Neural Models for Reasoning over Multiple Mentions Using Coreference. - Bhuwan Dhingra; Qiao Jin 001; Zhilin Yang 001; William W. Cohen; Ruslan Salakhutdinov (NAACL-HLT (2), 2018)

Deep Contextualized Biomedical Abbreviation Expansion. - Qiao Jin 001; Jinling Liu; Xinghua Lu 001 (BioNLP@ACL, 2019)

PubMedQA: A Dataset for Biomedical Research Question Answering. - Qiao Jin 001; Bhuwan Dhingra; Zhengping Liu; William W. Cohen; Xinghua Lu 001 (EMNLP/IJCNLP (1), 2019)

Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning. - Haohan Wang; Xiang Liu 017; Yifeng Tao; Wenting Ye; Qiao Jin 001; William W. Cohen; Eric P. Xing (PSB, 2019)

Probing Biomedical Embeddings from Language Models. - Qiao Jin 001; Bhuwan Dhingra; William W. Cohen; Xinghua Lu 001 (CoRR, 2019)

Tackling MeSH Indexing Dataset Shift with Time-Aware Concept Embedding Learning. - Qiao Jin 001; Haoyang Ding; Linfeng Li; Haitao Huang; Lei Wang; Jun Yan (DASFAA (3), 2020)

Predicting Clinical Trial Results by Implicit Evidence Integration. - Qiao Jin 001; Chuanqi Tan; Mosha Chen; Xiaozhong Liu; Songfang Huang (EMNLP (1), 2020)

Aliababa DAMO Academy at TREC Precision Medicine 2020: State-of-the-art Evidence Retriever for Precision Medicine with Expert-in-the-loop Active Learning. - Qiao Jin 001; Chuanqi Tan; Mosha Chen; Ming Yan 008; Songfang Huang; Ningyu Zhang 001; Xiaozhong Liu (TREC, 2020)

DiaKG: An Annotated Diabetes Dataset for Medical Knowledge Graph Construction. - Dejie Chang; Mosha Chen; Chaozhen Liu; Liping Liu; Dongdong Li; Wei Li 205; Fei Kong; Bangchang Liu; Xiaobin Luo; Ji Qi 003; Qiao Jin 001; Bin Xu 001 (CCKS, 2021)

Alibaba DAMO Academy at TREC Clinical Trials 2021: ExploringEmbedding-based First-stage Retrieval with TrialMatcher. - Qiao Jin 001; Chuanqi Tan; Zhengyun Zhao; Zheng Yuan 002; Songfang Huang (TREC, 2021)

Biomedical Question Answering: A Comprehensive Review. - Qiao Jin 001; Zheng Yuan 002; Guangzhi Xiong; Qianlan Yu; Chuanqi Tan; Mosha Chen; Songfang Huang; Xiaozhong Liu; Sheng Yu 002 (CoRR, 2021)

PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central. - Zhengyun Zhao; Qiao Jin 001; Sheng Yu 002 (CoRR, 2022)

Multi-stage Literature Retrieval System Trained by PubMed Search Logs for Biomedical Question Answering. - Ashley Shin; Qiao Jin 001; Zhiyong Lu (CLEF (Working Notes), 2023)

RAMM: Retrieval-augmented Biomedical Visual Question Answering with Multi-modal Pre-training. - Zheng Yuan 005; Qiao Jin 001; Chuanqi Tan; Zhengyun Zhao; Hongyi Yuan; Fei Huang 002; Songfang Huang (ACM Multimedia, 2023)

LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search. - Qiao Jin 001; Andrew Shin; Zhiyong Lu (SIGIR, 2023)

RAMM: Retrieval-augmented Biomedical Visual Question Answering with Multi-modal Pre-training. - Zheng Yuan 002; Qiao Jin 001; Chuanqi Tan; Zhengyun Zhao; Hongyi Yuan; Fei Huang 002; Songfang Huang (CoRR, 2023)

BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval. - Qiao Jin 001; Won Kim 003; Qingyu Chen 001; Donald C. Comeau; Lana Yeganova; W. John Wilbur; Zhiyong Lu (CoRR, 2023)

PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search. - Qiao Jin 001; Robert Leaman; Zhiyong Lu (CoRR, 2023)

Matching Patients to Clinical Trials with Large Language Models. - Qiao Jin 001; Zifeng Wang 008; Charalampos S. Floudas; Jimeng Sun 001; Zhiyong Lu (CoRR, 2023)

Leveraging Generative AI for Clinical Evidence Summarization Needs to Achieve Trustworthiness. - Gongbo Zhang; Qiao Jin 001; Denis Jered McInerney; Yong Chen 016; Fei Wang 001; Curtis L. Cole; Qian Yang 004; Yanshan Wang; Bradley A. Malin; Mor Peleg; Byron C. Wallace; Zhiyong Lu; et al. (CoRR, 2023)

Biomedical Question Answering: A Survey of Approaches and Challenges. - Qiao Jin 001; Zheng Yuan 002; Guangzhi Xiong; Qianlan Yu; Huaiyuan Ying; Chuanqi Tan; Mosha Chen; Songfang Huang; Xiaozhong Liu; Sheng Yu 002 (ACM Comput. Surv., 2023)

MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval. - Qiao Jin 001; Won Kim 003; Qingyu Chen 001; Donald C. Comeau; Lana Yeganova; W. John Wilbur; Zhiyong Lu (Bioinform., 2023)

Benchmarking Retrieval-Augmented Generation for Medicine. - Guangzhi Xiong; Qiao Jin 001; Zhiyong Lu; Aidong Zhang (ACL (Findings), 2024)

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for AI-generated Radiology Reports. - Qingqing Zhu; Xiuying Chen; Qiao Jin 001; Benjamin Hou; Tejas Sudharshan Mathai; Pritam Mukherjee; Xin Gao 001; Ronald M. Summers; Zhiyong Lu (ICHI, 2024)

MedCalc-Bench: Evaluating Large Language Models for Medical Calculations. - Nikhil Khandekar; Qiao Jin 001; Guangzhi Xiong; Soren Dunn; Serina S. Applebaum; Zain Anwar; Maame Sarfo-Gyamfi; Conrad W. Safranek; Abid A Anwar; Andrew Zhang; Aidan Gilson; Maxwell B. Singer; et al. (NeurIPS, 2024)

Response to Letter to Editor 'Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine'. - Shubo Tian; Qiao Jin 001; Zhiyong Lu (Briefings Bioinform., 2024)

Opportunities and challenges for ChatGPT and large language models in biomedicine and health. - Shubo Tian; Qiao Jin 001; Lana Yeganova; Po-Ting Lai; Qingqing Zhu; Xiuying Chen; Yifan Yang 006; Qingyu Chen 001; Won Kim 003; Donald C. Comeau; Rezarta Islamaj; Aadit Kapoor; et al. (Briefings Bioinform., 2024)

Hidden Flaws Behind Expert-Level Accuracy of GPT-4 Vision in Medicine. - Qiao Jin 001; Fangyuan Chen; Yiliang Zhou; Ziyang Xu; Justin M. Cheung; Robert Chen; Ronald M. Summers; Justin F. Rousseau; Peiyun Ni; Marc J. Landsman; Sally L. Baxter; Subhi J. Al'Aref; et al. (CoRR, 2024)

PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge. - Chih-Hsuan Wei; Alexis Allot; Po-Ting Lai; Robert Leaman; Shubo Tian; Ling Luo 001; Qiao Jin 001; Zhizheng Wang; Qingyu Chen 001; Zhiyong Lu (CoRR, 2024)

Unmasking and Quantifying Racial Bias of Large Language Models in Medical Report Generation. - Yifan Yang 006; Xiaoyu Liu 003; Qiao Jin 001; Furong Huang; Zhiyong Lu (CoRR, 2024)

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports. - Qingqing Zhu; Xiuying Chen; Qiao Jin 001; Benjamin Hou; Tejas Sudharshan Mathai; Pritam Mukherjee; Xin Gao 001; Ronald M. Summers; Zhiyong Lu (CoRR, 2024)

Quality of Answers of Generative Large Language Models vs Peer Patients for Interpreting Lab Test Results for Lay Patients: Evaluation Study. - Zhe He 001; Balu Bhasuran; Qiao Jin 001; Shubo Tian; Karim Hanna; Cindy Shavor; Lisbeth Y. Garcia Arguello; Patrick Murray; Zhiyong Lu (CoRR, 2024)

Harnessing PubMed User Query Logs for Post Hoc Explanations of Recommended Similar Articles. - Ashley Shin; Qiao Jin 001; James T. Anibal; Zhiyong Lu (CoRR, 2024)

Prioritizing Safeguarding Over Autonomy: Risks of LLM Agents for Science. - Xiangru Tang; Qiao Jin 001; Kunlun Zhu; Tongxin Yuan; Yichi Zhang; Wangchunshu Zhou; Meng Qu; Yilun Zhao 001; Jian Tang; Zhuosheng Zhang 001; Arman Cohan; Zhiyong Lu; et al. (CoRR, 2024)

AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning. - Qiao Jin 001; Zhizheng Wang; Yifan Yang 006; Qingqing Zhu; Donald Wright; Thomas Huang 003; W. John Wilbur; Zhe He 001; Andrew Taylor; Qingyu Chen 001; Zhiyong Lu (CoRR, 2024)

Decomposing Vision-based LLM Predictions for Auto-Evaluation with GPT-4. - Qingqing Zhu; Benjamin Hou; Tejas Sudharshan Mathai; Pritam Mukherjee; Qiao Jin 001; Xiuying Chen; Zhizheng Wang; Ruida Cheng; Ronald M. Summers; Zhiyong Lu (CoRR, 2024)

GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases. - Zhizheng Wang; Qiao Jin 001; Chih-Hsuan Wei; Shubo Tian; Po-Ting Lai; Qingqing Zhu; Chi-Ping Day; Christina Ross; Zhiyong Lu (CoRR, 2024)

Shadow and Light: Digitally Reconstructed Radiographs for Disease Classification. - Benjamin Hou; Qingqing Zhu; Tejas Sudharshan Mathai; Qiao Jin 001; Zhiyong Lu; Ronald M. Summers (CoRR, 2024)

Adversarial Attacks on Large Language Models in Medicine. - Yifan Yang 006; Qiao Jin 001; Furong Huang; Zhiyong Lu (CoRR, 2024)

Accelerating Clinical Evidence Synthesis with Large Language Models. - Zifeng Wang 008; Lang Cao; Benjamin P. Danek; Yichi Zhang; Qiao Jin 001; Zhiyong Lu; Jimeng Sun 001 (CoRR, 2024)

Improving Retrieval-Augmented Generation in Medicine with Iterative Follow-up Questions. - Guangzhi Xiong; Qiao Jin 001; Xiao Wang; Minjia Zhang; Zhiyong Lu; Aidong Zhang (CoRR, 2024)

Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology. - Aidan Gilson; Xuguang Ai; Thilaka Arunachalam; Ziyou Chen; Ki Xiong Cheong; Amisha D. Dave; Cameron Duic; Mercy Kibe; Annette Kaminaka; Minali Prasad; Fares Siddig; Maxwell B. Singer; et al. (CoRR, 2024)

Beyond Multiple-Choice Accuracy: Real-World Challenges of Implementing Large Language Models in Healthcare. - Yifan Yang 006; Qiao Jin 001; Qingqing Zhu; Zhizheng Wang; Francisco Erramuspe Álvarez; Nicholas Wan; Benjamin Hou; Zhiyong Lu (CoRR, 2024)

Demystifying Large Language Models for Medicine: A Primer. - Qiao Jin 001; Nicholas Wan; Robert Leaman; Shubo Tian; Zhizheng Wang; Yifan Yang 006; Zifeng Wang 008; Guangzhi Xiong; Po-Ting Lai; Qingqing Zhu; Benjamin Hou; Maame Sarfo-Gyamfi; et al. (CoRR, 2024)

Evaluating the Impact of Lab Test Results on Large Language Models Generated Differential Diagnoses from Clinical Case Vignettes. - Balu Bhasuran; Qiao Jin 001; Yuzhang Xie; Carl Yang 001; Karim Hanna; Jennifer Costa; Cindy Shavor; Zhiyong Lu; Zhe He 001 (CoRR, 2024)

Humans Continue to Outperform Large Language Models in Complex Clinical Decision-Making: A Study with Medical Calculators. - Nicholas Wan; Qiao Jin 001; Joey Chan; Guangzhi Xiong; Serina S. Applebaum; Aidan Gilson; Reid McMurry; R. Andrew Taylor; Aidong Zhang; Qingyu Chen 001; Zhiyong Lu (CoRR, 2024)

Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine. - Yifan Yang 006; Qiao Jin 001; Robert Leaman; Xiaoyu Liu 003; Guangzhi Xiong; Maame Sarfo-Gyamfi; Changlin Gong; Santiago Ferrière-Steinert; W. John Wilbur; Xiaojun Li; Jiaxin Yuan; Bang An 001; et al. (CoRR, 2024)

A MapReduce Approach to Effectively Utilize Long Context Information in Retrieval Augmented Language Models. - Gongbo Zhang; Zihan Xu; Qiao Jin 001; Fangyi Chen; Yilu Fang; Yi Liu 059; Justin F. Rousseau; Ziyang Xu; Zhiyong Lu; Chunhua Weng; Yifan Peng 002 (CoRR, 2024)

Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness. - Gongbo Zhang; Qiao Jin 001; Denis Jered McInerney; Yong Chen 016; Fei Wang 001; Curtis L. Cole; Qian Yang 004; Yanshan Wang; Bradley A. Malin; Mor Peleg; Byron C. Wallace; Zhiyong Lu; et al. (J. Biomed. Informatics, 2024)

Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. - Qiao Jin 001; Fangyuan Chen; Yiliang Zhou; Ziyang Xu; Justin M. Cheung; Robert Chen; Ronald M. Summers; Justin F. Rousseau; Peiyun Ni; Marc J. Landsman; Sally L. Baxter; Subhi J. Al'Aref; et al. (npj Digit. Medicine, 2024)

Closing the gap between open source and commercial large language models for medical evidence summarization. - Gongbo Zhang; Qiao Jin 001; Yiliang Zhou; Song Wang 026; Betina Idnay; Yiming Luo; Elizabeth Park; Jordan G. Nestor; Matthew E. Spotnitz; Ali Soroush; Thomas Campion; Zhiyong Lu; et al. (npj Digit. Medicine, 2024)

GeneGPT: augmenting large language models with domain tools for improved access to biomedical information. - Qiao Jin 001; Yifan Yang 006; Qingyu Chen 001; Zhiyong Lu (Bioinform., 2024)

Archive of PubTator 3.0 source code and trained models. - Chih-Hsuan Wei; Alexis Allot; Po-Ting Lai; Robert Leaman; Shubo Tian; Ling Luo 001; Qiao Jin 001; Zhizheng Wang; Qingyu Chen 001; Zhiyong Lu (Zenodo, 2024)

MedCite: Can Language Models Generate Verifiable Text for Medicine? - Xiao Wang; Mengjue Tan; Qiao Jin 001; Guangzhi Xiong; Yu Hu; Aidong Zhang; Zhiyong Lu; Minjia Zhang (ACL (Findings), 2025)

How well do multimodal LLMs interpret CT scans? An auto-evaluation framework for analyses. - Qingqing Zhu; Benjamin Hou; Tejas Sudharshan Mathai; Pritam Mukherjee; Qiao Jin 001; Xiuying Chen; Zhizheng Wang; Ruida Cheng; Ronald M. Summers; Zhiyong Lu (J. Biomed. Informatics, 2025)

Preliminary analysis of the impact of lab results on large language model generated differential diagnoses. - Balu Bhasuran; Qiao Jin 001; Yuzhang Xie; Carl Yang 001; Karim Hanna; Jennifer Costa; Cindy Shavor; Wenshan Han; Zhiyong Lu; Zhe He 001 (npj Digit. Medicine, 2025)

Leveraging long context in retrieval augmented language models for medical question answering. - Gongbo Zhang; Zihan Xu; Qiao Jin 001; Fangyi Chen; Yilu Fang; Yi Liu 059; Justin F. Rousseau; Ziyang Xu; Zhiyong Lu; Chunhua Weng; Yifan Peng 002 (npj Digit. Medicine, 2025)

A foundation model for human-AI collaboration in medical literature mining. - Zifeng Wang 008; Lang Cao; Qiao Jin 001; Joey Chan; Nicholas Wan; Behdad Afzali; Hyunjin Cho; Changin Choi; Mehdi Emamverdi; Manjot K. Gill; Sun-Hyung Kim; Yijia Li; et al. (CoRR, 2025)

RAG-Gym: Optimizing Reasoning and Search Agents with Process Supervision. - Guangzhi Xiong; Qiao Jin 001; Xiao Wang; Yin Fang; Haolin Liu; Yifan Yang 006; Fangyuan Chen; Zhixing Song; Dengyu Wang; Minjia Zhang; Zhiyong Lu; Aidong Zhang (CoRR, 2025)

Recommending Clinical Trials for Online Patient Cases using Artificial Intelligence. - Joey Chan; Qiao Jin 001; Nicholas Wan; Charalampos S. Floudas; Elisabetta Xue; Zhiyong Lu (CoRR, 2025)

Benchmarking Retrieval-Augmented Generation for Chemistry. - Xianrui Zhong; Bowen Jin; Siru Ouyang; Yanzhen Shen; Qiao Jin 001; Yin Fang; Zhiyong Lu; Jiawei Han 001 (CoRR, 2025)

TrialPanorama: Database and Benchmark for Systematic Review and Design of Clinical Trials. - Zifeng Wang 008; Qiao Jin 001; Jiacheng Lin; Junyi Gao; Jathurshan Pradeepkumar; Pengcheng Jiang; Benjamin P. Danek; Zhiyong Lu; Jimeng Sun 001 (CoRR, 2025)

Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning. - Yin Fang; Qiao Jin 001; Guangzhi Xiong; Bowen Jin; Xianrui Zhong; Siru Ouyang; Aidong Zhang; Jiawei Han 001; Zhiyong Lu (CoRR, 2025)

Knowledge-guided Contextual Gene Set Analysis Using Large Language Models. - Zhizheng Wang; Chi-Ping Day; Chih-Hsuan Wei; Qiao Jin 001; Robert Leaman; Yifan Yang 006; Shubo Tian; Aodong Qiu; Yin Fang; Qingqing Zhu; Xinghua Lu 001; Zhiyong Lu (CoRR, 2025)