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ORCIDQingyu Chen 0001
Person information
- affiliation: National Institutes of Health, USA
- affiliation (former): University of Melbourne, School of Computing and Information Systems, Australia
Other persons with the same name
- Qingyu Chen — disambiguation page
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Books and Theses
- 2017
[b1]Qingyu Chen
:
Duplication in biological databases: definitions, impacts and methods. University of Melbourne, Parkville, Victoria, Australia, 2017
Journal Articles
- 2026
- [j40]Zhenyue Qin, Yang Liu, Yu Yin, Jinyu Ding, Haoran Zhang, Anran Li, Dylan Campbell, Xuansheng Wu, Ke Zou, Tiarnan D. L. Keenan, Emily Y. Chew, Zhiyong Lu, Yih Chung Tham, Ninghao Liu, Xiuzhen Zhang, Qingyu Chen:
LMOD\(\boldsymbol{+}\): A Comprehensive Multimodal Dataset and Benchmark for Developing and Evaluating Multimodal Large Language Models in Ophthalmology. ACM Trans. Comput. Heal. 7(3): 52:1-52:38 (2026) - [j39]Yan Hu, Xu Zuo, Yujia Zhou, Xueqing Peng, Jimin Huang, Vipina Kuttichi Keloth, Vincent J. Zhang, Ruey-Ling Weng, Cathy Shyr, Qingyu Chen, Xiaoqian Jiang, Kirk E. Roberts, Hua Xu:
Information extraction from clinical notes: are we ready to switch to large language models? J. Am. Medical Informatics Assoc. 33(3): 553-562 (2026) - 2025
- [j38]Zhiyuan Wang, Jinhao Duan, Chenxi Yuan, Qingyu Chen, Tianlong Chen, Yue Zhang, Ren Wang, Xiaoshuang Shi, Kaidi Xu:
Word-Sequence Entropy: Towards uncertainty estimation in free-form medical question answering applications and beyond. Eng. Appl. Artif. Intell. 139: 109553 (2025) - [j37]Vipina Kuttichi Keloth, Salih Selek, Qingyu Chen, Christopher Gilman, Sunyang Fu, Yifang Dang, Xinghan Chen, Xinyue Hu, Yujia Zhou, Huan He, Jungwei W. Fan, Karen Wang, Cynthia Brandt, Cui Tao, Hongfang Liu, Hua Xu:
Social determinants of health extraction from clinical notes across institutions using large language models. npj Digit. Medicine 8(1) (2025) - [j36]Hyunjae Kim, Hyeon Hwang, Jiwoo Lee, Sihyeon Park, Dain Kim, Taewhoo Lee, Chanwoong Yoon, Jiwoong Sohn, Jungwoo Park, Olga Reykhart, Thomas Fetherston, Donghee Choi, Soo Heon Kwak, Qingyu Chen, Jaewoo Kang:
Small language models learn enhanced reasoning skills from medical textbooks. npj Digit. Medicine 8(1) (2025) - [j35]Hyunjae Kim, Hyeon Hwang, Jiwoo Lee, Sihyeon Park, Dain Kim, Taewhoo Lee, Chanwoong Yoon, Jiwoong Sohn, Jungwoo Park, Olga Reykhart, Thomas Fetherston, Donghee Choi, Soo Heon Kwak, Qingyu Chen, Jaewoo Kang:
Author Correction: Small language models learn enhanced reasoning skills from medical textbooks. npj Digit. Medicine 8(1) (2025) - [j34]Qianqian Xie, Qingyu Chen, Aokun Chen, Cheng Peng, Yan Hu, Fongci Lin, Xueqing Peng, Jimin Huang, Jeffrey Zhang, Vipina Kuttichi Keloth, Xinyu Zhou, Lingfei Qian, Huan He, Dennis L. Shung, Lucila Ohno-Machado, Yonghui Wu, Hua Xu, Jiang Bian:
Medical foundation large language models for comprehensive text analysis and beyond. npj Digit. Medicine 8(1) (2025) - 2024
- [j33]Shubo Tian, Qiao Jin, Lana Yeganova, Po-Ting Lai, Qingqing Zhu, Xiuying Chen, Yifan Yang, Qingyu Chen, Won Kim, Donald C. Comeau, Rezarta Islamaj, Aadit Kapoor, Xin Gao, Zhiyong Lu:
Opportunities and challenges for ChatGPT and large language models in biomedicine and health. Briefings Bioinform. 25(1) (2024) - [j32]Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu:
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information. Bioinform. 40(2) (2024) - [j31]Vipina Kuttichi Keloth, Yan Hu, Qianqian Xie, Xueqing Peng, Yan Wang, Andrew Zheng, Melih Selek, Kalpana Raja, Chih-Hsuan Wei, Qiao Jin, Zhiyong Lu, Qingyu Chen, Hua Xu:
Advancing entity recognition in biomedicine via instruction tuning of large language models. Bioinform. 40(4) (2024) - [j30]Shubo Tian, Qingyu Chen, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature. Bioinform. 40(11) (2024) - [j29]Aidan Gilson, Qingyu Chen, Ron A. Adelman:
Ophthalmic care may not align with patient need: An analysis on state-wide patient needs and provider density between 2008 and 2022. Int. J. Medical Informatics 185: 105411 (2024) - [j28]Yan Hu, Qingyu Chen, Jingcheng Du, Xueqing Peng, Vipina Kuttichi Keloth, Xu Zuo, Yujia Zhou, Zehan Li, Xiaoqian Jiang, Zhiyong Lu, Kirk Roberts, Hua Xu:
Improving large language models for clinical named entity recognition via prompt engineering. J. Am. Medical Informatics Assoc. 31(9): 1812-1820 (2024) - [j27]Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen:
Augmenting biomedical named entity recognition with general-domain resources. J. Biomed. Informatics 159: 104731 (2024) - 2023
- [j26]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu:
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. Bioinform. 39(5) (2023) - [j25]Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu:
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval. Bioinform. 39(10) (2023) - [j24]Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu:
BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets. J. Biomed. Informatics 146: 104487 (2023) - [j23]Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu:
LitCovid in 2022: an information resource for the COVID-19 literature. Nucleic Acids Res. 51(D1): 1512-1518 (2023) - [j22]Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. Patterns 4(1): 100659 (2023) - 2022
- [j21]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu:
Assigning species information to corresponding genes by a sequence labeling framework. Database J. Biol. Databases Curation 2022(2022) (2022) - [j20]Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep Vg, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database J. Biol. Databases Curation 2022(2022) (2022) - [j19]Andres Diaz-Pinto, Nishant Ravikumar, Rahman Attar, Avan Suinesiaputra, Yitian Zhao, Eylem Levelt, Erica Dall' Armellina, Marco Lorenzi, Qingyu Chen, Tiarnan D. L. Keenan, Elvira Agrón, Emily Y. Chew, Zhiyong Lu, Chris P. Gale, Richard P. Gale, Sven Plein, Alejandro F. Frangi:
Predicting myocardial infarction through retinal scans and minimal personal information. Nat. Mach. Intell. 4(1): 55-61 (2022) - [j18]Xiaoshuang Shi, Yifan Peng, Qingyu Chen, Tiarnan D. Keenan, Alisa T. Thavikulwat, Sungwon Lee, Yuxing Tang, Emily Y. Chew, Ronald M. Summers, Zhiyong Lu:
Robust convolutional neural networks against adversarial attacks on medical images. Pattern Recognit. 132: 108923 (2022) - [j17]Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu:
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation. IEEE ACM Trans. Comput. Biol. Bioinform. 19(5): 2584-2595 (2022) - 2021
- [j16]Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu:
Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration. J. Am. Medical Informatics Assoc. 28(6): 1135-1148 (2021) - [j15]Qingyu Chen, Alexis Allot, Zhiyong Lu:
LitCovid: an open database of COVID-19 literature. Nucleic Acids Res. 49(Database-Issue): D1534-D1540 (2021) - [j14]Alexis Allot, Kyubum Lee, Qingyu Chen, Ling Luo, Zhiyong Lu:
LitSuggest: a web-based system for literature recommendation and curation using machine learning. Nucleic Acids Res. 49(Webserver-Issue): 352-358 (2021) - 2020
- [j13]Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor:
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genom. Proteom. Bioinform. 18(2): 91-103 (2020) - [j12]Patrick Cheong-Iao Pang, Dana McKay, Shanton Chang, Qingyu Chen, Xiuzhen Zhang, Lishan Cui:
Privacy concerns of the Australian My Health Record: Implications for other large-scale opt-out personal health records. Inf. Process. Manag. 57(6): 102364 (2020) - [j11]Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu:
Better synonyms for enriching biomedical search. J. Am. Medical Informatics Assoc. 27(12): 1894-1902 (2020) - [j10]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. BMC Medical Informatics Decis. Mak. 20-S(1): 73 (2020) - [j9]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Predicting risk of late age-related macular degeneration using deep learning. npj Digit. Medicine 3 (2020) - [j8]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. 16(4) (2020) - 2019
- [j7]Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu:
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019: bay147 (2019) - [j6]Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu:
ML-Net: multi-label classification of biomedical texts with deep neural networks. J. Am. Medical Informatics Assoc. 26(11): 1279-1285 (2019) - [j5]Qingyu Chen, Xiuzhen Zhang, Yu Wan, Justin Zobel, Karin Verspoor:
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. J. Comput. Biol. 26(6): 605-617 (2019) - [j4]Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
LitSense: making sense of biomedical literature at sentence level. Nucleic Acids Res. 47(Webserver-Issue): W594-W599 (2019) - 2018
- [j3]Qingyu Chen, Nagesh C. Panyam, Aparna Elangovan, Karin Verspoor:
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics. Database J. Biol. Databases Curation 2018: bay122 (2018) - [j2]Qingyu Chen, Yu Wan, Xiuzhen Zhang, Yang Lei, Justin Zobel, Karin Verspoor:
Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. ACM J. Data Inf. Qual. 9(3): 17 (2018) - 2017
- [j1]Qingyu Chen, Justin Zobel, Karin Verspoor:
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. Database J. Biol. Databases Curation 2017: baw163 (2017)
Conference and Workshop Papers
- 2026
- [c32]Fan Gao, Sherry T. Tong, Jiwoong Sohn, Jiahao Huang, Junfeng Jiang, Ding Xia, Piyalitt Ittichaiwong, Kanyakorn Veerakanjana, Hyunjae Kim, Qingyu Chen, Edison Marrese-Taylor, Kazuma Kobayashi, Akiko Aizawa, Irene Li:
MED-COREASONER: Reducing Language Disparities in Medical Reasoning via Language-Informed Co-Reasoning. ACL (1) 2026: 24868-24888 - [c31]Zijie Liu, Xinyu Zhao, Jie Peng, Jinhao Duan, Zhuangdi Zhu, Qingyu Chen, Kaidi Xu, Xia Hu, Tianlong Chen:
Dialogue is Better Than Monologue: Instructing Meidcal LLMs via Strategic Conversations. EACL (Findings) 2026: 2858-2872 - [c30]Dain Kim, Jiwoo Lee, Jaehoon Yun, Yonghoe Koo, Qingyu Chen, Hyunjae Kim, Jaewoo Kang:
Benchmarking Direct Preference Optimization for Medical Large Vision-Language Models. EACL (Findings) 2026: 5052-5067 - 2025
- [c29]Yingjian Chen, Haoran Liu, Yinhong Liu, Jinxiang Xie, Rui Yang, Han Yuan, Yanran Fu, Peng Yuan Zhou, Qingyu Chen, James Caverlee, Irene Li:
GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking. ACL (1) 2025: 14976-14995 - [c28]Weihao Xuan, Rui Yang, Heli Qi, Qingcheng Zeng, Yunze Xiao, Aosong Feng, Dairui Liu, Yun Xing, Junjue Wang, Fan Gao, Jinghui Lu, Yuang Jiang, Huitao Li, Xin Li, Kunyu Yu, Ruihai Dong, Shangding Gu, Yuekang Li, Xiaofei Xie, Felix Juefei-Xu, Foutse Khomh, Osamu Yoshie, Qingyu Chen, Douglas Teodoro, Nan Liu, Randy Goebel, Lei Ma, Edison Marrese-Taylor, Shijian Lu, Yusuke Iwasawa, Yutaka Matsuo, Irene Li:
MMLU-ProX: A Multilingual Benchmark for Advanced Large Language Model Evaluation. EMNLP 2025: 1513-1532 - [c27]Jaehoon Yun, Jiwoong Sohn, Jungwoo Park, Hyunjae Kim, Xiangru Tang, Daniel Shao, Yonghoe Koo, Minhyeok Ko, Qingyu Chen, Mark Gerstein, Michael Moor, Jaewoo Kang:
Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards. EMNLP 2025: 16554-16571 - [c26]Hongyu Chen, Lingfei Qian, Xing He, Aokun Chen, Yu Huang, Qinling Gou, Yuxuan Wang, Yan Wang, Xuguang Ai, Yujia Zhou, Inessa Cohen, Qingyu Chen, Hua Xu, Jiang Bian:
Clinical Trial Eligibility Criteria Decomposition and Parsing with Large Language Models. MedInfo 2025: 688-692 - [c25]Puzhen Wu, Mingquan Lin, Qingyu Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Hexin Dong:
AMD-Mamba: A Phenotype-Aware Multi-modal Framework for Robust AMD Prognosis. MLMI@MICCAI 2025: 150-160 - [c24]Zhenyue Qin, Yu Yin, Dylan Campbell, Xuansheng Wu, Ke Zou, Ninghao Liu, Yih Chung Tham, Xiuzhen Zhang, Qingyu Chen:
LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models. NAACL (Findings) 2025: 2501-2522 - 2024
- [c23]Rui Yang, Haoran Liu, Edison Marrese-Taylor, Qingcheng Zeng, Yuhe Ke, Wanxin Li, Lechao Cheng, Qingyu Chen, James Caverlee, Yutaka Matsuo, Irene Li:
KG-Rank: Enhancing Large Language Models for Medical QA with Knowledge Graphs and Ranking Techniques. BioNLP@ACL 2024: 155-166 - [c22]Vimig Socrates, Thomas Huang, Xuguang Ai, Soraya Fereydooni, Qingyu Chen, R. Andrew Taylor, David Chartash:
Yale at "Discharge Me!": Evaluating Constrained Generation of Discharge Summaries with Unstructured and Structured Information. BioNLP@ACL 2024: 724-730 - [c21]Wenhan Han, Meng Fang, Zihan Zhang, Yu Yin, Zirui Song, Ling Chen, Mykola Pechenizkiy, Qingyu Chen:
MedINST: Meta Dataset of Biomedical Instructions. EMNLP (Findings) 2024: 8221-8240 - [c20]Nikhil Khandekar, Qiao Jin, 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, Amisha D. Dave, Andrew Taylor, Aidong Zhang, Qingyu Chen, Zhiyong Lu:
MedCalc-Bench: Evaluating Large Language Models for Medical Calculations. NeurIPS 2024 - 2023
- [c19]Amr S. Elsawy, Tiarnan D. Kenan, Qingyu Chen, Xiaoshuang Shi, Emily Y. Chew, Zhiyong Lu:
Attention-based 3D convolutional networks for detection of geographic atrophy from optical coherence tomography scans. Image Processing 2023 - 2022
- [c18]Qingyu Chen, 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, Michele Maiberger, Arnold Oshinsky, Brittany E. Powell, Boonkit Purt, Soo Shin, Hillary Steifel, Alisa T. Thavikulwat, Keith Wroblewski, Sirisha Koirala, Tom Murickan, Michael F. Chiang, Michelle R. Hribar, Emily Y. Chew, Zhiyong Lu:
Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows. AMIA 2022 - [c17]Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Amr S. Elsawy, Emily Y. Chew, Zhiyong Lu:
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. AMIA 2022 - [c16]Junghwan Lee, Tingyi Wanyan, Qingyu Chen, Tiarnan D. L. Keenan, Benjamin S. Glicksberg, Emily Y. Chew, Zhiyong Lu, Fei Wang, Yifan Peng:
Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning. MLMI@MICCAI 2022: 11-20 - 2021
- [c15]Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu:
AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation. AMIA 2021 - [c14]Qingyu Chen, Tiarnan D. Keenan, Emily Y. Chew, Zhiyong Lu:
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. AMIA 2021 - [c13]Gregory C. Ghahramani, Matthew Brendel, Mingquan Lin, Qingyu Chen, Tiarnan D. Keenan, Kun Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Fei Wang:
Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS. AMIA 2021 - [c12]Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu:
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors. AMIA 2021 - [c11]Yingying Zhu, Shuai Wang, Qingyu Chen, Sungwon Lee, Thomas C. Shen, Daniel C. Elton, Zhiyong Lu, Ronald M. Summers:
Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI. MLMI@MICCAI 2021: 101-109 - 2020
- [c10]Yifan Peng, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yuxing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald M. Summers, Zhiyong Lu:
Automatic recognition of abdominal lymph nodes from clinical text. ClinicalNLP@EMNLP 2020: 101-110 - [c9]Qingyu Chen, Tiarnan D. Keenan, Yifan Peng, Elvira Agrón, Christopher Hwang, Alisa T. Thavikulwat, Debora Lee, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Detection of reticular pseudodrusen using deep learning. AMIA 2020 - [c8]Yifan Peng, Qingyu Chen, Zhiyong Lu:
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. BioNLP 2020: 205-214 - 2019
- [c7]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs. AMIA 2019 - [c6]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Evaluation of Five Sentence Similarity Models on Electronic Medical Records. BCB 2019: 533 - [c5]Qingyu Chen, Yifan Peng, Zhiyong Lu:
BioSentVec: creating sentence embeddings for biomedical texts. ICHI 2019: 1-5 - 2018
- [c4]Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu:
Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. BCB 2018: 531-532 - 2017
- [c3]Qingyu Chen, Xiuzhen Zhang, Yu Wan, Justin Zobel, Karin Verspoor:
Sequence Clustering Methods and Completeness of Biological Database Search. BAI@IJCAI 2017: 8-14 - 2016
- [c2]Qingyu Chen, Yu Wan, Yang Lei, Justin Zobel, Karin Verspoor:
Evaluation of CD-HIT for constructing non-redundant databases. BIBM 2016: 703-706 - 2015
- [c1]Qingyu Chen, Justin Zobel, Karin Verspoor:
Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases. DTMBIO@CIKM 2015: 4-12
Data and Artifacts
- 2024
- [d1]Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu:
Archive of PubTator 3.0 source code and trained models. Zenodo, 2024
Informal and Other Publications
- 2026
- [i77]Rong Zhou, Dongping Chen, Zihan Jia, Yao Su, Yixin Liu, Yiwen Lu, Dongwei Shi, Yue Huang, Tianyang Xu, Yi Pan, Xinliang Li, Yohannes Abate, Qingyu Chen, Zhengzhong Tu, Yu Yang, Yu Zhang, Qingsong Wen, Gengchen Mai, Sunyang Fu, Jiachen Li, Xuyu Wang, Ziran Wang, Jing Huang, Tianming Liu, Yong Chen, Lichao Sun, Lifang He:
Digital Twin AI: Opportunities and Challenges from Large Language Models to World Models. CoRR abs/2601.01321 (2026) - [i76]Rui Yang, Huitao Li, Weihao Xuan, Heli Qi, Xin Li, Kunyu Yu, Yingjian Chen, Rongrong Wang, Jacques Behmoaras, Tianxi Cai, Bibhas Chakraborty, Qingyu Chen, Lionel Tim-Ee Cheng, Marie-Louise Damwanza, Chido Dzinotyiwei, Aosong Feng, Chuan Hong, Yusuke Iwasawa, Yuhe Ke, Linah Kitala, Taehoon Ko, Jisan Lee, Irene Li, Jonathan Chong Kai Liew, Hongfang Liu, Lian Leng Low, Edison Marrese-Taylor, Yutaka Matsuo, Isheanesu Misi, Yilin Ning, Jasmine Chiat Ling Ong, Marcus Eng Hock Ong, Enrico Petretto, Hossein Rouhizadeh, Abiram Sandralegar, Oren Schreier, Iain Bee Huat Tan, Patrick Tan, Daniel Shu Wei Ting, Junjue Wang, Chunhua Weng, Matthew Yu Heng Wong, Fang Wu, Yunze Xiao, Xuhai Xu, Qingcheng Zeng, Zhuo Zheng, Yifan Peng, Douglas Teodoro, Nan Liu:
Toward Global Large Language Models in Medicine. CoRR abs/2601.02186 (2026) - [i75]Fan Gao, Sherry T. Tong, Jiwoong Sohn, Jiahao Huang, Junfeng Jiang, Ding Xia, Piyalitt Ittichaiwong, Kanyakorn Veerakanjana, Hyunjae Kim, Qingyu Chen, Edison Marrese-Taylor, Kazuma Kobayashi, Akkiko Aizawa, Irene Li:
Med-CoReasoner: Reducing Language Disparities in Medical Reasoning via Language-Informed Co-Reasoning. CoRR abs/2601.08267 (2026) - [i74]Lingfei Qian, Mauro Giuffrè, Yan Wang, Huan He, Qianqian Xie, Xuguang Ai, Xeuqing Peng, Fan Ma, Ruey-Ling Weng, Donald Wright, Adan Wang, Qingyu Chen, Vipina Kuttichi Keloth, Hua Xu:
EHRNavigator: A Multi-Agent System for Patient-Level Clinical Question Answering over Heterogeneous Electronic Health Records. CoRR abs/2601.10020 (2026) - [i73]Hongyu He, Shaowen Xiang, Ye Zhang, Yingtao Zhu, Jin Zhang, Hao Deng, Emily Alsentzer, Yun Liu, Qingyu Chen, Kun-Hsing Yu, Andrew Marshall, Tingting Chen, Srinivas Anumasa, Daniel Ebner, Dean Ho, Kee Yuan Ngiam, Ching-Yu Cheng, Dianbo Liu:
AI-generated data contamination erodes pathological variability and diagnostic reliability. CoRR abs/2601.12946 (2026) - [i72]Dain Kim, Jiwoo Lee, Jaehoon Yun, Yonghoe Koo, Qingyu Chen, Hyunjae Kim, Jaewoo Kang:
Benchmarking Direct Preference Optimization for Medical Large Vision-Language Models. CoRR abs/2601.17918 (2026) - [i71]Anran Li, Yuanyuan Chen, Wenjun Long, Yu Yin, Yan Hu, Hyunjae Kim, Weipeng Zhou, Yujia Zhou, Hongyi Peng, Yang Ren, Xuguang Ai, Zhenyue Qin, Ming Hu, Xiaoxiao Li, Han Yu, Yih-Chung Tham, Lucila Ohno-Machado, Hua Xu, Qingyu Chen:
A Federated and Parameter-Efficient Framework for Large Language Model Training in Medicine. CoRR abs/2601.22124 (2026) - [i70]Ehsan Misaghi, Sean T. Berkowitz, Bing Yu Chen, Qingyu Chen, Renaud Duval, Pearse A. Keane, Danny A Mammo, Ariel Yuhan Ong, Mertcan Sevgi, Sumit Sharma, Sunil K. Srivastava, Yih Chung Tham, Fares Antaki:
Deliberative multi-agent large language models improve clinical reasoning in ophthalmology. CoRR abs/2603.21447 (2026) - [i69]Zhenyue Qin, Younjoon Chung, Elijah Lee, Wanyue Feng, Xuguang Ai, Serina S. Applebaum, Minjie Zou, Yang Liu, Pan Xiao, Mac Singer, Amisha D. Dave, Aidan Gilson, Tiarnan D. L. Keenan, Emily Y. Chew, Zhiyong Lu, Yih-Chung Tham, Ron Adelman, Luciano V. Del Priore, Qingyu Chen:
VOLMO: Versatile and Open Large Models for Ophthalmology. CoRR abs/2603.23953 (2026) - [i68]Tienyu Chang, Zhen Chen, Renjie Liang, Jinyu Ding, Jie Xu, Sunu Mathew, Amir Reza Hajrasouliha, Andrew J. Saykin, Ruogu Fang, Yu Huang, Jiang Bian, Qingyu Chen:
OphMAE: Bridging Volumetric and Planar Imaging with a Foundation Model for Adaptive Ophthalmological Diagnosis. CoRR abs/2605.02714 (2026) - [i67]Fan Ma, Yuntian Liu, Xiang Lan, Weipeng Zhou, Jun Ni, Mauro Giuffrè, Lingfei Qian, Xueqing Peng, Yujia Zhou, Ruey-Ling Weng, Huan He, Lu Li, Huiyuan Wang, Qingyu Chen, Andrew Loza, Laila Rasmy, Degui Zhi, Yuan Lu, Chenjie Zeng, Joshua C. Denny, Lee Schwamm, Daniella Meeker, Lucila Ohno-Machado, Yong Chen, Hua Xu:
Foundation Models to Unlock Real-World Evidence from Nationwide Medical Claims. CoRR abs/2605.02740 (2026) - [i66]Roy Jiang, Hyunjae Kim, Zhenyue Qin, Morten Lee, Margaret MacGibeny, Ailish Hanly, Angela Sadlowski, Shanin Chowdhury, Xuguang Ai, Jeffrey Gehlhausen, Qingyu Chen:
Are Multimodal LLMs Ready for Clinical Dermatology? A Real-World Evaluation in Dermatology. CoRR abs/2605.04098 (2026) - [i65]Peisong Zhang, Manqiang Peng, Yuxuan Wu, Pawit Phadungsaksawasdi, Wesley Yeung, Ye Zhang, Trang Nguyen, Qiang Zhang, Nan Liu, Meng Wang, Kee Yuan Ngiam, Yih-Chung Tham, Ching-Yu Cheng, Tianfan Fu, Qingyu Chen, Rosemary Ke, Chang Li, Wenzhuo Yang, Zhenghao Lu, Chunyou Lai, Yu Zhang, Sheng Zhong, Hao Deng, Dianbo Liu:
Resolving the bias-precision paradox with stochastic causal representation learning for personalized medicine. CoRR abs/2605.05706 (2026) - [i64]Zihan Guan, Qiao Jin, Guangzhi Xiong, Fangyuan Chen, Mengxuan Hu, Qingyu Chen, Yifan Peng, Zhiyong Lu, Anil Vullikanti:
Large Language Models Lack Temporal Awareness of Medical Knowledge. CoRR abs/2605.13045 (2026) - [i63]Yuang Fan, Lilin Xu, Millie Wu, Jingping Nie, Qingyu Chen, Yuzhe Yang, Zhuo Zhang, Xin Liu, Subigya Nepal, Xiaofan Jiang, Xuhai Orson Xu:
TimeSRL: Generalizable Time-Series Behavioral Modeling via Semantic RL-Tuned LLMs - A Case Study in Mental Health. CoRR abs/2605.21295 (2026) - [i62]Tianyu Liu, Allen Xin Wang, Antonia Panescu, Lisa Xinyi Chen, Wenxin Long, Xinyu Wei, Yueqian Jing, Ziyao Zeng, Jihang Chen, Sihan Jiang, Ziqing Wang, Siyi Gu, Siyu Chen, Xinyang Hu, Haoran Shao, Leqi Xu, Wangjie Zheng, Zhiyuan Cao, Ada Fang, Botao Yu, Kunyang Sun, Rex Ying, Arman Cohan, Qingyu Chen, Lingzhou Xue, Kaize Ding, Yuanqi Du, Wengong Jin, Zhuoran Yang, Marinka Zitnik, James Zou, Hua Xu, Hongyu Zhao:
Benchmarking AI Agents for Addressing Scientific Challenges Across Scales. CoRR abs/2606.12736 (2026) - [i61]Hyunjae Kim, Dain Kim, Pan Xiao, Serina S. Applebaum, Younjoon Chung, Xuguang Ai, Yu Yin, Roy Jiang, Yuexi Du, Yawen Wei, Yiming Kong, Tuo Guo, Zhiyuan Cao, Mengmeng Du, Yuelei Fu, Yan Hu, Rui Shi, Gui Yang, Kevin W. Jin, Yuntian Liu, Yuxuan Tian, Jonathan Marquez, Zhen Chen, Sheng Zhang, Hoifung Poon, Hua Xu, Jaewoo Kang, Qingyu Chen:
MedPMC: A Systematic Framework for Scaling High-Fidelity Medical Multimodal Data for Foundation Models. CoRR abs/2607.07673 (2026) - [i60]Fan Ma, Mauro Giuffrè, Donald Wright, Kent McCann, Mark Iscoe, Lingfei Qian, Mingyang Jiang, Chi Wing Ng, Na Hong, Huan He, Cathy Shyr, Qingyu Chen, Lee Schwamm, Lucila Ohno-Machado, Hua Xu:
A safety-oriented hypothetico-deductive framework for AI-assisted differential diagnosis. CoRR abs/2607.08038 (2026) - 2025
- [i59]Xinyao Ma, Rui Zhu, Zihao Wang, Jingwei Xiong, Qingyu Chen, Haixu Tang, L. Jean Camp, Lucila Ohno-Machado:
Enhancing Patient-Centric Communication: Leveraging LLMs to Simulate Patient Perspectives. CoRR abs/2501.06964 (2025) - [i58]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, Ziyou Chen, Dianbo Liu, Ron A. Adelman, Qingyu Chen, Yih Chung Tham:
Can OpenAI o1 Reason Well in Ophthalmology? A 6,990-Question Head-to-Head Evaluation Study. CoRR abs/2501.13949 (2025) - [i57]Zijie Liu, Xinyu Zhao, Jie Peng, Zhuangdi Zhu, Qingyu Chen, Xia Hu, Tianlong Chen:
Dialogue is Better Than Monologue: Instructing Medical LLMs via Strategical Conversations. CoRR abs/2501.17860 (2025) - [i56]Qingshan Hou, Yukun Zhou, Jocelyn Hui Lin Goh, Ke Zou, Samantha Min Er Yew, Sahana Srinivasan, Meng Wang, Thaddaeus Wai Soon Lo, Xiaofeng Lei, Siegfried K. Wagner, Mark A. Chia, Dawei Yang, Hongyang Jiang, Emma Anran Ran, Rui Santos, Gábor Márk Somfai, Juan Helen Zhou, Haoyu Chen, Qingyu Chen, Carol Yim-lui Cheung, Pearse A. Keane, Yih Chung Tham:
Is an Ultra Large Natural Image-Based Foundation Model Superior to a Retina-Specific Model for Detecting Ocular and Systemic Diseases? CoRR abs/2502.06289 (2025) - [i55]Yingjian Chen, Haoran Liu, Yinhong Liu, Rui Yang, Han Yuan, Yanran Fu, Pengyuan Zhou, Qingyu Chen, James Caverlee, Irene Li:
GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking. CoRR abs/2502.16514 (2025) - [i54]Weihao Xuan, Rui Yang, Heli Qi, Qingcheng Zeng, Yunze Xiao, Yun Xing, Junjue Wang, Huitao Li, Xin Li, Kunyu Yu, Nan Liu, Qingyu Chen, Douglas Teodoro, Edison Marrese-Taylor, Shijian Lu, Yusuke Iwasawa, Yutaka Matsuo, Irene Li:
MMLU-ProX: A Multilingual Benchmark for Advanced Large Language Model Evaluation. CoRR abs/2503.10497 (2025) - [i53]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, David Ziyou Chen, Dianbo Liu, Qingyu Chen, Yih Chung Tham:
Benchmarking Next-Generation Reasoning-Focused Large Language Models in Ophthalmology: A Head-to-Head Evaluation on 5,888 Items. CoRR abs/2504.11186 (2025) - [i52]Jaehoon Yun, Jiwoong Sohn, Jungwoo Park, Hyunjae Kim, Xiangru Tang, Yanjun Shao, Yonghoe Koo, Minhyeok Ko, Qingyu Chen, Mark Gerstein, Michael Moor, Jaewoo Kang:
Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards. CoRR abs/2506.11474 (2025) - [i51]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, Yibing Chen, Yiming Kong, Emily Yuelei Fu, Michelle Ongyong Hui, Kristen Nwanyanwu, Amisha D. Dave, Kelvin Zhenghao Li, Chen-Hsin Sun, Mark A. Chia, Gabriel Dawei Yang, Wendy Meihua Wong, David Ziyou Chen, Dianbo Liu, Maxwell B. Singer, Fares Antaki, Luciano V. Del Priore, Jost B. Jonas, Ron A. Adelman, Qingyu Chen, Yih-Chung Tham:
BEnchmarking LLMs for Ophthalmology (BELO) for Ophthalmological Knowledge and Reasoning. CoRR abs/2507.15717 (2025) - [i50]Fares Antaki, David Mikhail, Daniel Milad, Danny A Mammo, Sumit Sharma, Sunil K. Srivastava, Bing Yu Chen, Samir Touma, Mertcan Sevgi, Jonathan El-Khoury, Pearse A. Keane, Qingyu Chen, Yih Chung Tham, Renaud Duval:
Performance of GPT-5 Frontier Models in Ophthalmology Question Answering. CoRR abs/2508.09956 (2025) - [i49]Anran Li, Lingfei Qian, Mengmeng Du, Yu Yin, Yan Hu, Zihao Sun, Yihang Fu, Erica Stutz, Xuguang Ai, Qianqian Xie, Rui Zhu, Jimin Huang, Yifan Yang, Siru Liu, Yih-Chung Tham, Lucila Ohno-Machado, Hyunghoon Cho, Zhiyong Lu, Hua Xu, Qingyu Chen:
Memorization in Large Language Models in Medicine: Prevalence, Characteristics, and Implications. CoRR abs/2509.08604 (2025) - [i48]Zhenyue Qin, Yang Liu, Yu Yin, Jinyu Ding, Haoran Zhang, Anran Li, Dylan Campbell, Xuansheng Wu, Ke Zou, Tiarnan D. L. Keenan, Emily Y. Chew, Zhiyong Lu, Yih-Chung Tham, Ninghao Liu, Xiuzhen Zhang, Qingyu Chen:
LMOD+: A Comprehensive Multimodal Dataset and Benchmark for Developing and Evaluating Multimodal Large Language Models in Ophthalmology. CoRR abs/2509.25620 (2025) - [i47]Hyunjae Kim, Jiwoong Sohn, Aidan Gilson, Nicholas Cochran-Caggiano, Serina S. Applebaum, Heeju Jin, Seihee Park, Yujin Park, Jiyeong Park, Seoyoung Choi, Brittany Alexandra Herrera Contreras, Thomas Huang, Jaehoon Yun, Ethan F. Wei, Roy Jiang, Leah Colucci, Eric Lai, Amisha D. Dave, Tuo Guo, Maxwell B. Singer, Yonghoe Koo, Ron A. Adelman, James Zou, Andrew Taylor, Arman Cohan, Hua Xu, Qingyu Chen:
Rethinking Retrieval-Augmented Generation for Medicine: A Large-Scale, Systematic Expert Evaluation and Practical Insights. CoRR abs/2511.06738 (2025) - [i46]Yihang Fu, Lifang He, Qingyu Chen:
ManifoldFormer: Geometric Deep Learning for Neural Dynamics on Riemannian Manifolds. CoRR abs/2511.16828 (2025) - [i45]Zhen Chen, Yihang Fu, Gabriel Madera, Mauro Giuffrè, Serina S. Applebaum, Hyunjae Kim, Hua Xu, Qingyu Chen:
From Compound Figures to Composite Understanding: Developing a Multi-Modal LLM from Biomedical Literature with Medical Multiple-Image Benchmarking and Validation. CoRR abs/2511.22232 (2025) - 2024
- [i44]Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu:
PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge. CoRR abs/2401.11048 (2024) - [i43]Qianqian Xie, Qingyu Chen, Aokun Chen, Cheng Peng, Yan Hu, Fongci Lin, Xueqing Peng, Jimin Huang, Jeffrey Zhang, Vipina Kuttichi Keloth, Xingyu Zhou, Huan He, Lucila Ohno-Machado, Yonghui Wu, Hua Xu, Jiang Bian:
Me LLaMA: Foundation Large Language Models for Medical Applications. CoRR abs/2402.12749 (2024) - [i42]Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, W. John Wilbur, Zhe He, Andrew Taylor, Qingyu Chen, Zhiyong Lu:
AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning. CoRR abs/2402.13225 (2024) - [i41]Zhiyuan Wang, Jinhao Duan, Chenxi Yuan, Qingyu Chen, Tianlong Chen, Huaxiu Yao, Yue Zhang, Ren Wang, Kaidi Xu, Xiaoshuang Shi:
Word-Sequence Entropy: Towards Uncertainty Estimation in Free-Form Medical Question Answering Applications and Beyond. CoRR abs/2402.14259 (2024) - [i40]Rui Yang, Haoran Liu, Edison Marrese-Taylor, Qingcheng Zeng, Yuhe Ke, Wanxin Li, Lechao Cheng, Qingyu Chen, James Caverlee, Yutaka Matsuo, Irene Li:
KG-Rank: Enhancing Large Language Models for Medical QA with Knowledge Graphs and Ranking Techniques. CoRR abs/2403.05881 (2024) - [i39]Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen:
Augmenting Biomedical Named Entity Recognition with General-domain Resources. CoRR abs/2406.10671 (2024) - [i38]Nikhil Khandekar, Qiao Jin, 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, Amisha D. Dave, Andrew Taylor, Aidong Zhang, Qingyu Chen, Zhiyong Lu:
MedCalc-Bench: Evaluating Large Language Models for Medical Calculations. CoRR abs/2406.12036 (2024) - [i37]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, Wendy Wong, Qiao Jin, Tiarnan D. L. Keenan, Xia Hu, Emily Y. Chew, Zhiyong Lu, Hua Xu, Ron A. Adelman, Yih-Chung Tham, Qingyu Chen:
Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology. CoRR abs/2409.13902 (2024) - [i36]Anran Li, Yuanyuan Chen, Chao Ren, Wenhan Wang, Ming Hu, Tianlin Li, Han Yu, Qingyu Chen:
Federated Graph Learning with Adaptive Importance-based Sampling. CoRR abs/2409.14655 (2024) - [i35]Qingyu Chen, 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, Ellen Davis, William G. Gensheimer, David Grasic, Seema Gupta, Luis Haddock, Eleni Konstantinou, Tania Lamba, Michele Maiberger, Dimosthenis Mantopoulos, Mitul C. Mehta, Ayman G. Nahri, Mutaz AL-Nawaflh, Arnold Oshinsky, Brittany E. Powell, Boonkit Purt, Soo Shin, Hillary Stiefel, Alisa T. Thavikulwat, Keith Wroblewski, Tham Yih Chung, Chui Ming Gemmy Cheung, Ching-Yu Cheng, Emily Y. Chew, Michelle R. Hribar, Michael F. Chiang, Zhiyong Lu:
Towards Accountable AI-Assisted Eye Disease Diagnosis: Workflow Design, External Validation, and Continual Learning. CoRR abs/2409.15087 (2024) - [i34]Zhenyue Qin, Yu Yin, Dylan Campbell, Xuansheng Wu, Ke Zou, Yih-Chung Tham, Ninghao Liu, Xiuzhen Zhang, Qingyu Chen:
LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models. CoRR abs/2410.01620 (2024) - [i33]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, Hua Xu, Dianbo Liu, Ron A. Adelman, Yih-Chung Tham, Qingyu Chen:
Language Enhanced Model for Eye (LEME): An Open-Source Ophthalmology-Specific Large Language Model. CoRR abs/2410.03740 (2024) - [i32]Wenhan Han, Meng Fang, Zihan Zhang, Yu Yin, Zirui Song, Ling Chen, Mykola Pechenizkiy, Qingyu Chen:
MedINST: Meta Dataset of Biomedical Instructions. CoRR abs/2410.13458 (2024) - [i31]Qiao Jin, Nicholas Wan, Robert Leaman, Shubo Tian, Zhizheng Wang, Yifan Yang, Zifeng Wang, Guangzhi Xiong, Po-Ting Lai, Qingqing Zhu, Benjamin Hou, Maame Sarfo-Gyamfi, Gongbo Zhang, Aidan Gilson, Balu Bhasuran, Zhe He, Aidong Zhang, Jimeng Sun, Chunhua Weng, Ronald M. Summers, Qingyu Chen, Yifan Peng, Zhiyong Lu:
Demystifying Large Language Models for Medicine: A Primer. CoRR abs/2410.18856 (2024) - [i30]Nicholas Wan, Qiao Jin, Joey Chan, Guangzhi Xiong, Serina S. Applebaum, Aidan Gilson, Reid McMurry, R. Andrew Taylor, Aidong Zhang, Qingyu Chen, Zhiyong Lu:
Humans Continue to Outperform Large Language Models in Complex Clinical Decision-Making: A Study with Medical Calculators. CoRR abs/2411.05897 (2024) - [i29]Yan Hu, Xu Zuo, Yujia Zhou, Xueqing Peng, Jimin Huang, Vipina Kuttichi Keloth, Vincent J. Zhang, Ruey-Ling Weng, Qingyu Chen, Xiaoqian Jiang, Kirk E. Roberts, Hua Xu:
Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models? CoRR abs/2411.10020 (2024) - 2023
- [i28]Li Fang, Qingyu Chen, Chih-Hsuan Wei, Zhiyong Lu, Kai Wang:
Bioformer: an efficient transformer language model for biomedical text mining. CoRR abs/2302.01588 (2023) - [i27]Xinyue Hu, Lin Gu, Kazuma Kobayashi, Qiyuan An, Qingyu Chen, Zhiyong Lu, Chang Su, Tatsuya Harada, Yingying Zhu:
Interpretable Medical Image Visual Question Answering via Multi-Modal Relationship Graph Learning. CoRR abs/2302.09636 (2023) - [i26]Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu:
GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information. CoRR abs/2304.09667 (2023) - [i25]Qingyu Chen, Jingcheng Du, Yan Hu, Vipina Kuttichi Keloth, Xueqing Peng, Kalpana Raja, Rui Zhang, Zhiyong Lu, Hua Xu:
Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations. CoRR abs/2305.16326 (2023) - [i24]Shubo Tian, Qiao Jin, Lana Yeganova, Po-Ting Lai, Qingqing Zhu, Xiuying Chen, Yifan Yang, Qingyu Chen, Won Kim, Donald C. Comeau, Rezarta Islamaj, Aadit Kapoor, Xin Gao, Zhiyong Lu:
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health. CoRR abs/2306.10070 (2023) - [i23]Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu:
BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets. CoRR abs/2306.11189 (2023) - [i22]Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu:
BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval. CoRR abs/2307.00589 (2023) - [i21]Rui Yang, Edison Marrese-Taylor, Yuhe Ke, Lechao Cheng, Qingyu Chen, Irene Li:
Integrating UMLS Knowledge into Large Language Models for Medical Question Answering. CoRR abs/2310.02778 (2023) - [i20]Rui Yang, 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, Zhiyong Lu, Hua Xu, Qingyu Chen, Irene Li:
MedGen: A Python Natural Language Processing Toolkit for Medical Text Processing. CoRR abs/2311.16588 (2023) - 2022
- [i19]Qiyuan An, Ruijiang Li, Lin Gu, Hao Zhang, Qingyu Chen, Zhiyong Lu, Fei Wang, Yingying Zhu:
A Privacy-Preserving Unsupervised Domain Adaptation Framework for Clinical Text Analysis. CoRR abs/2201.07317 (2022) - [i18]Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu:
LitMC-BERT: transformer-based multi-label classification of biomedical literature with an application on COVID-19 literature curation. CoRR abs/2204.08649 (2022) - [i17]Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj Dogan, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. CoRR abs/2204.09781 (2022) - [i16]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Dogan, Zhiyong Lu:
Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework. CoRR abs/2205.03853 (2022) - [i15]Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. CoRR abs/2209.08124 (2022) - [i14]Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu:
LitCovid in 2022: an information resource for the COVID-19 literature. CoRR abs/2209.13428 (2022) - [i13]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu:
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning. CoRR abs/2211.16944 (2022) - 2020
- [i12]Yifan Peng, Qingyu Chen, Zhiyong Lu:
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. CoRR abs/2005.02799 (2020) - [i11]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Predicting risk of late age-related macular degeneration using deep learning. CoRR abs/2007.09550 (2020) - [i10]Lana Yeganova, Rezarta Islamaj Dogan, Qingyu Chen, Robert Leaman, Alexis Allot, Chih-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu:
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. CoRR abs/2008.03397 (2020) - [i9]Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu:
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). CoRR abs/2010.16413 (2020) - [i8]Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu:
Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration. CoRR abs/2011.05142 (2020) - 2019
- [i7]Tiarnan D. Keenan, Shazia Dharssi, Yifan Peng, Qingyu Chen, Elvira Agrón, Wai T. Wong, Zhiyong Lu, Emily Y. Chew:
A deep learning approach for automated detection of geographic atrophy from color fundus photographs. CoRR abs/1906.03153 (2019) - [i6]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. CoRR abs/1909.03044 (2019) - [i5]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR abs/1912.10846 (2019) - 2018
- [i4]Qingyu Chen, Yifan Peng, Zhiyong Lu:
BioSentVec: creating sentence embeddings for biomedical texts. CoRR abs/1810.09302 (2018) - [i3]Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu:
ML-Net: multi-label classification of biomedical texts with deep neural networks. CoRR abs/1811.05475 (2018) - [i2]Yifan Peng, Shazia Dharssi, Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs. CoRR abs/1811.07492 (2018) - [i1]Qingyu Chen, Yifan Peng, Tiarnan D. Keenan, Shazia Dharssi, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
A multi-task deep learning model for the classification of Age-related Macular Degeneration. CoRR abs/1812.00422 (2018)
Coauthor Index
Rezarta Islamaj Dogan
aka: Rezarta Islamaj
aka: Rezarta Islamaj
Tiarnan D. Keenan
aka: Tiarnan D. L. Keenan
aka: Tiarnan D. L. Keenan
[j40] [j33] [j32] [j31] [j30] [j28] [j27] [j26] [j25] [j24] [j23] [j22] [j21] [j20] [j19] [j18] [j17] [j16] [j15] [j14] [j11] [j10] [j9] [j8] [j7] [j6] [j4] [c25] [c20] [c19] [c18] [c17] [c16] [c15] [c14] [c13] [c12] [c11] [c10] [c9] [c8] [c7] [c6] [c5] [c4] [d1] [i69] [i64] [i49] [i48] [i44] [i42] [i39] [i38] [i37] [i35] [i31] [i30] [i28] [i27] [i26] [i25] [i24] [i23] [i22] [i20] [i19] [i18] [i17] [i16] [i15] [i14] [i13] [i12] [i11] [i10] [i9] [i8] [i7] [i6] [i5] [i4] [i3] [i2] [i1]
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