Selected Publications

Hejie Cui*, Lingjun Mao*, Xin Liang, Jieyu Zhang, Hui Ren, Quanzheng Li, Xiang Li, Carl Yang (2024). Biomedical Visual Instruction Tuning with Clinician Preference Alignment. The Conference on Neural Information Processing Systems (NeurIPS).

PDF Code Dataset Project Source Document

Yanbang Wang, Hejie Cui, Jon Kleinberg (2024). Microstructures and Accuracy of Graph Recall by Large Language Models. The Conference on Neural Information Processing Systems (NeurIPS). Abstract version accepted to International Conference on Computational Social Science (IC2S2) (Oral).

Hejie Cui, Zhuocheng Shen, Jieyu Zhang, Hui Shao, Lianhui Qin, Joyce C Ho, Carl Yang (2024). LLMs-based Few-Shot Disease Predictions using EHR: A Novel Approach Combining Predictive Agent Reasoning and Critical Agent Instruction. American Medical Informatics Association (AMIA) Annual Symposium (Oral).

Ziyang Zhang, Hejie Cui, Ran Xu, Yuzhang Xie, Joyce C Ho, Carl Yang (2024). TACCO: Task-guided Co-clustering of Clinical Concepts and Patient Visits for Disease Subtyping based on EHR Data. ACM International Conference on Knowledge Discovery and Data Mining (KDD).

Hejie Cui, Xuan Kan, Xiaoxiao Li, Ying Guo, Lifang He, Liang Zhan, Carl Yang (2024). Brain Network Analysis with Graph Neural Network. Tutorial at the IEEE International Symposium on Biomedical Imaging (ISBI).

Ran Xu, Hejie Cui, Yue Yu, Xuan Kan, Wenqi Shi, Yuchen Zhuang, Wei Jin, Joyce C Ho, Carl Yang (2023). Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models. Annual Meeting of the Association for Computational Linguistics (ACL-Findings).

Hejie Cui*, Xinyu Fang*, Zihan Zhang, Ran Xu, Xuan Kan, Xin Liu, Manling Li, Yangqiu Song, Carl Yang (2023). Open Visual Knowledge Extraction via Relation-Oriented Multimodality Model Prompting. Neural Information Processing Systems (NeurIPS).

Hejie Cui, Jiaying Lu, Shiyu Wang, Ran Xu, Wenjing Ma, Shaojun Yu, Yue Yu, Xuan Kan, Chen Ling, Tianfan Fu, Liang Zhao, Joyce C Ho, Fei Wang, Carl Yang (2023). A Review on Knowledge Graphs for Healthcare: Resources, Applications, and Promises. arXiv preprint.

Xuan Kan, Zimu Li, Hejie Cui, Yue Yu, Ran Xu, Shaojun Yu, Zilong Zhang, Ying Guo, Carl Yang (2023). R-Mixup: Riemannian Mixup for Biological Networks. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD).

Hejie Cui, Rongmei Lin, Nasser Zalmout, Chenwei Zhang, Jingbo Shang, Carl Yang, Xian Li (2023). PV2TEA: Patching Visual Modality to Textual-Established Information Extraction. Annual Meeting of the Association for Computational Linguistics (ACL-Findings).

Yi Yang, Hejie Cui, Carl Yang (2023). PTGB: Pre-Train Graph Neural Networks for Brain Network Analysis. The Conference on Health, Inference, and Learning (CHIL) (Oral).

Hejie Cui, Xuan Kan, Xiaoxiao Li, Lifang He, Liang Zhan, Ying Guo, Carl Yang (2023). Brain Network Analysis with Graph Neural Network. Tutorial at the International Conference on Intelligent Biology and Medicine (ICIBM).

Ran Xu, Yue Yu, Hejie Cui, Xuan Kan, Yanqiao Zhu, Joyce C Ho, Chao Zhang, Carl Yang (2023). Neighborhood-regularized Self-Training for Learning with Few Labels. The AAAI International Conference on Artificial Intelligence (AAAI) (Oral).

Hejie Cui, Wei Dai, Yanqiao Zhu, Xuan Kan, Antonio Aodong Chen Gu, Joshua Lukemire, Liang Zhan, Lifang He, Ying Guo, Carl Yang (2022). BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networks. IEEE Transactions on Medical Imaging (TMI) (IF: 11.037).

Xuan Kan, Wei Dai, Hejie Cui, Zilong Zhang, Ying Guo, Carl Yang (2022). Brain Network Transformer. The Conference on Neural Information Processing Systems (NeurIPS) (Spotlight).

Hejie Cui, Zijie Lu, Pan Li, Carl Yang (2022). On Positional and Structural Node Features for Graph Neural Networks on Non-attributed Graphs. The International Conference on Information and Knowledge Management (CIKM) (Most Influential CIKM Paper of 2022).

Hejie Cui, Wei Dai, Yanqiao Zhu, Xiaoxiao Li, Lifang He, Carl Yang (2022). Interpretable GNNs for Connectome-Based Brain Disorder Analysis. The International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) (Oral).

Xuan Kan, Hejie Cui, Joshua Lukemire, Ying Guo, Carl Yang (2022). FBNetGen: Task-aware GNN-based fMRI Analysis via Functional Brain Network Generation. The International Conference on Medical Imaging with Deep Learning (MIDL) (Oral).

Hejie Cui, Jiaying Lu, Yao Ge, Carl Yang (2022). How Can Graph Neural Networks Help Document Retrieval: A Case Study on CORD19 with Concept Map Generation. The European Conference on Information Retrieval (ECIR).

Xuan Kan, Hejie Cui, Carl Yang (2021). Zero-Shot Scene Graph Relation Prediction through Commonsense Knowledge Integration. The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML).

Hejie Cui, Xinglong Liu, Ning Huang (2019). Pulmonary Vessel Segmentation based on Orthogonal Fused U-Net++ of Chest CT Images. The International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI).