TIPS: “^” means “Equal Contribution”; “*” means “Contact Author”;

Pre-prints

• [BIORXIV] CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks. Guihai Feng, Xin Qin, Jiahao Zhang, Wuliang Huang, Yiyang Zhang, Wentao Cui, Shirui Li, Yao Chen, Wenhao Liu, Yao Tian, Yana Liu, Jingxi Dong, Ping Xu, Zhenpeng Man, Guole Liu, Zhongming Liang, Xinlong Jiang, Xiaodong Yang, Pengfei Wang, Ge Yang, Hongmei Wang, Xuezhi Wang, Ming-Han Tong, Yuanchun Zhou, Shihua Zhang, Yiqiang Chen, Yong Wang, Xin Li. 

• [ARXIV] Graph Soft-Contrastive Learning via Neighborhood Ranking. Zhiyuan Ning, Pengfei Wang, Pengyang Wang, Ziyue Qiao, Wei Fan, Denghui Zhang, Yi Du, Yuanchun Zhou. 

Publications 

2025

• [Advanced Science]  scCompass: An integrated cross-species scRNA-seq database for AI-ready. Pengfei Wang, Wenhao Liu, Jiajia Wang, Yana Liu, Pengjiang Li, Ping Xu, Wentao Cui, Ran Zhang, Qingqing Long, Zhilong Hu, Chen Fang, Jingxi Dong, Chunyang Zhang, Yan Chen, Chengrui Wang, Guole Liu, Hanyu Xie, Yiyang Zhang, Meng Xiao, Shubai Chen, X-Compass Consortium, Yiqiang Chen, Ge Yang, Shihua Zhang, Zhen Meng, Xuezhi Wang, Guihai Feng, Xin Li, Yuanchun Zhou. Advanced Science, 2025. 

• [AAAI] Motif-Oriented Representation Learning with Topology Refinement for Drug-Drug Interaction Prediction. Ran Zhang, Xuezhi Wang, Guannan Liu, Pengyang Wang, Yuanchun Zhou, Pengfei Wang*.  Proceedings of the AAAI Conference on Artificial Intelligence. 2025. 

• [Mathematics] Next Arrival and Destination Prediction via Spatiotemporal Embedding with Urban Geography and Human Mobility Data. Pengjiang Li, Zaitian Wang, Xinhao Zhang, Pengfei Wang, Kunpeng Liu. Mathematics, 2025. 

2024

• [Cell Research (Coevr story)] GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model. Xiaodong Yang, Guole Liu, Guihai Feng, Dechao Bu, Pengfei Wang, Jie Jiang, Shubai Chen, Qinmeng Yang, Yiyang Zhang, Zhenpeng Man, Zhongming Liang, Zichen Wang, Yaning Li, Zheng Li, Yana Liu, Yao Tian, Ao Li, Jingxi Dong, Zhilong Hu, Chen Fang, Hefan Miao, Lina Cui, Zixu Deng, Haiping Jiang, Wentao Cui, Jiahao Zhang, Zhaohui Yang, Handong Li, Xingjian He, Liqun Zhong, Jiaheng Zhou, Zijian Wang, Qingqing Long, Ping Xu, Hongmei Wang, Zhen Meng, Xuezhi Wang, Yangang Wang, Yong Wang, Shihua Zhang, Jingtao Guo, Yi Zhao, Yuanchun Zhou, Fei Li, Jing Liu, Yiqiang Chen, Ge Yang, Xin Li. Cell Research, 2024, 34(12): 830-845.

• [IJCAI] Make Graph Neural Networks Great Again: A Generic Integration Paradigm of Topology-Free Patterns for Traffic Speed Prediction. Yicheng Zhou^, Pengfei Wang^, Hao Dong, Denghui Zhang, Dingqi Yang, Yanjie Fu, Pengyang Wang. The 33rd International Joint Conference on Artificial Intelligence, 2024.  

• [IJCAI] FedGCS: A Generative Framework for Efficient Client Selection in Federated Learning via Gradient-based Optimization. Zhiyuan Ning, Chunlin Tian, Meng Xiao, Wei Fan, Pengyang Wang, Li Li*, Pengfei Wang*, Yuanchun Zhou. The 33rd International Joint Conference on Artificial Intelligence, 2024. 

• [IJCAI] TFWT: Tabular Feature Weighting with Transformer. Xinhao Zhang, Zaitian Wang, Lu Jiang, Wanfu Gao, Pengfei Wang*, Kunpeng Liu*. The 33rd International Joint Conference on Artificial Intelligence, 2024. 

• [WWW] Unveiling Delay Effects in Traffic Forecasting: A Perspective from Spatial-Temporal Delay Differential Equations. Qingqing Long, Zheng Fang, Chen Fang, Chong Chen, Pengfei Wang*, Yuanchun Zhou. The 2024 ACM Web Conference. 

• [AIJ] Temporal Inductive Path Neural Network for Temporal Knowledge Graph Reasoning. Hao Dong^, Pengyang Wang*, Meng Xiao, Zhiyuan Ning, Pengfei Wang*, Yuanchun Zhou. Artificial Intelligence, 2024. 

• [DASFAA] scCDCG: Efficient Deep Structural Clustering for single-cell RNA-seq via Deep Cut-informed Graph Embedding. Ping Xu, Zhiyuan Ning, Meng Xiao, Guihai Feng, Xin Li, Yuanchun Zhou, Pengfei Wang*. The 29th International Conference on Database Systems for Advanced Applications, 2024.

• [DASFAA] M2Mol: Multi-View Multi-Granularity Molecular Representation Learning for Property Prediction. Ran Zhang, Xuezhi Wang, Kunpeng Liu, Yuanchun Zhou, Pengfei Wang*. The 29th International Conference on Database Systems for Advanced Applications, 2024. 

2023

• [IJCAI] Adaptive Path-Memory Network for Temporal Knowledge Graph Reasoning. Hao Dong, Zhiyuan Ning, Pengyang Wang, Ziyue Qiao, Pengfei Wang*, Yuanchun Zhou, Yanjie Fu. The 32rd International Joint Conference on Artificial Intelligence, 2023. 

• [Briefings in Bioinformatics] HTCL-DDI: a hierarchical triple-view contrastive learning framework for drug–drug interaction prediction. Ran Zhang, Xuezhi Wang, Pengfei Wang*, Zhen Meng, Wenjuan Cui, Yuanchun Zhou. Briefings in Bioinformatics.

• [TWEB] Deep Adaptive Graph Clustering via von Mises-Fisher Distributions. Pengfei Wang, Daqing Wu, Chong Chen, Kunpeng Liu, Yanjie Fu, Jianqiang Huang, Yuanchun Zhou, Jianfeng Zhan, Xiansheng Hua. ACM Transactions on the Web.

• [TWEB] A Dual-Channel Semi-Supervised Learning Framework on Graphs via Knowledge Transfer and Meta-Learning. Ziyue Qiao, Pengyang Wang, Pengfei Wang, Zhiyuan Ning, Yanjie Fu, Yi Du, Yuanchun Zhou, Jianqiang Huang, Xian-Sheng Hua, Hui Xiong. ACM Transactions on the Web.

• [SDM] Hierarchical Reinforced Urban Planning: Jointly Steering Region and Block Configurations. Pengfei Wang, Daniel Wang, Kunpeng Liu, Dongjie Wang, Yuanchun Zhou, Leilei Sun, Yanjie Fu. Proceedings of the 2023 SIAM International Conference on Data Mining (SDM).

• [SDM] Traceable Automatic Feature Transformation via Cascading Actor-Critic Agents. Meng Xiao, Dongjie Wang, Min Wu, Ziyue Qiao, Pengfei Wang, Kunpeng Liu, Yuanchun Zhou, Yanjie Fu. Proceedings of the 2023 SIAM International Conference on Data Mining (SDM). 

• [Remote Sensing] Dynamic High-Resolution Network for Semantic Segmentation in Remote-Sensing Images. Shichen Guo, Qi Yang, Shiming Xiang, Pengfei Wang, Xuezhi Wang. Remote Sensing.

2022

• [SDM] Unifying Human Mobility Forecasting and Trajectory Semantics Augmentation via Hawkes Process Based LSTM. Pengfei Wang, K Liu, Y Zhou, Y Fu. Proceedings of the 2022 SIAM International Conference on Data Mining (SDM).

2021

• [ICDM] Efficient Reinforced Feature Selection via Early Stopping Traverse Strategy. K Liu^, Pengfei Wang^, D Wang, W Du, DO Wu, Y Fu2021 IEEE International Conference on Data Mining (ICDM).

• [ICDM] Composition-Enhanced Graph Collaborative Filtering for Multi-behavior Recommendation. D Wu, X Luo, Z Ma, C Chen, Pengfei Wang, M Deng, J Ma2021 IEEE International Conference on Data Mining (ICDM).

• [TKDE] Urban Traffic Light Control via Active Multi-agent Communication and Supply-Demand Modeling. X Guo, Z Yu, Pengfei Wang, Z Jin, J Huang, D Cai, X He, X HuaIEEE Transactions on Knowledge and Data Engineering.

2020

• [ICDM] Tree Structure-Aware Graph Representation Learning via Integrated Hierarchical Aggregation and Relational Metric Learning. Z Qiao, P Wang, Y Fu, Y Du, Pengfei Wang, Y Zhou. 2020 IEEE International Conference on Data Mining (ICDM).

2019

• [KDD] Automating Feature Subspace Exploration via Multi-Agent Reinforcement Learning. K Liu, Y Fu, P Wang, L Wu, R Bo, X Li. Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining.

• [Big Data] Unsupervised Author Disambiguation using Heterogeneous Graph Convolutional Network Embedding. Z Qiao, Y Du, Y Fu, Pengfei Wang, Y Zhou2019 IEEE International Conference on Big Data (Big Data).

2018

• [KDD] You Are How You Drive: Peer and Temporal-Aware Representation Learning for Driving Behavior Analysis. P Wang, Y Fu, J Zhang, Pengfei Wang, Y Zheng, C AggarwalProceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining.

2017

• [KDD] Human Mobility Synchronization and Trip Purpose Detection with Mixture of Hawkes Processes. Pengfei Wang^, Y Fu^, G Liu, W Hu, C AggarwalProceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining.

• [TIST] Spotting trip purposes from taxi trajectories: A general probabilistic model. Pengfei Wang, G Liu, Y Fu, Y Zhou, J Li. ACM Transactions on Intelligent Systems and Technology (TIST).

• [Neurocomputing] An algorithm for event detection based on social media data. W Cui, Pengfei Wang, Y Du, X Chen, D Guo, J Li, Y Zhou Neurocomputing.

2016

• [DASSFA] How to use the social media data in assisting restaurant recommendation. W Cui, Pengfei Wang, X Chen, Y Du, D Guo, Y Zhou, J LiInternational Conference on Database Systems for Advanced Applications.