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)

Counterfactual and Factual Reasoning over Hypergraphs for Interpretable Clinical Predictions on EHR. - Ran Xu 002; Yue Yu 001; Chao Zhang 014; Mohammed K. Ali; Joyce C. Ho; Carl Yang 001 (ML4H@NeurIPS, 2022)

Cold-Start Data Selection for Few-shot Language Model Fine-tuning: A Prompt-Based Uncertainty Propagation Approach. - Yue Yu 001; Rongzhi Zhang; Ran Xu 002; Jieyu Zhang 001; Jiaming Shen; Chao Zhang 014 (CoRR, 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)

Cold-Start Data Selection for Better Few-shot Language Model Fine-tuning: A Prompt-based Uncertainty Propagation Approach. - Yue Yu 001; Rongzhi Zhang; Ran Xu 002; Jieyu Zhang 001; Jiaming Shen; Chao Zhang 014 (ACL (1), 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)

Weakly-Supervised Scientific Document Classification via Retrieval-Augmented Multi-Stage Training. - Ran Xu 002; Yue Yu 001; Joyce C. Ho; Carl Yang 001 (SIGIR, 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)

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)

RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records. - Ran Xu 002; Wenqi Shi; Yue Yu 001; Yuchen Zhuang; Bowen Jin; May Dongmei Wang; Joyce C. Ho; Carl Yang 001 (ACL (Short Papers), 2024)

From Basic to Extra Features: Hypergraph Transformer Pretrain-then-Finetuning for Balanced Clinical Predictions on EHR. - Ran Xu 002; Yiwen Lu; Chang Liu; Yong Chen 016; Yan Sun; Xiao Hu 002; Joyce C. Ho; Carl Yang 001 (CHIL, 2024)

BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers. - Ran Xu 002; Wenqi Shi; Yue Yu 001; Yuchen Zhuang; Yanqiao Zhu 001; May Dongmei Wang; Joyce C. Ho; Chao Zhang 014; Carl Yang 001 (EMNLP, 2024)

MedAdapter: Efficient Test-Time Adaptation of Large Language Models Towards Medical Reasoning. - Wenqi Shi; Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Haotian Sun; Hang Wu; Carl Yang 001; May Dongmei Wang (EMNLP, 2024)

EHRAgent: Code Empowers Large Language Models for Few-shot Complex Tabular Reasoning on Electronic Health Records. - Wenqi Shi; Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Jieyu Zhang 001; Hang Wu; Yuanda Zhu; Joyce C. Ho; Carl Yang 001; May Dongmei Wang (EMNLP, 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)

EHRAgent: Code Empowers Large Language Models for Complex Tabular Reasoning on Electronic Health Records. - Wenqi Shi; Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Jieyu Zhang 001; Hang Wu; Yuanda Zhu; Joyce C. Ho; Carl Yang 001; May D. Wang (CoRR, 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)

MedAdapter: Efficient Test-Time Adaptation of Large Language Models towards Medical Reasoning. - Wenqi Shi; Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Hang Wu; Carl Yang 001; May D. Wang (CoRR, 2024)

Boosting Reward Model with Preference-Conditional Multi-Aspect Synthetic Data Generation. - Jiaming Shen; Ran Xu 002; Yennie Jun; Zhen Qin 001; Tianqi Liu 002; Carl Yang 001; Yi Liang; Simon Baumgartner; Michael Bendersky (CoRR, 2024)

SimRAG: Self-Improving Retrieval-Augmented Generation for Adapting Large Language Models to Specialized Domains. - Ran Xu 002; Hui Liu 003; Sreyashi Nag; Zhenwei Dai; Yaochen Xie; Xianfeng Tang; Chen Luo 003; Yang Li 055; Joyce C. Ho; Carl Yang 001; Qi He 002 (CoRR, 2024)

Knowledge Graph and Large Language Model Co-learning via Structure-oriented Retrieval Augmented Generation. - Carl Yang 001; Ran Xu 002; Linhao Luo; Shirui Pan (IEEE Data Eng. Bull., 2024)

SimRAG: Self-Improving Retrieval-Augmented Generation for Adapting Large Language Models to Specialized Domains. - Ran Xu 002; Hui Liu 031; Sreyashi Nag; Zhenwei Dai; Yaochen Xie; Xianfeng Tang; Chen Luo 003; Yang Li 055; Joyce C. Ho; Carl Yang 001; Qi He 002 (NAACL (Long Papers), 2025)

MedAssist: LLM-Empowered Medical Assistant for Assisting the Scrutinization and Comprehension of Electronic Health Records. - Ran Xu 002; Wenqi Shi; Jonathan Wang; Jasmine Zhou; Carl Yang 001 (WWW (Companion Volume), 2025)

Collab-RAG: Boosting Retrieval-Augmented Generation for Complex Question Answering via White-Box and Black-Box LLM Collaboration. - Ran Xu 002; Wenqi Shi; Yuchen Zhuang; Yue Yu 001; Joyce C. Ho; Haoyu Wang; Carl Yang 001 (CoRR, 2025)

MedAgentGym: Training LLM Agents for Code-Based Medical Reasoning at Scale. - Ran Xu 002; Yuchen Zhuang; Yishan Zhong; Yue Yu 001; Xiangru Tang; Hang Wu; May D. Wang; Peifeng Ruan; Donghan Yang; Tao Wang 006; Guanghua Xiao; Carl Yang 001; et al. (CoRR, 2025)

HypKG: Hypergraph-based Knowledge Graph Contextualization for Precision Healthcare. - Yuzhang Xie; Xu Han; Ran Xu 002; Xiao Hu 002; Jiaying Lu 001; Carl Yang 001 (CoRR, 2025)

RAG in the Wild: On the (In)effectiveness of LLMs with Mixture-of-Knowledge Retrieval Augmentation. - Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Haoyu Wang; Wenqi Shi; Carl Yang 001 (CoRR, 2025)