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ORCIDQingyu Chen 0001
Person information
- affiliation: National Institutes of Health, USA
- affiliation (former): University of Melbourne, School of Computing and Information Systems, Australia
Other persons with the same name
- Qingyu Chen — disambiguation page
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2020 – today
- 2023
[j22]Robert Leaman
, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. Patterns 4(1): 100659 (2023)- [i22]Li Fang, Qingyu Chen, Chih-Hsuan Wei, Zhiyong Lu, Kai Wang:
Bioformer: an efficient transformer language model for biomedical text mining. CoRR abs/2302.01588 (2023) - [i21]Xinyue Hu, Lin Gu, Kazuma Kobayashi, Qiyuan An, Qingyu Chen, Zhiyong Lu, Chang Su, Tatsuya Harada, Yingying Zhu:
Interpretable Medical Image Visual Question Answering via Multi-Modal Relationship Graph Learning. CoRR abs/2302.09636 (2023) - [i20]Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu:
GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information. CoRR abs/2304.09667 (2023) - 2022
- [j21]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu:
Assigning species information to corresponding genes by a sequence labeling framework. Database J. Biol. Databases Curation 2022(2022) (2022) - [j20]Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep Vg, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database J. Biol. Databases Curation 2022(2022) (2022) - [j19]Andres Diaz-Pinto, Nishant Ravikumar, Rahman Attar, Avan Suinesiaputra, Yitian Zhao, Eylem Levelt, Erica Dall' Armellina, Marco Lorenzi, Qingyu Chen, Tiarnan D. L. Keenan, Elvira Agrón, Emily Y. Chew, Zhiyong Lu, Chris P. Gale, Richard P. Gale, Sven Plein, Alejandro F. Frangi:
Predicting myocardial infarction through retinal scans and minimal personal information. Nat. Mach. Intell. 4(1): 55-61 (2022) - [j18]Xiaoshuang Shi, Yifan Peng, Qingyu Chen, Tiarnan D. Keenan, Alisa T. Thavikulwat, Sungwon Lee, Yuxing Tang, Emily Y. Chew, Ronald M. Summers, Zhiyong Lu:
Robust convolutional neural networks against adversarial attacks on medical images. Pattern Recognit. 132: 108923 (2022) - [j17]Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu:
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation. IEEE ACM Trans. Comput. Biol. Bioinform. 19(5): 2584-2595 (2022) - [c18]Qingyu Chen, Tiarnan D. Keenan, Alexis Allot, Sanjeeb Bhandari, Geoff Broadhead, Chantal Cousineau-Krieger, Ellen Davis, William G. Gensheimer, David Grasic, Seema Gupta, Eleni Konstantinou, Tania Lamba, Michele Maiberger, Arnold Oshinsky, Brittany Powell, Boonkit Purt, Soo Shin, Hillary Steifel, Alisa T. Thavikulwat, Keith Wroblewski, Sirisha Koirala, Tom Murickan, Michael F. Chiang, Michelle R. Hribar, Emily Y. Chew, Zhiyong Lu:
Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows. AMIA 2022 - [c17]Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Amr S. Elsawy, Emily Y. Chew, Zhiyong Lu:
Deep learning automated diagnosis and quantitative classification of cataract type and severity: quantifying the effectiveness and usability of deep learning-assisted disease diagnosis models with 14 ophthalmologists and multi-center validations. AMIA 2022 - [c16]Junghwan Lee, Tingyi Wanyan, Qingyu Chen, Tiarnan D. L. Keenan, Benjamin S. Glicksberg, Emily Y. Chew, Zhiyong Lu, Fei Wang, Yifan Peng:
Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning. MLMI@MICCAI 2022: 11-20 - [i19]Qiyuan An, Ruijiang Li, Lin Gu, Hao Zhang, Qingyu Chen, Zhiyong Lu, Fei Wang, Yingying Zhu:
A Privacy-Preserving Unsupervised Domain Adaptation Framework for Clinical Text Analysis. CoRR abs/2201.07317 (2022) - [i18]Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu:
LitMC-BERT: transformer-based multi-label classification of biomedical literature with an application on COVID-19 literature curation. CoRR abs/2204.08649 (2022) - [i17]Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj Dogan, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. CoRR abs/2204.09781 (2022) - [i16]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Dogan, Zhiyong Lu:
Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework. CoRR abs/2205.03853 (2022) - [i15]Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. CoRR abs/2209.08124 (2022) - [i14]Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu:
LitCovid in 2022: an information resource for the COVID-19 literature. CoRR abs/2209.13428 (2022) - [i13]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu:
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning. CoRR abs/2211.16944 (2022) - 2021
- [j16]Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu:
Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration. J. Am. Medical Informatics Assoc. 28(6): 1135-1148 (2021) - [j15]Qingyu Chen, Alexis Allot, Zhiyong Lu:
LitCovid: an open database of COVID-19 literature. Nucleic Acids Res. 49(Database-Issue): D1534-D1540 (2021) - [j14]Alexis Allot, Kyubum Lee, Qingyu Chen, Ling Luo, Zhiyong Lu:
LitSuggest: a web-based system for literature recommendation and curation using machine learning. Nucleic Acids Res. 49(Webserver-Issue): 352-358 (2021) - [c15]Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu:
AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation. AMIA 2021 - [c14]Qingyu Chen, Tiarnan D. Keenan, Emily Y. Chew, Zhiyong Lu:
Deep learning detection of reticular pseudodrusen using multi-modal, multi-task, and multi-attention mechanisms: towards automated and accessible classification of age-related macular degeneration. AMIA 2021 - [c13]Gregory C. Ghahramani, Matthew Brendel, Mingquan Lin, Qingyu Chen, Tiarnan D. Keenan, Kun Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Fei Wang:
Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS. AMIA 2021 - [c12]Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu:
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors. AMIA 2021 - [c11]Yingying Zhu, Shuai Wang, Qingyu Chen, Sungwon Lee, Thomas C. Shen, Daniel C. Elton, Zhiyong Lu, Ronald M. Summers:
Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI. MLMI@MICCAI 2021: 101-109 - 2020
- [j13]Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor:
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genom. Proteom. Bioinform. 18(2): 91-103 (2020) - [j12]Patrick Cheong-Iao Pang, Dana McKay, Shanton Chang, Qingyu Chen, Xiuzhen Zhang, Lishan Cui:
Privacy concerns of the Australian My Health Record: Implications for other large-scale opt-out personal health records. Inf. Process. Manag. 57(6): 102364 (2020) - [j11]Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu:
Better synonyms for enriching biomedical search. J. Am. Medical Informatics Assoc. 27(12): 1894-1902 (2020) - [j10]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. BMC Medical Informatics Decis. Mak. 20-S(1): 73 (2020) - [j9]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Predicting risk of late age-related macular degeneration using deep learning. npj Digit. Medicine 3 (2020) - [j8]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. 16(4) (2020) - [c10]Yifan Peng, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yuxing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald M. Summers, Zhiyong Lu:
Automatic recognition of abdominal lymph nodes from clinical text. ClinicalNLP@EMNLP 2020: 101-110 - [c9]Qingyu Chen, Tiarnan D. Keenan, Yifan Peng, Elvira Agrón, Christopher Hwang, Alisa T. Thavikulwat, Debora Lee, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Detection of reticular pseudodrusen using deep learning. AMIA 2020 - [c8]Yifan Peng, Qingyu Chen, Zhiyong Lu:
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. BioNLP 2020: 205-214 - [i12]Yifan Peng, Qingyu Chen, Zhiyong Lu:
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. CoRR abs/2005.02799 (2020) - [i11]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Predicting risk of late age-related macular degeneration using deep learning. CoRR abs/2007.09550 (2020) - [i10]Lana Yeganova, Rezarta Islamaj Dogan, Qingyu Chen, Robert Leaman, Alexis Allot, Chih-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu:
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. CoRR abs/2008.03397 (2020) - [i9]Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu:
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). CoRR abs/2010.16413 (2020) - [i8]Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu:
Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration. CoRR abs/2011.05142 (2020)
2010 – 2019
- 2019
- [j7]Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu:
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019: bay147 (2019) - [j6]Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu:
ML-Net: multi-label classification of biomedical texts with deep neural networks. J. Am. Medical Informatics Assoc. 26(11): 1279-1285 (2019) - [j5]Qingyu Chen, Xiuzhen Zhang, Yu Wan, Justin Zobel, Karin Verspoor:
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. J. Comput. Biol. 26(6): 605-617 (2019) - [j4]Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
LitSense: making sense of biomedical literature at sentence level. Nucleic Acids Res. 47(Webserver-Issue): W594-W599 (2019) - [c7]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs. AMIA 2019 - [c6]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Evaluation of Five Sentence Similarity Models on Electronic Medical Records. BCB 2019: 533 - [c5]Qingyu Chen, Yifan Peng, Zhiyong Lu:
BioSentVec: creating sentence embeddings for biomedical texts. ICHI 2019: 1-5 - [i7]Tiarnan D. Keenan, Shazia Dharssi, Yifan Peng, Qingyu Chen, Elvira Agrón, Wai T. Wong, Zhiyong Lu, Emily Y. Chew:
A deep learning approach for automated detection of geographic atrophy from color fundus photographs. CoRR abs/1906.03153 (2019) - [i6]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. CoRR abs/1909.03044 (2019) - [i5]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR abs/1912.10846 (2019) - 2018
- [j3]Qingyu Chen, Nagesh C. Panyam, Aparna Elangovan, Karin Verspoor:
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics. Database J. Biol. Databases Curation 2018: bay122 (2018) - [j2]Qingyu Chen, Yu Wan, Xiuzhen Zhang, Yang Lei, Justin Zobel, Karin Verspoor:
Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. ACM J. Data Inf. Qual. 9(3): 17 (2018) - [c4]Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu:
Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. BCB 2018: 531-532 - [i4]Qingyu Chen, Yifan Peng, Zhiyong Lu:
BioSentVec: creating sentence embeddings for biomedical texts. CoRR abs/1810.09302 (2018) - [i3]Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu:
ML-Net: multi-label classification of biomedical texts with deep neural networks. CoRR abs/1811.05475 (2018) - [i2]Yifan Peng, Shazia Dharssi, Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs. CoRR abs/1811.07492 (2018) - [i1]Qingyu Chen, Yifan Peng, Tiarnan D. Keenan, Shazia Dharssi, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
A multi-task deep learning model for the classification of Age-related Macular Degeneration. CoRR abs/1812.00422 (2018) - 2017
- [b1]Qingyu Chen:
Duplication in biological databases: definitions, impacts and methods. University of Melbourne, Parkville, Victoria, Australia, 2017 - [j1]Qingyu Chen, Justin Zobel, Karin Verspoor:
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. Database J. Biol. Databases Curation 2017: baw163 (2017) - [c3]Qingyu Chen, Xiuzhen Zhang, Yu Wan, Justin Zobel, Karin Verspoor:
Sequence Clustering Methods and Completeness of Biological Database Search. BAI@IJCAI 2017: 8-14 - 2016
- [c2]Qingyu Chen, Yu Wan, Yang Lei, Justin Zobel, Karin Verspoor:
Evaluation of CD-HIT for constructing non-redundant databases. BIBM 2016: 703-706 - 2015
- [c1]Qingyu Chen, Justin Zobel, Karin Verspoor:
Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases. DTMBIO@CIKM 2015: 4-12
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