ZHIYONG LU

Also affiliated with State Administration of Cultural Heritage, United States National Library of Medicine, National Institute of Nursing Research

Biochemistry, Genetics and Molecular BiologyComputer Science

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

63.3Author DataRank

Indexed papers

26in 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 26 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.

ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases

2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)(2017)10.1109/cvpr.2017.369

Top 1%

10.4DataRank

Top 1%3374 citations

Yifan Peng, Le Lu, ZHIYONG LU, Mohammadhadi Bagheri, Ronald M. Summers +1 more

Papers

Driven by 147 papers — median percentile 78. Top paper: “Opportunities and obstacles for deep learning in biology and medicine”.

Opportunities and obstacles for deep learning in biology and medicine

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/142760

N/A

11.2DataRank · unranked

310 citations

Daniel S. Himmelstein, Brett K. Beaulieu‐Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way +31 more

ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases

2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)(2017)10.1109/cvpr.2017.369

Top 1%

10.4DataRank

Top 1%3374 citations

Yifan Peng, Le Lu, ZHIYONG LU, Mohammadhadi Bagheri, Ronald M. Summers +1 more

Database resources of the national center for biotechnology information

Nucleic Acids Research(2021)10.1093/nar/gkab1112

Top 2%

7.6DataRank

Top 2%3013 citations

Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau +20 more

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

Database resources of the National Center for Biotechnology Information

Nucleic Acids Research(2020)10.1093/nar/gkaa892

Top 3%

6.3DataRank

Top 3%1019 citations

Jeffrey Beck, Evan E. Bolton, Devon Bourexis, J. Rodney Brister, Kathi Canese +20 more

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

Database resources of the National Center for Biotechnology Information

Nucleic Acids Research(2023)10.1093/nar/gkad1044

Top 4%

5.4DataRank

Top 4%363 citations

Jeffrey Beck, Evan E. Bolton, J. Rodney Brister, Jessica Chan, Donald C. Comeau +36 more

Database resources of the National Center for Biotechnology Information in 2023

Nucleic Acids Research(2022)10.1093/nar/gkac1032

Top 4%

5.3DataRank

Top 4%471 citations

Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau +27 more

BioRED: a rich biomedical relation extraction dataset

Briefings in Bioinformatics(2022)10.1093/bib/bbac282

Top 5%

4.3DataRank

Top 5%154 citations

Po‐Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, ZHIYONG LU, Ling Luo

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

COVID-19-CT-CXR: A Freely Accessible and Weakly Labeled Chest X-Ray and CT Image Collection on COVID-19 From Biomedical Literature

IEEE Transactions on Big Data(2020)10.1109/tbdata.2020.3035935

Top 6%

3.6DataRank

Top 6%89 citations

Yuxing Tang, Sungwon Lee, Yingying Zhu, Ronald M. Summers, ZHIYONG LU +1 more

PubMed and beyond: biomedical literature search in the age of artificial intelligence

EBioMedicine(2024)10.1016/j.ebiom.2024.104988

N/A

2.8DataRank · unranked

119 citations

Robert Leaman, ZHIYONG LU, Qiao Jin

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

Large language models in biomedicine and health: current research landscape and future directions

Journal of the American Medical Informatics Association(2024)10.1093/jamia/ocae202

N/A

2.0DataRank · unranked

79 citations

Yifan Peng, Trevor Cohen, Marzyeh Ghassemi, Chunhua Weng, Shubo Tian +1 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

A roadmap for the functional annotation of protein families: a community perspective

Database(2022)10.1093/database/baac062

Top 14%

1.5DataRank

Top 14%63 citations

Rocío Amorín, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian K. Blaby +54 more

NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition

Journal of Biomedical Informatics(2021)10.1016/j.jbi.2021.103779

Top 17%

1.2DataRank

Top 17%33 citations

Chih-Hsuan Wei, David S. Cissel, Nicholas Miliaras, Olga Printseva, Oleg Rodionov +4 more

Improving model fairness in image-based computer-aided diagnosis

Nature Communications(2023)10.1038/s41467-023-41974-4

N/A

1.2DataRank · unranked

29 citations

Tianhao Li, Yifan Yang, Gregory Holste, Ying Ding, Sarah H. Van Tassel +7 more

Opportunities and obstacles for deep learning in biology and medicine

Journal of The Royal Society Interface(2018)10.1098/rsif.2017.0387

N/A

1.2DataRank · unranked

2203 citations

Daniel S. Himmelstein, Brett K. Beaulieu‐Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way +31 more

A survey of current trends in computational drug repositioning

Briefings in Bioinformatics(2015)10.1093/bib/bbv020

N/A

0.953DataRank · unranked

573 citations

Si Zheng, BIN CHEN, Atul Janardhan Butte, S. Joshua Swamidass, ZHIYONG LU +1 more

EnzChemRED, a rich enzyme chemistry relation extraction dataset

Scientific Data(2024)10.1038/s41597-024-03835-7

Top 21%

0.945DataRank

Top 21%11 citations

Elisabeth Coudert, Lucila Aimo, Kristian B. Axelsen, Lionel Breuza, Edouard de Castro +14 more

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

TeamTat: a collaborative text annotation tool

Nucleic Acids Research(2020)10.1093/nar/gkaa333

N/A

0.652DataRank · unranked

76 citations

Dongseop Kwon, Sun Kim, ZHIYONG LU, Rezarta Islamaj

Leveraging long context in retrieval augmented language models for medical question answering

npj Digital Medicine(2025)10.1038/s41746-025-01651-w

N/A

0.614DataRank · unranked

59 citations

Zihan Xu, Qiao Jin, Fangyi Chen, Yilu Fang, Yi Liu +6 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

A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2

(2020)10.18653/v1/2020.nlpcovid19-2.32

Top 35%

0.559DataRank

Top 35%7 citations

ZHIYONG LU, Robert Leaman

Utilizing Longitudinal Chest X-Rays and Reports to Pre-fill Radiology Reports

Lecture notes in computer science(2023)10.1007/978-3-031-43904-9_19

N/A

0.500DataRank · unranked

27 citations

Tejas Sudharshan Mathai, Pritam Mukherjee, Yifan Peng, Ronald M. Summers, ZHIYONG LU +1 more

PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology

Journal of Biomedical Informatics(2022)10.1016/j.jbi.2022.104059

Top 41%

0.469DataRank

Top 41%6 citations

Ling Luo, Po‐Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar +5 more

A foundation model for human-AI collaboration in medical literature mining

Nature Communications(2025)10.1038/s41467-025-62058-5

N/A

0.442DataRank · unranked

18 citations

Lang Cao, Qiao Jin, Joey Wing Yan Chan, Nicholas Wan, Behdad Afzali +18 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

Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine

PubMed(2024)10.48550/arxiv.2401.08396

N/A

0.355DataRank · unranked

2 citations

Fangyuan Chen, Yiliang Zhou, Ziyang Xu, Justin M. Cheung, Robert F. Chen +13 more

Adversarial Attacks on Large Language Models in Medicine

PubMed(2024)10.48550/arxiv.2406.12259

N/A

0.334DataRank · unranked

5 citations

Qiao Jin, Furong Huang, ZHIYONG LU, Yifan Yang

LitSense 2.0: AI-powered biomedical information retrieval with sentence and passage level knowledge discovery

Nucleic Acids Research(2025)10.1093/nar/gkaf417

Top 54%

0.312DataRank

Top 54%7 citations

Won Bae Kim, Shubo Tian, Donald C. Comeau, W. John Wilbur, ZHIYONG LU +1 more

Universal lymph node detection in T2 MRI using neural networks

International Journal of Computer Assisted Radiology and Surgery(2022)10.1007/s11548-022-02782-1

N/A

0.312DataRank · unranked

7 citations

Sungwon Lee, Thomas C. Shen, ZHIYONG LU, Ronald M. Summers, Tejas Sudharshan Mathai

Enhancing biomedical relation extraction with directionality

Bioinformatics(2025)10.1093/bioinformatics/btaf226

N/A

0.309DataRank · unranked

5 citations

Chih-Hsuan Wei, Shubo Tian, Robert Leaman, ZHIYONG LU, Po‐Ting Lai

Assessing Artificial Intelligence (AI) Implementation for Assisting Gene Linking (at the National Library of Medicine)

JAMIA Open(2024)10.1093/jamiaopen/ooae129

Top 56%

0.293DataRank

Top 56%3 citations

Chih-Hsuan Wei, Po‐Ting Lai, Melanie Huston, Cathleen Coss, Preeti Gokal Kochar +9 more

The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop

Database(2024)10.1093/database/baae071

Top 62%

0.227DataRank

Top 62%3 citations

Chih-Hsuan Wei, Po‐Ting Lai, Ling Luo, Cathleen Coss, Preeti Gokal Kochar +7 more

Environment Scan of Generative AI Infrastructure for Clinical and Translational Science

arXiv (Cornell University)(2024)10.48550/arxiv.2410.12793

Top 62%

0.222DataRank

Top 62%2 citations

Zihan Xu, William G. Adams, Mohammad Adibuzzaman, Nicholas R. Anderson, Neil Bahroos +52 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

Shadow and Light: Digitally Reconstructed Radiographs for Disease Classification

arXiv (Cornell University)(2024)10.48550/arxiv.2406.03688

Top 71%

0.130DataRank

Top 71%1 citations

Qingqing Zhu, Tejas Sudarshan Mathai, Qiao Jin, ZHIYONG LU, R. Summers +1 more

COMPUTATIONAL DRUG REPOSITIONING

Biocomputing 2013(2012)10.1142/9789814447973_0001

N/A

0.104DataRank · unranked

1 citations

PANKAJ AGARWAL, Atul Janardhan Butte, ZHIYONG LU

COMPUTATIONAL APPROACHES TO DRUG REPURPOSING AND PHARMACOLOG- SESSION INTRODUCTION

Biocomputing 2014(2013)10.1142/9789814583220_0011

N/A

0.104DataRank · unranked

1 citations

ZHIYONG LU, PANKAJ AGARWAL, Atul Janardhan Butte, S. Joshua Swamidass

PSB 2019 Workshop on Text Mining and Visualization for Precision Medicine

Biocomputing 2019(2018)10.1142/9789813279827_0042

N/A

0.104DataRank · unranked

1 citations

ZHIYONG LU, Robert Leaman, Davy Weissenbacher, Mary Regina Boland, Yong Chen +14 more

Correspondence on “Comparison of literature mining tools for variant classification: Through the lens of 50 RYR1 variants” by Wermers et al

Genetics in Medicine(2024)10.1016/j.gim.2024.101208

N/A

0.104DataRank · unranked

1 citations

Lon Phan, Timothy Hefferon, Melissa Landrum, Heidi L. Rehm, ZHIYONG LU +1 more

tmVar 3.0: an improved variant concept recognition and normalization tool

Bioinformatics(2022)10.1093/bioinformatics/btac537

N/A

0DataRank · unranked

25 citations

Alexis Allot, Kevin Riehle, Aleksandar Milosavljević, ZHIYONG LU, Chih-Hsuan Wei

Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images

Medical Image Analysis(2022)10.1016/j.media.2021.102345

N/A

0DataRank · unranked

28 citations

Yingying Zhu, Sung Won Lee, Daniel C. Elton, Thomas C. Shen, Youbao Tang +4 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

A sequence labeling framework for extracting drug–protein relations from biomedical literature

Database(2022)10.1093/database/baac058

N/A

0DataRank · unranked

4 citations

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

A Sequence Labeling Framework for Extracting Drug-Protein Relations from Biomedical Literature

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.31.486574

N/A

0DataRank · unranked

0 citations

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

Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction

Research Square(2022)10.21203/rs.3.rs-958135/v2

N/A

0DataRank · unranked

0 citations

Lei Liu, Hongmei Jiang, Yifan Peng, Yishu Wei, Zhiyang Zhou +13 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

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

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

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

A scoping review on multimodal deep learning in biomedical images and texts

Journal of Biomedical Informatics(2023)10.1016/j.jbi.2023.104482

N/A

0DataRank · unranked

54 citations

Mingquan Lin, Qingqing Zhu, Qianqian Xie, Fei Wang, ZHIYONG LU +2 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

GNorm2: an improved gene name recognition and normalization system

Bioinformatics(2023)10.1093/bioinformatics/btad599

N/A

0DataRank · unranked

42 citations

Ling Luo, Rezarta Islamaj, Po‐Ting Lai, ZHIYONG LU, Chih-Hsuan Wei

Tracking genetic variants in the biomedical literature using LitVar 2.0

Nature Genetics(2023)10.1038/s41588-023-01414-x

N/A

0DataRank · unranked

40 citations

Chih-Hsuan Wei, Lon Phan, Timothy Hefferon, Melissa Landrum, Heidi L. Rehm +2 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

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

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

Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction

BMC Medical Research Methodology(2023)10.1186/s12874-022-01829-w

N/A

0DataRank · unranked

17 citations

Lei Liu, Hongmei Jiang, Yifan Peng, Yishu Wei, Zhiyang Zhou +13 more

Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII

Database(2023)10.1093/database/baad005

N/A

0DataRank · unranked

15 citations

Rezarta Islamaj, Virginia Adams, Mohammed Alliheedi, João Rafael Almeida, Rui Antunes +16 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

Universal detection and segmentation of lymph nodes in multi-parametric MRI

International Journal of Computer Assisted Radiology and Surgery(2023)10.1007/s11548-023-02954-7

N/A

0DataRank · unranked

6 citations

Sungwon Lee, Thomas C. Shen, Daniel C. Elton, ZHIYONG LU, Ronald M. Summers +1 more

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts

Bioinformatics(2023)10.1093/bioinformatics/btad716

N/A

0DataRank · unranked

3 citations

Honghan Wu, Marcel E. Dinger, Daniel Daniš, Coleman Hilton, Anita Bagley +5 more

Matching Patients to Clinical Trials with Large Language Models

PubMed(2023)10.48550/arxiv.2307.15051

N/A

0DataRank · unranked

42 citations

Zifeng Wang, Charalampos S. Floudas, Fangyuan Chen, Changlin Gong, Dara Bracken‐Clarke +5 more

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

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

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

LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search

PubMed(2023)10.1145/3539618.3592005

N/A

0DataRank · unranked

10 citations

Ashley Shin, ZHIYONG LU, Qiao Jin

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

PubMed and Beyond: Biomedical Literature Search in the Age of Artificial Intelligence

arXiv (Cornell University)(2023)10.48550/arxiv.2307.09683

N/A

0DataRank · unranked

4 citations

Robert Leaman, ZHIYONG LU, Qiao Jin

Leveraging Generative AI for Clinical Evidence Summarization Needs to Ensure Trustworthiness

arXiv (Cornell University)(2023)10.48550/arxiv.2311.11211

N/A

0DataRank · unranked

2 citations

Qiao Jin, Denis Jered McInerney, Chen, Yong, Fei Wang, Curtis L. Cole +9 more

Measuring the relative importance of full text sections for information retrieval from scientific literature.

(2021)10.18653/v1/2021.bionlp-1.27

N/A

0DataRank · unranked

3 citations

Won Gyu Kim, Donald C. Comeau, W. John Wilbur, ZHIYONG LU, Lana Yeganova

LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search

arXiv (Cornell University)(2023)10.48550/arxiv.2304.04590

N/A

0DataRank · unranked

1 citations

Shin, Ashley, ZHIYONG LU, Qiao Jin

Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge

PubMed(2023)10.48550/arxiv.2310.16112

Top 100%

0DataRank

Top 100%0 citations

Yiliang Zhou, Song Wang, Ajay Jaiswal, Mingquan Lin, Sherry Zhuge +20 more

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

Matching patients to clinical trials with large language models

Nature Communications(2024)10.1038/s41467-024-53081-z

N/A

0DataRank · unranked

213 citations

Zifeng Wang, Charalampos S. Floudas, Fangyuan Chen, Changlin Gong, Dara Bracken‐Clarke +5 more

NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature

Scientific Data(2021)10.1038/s41597-021-00875-1

N/A

0DataRank · unranked

70 citations

Robert Leaman, Sun Kim, Dongseop Kwon, Chih-Hsuan Wei, Donald C. Comeau +14 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

Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine

npj Digital Medicine(2024)10.1038/s41746-024-01185-7

N/A

0DataRank · unranked

120 citations

Fangyuan Chen, Yiliang Zhou, Ziyang Xu, Justin M. Cheung, Robert F. Chen +13 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

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

Unmasking and quantifying racial bias of large language models in medical report generation

Communications Medicine(2024)10.1038/s43856-024-00601-z

N/A

0DataRank · unranked

82 citations

Xiaoyu Liu, Qiao Jin, Furong Huang, ZHIYONG LU, Yifan Yang

A survey of recent methods for addressing AI fairness and bias in biomedicine

Journal of Biomedical Informatics(2024)10.1016/j.jbi.2024.104646

N/A

0DataRank · unranked

77 citations

Mingquan Lin, Han Zhao, Yifan Peng, Furong Huang, ZHIYONG LU +1 more

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

Closing the gap between open source and commercial large language models for medical evidence summarization

npj Digital Medicine(2024)10.1038/s41746-024-01239-w

N/A

0DataRank · unranked

73 citations

Qiao Jin, Yiliang Zhou, Song Wang, Betina Idnay, Hanley Ong +9 more

Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study

Journal of Medical Internet Research(2024)10.2196/56655

N/A

0DataRank · unranked

50 citations

Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor +4 more

Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness

Journal of Biomedical Informatics(2024)10.1016/j.jbi.2024.104640

N/A

0DataRank · unranked

37 citations

Qiao Jin, Denis Jered McInerney, Yong Chen, Fei Wang, Curtis L. Cole +9 more

Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge

Medical Image Analysis(2024)10.1016/j.media.2024.103224

N/A

0DataRank · unranked

37 citations

Yiliang Zhou, Song Wang, Ajay Jaiswal, Mingquan Lin, Sherry Zhuge +20 more

Generalized Zero-Shot Chest X-Ray Diagnosis Through Trait-Guided Multi-View Semantic Embedding With Self-Training

IEEE Transactions on Medical Imaging(2021)10.1109/tmi.2021.3054817

N/A

0DataRank · unranked

43 citations

Thomas C. Shen, Sungwon Lee, Niranjan Balachandar, Yifan Peng, ZHIYONG LU +2 more

Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling

npj Digital Medicine(2024)10.1038/s41746-024-01207-4

N/A

0DataRank · unranked

22 citations

Mingquan Lin, Ruiwen Zhou, Fei Wang, Lei Liu, Qi Yan +7 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

PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology

Bioinformatics(2021)10.1093/bioinformatics/btab019

N/A

0DataRank · unranked

78 citations

Shankai Yan, Po‐Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar +5 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

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

Detection of abdominopelvic lymph nodes in multi-parametric MRI

Computerized Medical Imaging and Graphics(2024)10.1016/j.compmedimag.2024.102363

N/A

0DataRank · unranked

2 citations

Thomas C. Shen, Daniel C. Elton, Sungwon Lee, ZHIYONG LU, Ronald M. Summers +1 more

Response to Letter to Editor ‘Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine’

Briefings in Bioinformatics(2024)10.1093/bib/bbae211

N/A

0DataRank · unranked

1 citations

Qiao Jin, ZHIYONG LU, Shubo Tian

Benchmarking Retrieval-Augmented Generation for Medicine

(2024)10.18653/v1/2024.findings-acl.372

N/A

0DataRank · unranked

229 citations

Qiao Jin, ZHIYONG LU, Aidong Zhang, Guangzhi Xiong

Benchmarking Retrieval-Augmented Generation for Medicine

arXiv (Cornell University)(2024)10.48550/arxiv.2402.13178

N/A

0DataRank · unranked

23 citations

Qiao Jin, ZHIYONG LU, Aidong Zhang, Guangzhi Xiong

Risks of AI Scientists: Prioritizing Safeguarding Over Autonomy

arXiv (Cornell University)(2024)10.48550/arxiv.2402.04247

N/A

0DataRank · unranked

13 citations

Qiao Jin, Kunlun Zhu, Tongxin Yuan, Yichi Zhang, Wangchunshu Zhou +8 more

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for AI-generated Radiology Reports

PubMed(2024)10.1109/ichi61247.2024.00058

N/A

0DataRank · unranked

12 citations

Xiuying Chen, Qiao Jin, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee +4 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

Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology

arXiv (Cornell University)(2024)10.48550/arxiv.2409.13902

N/A

0DataRank · unranked

6 citations

X. C. Ai, Thilaka Arunachalam, Chen, Ziyou, Ki Xiong Cheong, Amisha Dave +17 more

Unmasking and Quantifying Racial Bias of Large Language Models in Medical Report Generation

PubMed(2024)10.48550/arxiv.2401.13867

N/A

0DataRank · unranked

5 citations

Xiaoyu Liu, Qiao Jin, Furong Huang, ZHIYONG LU, Y. F. Yang

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports

PubMed(2024)10.48550/arxiv.2401.16578

N/A

0DataRank · unranked

5 citations

Xiuying Chen, Qiao Jin, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee +4 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

Loss-Based Attention for Interpreting Image-Level Prediction of Convolutional Neural Networks

IEEE Transactions on Image Processing(2020)10.1109/tip.2020.3046875

N/A

0DataRank · unranked

43 citations

Fuyong Xing, Kaidi Xu, Pingjun Chen, Yun Liang, ZHIYONG LU +2 more

Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine

arXiv (Cornell University)(2024)10.48550/arxiv.2411.14487

N/A

0DataRank · unranked

3 citations

Qiao Jin, Robert Leaman, Xiaoyu Liu, Guangzhi Xiong, Maame Sarfo-Gyamfi +13 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

GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases

PubMed(2024)10.48550/arxiv.2405.16205

N/A

0DataRank · unranked

2 citations

Qiao Jin, Chih-Hsuan Wei, Shubo Tian, Po‐Ting Lai, Qingqing Zhu +4 more

Closing the gap between open-source and commercial large language models for medical evidence summarization

arXiv (Cornell University)(2024)10.48550/arxiv.2408.00588

N/A

0DataRank · unranked

2 citations

Qiao Jin, Yiliang Zhou, Song Wang, Betina Idnay, Hanley Ong +9 more

Ten tips for a text-mining-ready article: How to improve automated discoverability and interpretability

PLoS Biology(2020)10.1371/journal.pbio.3000716

N/A

0DataRank · unranked

13 citations

Chih-Hsuan Wei, Alexis Allot, ZHIYONG LU, Robert Leaman

Entry-level guide to the use of large language models for medical research

PubMed(2024)10.48550/arxiv.2410.18856

N/A

0DataRank · unranked

2 citations

Nicholas Wan, Robert Leaman, Shubo Tian, Zhizheng Wang, Yifan Yang +18 more

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

Universal Lymph Node Detection in Multiparametric MRI with Selective Augmentation

arXiv (Cornell University)(2025)10.48550/arxiv.2504.05196

N/A

0DataRank · unranked

0 citations

Sungwon Lee, Thomas C. Shen, ZHIYONG LU, Ronald M. Summers, Tejas Sudharshan Mathai

Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling

arXiv (Cornell University)(2024)10.48550/arxiv.2405.08780

N/A

0DataRank · unranked

0 citations

Mingquan Lin, Ruiwen Zhou, Fei Wang, Lei Liu, Qi Yan +7 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

Beyond Multiple-Choice Accuracy: Real-World Challenges of Implementing Large Language Models in Healthcare

arXiv (Cornell University)(2024)10.48550/arxiv.2410.18460

N/A

0DataRank · unranked

0 citations

Qiao Jin, Qingqing Zhu, Zhizheng Wang, Francisco Álvarez, Nicholas Wan +3 more

Evaluating the Impact of Lab Test Results on Large Language Models Generated Differential Diagnoses from Clinical Case Vignettes

arXiv (Cornell University)(2024)10.48550/arxiv.2411.02523

N/A

0DataRank · unranked

0 citations

Qiao Jin, Yuzhang Xie, Carl Yang, Karim Hanna, Jennifer Costa +4 more

A MapReduce Approach to Effectively Utilize Long Context Information in Retrieval Augmented Language Models

arXiv (Cornell University)(2024)10.48550/arxiv.2412.15271

N/A

0DataRank · unranked

0 citations

Zihan Xu, Qiao Jin, Fangyi Chen, Yilu Fang, Yi Liu +6 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

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

Accelerating clinical evidence synthesis with large language models

npj Digital Medicine(2025)10.1038/s41746-025-01840-7

N/A

0DataRank · unranked

43 citations

Lang Cao, Benjamin Danek, Qiao Jin, ZHIYONG LU, Jimeng Sun +1 more

GeneAgent: self-verification language agent for gene-set analysis using domain databases

Nature Methods(2025)10.1038/s41592-025-02748-6

N/A

0DataRank · unranked

41 citations

Qiao Jin, Chih-Hsuan Wei, Shubo Tian, Po‐Ting Lai, Qingqing Zhu +5 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

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

One Year On: Assessing Progress of Multimodal Large Language Model Performance on RSNA 2024 Case of the Day Questions

Radiology(2025)10.1148/radiol.250617

N/A

0DataRank · unranked

11 citations

Pritam Mukherjee, Vivek Batheja, Kenneth C. Wang, Ronald M. Summers, ZHIYONG LU +1 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

Environment scan of generative AI infrastructure for clinical and translational science

npj Health Systems(2025)10.1038/s44401-024-00009-w

N/A

0DataRank · unranked

9 citations

Zihan Xu, William G. Adams, Mohammad Adibuzzaman, Nicholas R. Anderson, Neil Bahroos +52 more

Adversarial prompt and fine-tuning attacks threaten medical large language models

Nature Communications(2025)10.1038/s41467-025-64062-1

N/A

0DataRank · unranked

8 citations

Qiao Jin, Furong Huang, ZHIYONG LU, Yifan Yang

Recent advances in biomedical literature mining

Briefings in Bioinformatics(2020)10.1093/bib/bbaa057

N/A

0DataRank · unranked

131 citations

Chang Su, ZHIYONG LU, Fei Wang, Sendong Zhao

How well do multimodal LLMs interpret CT scans? An auto-evaluation framework for analyses

Journal of Biomedical Informatics(2025)10.1016/j.jbi.2025.104864

N/A

0DataRank · unranked

7 citations

Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Qiao Jin, Xiuying Chen +5 more

CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray

Medical Image Analysis(2025)10.1016/j.media.2025.103739

N/A

0DataRank · unranked

6 citations

Gregory Holste, Song Wang, Yiliang Zhou, Yishu Wei, Imon Banerjee +29 more

Automated abnormality classification of chest radiographs using deep convolutional neural networks

npj Digital Medicine(2020)10.1038/s41746-020-0273-z

N/A

0DataRank · unranked

255 citations

Youbao Tang, Yifan Peng, Ke Yan, Mohammadhadi Bagheri, Bernadette Redd +6 more

The Dawn of the AI Co-Scientist: A Comprehensive Survey of Biomedical and Chemical Multimodal Agents and Their Applications

(2025)10.36227/techrxiv.176057860.08604810/v1

N/A

0DataRank · unranked

1 citations

Yao Ge, Qingqing Zhu, ZHIYONG LU, Qingyun Wang

Benchmarking Retrieval-Augmented Generation for Chemistry

arXiv (Cornell University)(2025)10.48550/arxiv.2505.07671

N/A

0DataRank · unranked

1 citations

Bowen Jin, Siru Ouyang, Yanzhen Shen, Qiao Jin, Yin Fang +3 more

Enhancing Biomedical Relation Extraction with Directionality

arXiv (Cornell University)(2025)10.48550/arxiv.2501.14079

N/A

0DataRank · unranked

0 citations

Chih-Hsuan Wei, Shubo Tian, Robert Leaman, ZHIYONG LU, Po‐Ting Lai

LabQAR: A Manually Curated Dataset for Question Answering on Laboratory Test Reference Ranges and Interpretation

medRxiv(2025)10.1101/2025.06.03.25328882

Top 100%

0DataRank

Top 100%0 citations

Qiao Jin, Angelique Deville, Yonghui Wu, Karim Hanna, ZHIYONG LU +2 more

FAIR-SMART expands access to supplementary materials for research transparency

PLoS Biology(2025)10.1371/journal.pbio.3003428

N/A

0DataRank · unranked

0 citations

Robert Leaman, Po-Ting Lai, D. C. Comeau, Shubo Tian, ZHIYONG LU +1 more

Towards a unified search: Improving PubMed retrieval with full text

Journal of Biomedical Informatics(2022)10.1016/j.jbi.2022.104211

N/A

0DataRank · unranked

10 citations

Lana Yeganova, Donald C. Comeau, W. John Wilbur, ZHIYONG LU, Won Bae Kim

ZHIYONG LU

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