Qingyu Chen

United States National Library of Medicine

Also affiliated with Yale University, Zhejiang University

Computer ScienceBiochemistry, Genetics and Molecular BiologyMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

15.4Author DataRank

Indexed papers

10in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 10 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

LitCovid: an open database of COVID-19 literature

Nucleic Acids Research(2020)10.1093/nar/gkaa952

Top 3%

6.9DataRank

Top 3%276 citations

Alexis Allot, ZHIYONG LU, Qingyu Chen

Papers

Driven by 60 papers — median percentile 69. Top paper: “LitCovid: an open database of COVID-19 literature”.

LitCovid: an open database of COVID-19 literature

Nucleic Acids Research(2020)10.1093/nar/gkaa952

Top 3%

6.9DataRank

Top 3%276 citations

Alexis Allot, ZHIYONG LU, Qingyu Chen

MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval

Bioinformatics(2023)10.1093/bioinformatics/btad651

N/A

5.8DataRank · unranked

144 citations

Won Bae Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur +2 more

PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge

Nucleic Acids Research(2024)10.1093/nar/gkae235

Top 6%

3.8DataRank

Top 6%167 citations

Alexis Allot, Po‐Ting Lai, Robert Leaman, Shubo Tian, Ling Luo +5 more

Artificial Intelligence in Action: Addressing the COVID-19 Pandemic with Natural Language Processing

Annual Review of Biomedical Data Science(2021)10.1146/annurev-biodatasci-021821-061045

N/A

2.6DataRank · unranked

65 citations

Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan +2 more

Benchmarking large language models for biomedical natural language processing applications and recommendations

Nature Communications(2025)10.1038/s41467-025-56989-2

N/A

2.5DataRank · unranked

139 citations

Yan Hu, Xueqing Peng, Qianqian Xie, Qiao Jin, Aidan Gilson +16 more

Medical foundation large language models for comprehensive text analysis and beyond

npj Digital Medicine(2025)10.1038/s41746-025-01533-1

N/A

1.7DataRank · unranked

61 citations

Qingyu Chen, Aokun Chen, Peng Cheng, Yan Hu, Fongci Lin +13 more

LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation

IEEE/ACM Transactions on Computational Biology and Bioinformatics(2022)10.1109/tcbb.2022.3173562

Top 13%

1.6DataRank

Top 13%40 citations

Jingcheng Du, Alexis Allot, ZHIYONG LU, Qingyu Chen

LitCovid in 2022: an information resource for the COVID-19 literature

Nucleic Acids Research(2022)10.1093/nar/gkac1005

Top 22%

0.909DataRank

Top 22%31 citations

Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio +3 more

Improving large language models for clinical named entity recognition via prompt engineering

Journal of the American Medical Informatics Association(2024)10.1093/jamia/ocad259

N/A

0.853DataRank · unranked

293 citations

Qingyu Chen, Jingcheng Du, Xueqing Peng, Vipina K. Keloth, Xu Zuo +7 more

An Updated Simplified Severity Scale for Age-Related Macular Degeneration Incorporating Reticular Pseudodrusen

Ophthalmology(2024)10.1016/j.ophtha.2024.04.011

N/A

0.811DataRank · unranked

33 citations

Amitha Domalpally, Qingyu Chen, ZHIYONG LU, Emily Y. Chew, Tiarnán D L Keenan +1 more

Deep-GA-Net for Accurate and Explainable Detection of Geographic Atrophy on OCT Scans

Ophthalmology Science(2023)10.1016/j.xops.2023.100311

Top 30%

0.656DataRank

Top 30%13 citations

Tiarnán D L Keenan, Qingyu Chen, Xioashuang Shi, Alisa T. Thavikulwat, S. Bhandari +3 more

Archive of PubTator 3.0 source code and trained models

PubMed(2024)10.48550/arxiv.2401.11048

Top 32%

0.613DataRank

Top 32%3 citations

Alexis Allot, Po‐Ting Lai, Robert Leaman, Shubo Tian, Ling Luo +5 more

LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models

PubMed(2025)10.18653/v1/2025.findings-naacl.135

Top 48%

0.377DataRank

Top 48%9 citations

Yu Yin, Dylan Campbell, Xuansheng Wu, Ke Zou, Ninghao Liu +4 more

A deep network DeepOpacityNet for detection of cataracts from color fundus photographs

Communications Medicine(2023)10.1038/s43856-023-00410-w

N/A

0.360DataRank · unranked

10 citations

Tiarnán D L Keenan, Qingyu Chen, Alisa T. Thavikulwat, S. Bhandari, Ten Cheer Quek +6 more

LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models

arXiv (Cornell University)(2024)10.48550/arxiv.2410.01620

Top 62%

0.233DataRank

Top 62%3 citations

Yu Yin, Dylan Campbell, Xuansheng Wu, Ke Zou, Yih Chung Tham +4 more

PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature

Bioinformatics(2024)10.1093/bioinformatics/btae672

Top 63%

0.221DataRank

Top 63%3 citations

Qingyu Chen, Donald C. Comeau, W. John Wilbur, ZHIYONG LU, Shubo Tian

Ascle: A Python Natural Language Processing Toolkit for Medical Text Generation

arXiv (Cornell University)(2023)10.48550/arxiv.2311.16588

N/A

0.177DataRank · unranked

2 citations

Qingcheng Zeng, Keen You, Yujie Qiao, Lucas Huang, Chia-Chun Hsieh +11 more

BEnchmarking Large Language Models for Ophthalmology (BELO): An Expert-Curated Data Set and Evaluation Framework for Knowledge and Reasoning

Ophthalmology Science(2025)10.1016/j.xops.2025.101050

Top 78%

0.104DataRank

Top 78%1 citations

Xuguang Ai, Thaddaeus Wai Soon Lo, Aidan Gilson, Minjie Zou, Ke Zou +27 more

Reticular Pseudodrusen Status, ARMS2/HTRA1 Genotype, and Geographic Atrophy Enlargement

Ophthalmology(2022)10.1016/j.ophtha.2022.11.026

N/A

0DataRank · unranked

39 citations

Amitha Domalpally, Catherine A. Cukras, Traci E. Clemons, Qingyu Chen, Anand Swaroop +4 more

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations

Database(2022)10.1093/database/baac069

N/A

0DataRank · unranked

41 citations

Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Fang Li +34 more

Comprehensively identifying Long Covid articles with human-in-the-loop machine learning

Patterns(2022)10.1016/j.patter.2022.100659

N/A

0DataRank · unranked

5 citations

Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, ZHIYONG LU +1 more

Opportunities and challenges for ChatGPT and large language models in biomedicine and health

Briefings in Bioinformatics(2023)10.1093/bib/bbad493

N/A

0DataRank · unranked

354 citations

Qiao Jin, Lana Yeganova, Po‐Ting Lai, Qingqing Zhu, Xiuying Chen +9 more

AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning

Bioinformatics(2023)10.1093/bioinformatics/btad310

N/A

0DataRank · unranked

70 citations

Chih-Hsuan Wei, Po‐Ting Lai, Robert Leaman, Qingyu Chen, ZHIYONG LU +1 more

BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets

Journal of Biomedical Informatics(2023)10.1016/j.jbi.2023.104487

N/A

0DataRank · unranked

51 citations

Chih-Hsuan Wei, Ling Luo, Qingyu Chen, ZHIYONG LU, Po‐Ting Lai

From function to translation: Decoding genetic susceptibility to human diseases via artificial intelligence

Cell Genomics(2023)10.1016/j.xgen.2023.100320

N/A

0DataRank · unranked

20 citations

Peixing Wan, Qingyu Chen, ZHIYONG LU, Jiyeon Choi, Erping Long

Benchmarking large language models for biomedical natural language processing applications and recommendations

arXiv (Cornell University)(2023)10.48550/arxiv.2305.16326

N/A

0DataRank · unranked

41 citations

Yan Hu, Xueqing Peng, Xie, Qianqian, Jin, Qiao, Gilson, Aidan +16 more

Bioformer: an efficient transformer language model for biomedical text mining

PubMed(2023)10.48550/arxiv.2302.01588

N/A

0DataRank · unranked

15 citations

Qingyu Chen, Chih-Hsuan Wei, ZHIYONG LU, Kai Wang, Fang Li

MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval

arXiv (Cornell University)(2023)10.48550/arxiv.2307.00589

N/A

0DataRank · unranked

9 citations

Won Bae Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur +2 more

GeneGPT: augmenting large language models with domain tools for improved access to biomedical information

Bioinformatics(2024)10.1093/bioinformatics/btae075

N/A

0DataRank · unranked

158 citations

Yifan Yang, Qingyu Chen, ZHIYONG LU, Qiao Jin

Advancing entity recognition in biomedicine via instruction tuning of large language models

Bioinformatics(2024)10.1093/bioinformatics/btae163

N/A

0DataRank · unranked

95 citations

Yan Hu, Qianqian Xie, Xueqing Peng, Yan Wang, Andrew Zheng +8 more

Deep-Reticular Pseudodrusen-Net: A 3-Dimensional Deep Network for Detection of Reticular Pseudodrusen on OCT Scans

Ophthalmology Science(2024)10.1016/j.xops.2024.100655

N/A

0DataRank · unranked

3 citations

Tiarnán D L Keenan, Alisa T. Thavikulwat, Amy Q. Lu, Sunil Bellur, Souvick Mukherjee +5 more

Ophthalmic care may not align with patient need: An analysis on state-wide patient needs and provider density between 2008 and 2022

International Journal of Medical Informatics(2024)10.1016/j.ijmedinf.2024.105411

N/A

0DataRank · unranked

1 citations

Qingyu Chen, Ron A. Adelman, Aidan Gilson

Me-LLaMA: Foundation Large Language Models for Medical Applications

Research Square(2024)10.21203/rs.3.rs-4240043/v1

N/A

0DataRank · unranked

55 citations

Qingyu Chen, Aokun Chen, Peng Cheng, Yan Hu, Fongci Lin +11 more

MedCalc-Bench: Evaluating Large Language Models for Medical Calculations

arXiv (Cornell University)(2024)10.52202/079017-2690

N/A

0DataRank · unranked

6 citations

Qiao Jin, Guangzhi Xiong, S.M. Dunn, Serina Applebaum, Zain Anwar +12 more

Augmenting Biomedical Named Entity Recognition with General-domain Resources

arXiv (Cornell University)(2024)10.48550/arxiv.2406.10671

N/A

0DataRank · unranked

0 citations

Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, ZHIYONG LU +4 more

AgentMD: Empowering language agents for risk prediction with large-scale clinical tool learning

Nature Communications(2025)10.1038/s41467-025-64430-x

N/A

0DataRank · unranked

13 citations

Zhizheng Wang, Yifan Yang, Qingqing Zhu, D. Wright, Thomas Huang +9 more

AI Workflow, External Validation, and Development in Eye Disease Diagnosis

JAMA Network Open(2025)10.1001/jamanetworkopen.2025.17204

N/A

0DataRank · unranked

10 citations

Tiarnán D L Keenan, Elvira Agrón, Alexis Allot, Emily Guan, Bryant Duong +34 more

Integrating rule-based NLP and large language models for statin information extraction from clinical notes

International Journal of Medical Informatics(2025)10.1016/j.ijmedinf.2025.106104

N/A

0DataRank · unranked

10 citations

Allison B. McCoy, Qingyu Chen, Adam Wright, Siru Liu

Performance of GPT-5 Frontier Models in Ophthalmology Question Answering

Ophthalmology Science(2025)10.1016/j.xops.2025.101034

N/A

0DataRank · unranked

3 citations

David Mikhail, Daniel Milad, Danny A. Mammo, Sumit Sharma, Sunil K. Srivastava +9 more

Genotype‐by‐sex interaction analyses for alcohol use disorder across biobanks

Alcohol Clinical and Experimental Research(2025)10.1111/acer.70173

N/A

0DataRank · unranked

1 citations

Lu Wang, Zhongzheng Mao, P. J. Michael Deans, Rachel L. Kember, Qingyu Chen +12 more

GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking

PubMed(2025)10.18653/v1/2025.acl-long.729

N/A

0DataRank · unranked

5 citations

Haoran Liu, Yinhong Liu, Jinxiang Xie, Rui Yang, Han Yuan +6 more

Rethinking Retrieval-Augmented Generation for Medicine: A Large-Scale, Systematic Expert Evaluation and Practical Insights

arXiv (Cornell University)(2025)10.48550/arxiv.2511.06738

N/A

0DataRank · unranked

1 citations

Jiwoong Sohn, Aidan Gilson, Nicholas Cochran-Caggiano, Serina Applebaum, Jin, Heeju +22 more

Mixture-of-Shape-Experts (MoSE): End-to-End Shape Dictionary Framework to Prompt SAM for Generalizable Medical Segmentation

PubMed(2025)10.1109/cvprw67362.2025.00642

N/A

0DataRank · unranked

0 citations

Xiaoqi Zhao, Jonghye Woo, Jinsong Ouyang, Georges El Fakhri, Qingyu Chen +2 more

Predicting risk of late age-related macular degeneration using deep learning

npj Digital Medicine(2020)10.1038/s41746-020-00317-z

N/A

0DataRank · unranked

69 citations

Tiarnán D L Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong +3 more

BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007617

N/A

0DataRank · unranked

65 citations

Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, ZHIYONG LU +1 more

Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records

BMC Medical Informatics and Decision Making(2020)10.1186/s12911-020-1044-0

N/A

0DataRank · unranked

21 citations

Jingcheng Du, Sun Kim, W. John Wilbur, ZHIYONG LU, Qingyu Chen

Better synonyms for enriching biomedical search

Journal of the American Medical Informatics Association(2020)10.1093/jamia/ocaa151

N/A

0DataRank · unranked

12 citations

Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, ZHIYONG LU +1 more

Deep Learning Automated Detection of Reticular Pseudodrusen from Fundus Autofluorescence Images or Color Fundus Photographs in AREDS2

Ophthalmology(2020)10.1016/j.ophtha.2020.05.036

N/A

0DataRank · unranked

44 citations

Qingyu Chen, Yifan Peng, Amitha Domalpally, Elvira Agrón, C.‐K. HWANG +7 more

Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration

Journal of the American Medical Informatics Association(2020)10.1093/jamia/ocaa302

N/A

0DataRank · unranked

41 citations

Tiarnán D L Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally +12 more

An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining

(2020)10.18653/v1/2020.bionlp-1.22

N/A

0DataRank · unranked

95 citations

Qingyu Chen, ZHIYONG LU, Yifan Peng

Automatic recognition of abdominal lymph nodes from clinical text

(2020)10.18653/v1/2020.clinicalnlp-1.12

N/A

0DataRank · unranked

6 citations

Sung-Won Lee, Daniel C. Elton, Thomas C. Shen, Yuxing Tang, Qingyu Chen +5 more

LitSuggest: a web-based system for literature recommendation and curation using machine learning

Nucleic Acids Research(2021)10.1093/nar/gkab326

N/A

0DataRank · unranked

63 citations

Kyubum Lee, Qingyu Chen, Ling Luo, ZHIYONG LU, Alexis Allot

Improving Interpretability in Machine Diagnosis

Ophthalmology Science(2021)10.1016/j.xops.2021.100038

N/A

0DataRank · unranked

22 citations

Tiarnán D L Keenan, Qingyu Chen, Tharindu De Silva, Alisa T. Thavikulwat, Geoffrey Broadhead +5 more

Benchmarking Effectiveness and Efficiency of Deep Learning Models for Semantic Textual Similarity in the Clinical Domain: Validation Study

JMIR Medical Informatics(2021)10.2196/27386

N/A

0DataRank · unranked

19 citations

Alex Rankine, Yifan Peng, Elaheh Aghaarabi, ZHIYONG LU, Qingyu Chen

Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS

medRxiv(2021)10.1101/2021.08.26.21262548

N/A

0DataRank · unranked

9 citations

Matthew Brendel, Mingquan Lin, Qingyu Chen, Tiarnán D L Keenan, Kun Chen +5 more

Referee report. For: KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications [version 1; peer review: 1 approved with reservations]

Faculty of 1000 Research Ltd(2021)10.5256/f1000research.28167.r82000

N/A

0DataRank · unranked

0 citations

Qingyu Chen

Reticular Pseudodrusen: The Third Macular Risk Feature for Progression to Late Age-Related Macular Degeneration

Ophthalmology(2022)10.1016/j.ophtha.2022.05.021

N/A

0DataRank · unranked

78 citations

Amitha Domalpally, Catherine A. Cukras, Traci E. Clemons, Qingyu Chen, ZHIYONG LU +3 more

DeepLensNet: Deep Learning Automated Diagnosis and Quantitative Classification of Cataract Type and Severity

Ophthalmology(2022)10.1016/j.ophtha.2021.12.017

N/A

0DataRank · unranked

75 citations

Qingyu Chen, Elvira Agrón, Yih Chung Tham, Jocelyn Hui Lin Goh, Xiaofeng Lei +47 more

Detecting visually significant cataract using retinal photograph-based deep learning

Nature Aging(2022)10.1038/s43587-022-00171-6

N/A

0DataRank · unranked

51 citations

Jocelyn Hui Lin Goh, Ayesha Anees, Xiaofeng Lei, Tyler Hyungtaek Rim, Miao-Li Chee +22 more

Robust convolutional neural networks against adversarial attacks on medical images

Pattern Recognition(2022)10.1016/j.patcog.2022.108923

N/A

0DataRank · unranked

46 citations

Yifan Peng, Qingyu Chen, Tiarnán D L Keenan, Alisa T. Thavikulwat, Sungwon Lee +5 more

Qingyu Chen

Indexed papers

Top data-sharing exemplar

Papers