A Method to Predict the Performance and Storage of Executing Contract for Ethereum Consortium-Blockchain. - Huijuan Zhang; Chengxin Jin; Hejie Cui (ICBC, 2018)

Pulmonary Vessel Segmentation Based on Orthogonal Fused U-Net++ of Chest CT Images. - Hejie Cui; Xinglong Liu; Ning Huang (MICCAI (6), 2019)

Zero-Shot Scene Graph Relation Prediction Through Commonsense Knowledge Integration. - Xuan Kan; Hejie Cui; Carl Yang 001 (ECML/PKDD (2), 2021)

BrainNNExplainer: An Interpretable Graph Neural Network Framework for Brain Network based Disease Analysis. - Hejie Cui; Wei Dai 013; Yanqiao Zhu 001; Xiaoxiao Li; Lifang He 001; Carl Yang 001 (CoRR, 2021)

Effective and Interpretable fMRI Analysis via Functional Brain Network Generation. - Xuan Kan; Hejie Cui; Ying Guo 003; Carl Yang 001 (CoRR, 2021)

Structure-Aware Hard Negative Mining for Heterogeneous Graph Contrastive Learning. - Yanqiao Zhu 001; Yichen Xu; Hejie Cui; Carl Yang 001; Qiang Liu 006; Shu Wu (CoRR, 2021)

Multi-View Brain Network Analysis with Cross-View Missing Network Generation. - Gongxu Luo; Chenyang Li; Hejie Cui; Lichao Sun 001; Lifang He 001; Carl Yang 001 (BIBM, 2022)

BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networks (Extended Abstract). - Hejie Cui; Wei Dai 013; Yanqiao Zhu 001; Xuan Kan; Antonio Aodong Chen Gu; Joshua Lukemire; Liang Zhan; Lifang He 001; Ying Guo 003; Carl Yang 001 (IEEE Big Data, 2022)

Transformer-Based Hierarchical Clustering for Brain Network Analysis (Extended Abstract). - Wei Dai 013; Hejie Cui; Xuan Kan; Ying Guo 003; Carl Yang 001 (IEEE Big Data, 2022)

Pre-train Graph Neural Networks for Brain Network Analysis (Extended Abstract). - Yi Yang 094; Hejie Cui; Carl Yang 001 (IEEE Big Data, 2022)

Learning Task-Aware Effective Brain Connectivity for fMRI Analysis with Graph Neural Networks (Extended Abstract). - Yue Yu 001; Xuan Kan; Hejie Cui; Ran Xu 002; Yujia Zheng 001; Xiangchen Song; Yanqiao Zhu 001; Kun Zhang 001; Razieh Nabi; Ying Guo 003; Chao Zhang 014; Carl Yang 001 (IEEE Big Data, 2022)

On Positional and Structural Node Features for Graph Neural Networks on Non-attributed Graphs. - Hejie Cui; Zijie Lu; Pan Li 005; Carl Yang 001 (CIKM, 2022)

How Can Graph Neural Networks Help Document Retrieval: A Case Study on CORD19 with Concept Map Generation. - Hejie Cui; Jiaying Lu 001; Yao Ge 003; Carl Yang 001 (ECIR (2), 2022)

Joint Embedding of Structural and Functional Brain Networks with Graph Neural Networks for Mental Illness Diagnosis. - Yanqiao Zhu 001; Hejie Cui; Lifang He 001; Lichao Sun 001; Carl Yang 001 (EMBC, 2022)

Data-Efficient Brain Connectome Analysis via Multi-Task Meta-Learning. - Yi Yang 094; Yanqiao Zhu 001; Hejie Cui; Xuan Kan; Lifang He 001; Ying Guo 003; Carl Yang 001 (KDD, 2022)

Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysis. - Hejie Cui; Wei Dai 013; Yanqiao Zhu 001; Xiaoxiao Li; Lifang He 001; Carl Yang 001 (MICCAI (8), 2022)

FBNETGEN: Task-aware GNN-based fMRI Analysis via Functional Brain Network Generation. - Xuan Kan; Hejie Cui; Joshua Lukemire; Ying Guo 003; Carl Yang 001 (MIDL, 2022)

Brain Network Transformer. - Xuan Kan; Wei Dai 013; Hejie Cui; Zilong Zhang; Ying Guo 003; Carl Yang 001 (NeurIPS, 2022)

Structure-Enhanced Heterogeneous Graph Contrastive Learning. - Yanqiao Zhu 001; Yichen Xu; Hejie Cui; Carl Yang 001; Qiang Liu 006; Shu Wu (SDM, 2022)

Learning Task-Aware Effective Brain Connectivity for fMRI Analysis with Graph Neural Networks. - Yue Yu 001; Xuan Kan; Hejie Cui; Ran Xu 002; Yujia Zheng 001; Xiangchen Song; Yanqiao Zhu 001; Kun Zhang 001; Razieh Nabi; Ying Guo 003; Chao Zhang 014; Carl Yang 001 (CoRR, 2022)

Neighborhood-Regularized Self-Training for Learning with Few Labels. - Ran Xu 002; Yue Yu 001; Hejie Cui; Xuan Kan; Yanqiao Zhu 001; Joyce C. Ho; Chao Zhang 014; Carl Yang 001 (AAAI, 2023)

PV2TEA: Patching Visual Modality to Textual-Established Information Extraction. - Hejie Cui; Rongmei Lin; Nasser Zalmout; Chenwei Zhang; Jingbo Shang; Carl Yang 001; Xian Li (ACL (Findings), 2023)

Dynamic Brain Transformer with Multi-Level Attention for Functional Brain Network Analysis. - Xuan Kan; Antonio Aodong Chen Gu; Hejie Cui; Ying Guo 003; Carl Yang 001 (BHI, 2023)

PTGB: Pre-Train Graph Neural Networks for Brain Network Analysis. - Yi Yang 094; Hejie Cui; Carl Yang 001 (CHIL, 2023)

Transformer-Based Hierarchical Clustering for Brain Network Analysis. - Wei Dai 013; Hejie Cui; Xuan Kan; Ying Guo 003; Sanne J. H. van Rooij; Carl Yang 001 (ISBI, 2023)

Deep Dag Learning of Effective Brain Connectivity for FMRI Analysis. - Yue Yu 001; Xuan Kan; Hejie Cui; Ran Xu 002; Yujia Zheng 001; Xiangchen Song; Yanqiao Zhu 001; Kun Zhang 001; Razieh Nabi; Ying Guo 003; Chao Zhang 014; Carl Yang 001 (ISBI, 2023)

R-Mixup: Riemannian Mixup for Biological Networks. - Xuan Kan; Zimu Li; Hejie Cui; Yue Yu 001; Ran Xu 002; Shaojun Yu; Zilong Zhang; Ying Guo 003; Carl Yang 001 (KDD, 2023)

Open Visual Knowledge Extraction via Relation-Oriented Multimodality Model Prompting. - Hejie Cui; Xinyu Fang; Zihan Zhang; Ran Xu 002; Xuan Kan; Xin Liu 039; Yue Yu 001; Manling Li; Yangqiu Song; Carl Yang 001 (NeurIPS, 2023)

Beyond One-Model-Fits-All: A Survey of Domain Specialization for Large Language Models. - Chen Ling 003; Xujiang Zhao; Jiaying Lu 001; Chengyuan Deng; Can Zheng; Junxiang Wang; Tanmoy Chowdhury; Yun Li 005; Hejie Cui; Xuchao Zhang; Tianjiao Zhao; Amit Panalkar; et al. (CoRR, 2023)

A Survey on Knowledge Graphs for Healthcare: Resources, Applications, and Promises. - Hejie Cui; Jiaying Lu 001; Shiyu Wang 002; Ran Xu 002; Wenjing Ma; Shaojun Yu; Yue Yu 001; Xuan Kan; Chen Ling 003; Joyce C. Ho; Fei Wang; Carl Yang 001 (CoRR, 2023)

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models. - Ran Xu 002; Hejie Cui; Yue Yu 001; Xuan Kan; Wenqi Shi; Yuchen Zhuang; Wei Jin 009; Joyce C. Ho; Carl Yang 001 (CoRR, 2023)

BrainGB: A Benchmark for Brain Network Analysis With Graph Neural Networks. - Hejie Cui; Wei Dai 013; Yanqiao Zhu 001; Xuan Kan; Antonio Aodong Chen Gu; Joshua Lukemire; Liang Zhan; Lifang He 001; Ying Guo 003; Carl Yang 001 (IEEE Trans. Medical Imaging, 2023)

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models. - Ran Xu 002; Hejie Cui; Yue Yu 001; Xuan Kan; Wenqi Shi; Yuchen Zhuang; May Dongmei Wang; Wei Jin 009; Joyce C. Ho; Carl Yang 001 (ACL (Findings), 2024)

Multi-task Learning for Brain Network Analysis in the ABCD Study. - Xuan Kan; Hejie Cui; Keqi Han; Ying Guo 003; Carl Yang 001 (BHI, 2024)

TACCO: Task-guided Co-clustering of Clinical Concepts and Patient Visits for Disease Subtyping based on EHR Data. - Ziyang Zhang; Hejie Cui; Ran Xu 002; Yuzhang Xie; Joyce C. Ho; Carl Yang 001 (KDD, 2024)

Biomedical Visual Instruction Tuning with Clinician Preference Alignment. - Hejie Cui; Lingjun Mao; Xin Liang; Jieyu Zhang 001; Hui Ren 001; Quanzheng Li; Xiang Li 001; Carl Yang 001 (NeurIPS, 2024)

Microstructures and Accuracy of Graph Recall by Large Language Models. - Yanbang Wang; Hejie Cui; Jon M. Kleinberg (NeurIPS, 2024)

Multimodal Fusion of EHR in Structures and Semantics: Integrating Clinical Records and Notes with Hypergraph and LLM. - Hejie Cui; Xinyu Fang; Ran Xu 002; Xuan Kan; Joyce C. Ho; Carl Yang 001 (CoRR, 2024)

LLMs-based Few-Shot Disease Predictions using EHR: A Novel Approach Combining Predictive Agent Reasoning and Critical Agent Instruction. - Hejie Cui; Zhuocheng Shen; Jieyu Zhang 001; Hui Shao; Lianhui Qin; Joyce C. Ho; Carl Yang 001 (CoRR, 2024)

A review on knowledge graphs for healthcare: Resources, applications, and promises. - Hejie Cui; Jiaying Lu 001; Ran Xu 002; Shiyu Wang 002; Wenjing Ma; Yue Yu 001; Shaojun Yu; Xuan Kan; Chen Ling 003; Liang Zhao 002; Zhaohui S. Qin; Joyce C. Ho; et al. (J. Biomed. Informatics, 2025)

Recent Advances, Applications and Open Challenges in Machine Learning for Health: Reflections from Research Roundtables at ML4H 2024 Symposium. - Amin Adibi; Xu Cao; Zongliang Ji; Jivat Neet Kaur; Winston Chen; Elizabeth Healey; Brighton Nuwagira; Wenqian Ye; Geoffrey Woollard; Maxwell A. Xu; Hejie Cui; Johnny Xi; et al. (CoRR, 2025)

TIMER: Temporal Instruction Modeling and Evaluation for Longitudinal Clinical Records. - Hejie Cui; Alyssa Unell; Bowen Chen; Jason Alan Fries; Emily Alsentzer; Sanmi Koyejo; Nigam Shah (CoRR, 2025)

CLIMB: Data Foundations for Large Scale Multimodal Clinical Foundation Models. - Wei Dai 013; Peilin Chen; Malinda Lu; Daniel Li; Haowen Wei; Hejie Cui; Paul Pu Liang (CoRR, 2025)

MedHELM: Holistic Evaluation of Large Language Models for Medical Tasks. - Suhana Bedi; Hejie Cui; Miguel Fuentes; Alyssa Unell; Michael Wornow; Juan M. Banda; Nikesh Kotecha; Timothy Keyes; Yifan Mai 001; Mert Oez; Hao Qiu; Shrey Jain; et al. (CoRR, 2025)

KERAP: A Knowledge-Enhanced Reasoning Approach for Accurate Zero-shot Diagnosis Prediction Using Multi-agent LLMs. - Yuzhang Xie; Hejie Cui; Ziyang Zhang; Jiaying Lu 001; Kai Shu; Fadi B. Nahab; Xiao-Hu Zhou; Carl Yang 001 (CoRR, 2025)