu, Xianghao Zhan, Ziheng Duan, Yi Wu, Rumeng Wu, Xiaoqing Guan, Zhan Wang, You Wang, Guang Li (2021). Classifying herbal medicine origins by temporal and spectral data mining of electronic nose.

Yifu Zhou, Ziheng Duan, Haoyan Xu, Jie Feng, Anni Ren, Yueyang Wang, Xiaoqian Wang (2020). Parallel Extraction of Long-term Trends and Short-term Fluctuation Framework for Multivariate Time Series Forecasting.

Haoyan Xu, Runjian Chen, Yunsheng Bai, Ziheng Duan, Jie Feng, Ke Luo, Yizhou Sun, Wei Wang (2020). CoSimGNN: Towards Large-scale Graph Similarity Computation.

Boxing Wang, Chunlin Zhou, Ziheng Duan, Qichao Zhu, Jun Wu, Rong Xiong (2019). Untethered quadrupedal hopping and bounding on a trampoline. Frontiers of Mechanical Engineering.

Yueyang Wang, Ziheng Duan, Binbing Liao, Fei Wu, Yueting Zhuang (2019). Heterogeneous Attributed Network Embedding with Graph Convolutional Networks. AAAI-2019.