Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases. - Qingyu Chen 001; Justin Zobel; Karin Verspoor (DTMBIO@CIKM, 2015)

Evaluation of CD-HIT for constructing non-redundant databases. - Qingyu Chen 001; Yu Wan 001; Yang Lei 003; Justin Zobel; Karin Verspoor (BIBM, 2016)

Sequence Clustering Methods and Completeness of Biological Database Search. - Qingyu Chen 001; Xiuzhen Zhang 001; Yu Wan 001; Justin Zobel; Karin Verspoor (BAI@IJCAI, 2017)

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. - Qingyu Chen 001; Justin Zobel; Karin Verspoor (Database J. Biol. Databases Curation, 2017)

Duplication in biological databases: definitions, impacts and methods. - Qingyu Chen 001 (2017)

Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. - Qingyu Chen 001; Sun Kim; W. John Wilbur; Zhiyong Lu (BCB, 2018)

BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics. - Qingyu Chen 001; Nagesh C. Panyam; Aparna Elangovan; Karin Verspoor (Database J. Biol. Databases Curation, 2018)

DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs. - Yifan Peng 002; Shazia Dharssi; Qingyu Chen 001; Tiarnan D. Keenan; Elvira Agrón; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (CoRR, 2018)

A multi-task deep learning model for the classification of Age-related Macular Degeneration. - Qingyu Chen 001; Yifan Peng 002; Tiarnan D. Keenan; Shazia Dharssi; Elvira Agrón; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (CoRR, 2018)

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. - Qingyu Chen 001; Yu Wan 001; Xiuzhen Zhang 001; Yang Lei 003; Justin Zobel; Karin Verspoor (ACM J. Data Inf. Qual., 2018)

A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs. - Yifan Peng 002; Tiarnan D. Keenan; Qingyu Chen 001; Elvira Agrón; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (AMIA, 2019)

Evaluation of Five Sentence Similarity Models on Electronic Medical Records. - Qingyu Chen 001; Jingcheng Du; Sun Kim; W. John Wilbur; Zhiyong Lu (BCB, 2019)

BioSentVec: creating sentence embeddings for biomedical texts. - Qingyu Chen 001; Yifan Peng 002; Zhiyong Lu (ICHI, 2019)

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. - Rezarta Islamaj Dogan; Sun Kim; Andrew Chatr-aryamontri; Chih-Hsuan Wei; Donald C. Comeau; Rui Antunes 002; Sérgio Matos; Qingyu Chen 001; Aparna Elangovan; Nagesh C. Panyam; Karin Verspoor; Hongfang Liu; et al. (Database J. Biol. Databases Curation, 2019)

A deep learning approach for automated detection of geographic atrophy from color fundus photographs. - Tiarnan D. Keenan; Shazia Dharssi; Yifan Peng 002; Qingyu Chen 001; Elvira Agrón; Wai T. Wong; Zhiyong Lu; Emily Y. Chew (CoRR, 2019)

ML-Net: multi-label classification of biomedical texts with deep neural networks. - Jingcheng Du; Qingyu Chen 001; Yifan Peng 002; Yang Xiang 003; Cui Tao; Zhiyong Lu (J. Am. Medical Informatics Assoc., 2019)

Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. - Qingyu Chen 001; Xiuzhen Zhang 001; Yu Wan 001; Justin Zobel; Karin Verspoor (J. Comput. Biol., 2019)

LitSense: making sense of biomedical literature at sentence level. - Alexis Allot; Qingyu Chen 001; Sun Kim; Roberto Vera Alvarez; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (Nucleic Acids Res., 2019)

Automatic recognition of abdominal lymph nodes from clinical text. - Yifan Peng 002; Sungwon Lee 003; Daniel C. Elton; Thomas C. Shen; Yuxing Tang; Qingyu Chen 001; Shuai Wang; Yingying Zhu 003; Ronald M. Summers; Zhiyong Lu (ClinicalNLP@EMNLP, 2020)

Detection of reticular pseudodrusen using deep learning. - Qingyu Chen 001; Tiarnan D. Keenan; Yifan Peng 002; Elvira Agrón; Christopher Hwang; Alisa T. Thavikulwat; Debora Lee; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (AMIA, 2020)

An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. - Yifan Peng 002; Qingyu Chen 001; Zhiyong Lu (BioNLP, 2020)

Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. - Lana Yeganova; Rezarta Islamaj Dogan; Qingyu Chen 001; Robert Leaman; Alexis Allot; Chih-Hsuan Wei; Donald C. Comeau; Won Kim 003; Yifan Peng 002; W. John Wilbur; Zhiyong Lu (CoRR, 2020)

Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). - Qingyu Chen 001; Robert Leaman; Alexis Allot; Ling Luo 001; Chih-Hsuan Wei; Shankai Yan; Zhiyong Lu (CoRR, 2020)

Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration. - Qingyu Chen 001; Tiarnan D. L. Keenan; Alexis Allot; Yifan Peng 002; Elvira Agrón; Amitha Domalpally; Caroline C. W. Klaver; Daniel T. Luttikhuizen; Marcus H. Colyer; Catherine A. Cukras; Henry E. Wiley; M. Teresa Magone; et al. (CoRR, 2020)

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. - Qingyu Chen 001; Ramona Britto; Ivan Erill; Constance J. Jeffery; Arthur Liberzon; Michele Magrane; Jun-ichi Onami; Marc Robinson-Rechavi; Jana Sponarova; Justin Zobel; Karin Verspoor (Genom. Proteom. Bioinform., 2020)

Privacy concerns of the Australian My Health Record: Implications for other large-scale opt-out personal health records. - Patrick Cheong-Iao Pang; Dana McKay; Shanton Chang; Qingyu Chen 001; Xiuzhen Zhang 001; Lishan Cui (Inf. Process. Manag., 2020)

Better synonyms for enriching biomedical search. - Lana Yeganova; Sun Kim; Qingyu Chen 001; Grigory Balasanov; W. John Wilbur; Zhiyong Lu (J. Am. Medical Informatics Assoc., 2020)

Predicting risk of late age-related macular degeneration using deep learning. - Yifan Peng 002; Tiarnan D. Keenan; Qingyu Chen 001; Elvira Agrón; Alexis Allot; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (npj Digit. Medicine, 2020)

BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. - Qingyu Chen 001; Kyubum Lee; Shankai Yan; Sun Kim; Chih-Hsuan Wei; Zhiyong Lu (PLoS Comput. Biol., 2020)

Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. - Qingyu Chen 001; Jingcheng Du; Sun Kim; W. John Wilbur; Zhiyong Lu (BMC Medical Informatics Decis. Mak., 2020)

AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation. - Qingyu Chen 001; Jingcheng Du; Alexis Allot; Zhiyong Lu (AMIA, 2021)

Deep learning detection of reticular pseudodrusen using multi-modal, multi-task, and multi-attention mechanisms: towards automated and accessible classification of age-related macular degeneration. - Qingyu Chen 001; Tiarnan D. Keenan; Emily Y. Chew; Zhiyong Lu (AMIA, 2021)

Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS. - Gregory C. Ghahramani; Matthew Brendel; Mingquan Lin; Qingyu Chen 001; Tiarnan D. Keenan; Kun Chen 002; Emily Y. Chew; Zhiyong Lu; Yifan Peng 002; Fei Wang 001 (AMIA, 2021)

Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors. - Robert Leaman; Qingyu Chen 001; Alexis Allot; Zhiyong Lu (AMIA, 2021)

Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI. - Yingying Zhu 003; Shuai Wang; Qingyu Chen 001; Sungwon Lee 003; Thomas C. Shen; Daniel C. Elton; Zhiyong Lu; Ronald M. Summers (MLMI@MICCAI, 2021)

Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration. - Qingyu Chen 001; Tiarnan D. L. Keenan; Alexis Allot; Yifan Peng 002; Elvira Agrón; Amitha Domalpally; Caroline C. W. Klaver; Daniel T. Luttikhuizen; Marcus H. Colyer; Catherine A. Cukras; Henry E. Wiley; M. Teresa Magone; et al. (J. Am. Medical Informatics Assoc., 2021)

LitCovid: an open database of COVID-19 literature. - Qingyu Chen 001; Alexis Allot; Zhiyong Lu (Nucleic Acids Res., 2021)

LitSuggest: a web-based system for literature recommendation and curation using machine learning. - Alexis Allot; Kyubum Lee; Qingyu Chen 001; Ling Luo 001; Zhiyong Lu (Nucleic Acids Res., 2021)

Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows. - Qingyu Chen 001; Tiarnan D. Keenan; Alexis Allot; Sanjeeb Bhandari; Geoff Broadhead; Chantal Cousineau-Krieger; Ellen Davis; William G. Gensheimer; David Grasic; Seema Gupta; Eleni Konstantinou; Tania Lamba; et al. (AMIA, 2022)

Deep learning automated diagnosis and quantitative classification of cataract type and severity: quantifying the effectiveness and usability of deep learning-assisted disease diagnosis models with 14 ophthalmologists and multi-center validations. - Qingyu Chen 001; Tiarnan D. Keenan; Elvira Agrón; Amr S. Elsawy; Emily Y. Chew; Zhiyong Lu (AMIA, 2022)

Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning. - Junghwan Lee; Tingyi Wanyan; Qingyu Chen 001; Tiarnan D. L. Keenan; Benjamin S. Glicksberg; Emily Y. Chew; Zhiyong Lu; Fei Wang 001; Yifan Peng 002 (MLMI@MICCAI, 2022)

Assigning species information to corresponding genes by a sequence labeling framework. - Ling Luo 001; Chih-Hsuan Wei; Po-Ting Lai; Qingyu Chen 001; Rezarta Islamaj; Zhiyong Lu (Database J. Biol. Databases Curation, 2022)

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Rezarta Islamaj; Jingcheng Du; Li Fang; Wang Kai; Shuo Xu 001; Yuefu Zhang; Parsa Bagherzadeh; Sabine Bergler; Aakash Bhatnagar; et al. (Database J. Biol. Databases Curation, 2022)

A Privacy-Preserving Unsupervised Domain Adaptation Framework for Clinical Text Analysis. - Qiyuan An; Ruijiang Li; Lin Gu 003; Hao Zhang 050; Qingyu Chen 001; Zhiyong Lu; Fei Wang 001; Yingying Zhu 003 (CoRR, 2022)

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Rezarta Islamaj Dogan; Jingcheng Du; Li Fang; Wang Kai; Shuo Xu 001; Yuefu Zhang; Parsa Bagherzadeh; Sabine Bergler; Aakash Bhatnagar; et al. (CoRR, 2022)

Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. - Robert Leaman; Rezarta Islamaj Dogan; Alexis Allot; Qingyu Chen 001; W. John Wilbur; Zhiyong Lu (CoRR, 2022)

Predicting myocardial infarction through retinal scans and minimal personal information. - Andres Diaz-Pinto; Nishant Ravikumar; Rahman Attar; Avan Suinesiaputra; Yitian Zhao; Eylem Levelt; Erica Dall' Armellina; Marco Lorenzi; Qingyu Chen 001; Tiarnan D. L. Keenan; Elvira Agrón; Emily Y. Chew; et al. (Nat. Mach. Intell., 2022)

Robust convolutional neural networks against adversarial attacks on medical images. - Xiaoshuang Shi; Yifan Peng 002; Qingyu Chen 001; Tiarnan D. Keenan; Alisa T. Thavikulwat; Sungwon Lee 003; Yuxing Tang; Emily Y. Chew; Ronald M. Summers; Zhiyong Lu (Pattern Recognit., 2022)

LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation. - Qingyu Chen 001; Jingcheng Du; Alexis Allot; Zhiyong Lu (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Attention-based 3D convolutional networks for detection of geographic atrophy from optical coherence tomography scans. - Amr S. Elsawy; Tiarnan D. Kenan; Qingyu Chen 001; Xiaoshuang Shi; Emily Y. Chew; Zhiyong Lu (Image Processing, 2023)

Bioformer: an efficient transformer language model for biomedical text mining. - Li Fang; Qingyu Chen 001; Chih-Hsuan Wei; Zhiyong Lu; Kai Wang (CoRR, 2023)

Interpretable Medical Image Visual Question Answering via Multi-Modal Relationship Graph Learning. - Xinyue Hu 002; Lin Gu 003; Kazuma Kobayashi; Qiyuan An; Qingyu Chen 001; Zhiyong Lu; Chang Su 002; Tatsuya Harada; Yingying Zhu 004 (CoRR, 2023)

Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations. - Qingyu Chen 001; Jingcheng Du; Yan Hu; Vipina Kuttichi Keloth; Xueqing Peng; Kalpana Raja; Rui Zhang 028; Zhiyong Lu; Hua Xu 001 (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)

Integrating UMLS Knowledge into Large Language Models for Medical Question Answering. - Rui Yang 016; Edison Marrese-Taylor; Yuhe Ke; Lechao Cheng; Qingyu Chen 001; Irene Li (CoRR, 2023)

MedGen: A Python Natural Language Processing Toolkit for Medical Text Processing. - Rui Yang 016; Qingcheng Zeng; Keen You; Yujie Qiao; Lucas Huang; Chiachun Hsieh; Benjamin Rosand; Jeremy Goldwasser; Amisha D. Dave; Tiarnan D. L. Keenan; Emily Y. Chew; Dragomir Radev; et al. (CoRR, 2023)

LitCovid in 2022: an information resource for the COVID-19 literature. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Chih-Hsuan Wei; Elaheh Aghaarabi; John J. Guerrerio; Lilly Xu; Zhiyong Lu (Nucleic Acids Res., 2023)

Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. - Robert Leaman; Rezarta Islamaj; Alexis Allot; Qingyu Chen 001; W. John Wilbur; Zhiyong Lu (Patterns, 2023)

AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. - Ling Luo 001; Chih-Hsuan Wei; Po-Ting Lai; Robert Leaman; Qingyu Chen 001; Zhiyong Lu (Bioinform., 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)

BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets. - Po-Ting Lai; Chih-Hsuan Wei; Ling Luo 001; Qingyu Chen 001; Zhiyong Lu (J. Biomed. Informatics, 2023)

Yale at "Discharge Me!": Evaluating Constrained Generation of Discharge Summaries with Unstructured and Structured Information. - Vimig Socrates; Thomas Huang 003; Xuguang Ai; Soraya Fereydooni; Qingyu Chen 001; R. Andrew Taylor; David Chartash (BioNLP@ACL, 2024)

KG-Rank: Enhancing Large Language Models for Medical QA with Knowledge Graphs and Ranking Techniques. - Rui Yang 016; Haoran Liu; Edison Marrese-Taylor; Qingcheng Zeng; Yuhe Ke; Wanxin Li; Lechao Cheng; Qingyu Chen 001; James Caverlee; Yutaka Matsuo; Irene Li (BioNLP@ACL, 2024)

MedINST: Meta Dataset of Biomedical Instructions. - Wenhan Han; Meng Fang; Zihan Zhang; Yu Yin; Zirui Song; Ling Chen 006; Mykola Pechenizkiy; Qingyu Chen 001 (EMNLP (Findings), 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)

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)

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)

Me LLaMA: Foundation Large Language Models for Medical Applications. - Qianqian Xie; Qingyu Chen 001; Aokun Chen; Cheng Peng 009; Yan Hu; Fongci Lin; Xueqing Peng; Jimin Huang; Jeffrey Zhang 010; Vipina Kuttichi Keloth; Xingyu Zhou; Huan He; 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)

Word-Sequence Entropy: Towards Uncertainty Estimation in Free-Form Medical Question Answering Applications and Beyond. - Zhiyuan Wang; Jinhao Duan; Chenxi Yuan; Qingyu Chen 001; Tianlong Chen 001; Huaxiu Yao; Yue Zhang; Ren Wang 008; Kaidi Xu; Xiaoshuang Shi (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)

Towards Accountable AI-Assisted Eye Disease Diagnosis: Workflow Design, External Validation, and Continual Learning. - Qingyu Chen 001; Tiarnan D. L. Keenan; Elvira Agrón; Alexis Allot; Emily Guan; Bryant Duong; Amr S. Elsawy; Benjamin Hou; Cancan Xue; Sanjeeb Bhandari; Geoff Broadhead; Chantal Cousineau-Krieger; et al. (CoRR, 2024)

Language Enhanced Model for Eye (LEME): An Open-Source Ophthalmology-Specific Large Language Model. - Aidan Gilson; Xuguang Ai; Qianqian Xie; Sahana Srinivasan; Krithi Pushpanathan; Maxwell B. Singer; Jimin Huang; Hyunjae Kim; Erping Long; Peixing Wan; Luciano V. Del Priore; Lucila Ohno-Machado; et al. (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)

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)

Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models? - Yan Hu; Xu Zuo; Yujia Zhou 003; Xueqing Peng; Jimin Huang; Vipina Kuttichi Keloth; Vincent J. Zhang; Ruey-Ling Weng; Qingyu Chen 001; Xiaoqian Jiang; Kirk E. Roberts; Hua Xu 001 (CoRR, 2024)

Ophthalmic care may not align with patient need: An analysis on state-wide patient needs and provider density between 2008 and 2022. - Aidan Gilson; Qingyu Chen 001; Ron A. Adelman (Int. J. Medical Informatics, 2024)

Improving large language models for clinical named entity recognition via prompt engineering. - Yan Hu; Qingyu Chen 001; Jingcheng Du; Xueqing Peng; Vipina Kuttichi Keloth; Xu Zuo; Yujia Zhou 003; Zehan Li; Xiaoqian Jiang; Zhiyong Lu; Kirk Roberts; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2024)

Augmenting biomedical named entity recognition with general-domain resources. - Yu Yin; Hyunjae Kim; Xiao Xiao; Chih-Hsuan Wei; Jaewoo Kang; Zhiyong Lu; Hua Xu 001; Meng Fang; Qingyu Chen 001 (J. Biomed. Informatics, 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)

GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking. - Yingjian Chen; Haoran Liu; Yinhong Liu; Jinxiang Xie; Rui Yang 016; Han Yuan; Yanran Fu; Peng Yuan Zhou; Qingyu Chen 001; James Caverlee; Irene Li (ACL (1), 2025)

LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models. - Zhenyue Qin; Yu Yin; Dylan Campbell; Xuansheng Wu; Ke Zou; Ninghao Liu; Yih Chung Tham; Xiuzhen Zhang 001; Qingyu Chen 001 (NAACL (Findings), 2025)

Word-Sequence Entropy: Towards uncertainty estimation in free-form medical question answering applications and beyond. - Zhiyuan Wang; Jinhao Duan; Chenxi Yuan; Qingyu Chen 001; Tianlong Chen 001; Yue Zhang; Ren Wang 008; Xiaoshuang Shi; Kaidi Xu (Eng. Appl. Artif. Intell., 2025)

Social determinants of health extraction from clinical notes across institutions using large language models. - Vipina Kuttichi Keloth; Salih Selek; Qingyu Chen 001; Christopher Gilman; Sunyang Fu; Yifang Dang; Xinghan Chen; Xinyue Hu 002; Yujia Zhou 003; Huan He; Jungwei W. Fan 001; Karen Wang; et al. (npj Digit. Medicine, 2025)

Small language models learn enhanced reasoning skills from medical textbooks. - Hyunjae Kim; Hyeon Hwang; Jiwoo Lee; Sihyeon Park; Dain Kim; Taewhoo Lee; Chanwoong Yoon; Jiwoong Sohn; Jungwoo Park; Olga Reykhart; Thomas Fetherston; Donghee Choi; et al. (npj Digit. Medicine, 2025)

Author Correction: Small language models learn enhanced reasoning skills from medical textbooks. - Hyunjae Kim; Hyeon Hwang; Jiwoo Lee; Sihyeon Park; Dain Kim; Taewhoo Lee; Chanwoong Yoon; Jiwoong Sohn; Jungwoo Park; Olga Reykhart; Thomas Fetherston; Donghee Choi; et al. (npj Digit. Medicine, 2025)

Medical foundation large language models for comprehensive text analysis and beyond. - Qianqian Xie; Qingyu Chen 001; Aokun Chen; Cheng Peng 009; Yan Hu; Fongci Lin; Xueqing Peng; Jimin Huang; Jeffrey Zhang 010; Vipina Kuttichi Keloth; Xinyu Zhou; Lingfei Qian; et al. (npj Digit. Medicine, 2025)

Enhancing Patient-Centric Communication: Leveraging LLMs to Simulate Patient Perspectives. - Xinyao Ma; Rui Zhu; Zihao Wang; Jingwei Xiong; Qingyu Chen 001; Haixu Tang; L. Jean Camp; Lucila Ohno-Machado (CoRR, 2025)

Can OpenAI o1 Reason Well in Ophthalmology? A 6,990-Question Head-to-Head Evaluation Study. - Sahana Srinivasan; Xuguang Ai; Minjie Zou; Ke Zou; Hyunjae Kim; Thaddaeus Wai Soon Lo; Krithi Pushpanathan; Yiming Kong; Anran Li; Maxwell B. Singer; Kai Jin; Fares Antaki; et al. (CoRR, 2025)

Dialogue is Better Than Monologue: Instructing Medical LLMs via Strategical Conversations. - Zijie Liu; Xinyu Zhao; Jie Peng 002; Zhuangdi Zhu; Qingyu Chen 001; Xia Hu 001; Tianlong Chen 001 (CoRR, 2025)

Is an Ultra Large Natural Image-Based Foundation Model Superior to a Retina-Specific Model for Detecting Ocular and Systemic Diseases? - Qingshan Hou; Yukun Zhou; Jocelyn Hui Lin Goh; Ke Zou; Samantha Min Er Yew; Sahana Srinivasan; Meng Wang 001; Thaddaeus Wai Soon Lo; Xiaofeng Lei; Siegfried K. Wagner; Mark A. Chia; Dawei Yang; et al. (CoRR, 2025)

GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking. - Yingjian Chen; Haoran Liu; Yinhong Liu; Rui Yang 016; Han Yuan; Yanran Fu; Pengyuan Zhou; Qingyu Chen 001; James Caverlee; Irene Li (CoRR, 2025)

MMLU-ProX: A Multilingual Benchmark for Advanced Large Language Model Evaluation. - Weihao Xuan; Rui Yang 016; Heli Qi; Qingcheng Zeng; Yunze Xiao; Yun Xing; Junjue Wang; Huitao Li; Xin Li 079; Kunyu Yu; Nan Liu 003; Qingyu Chen 001; et al. (CoRR, 2025)

Benchmarking Next-Generation Reasoning-Focused Large Language Models in Ophthalmology: A Head-to-Head Evaluation on 5,888 Items. - Minjie Zou; Sahana Srinivasan; Thaddaeus Wai Soon Lo; Ke Zou; Gabriel Dawei Yang; Xuguang Ai; Hyunjae Kim; Maxwell B. Singer; Fares Antaki; Kelvin Li; Robert Chang; Marcus Tan; et al. (CoRR, 2025)

Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards. - Jaehoon Yun; Jiwoong Sohn; Jungwoo Park; Hyunjae Kim; Xiangru Tang; Yanjun Shao; Yonghoe Koo; Minhyeok Ko; Qingyu Chen 001; Mark Gerstein; Michael Moor; Jaewoo Kang (CoRR, 2025)

BEnchmarking LLMs for Ophthalmology (BELO) for Ophthalmological Knowledge and Reasoning. - Sahana Srinivasan; Xuguang Ai; Thaddaeus Wai Soon Lo; Aidan Gilson; Minjie Zou; Ke Zou; Hyunjae Kim; Mingjia Yang; Krithi Pushpanathan; Samantha Min Er Yew; Wan Ting Loke; Jocelyn Hui Lin Goh; et al. (CoRR, 2025)

Performance of GPT-5 Frontier Models in Ophthalmology Question Answering. - Fares Antaki; David Mikhail; Daniel Milad; Danny A Mammo; Sumit Sharma 005; Sunil K. Srivastava; Bing Yu Chen; Samir Touma; Mertcan Sevgi; Jonathan El-Khoury; Pearse A. Keane; Qingyu Chen 001; et al. (CoRR, 2025)