Qingyu Chen

138 papers A* 3B 1Misc 8Journal 106Unranked 19
YearRankTypeTitle / Venue / Authors
2026 J jnl
A Federated and Parameter-Efficient Framework for Large Language Model Training in Medicine.
CoRR
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
2026 J jnl
AI-generated data contamination erodes pathological variability and diagnostic reliability.
CoRR
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
2026 — conf
Benchmarking Direct Preference Optimization for Medical Large Vision-Language Models.
EACL (Findings)
Dain Kim, Jiwoo Lee, Jaehoon Yun, Yonghoe Koo, Qingyu Chen, Hyunjae Kim, Jaewoo Kang
2026 J jnl
Benchmarking Direct Preference Optimization for Medical Large Vision-Language Models.
CoRR
Dain Kim, Jiwoo Lee, Jaehoon Yun, Yonghoe Koo, Qingyu Chen, Hyunjae Kim, Jaewoo Kang
2026 J jnl
Deliberative multi-agent large language models improve clinical reasoning in ophthalmology.
CoRR
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
2026 — conf
Dialogue is Better Than Monologue: Instructing Meidcal LLMs via Strategic Conversations.
EACL (Findings)
Zijie Liu, Xinyu Zhao, Jie Peng, Jinhao Duan, Zhuangdi Zhu, Qingyu Chen, Kaidi Xu, Xia Hu, Tianlong Chen
2026 J jnl
Digital Twin AI: Opportunities and Challenges from Large Language Models to World Models.
CoRR
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
2026 J jnl
EHRNavigator: A Multi-Agent System for Patient-Level Clinical Question Answering over Heterogeneous Electronic Health Records.
CoRR
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
2026 J jnl
Information extraction from clinical notes: are we ready to switch to large language models?
J. Am. Medical Informatics Assoc.
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
2026 J jnl
Med-CoReasoner: Reducing Language Disparities in Medical Reasoning via Language-Informed Co-Reasoning.
CoRR
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
2026 J jnl
Toward Global Large Language Models in Medicine.
CoRR
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
2026 J jnl
VOLMO: Versatile and Open Large Models for Ophthalmology.
CoRR
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
2025 — conf
AMD-Mamba: A Phenotype-Aware Multi-modal Framework for Robust AMD Prognosis.
MLMI@MICCAI
Puzhen Wu, Mingquan Lin, Qingyu Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Hexin Dong
2025 J jnl
Author Correction: Small language models learn enhanced reasoning skills from medical textbooks.
npj Digit. Medicine
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
2025 J jnl
BEnchmarking LLMs for Ophthalmology (BELO) for Ophthalmological Knowledge and Reasoning.
CoRR
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
2025 J jnl
Benchmarking Next-Generation Reasoning-Focused Large Language Models in Ophthalmology: A Head-to-Head Evaluation on 5,888 Items.
CoRR
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
2025 J jnl
Can OpenAI o1 Reason Well in Ophthalmology? A 6,990-Question Head-to-Head Evaluation Study.
CoRR
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
2025 — conf
Clinical Trial Eligibility Criteria Decomposition and Parsing with Large Language Models.
MedInfo
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
2025 J jnl
Dialogue is Better Than Monologue: Instructing Medical LLMs via Strategical Conversations.
CoRR
Zijie Liu, Xinyu Zhao, Jie Peng, Zhuangdi Zhu, Qingyu Chen, Xia Hu, Tianlong Chen
2025 J jnl
Enhancing Patient-Centric Communication: Leveraging LLMs to Simulate Patient Perspectives.
CoRR
Xinyao Ma, Rui Zhu, Zihao Wang, Jingwei Xiong, Qingyu Chen, Haixu Tang, L. Jean Camp, Lucila Ohno-Machado
2025 J jnl
From Compound Figures to Composite Understanding: Developing a Multi-Modal LLM from Biomedical Literature with Medical Multiple-Image Benchmarking and Validation.
CoRR
Zhen Chen, Yihang Fu, Gabriel Madera, Mauro Giuffrè, Serina S. Applebaum, Hyunjae Kim, Hua Xu, Qingyu Chen
2025 — conf
GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking.
ACL (1)
Yingjian Chen, Haoran Liu, Yinhong Liu, Jinxiang Xie, Rui Yang, Han Yuan, Yanran Fu, Peng Yuan Zhou, Qingyu Chen, James Caverlee, Irene Li
2025 J jnl
GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking.
CoRR
Yingjian Chen, Haoran Liu, Yinhong Liu, Rui Yang, Han Yuan, Yanran Fu, Pengyuan Zhou, Qingyu Chen, James Caverlee, Irene Li
2025 J jnl
Is an Ultra Large Natural Image-Based Foundation Model Superior to a Retina-Specific Model for Detecting Ocular and Systemic Diseases?
CoRR
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
2025 J jnl
LMOD+: A Comprehensive Multimodal Dataset and Benchmark for Developing and Evaluating Multimodal Large Language Models in Ophthalmology.
CoRR
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
2025 — conf
LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models.
NAACL (Findings)
Zhenyue Qin, Yu Yin, Dylan Campbell, Xuansheng Wu, Ke Zou, Ninghao Liu, Yih Chung Tham, Xiuzhen Zhang, Qingyu Chen
2025 A* conf
MMLU-ProX: A Multilingual Benchmark for Advanced Large Language Model Evaluation.
EMNLP
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
2025 J jnl
MMLU-ProX: A Multilingual Benchmark for Advanced Large Language Model Evaluation.
CoRR
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
2025 J jnl
ManifoldFormer: Geometric Deep Learning for Neural Dynamics on Riemannian Manifolds.
CoRR
Yihang Fu, Lifang He, Qingyu Chen
2025 A* conf
Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards.
EMNLP
Jaehoon Yun, Jiwoong Sohn, Jungwoo Park, Hyunjae Kim, Xiangru Tang, Daniel Shao, Yonghoe Koo, Minhyeok Ko, Qingyu Chen, Mark Gerstein, Michael Moor, Jaewoo Kang
2025 J jnl
Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards.
CoRR
Jaehoon Yun, Jiwoong Sohn, Jungwoo Park, Hyunjae Kim, Xiangru Tang, Yanjun Shao, Yonghoe Koo, Minhyeok Ko, Qingyu Chen, Mark Gerstein, Michael Moor, Jaewoo Kang
2025 J jnl
Medical foundation large language models for comprehensive text analysis and beyond.
npj Digit. Medicine
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
2025 J jnl
Memorization in Large Language Models in Medicine: Prevalence, Characteristics, and Implications.
CoRR
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
2025 J jnl
Performance of GPT-5 Frontier Models in Ophthalmology Question Answering.
CoRR
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
2025 J jnl
Rethinking Retrieval-Augmented Generation for Medicine: A Large-Scale, Systematic Expert Evaluation and Practical Insights.
CoRR
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
2025 J jnl
Small language models learn enhanced reasoning skills from medical textbooks.
npj Digit. Medicine
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
2025 J jnl
Social determinants of health extraction from clinical notes across institutions using large language models.
npj Digit. Medicine
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
2025 J jnl
Word-Sequence Entropy: Towards uncertainty estimation in free-form medical question answering applications and beyond.
Eng. Appl. Artif. Intell.
Zhiyuan Wang, Jinhao Duan, Chenxi Yuan, Qingyu Chen, Tianlong Chen, Yue Zhang, Ren Wang, Xiaoshuang Shi, Kaidi Xu
2024 J jnl
Advancing entity recognition in biomedicine via instruction tuning of large language models.
Bioinform.
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
2024 J jnl
AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning.
CoRR
Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, W. John Wilbur, Zhe He, Andrew Taylor, Qingyu Chen, Zhiyong Lu
2024 J jnl
Augmenting Biomedical Named Entity Recognition with General-domain Resources.
CoRR
Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen
2024 J jnl
Augmenting biomedical named entity recognition with general-domain resources.
J. Biomed. Informatics
Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen
2024 J jnl
Demystifying Large Language Models for Medicine: A Primer.
CoRR
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
2024 J jnl
Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology.
CoRR
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
2024 J jnl
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information.
Bioinform.
Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu
2024 J jnl
Humans Continue to Outperform Large Language Models in Complex Clinical Decision-Making: A Study with Medical Calculators.
CoRR
Nicholas Wan, Qiao Jin, Joey Chan, Guangzhi Xiong, Serina S. Applebaum, Aidan Gilson, Reid McMurry, R. Andrew Taylor, Aidong Zhang, Qingyu Chen, Zhiyong Lu
2024 J jnl
Improving large language models for clinical named entity recognition via prompt engineering.
J. Am. Medical Informatics Assoc.
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
2024 J jnl
Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models?
CoRR
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
2024 — conf
KG-Rank: Enhancing Large Language Models for Medical QA with Knowledge Graphs and Ranking Techniques.
BioNLP@ACL
Rui Yang, Haoran Liu, Edison Marrese-Taylor, Qingcheng Zeng, Yuhe Ke, Wanxin Li, Lechao Cheng, Qingyu Chen, James Caverlee, Yutaka Matsuo, Irene Li
2024 J jnl
KG-Rank: Enhancing Large Language Models for Medical QA with Knowledge Graphs and Ranking Techniques.
CoRR
Rui Yang, Haoran Liu, Edison Marrese-Taylor, Qingcheng Zeng, Yuhe Ke, Wanxin Li, Lechao Cheng, Qingyu Chen, James Caverlee, Yutaka Matsuo, Irene Li
2024 J jnl
LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models.
CoRR
Zhenyue Qin, Yu Yin, Dylan Campbell, Xuansheng Wu, Ke Zou, Yih-Chung Tham, Ninghao Liu, Xiuzhen Zhang, Qingyu Chen
2024 J jnl
Language Enhanced Model for Eye (LEME): An Open-Source Ophthalmology-Specific Large Language Model.
CoRR
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
2024 J jnl
Me LLaMA: Foundation Large Language Models for Medical Applications.
CoRR
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
2024 A* conf
MedCalc-Bench: Evaluating Large Language Models for Medical Calculations.
NeurIPS
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
2024 J jnl
MedCalc-Bench: Evaluating Large Language Models for Medical Calculations.
CoRR
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
2024 — conf
MedINST: Meta Dataset of Biomedical Instructions.
EMNLP (Findings)
Wenhan Han, Meng Fang, Zihan Zhang, Yu Yin, Zirui Song, Ling Chen, Mykola Pechenizkiy, Qingyu Chen
2024 J jnl
MedINST: Meta Dataset of Biomedical Instructions.
CoRR
Wenhan Han, Meng Fang, Zihan Zhang, Yu Yin, Zirui Song, Ling Chen, Mykola Pechenizkiy, Qingyu Chen
2024 J jnl
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
Aidan Gilson, Qingyu Chen, Ron A. Adelman
2024 J jnl
Opportunities and challenges for ChatGPT and large language models in biomedicine and health.
Briefings Bioinform.
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
2024 J jnl
PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature.
Bioinform.
Shubo Tian, Qingyu Chen, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2024 J jnl
PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge.
CoRR
Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
2024 J jnl
Towards Accountable AI-Assisted Eye Disease Diagnosis: Workflow Design, External Validation, and Continual Learning.
CoRR
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
2024 J jnl
Word-Sequence Entropy: Towards Uncertainty Estimation in Free-Form Medical Question Answering Applications and Beyond.
CoRR
Zhiyuan Wang, Jinhao Duan, Chenxi Yuan, Qingyu Chen, Tianlong Chen, Huaxiu Yao, Yue Zhang, Ren Wang, Kaidi Xu, Xiaoshuang Shi
2024 — conf
Yale at "Discharge Me!": Evaluating Constrained Generation of Discharge Summaries with Unstructured and Structured Information.
BioNLP@ACL
Vimig Socrates, Thomas Huang, Xuguang Ai, Soraya Fereydooni, Qingyu Chen, R. Andrew Taylor, David Chartash
2023 J jnl
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning.
Bioinform.
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
2023 B conf
Attention-based 3D convolutional networks for detection of geographic atrophy from optical coherence tomography scans.
Image Processing
Amr S. Elsawy, Tiarnan D. Kenan, Qingyu Chen, Xiaoshuang Shi, Emily Y. Chew, Zhiyong Lu
2023 J jnl
BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval.
CoRR
Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu
2023 J jnl
BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets.
CoRR
Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu
2023 J jnl
BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets.
J. Biomed. Informatics
Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu
2023 J jnl
Bioformer: an efficient transformer language model for biomedical text mining.
CoRR
Li Fang, Qingyu Chen, Chih-Hsuan Wei, Zhiyong Lu, Kai Wang
2023 J jnl
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning.
Patterns
Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2023 J jnl
GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information.
CoRR
Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu
2023 J jnl
Integrating UMLS Knowledge into Large Language Models for Medical Question Answering.
CoRR
Rui Yang, Edison Marrese-Taylor, Yuhe Ke, Lechao Cheng, Qingyu Chen, Irene Li
2023 J jnl
Interpretable Medical Image Visual Question Answering via Multi-Modal Relationship Graph Learning.
CoRR
Xinyue Hu, Lin Gu, Kazuma Kobayashi, Qiyuan An, Qingyu Chen, Zhiyong Lu, Chang Su, Tatsuya Harada, Yingying Zhu
2023 J jnl
Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations.
CoRR
Qingyu Chen, Jingcheng Du, Yan Hu, Vipina Kuttichi Keloth, Xueqing Peng, Kalpana Raja, Rui Zhang, Zhiyong Lu, Hua Xu
2023 J jnl
LitCovid in 2022: an information resource for the COVID-19 literature.
Nucleic Acids Res.
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
2023 J jnl
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval.
Bioinform.
Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu
2023 J jnl
MedGen: A Python Natural Language Processing Toolkit for Medical Text Processing.
CoRR
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
2023 J jnl
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health.
CoRR
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
2022 J jnl
A Privacy-Preserving Unsupervised Domain Adaptation Framework for Clinical Text Analysis.
CoRR
Qiyuan An, Ruijiang Li, Lin Gu, Hao Zhang, Qingyu Chen, Zhiyong Lu, Fei Wang, Yingying Zhu
2022 J jnl
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning.
CoRR
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
2022 J jnl
Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework.
CoRR
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Dogan, Zhiyong Lu
2022 J jnl
Assigning species information to corresponding genes by a sequence labeling framework.
Database J. Biol. Databases Curation
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu
2022 Misc conf
Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows.
AMIA
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
2022 J jnl
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning.
CoRR
Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2022 Misc conf
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
Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Amr S. Elsawy, Emily Y. Chew, Zhiyong Lu
2022 J jnl
LitCovid in 2022: an information resource for the COVID-19 literature.
CoRR
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
2022 J jnl
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation.
IEEE ACM Trans. Comput. Biol. Bioinform.
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2022 J jnl
LitMC-BERT: transformer-based multi-label classification of biomedical literature with an application on COVID-19 literature curation.
CoRR
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2022 J jnl
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
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
2022 J jnl
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
CoRR
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
2022 — conf
Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning.
MLMI@MICCAI
Junghwan Lee, Tingyi Wanyan, Qingyu Chen, Tiarnan D. L. Keenan, Benjamin S. Glicksberg, Emily Y. Chew, Zhiyong Lu, Fei Wang, Yifan Peng
2022 J jnl
Predicting myocardial infarction through retinal scans and minimal personal information.
Nat. Mach. Intell.
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
2022 J jnl
Robust convolutional neural networks against adversarial attacks on medical images.
Pattern Recognit.
Xiaoshuang Shi, Yifan Peng, Qingyu Chen, Tiarnan D. Keenan, Alisa T. Thavikulwat, Sungwon Lee, Yuxing Tang, Emily Y. Chew, Ronald M. Summers, Zhiyong Lu
2021 Misc conf
AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation.
AMIA
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2021 Misc conf
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
Qingyu Chen, Tiarnan D. Keenan, Emily Y. Chew, Zhiyong Lu
2021 — conf
Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI.
MLMI@MICCAI
Yingying Zhu, Shuai Wang, Qingyu Chen, Sungwon Lee, Thomas C. Shen, Daniel C. Elton, Zhiyong Lu, Ronald M. Summers
2021 J jnl
LitCovid: an open database of COVID-19 literature.
Nucleic Acids Res.
Qingyu Chen, Alexis Allot, Zhiyong Lu
2021 J jnl
LitSuggest: a web-based system for literature recommendation and curation using machine learning.
Nucleic Acids Res.
Alexis Allot, Kyubum Lee, Qingyu Chen, Ling Luo, Zhiyong Lu
2021 Misc conf
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors.
AMIA
Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu
2021 Misc conf
Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS.
AMIA
Gregory C. Ghahramani, Matthew Brendel, Mingquan Lin, Qingyu Chen, Tiarnan D. Keenan, Kun Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Fei Wang
2021 J jnl
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.
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
2020 — conf
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining.
BioNLP
Yifan Peng, Qingyu Chen, Zhiyong Lu
2020 J jnl
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining.
CoRR
Yifan Peng, Qingyu Chen, Zhiyong Lu
2020 J jnl
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP).
CoRR
Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
2020 — conf
Automatic recognition of abdominal lymph nodes from clinical text.
ClinicalNLP@EMNLP
Yifan Peng, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yuxing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald M. Summers, Zhiyong Lu
2020 J jnl
Better synonyms for enriching biomedical search.
J. Am. Medical Informatics Assoc.
Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu
2020 J jnl
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.
PLoS Comput. Biol.
Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
2020 J jnl
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.
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2020 Misc conf
Detection of reticular pseudodrusen using deep learning.
AMIA
Qingyu Chen, Tiarnan D. Keenan, Yifan Peng, Elvira Agrón, Christopher Hwang, Alisa T. Thavikulwat, Debora Lee, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2020 J jnl
Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration.
CoRR
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
2020 J jnl
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view.
CoRR
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
2020 J jnl
Predicting risk of late age-related macular degeneration using deep learning.
CoRR
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2020 J jnl
Predicting risk of late age-related macular degeneration using deep learning.
npj Digit. Medicine
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2020 J jnl
Privacy concerns of the Australian My Health Record: Implications for other large-scale opt-out personal health records.
Inf. Process. Manag.
Patrick Cheong-Iao Pang, Dana McKay, Shanton Chang, Qingyu Chen, Xiuzhen Zhang, Lishan Cui
2020 J jnl
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases.
Genom. Proteom. Bioinform.
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
2019 J jnl
A deep learning approach for automated detection of geographic atrophy from color fundus photographs.
CoRR
Tiarnan D. Keenan, Shazia Dharssi, Yifan Peng, Qingyu Chen, Elvira Agrón, Wai T. Wong, Zhiyong Lu, Emily Y. Chew
2019 Misc conf
A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs.
AMIA
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2019 J jnl
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale.
CoRR
Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
2019 — conf
BioSentVec: creating sentence embeddings for biomedical texts.
ICHI
Qingyu Chen, Yifan Peng, Zhiyong Lu
2019 J jnl
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records.
CoRR
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2019 — conf
Evaluation of Five Sentence Similarity Models on Electronic Medical Records.
BCB
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2019 J jnl
LitSense: making sense of biomedical literature at sentence level.
Nucleic Acids Res.
Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2019 J jnl
ML-Net: multi-label classification of biomedical texts with deep neural networks.
J. Am. Medical Informatics Assoc.
Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu
2019 J jnl
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.
Database J. Biol. Databases Curation
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
2019 J jnl
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.
J. Comput. Biol.
Qingyu Chen, Xiuzhen Zhang, Yu Wan, Justin Zobel, Karin Verspoor
2018 J jnl
A multi-task deep learning model for the classification of Age-related Macular Degeneration.
CoRR
Qingyu Chen, Yifan Peng, Tiarnan D. Keenan, Shazia Dharssi, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2018 J jnl
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics.
Database J. Biol. Databases Curation
Qingyu Chen, Nagesh C. Panyam, Aparna Elangovan, Karin Verspoor
2018 J jnl
BioSentVec: creating sentence embeddings for biomedical texts.
CoRR
Qingyu Chen, Yifan Peng, Zhiyong Lu
2018 J jnl
Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases.
ACM J. Data Inf. Qual.
Qingyu Chen, Yu Wan, Xiuzhen Zhang, Yang Lei, Justin Zobel, Karin Verspoor
2018 J jnl
DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs.
CoRR
Yifan Peng, Shazia Dharssi, Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2018 J jnl
ML-Net: multi-label classification of biomedical texts with deep neural networks.
CoRR
Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu
2018 — conf
Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents.
BCB
Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu
2017 J jnl
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.
Database J. Biol. Databases Curation
Qingyu Chen, Justin Zobel, Karin Verspoor
2017 — —
Duplication in biological databases: definitions, impacts and methods.
Qingyu Chen
2017 — conf
Sequence Clustering Methods and Completeness of Biological Database Search.
BAI@IJCAI
Qingyu Chen, Xiuzhen Zhang, Yu Wan, Justin Zobel, Karin Verspoor
2016 — conf
Evaluation of CD-HIT for constructing non-redundant databases.
BIBM
Qingyu Chen, Yu Wan, Yang Lei, Justin Zobel, Karin Verspoor
2015 — conf
Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases.
DTMBIO@CIKM
Qingyu Chen, Justin Zobel, Karin Verspoor