Qingyu Chen
Orcid: 0000-0002-6036-1516Affiliations:
- National Institutes of Health, USA
- University of Melbourne, School of Computing and Information Systems, Australia (former)
According to our database1,
Qingyu Chen authored at least 120 papers
between 2015 and 2026.
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Bibliography
2026
Deliberative multi-agent large language models improve clinical reasoning in ophthalmology.
CoRR, March, 2026
A Federated and Parameter-Efficient Framework for Large Language Model Training in Medicine.
CoRR, January, 2026
AI-generated data contamination erodes pathological variability and diagnostic reliability.
CoRR, January, 2026
EHRNavigator: A Multi-Agent System for Patient-Level Clinical Question Answering over Heterogeneous Electronic Health Records.
CoRR, January, 2026
Med-CoReasoner: Reducing Language Disparities in Medical Reasoning via Language-Informed Co-Reasoning.
CoRR, January, 2026
Digital Twin AI: Opportunities and Challenges from Large Language Models to World Models.
CoRR, January, 2026
Information extraction from clinical notes: are we ready to switch to large language models?
J. Am. Medical Informatics Assoc., 2026
Dialogue is Better Than Monologue: Instructing Meidcal LLMs via Strategic Conversations.
Proceedings of the Findings of the Association for Computational Linguistics: EACL 2026, 2026
Benchmarking Direct Preference Optimization for Medical Large Vision-Language Models.
Proceedings of the Findings of the Association for Computational Linguistics: EACL 2026, 2026
2025
From Compound Figures to Composite Understanding: Developing a Multi-Modal LLM from Biomedical Literature with Medical Multiple-Image Benchmarking and Validation.
CoRR, November, 2025
CoRR, November, 2025
Rethinking Retrieval-Augmented Generation for Medicine: A Large-Scale, Systematic Expert Evaluation and Practical Insights.
CoRR, November, 2025
LMOD+: A Comprehensive Multimodal Dataset and Benchmark for Developing and Evaluating Multimodal Large Language Models in Ophthalmology.
CoRR, September, 2025
Memorization in Large Language Models in Medicine: Prevalence, Characteristics, and Implications.
CoRR, September, 2025
CoRR, August, 2025
BEnchmarking LLMs for Ophthalmology (BELO) for Ophthalmological Knowledge and Reasoning.
CoRR, July, 2025
CoRR, June, 2025
Benchmarking Next-Generation Reasoning-Focused Large Language Models in Ophthalmology: A Head-to-Head Evaluation on 5,888 Items.
CoRR, April, 2025
CoRR, March, 2025
GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking.
CoRR, February, 2025
Is an Ultra Large Natural Image-Based Foundation Model Superior to a Retina-Specific Model for Detecting Ocular and Systemic Diseases?
CoRR, February, 2025
Dialogue is Better Than Monologue: Instructing Medical LLMs via Strategical Conversations.
CoRR, January, 2025
Can OpenAI o1 Reason Well in Ophthalmology? A 6,990-Question Head-to-Head Evaluation Study.
CoRR, January, 2025
Enhancing Patient-Centric Communication: Leveraging LLMs to Simulate Patient Perspectives.
CoRR, January, 2025
npj Digit. Medicine, 2025
Author Correction: Small language models learn enhanced reasoning skills from medical textbooks.
npj Digit. Medicine, 2025
npj Digit. Medicine, 2025
Social determinants of health extraction from clinical notes across institutions using large language models.
npj Digit. Medicine, 2025
Word-Sequence Entropy: Towards uncertainty estimation in free-form medical question answering applications and beyond.
Eng. Appl. Artif. Intell., 2025
LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models.
Proceedings of the Findings of the Association for Computational Linguistics: NAACL 2025, Albuquerque, New Mexico, USA, April 29, 2025
Proceedings of the Machine Learning in Medical Imaging - 16th International Workshop, 2025
Clinical Trial Eligibility Criteria Decomposition and Parsing with Large Language Models.
Proceedings of the MEDINFO 2025 - Healthcare Smart × Medicine Deep, 2025
Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing, 2025
Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing, 2025
GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking.
Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), 2025
2024
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information.
Bioinform., February, 2024
Opportunities and challenges for ChatGPT and large language models in biomedicine and health.
Briefings Bioinform., January, 2024
J. Biomed. Informatics, 2024
Improving large language models for clinical named entity recognition via prompt engineering.
J. Am. Medical Informatics Assoc., 2024
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, 2024
Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models?
CoRR, 2024
Humans Continue to Outperform Large Language Models in Complex Clinical Decision-Making: A Study with Medical Calculators.
CoRR, 2024
Language Enhanced Model for Eye (LEME): An Open-Source Ophthalmology-Specific Large Language Model.
CoRR, 2024
Towards Accountable AI-Assisted Eye Disease Diagnosis: Workflow Design, External Validation, and Continual Learning.
CoRR, 2024
Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology.
CoRR, 2024
Word-Sequence Entropy: Towards Uncertainty Estimation in Free-Form Medical Question Answering Applications and Beyond.
CoRR, 2024
AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning.
CoRR, 2024
CoRR, 2024
PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature.
Bioinform., 2024
Advancing entity recognition in biomedicine via instruction tuning of large language models.
Bioinform., 2024
Proceedings of the Advances in Neural Information Processing Systems 37: Annual Conference on Neural Information Processing Systems 2024, 2024
Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2024, 2024
KG-Rank: Enhancing Large Language Models for Medical QA with Knowledge Graphs and Ranking Techniques.
Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, 2024
Yale at "Discharge Me!": Evaluating Constrained Generation of Discharge Summaries with Unstructured and Structured Information.
Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, 2024
2023
BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets.
J. Biomed. Informatics, October, 2023
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval.
Bioinform., October, 2023
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning.
Bioinform., May, 2023
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning.
Patterns, January, 2023
Nucleic Acids Res., January, 2023
CoRR, 2023
Integrating UMLS Knowledge into Large Language Models for Medical Question Answering.
CoRR, 2023
BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval.
CoRR, 2023
Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations.
CoRR, 2023
Interpretable Medical Image Visual Question Answering via Multi-Modal Relationship Graph Learning.
CoRR, 2023
CoRR, 2023
Attention-based 3D convolutional networks for detection of geographic atrophy from optical coherence tomography scans.
Proceedings of the Medical Imaging 2023: Image Processing, 2023
2022
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
Pattern Recognit., 2022
Predicting myocardial infarction through retinal scans and minimal personal information.
Nat. Mach. Intell., 2022
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning.
CoRR, 2022
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
CoRR, 2022
A Privacy-Preserving Unsupervised Domain Adaptation Framework for Clinical Text Analysis.
CoRR, 2022
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
Assigning species information to corresponding genes by a sequence labeling framework.
Database J. Biol. Databases Curation, 2022
Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning.
Proceedings of the Machine Learning in Medical Imaging - 13th International Workshop, 2022
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.
Proceedings of the AMIA 2022, 2022
Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows.
Proceedings of the AMIA 2022, 2022
2021
LitSuggest: a web-based system for literature recommendation and curation using machine learning.
Nucleic Acids Res., 2021
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., 2021
Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI.
Proceedings of the Machine Learning in Medical Imaging - 12th International Workshop, 2021
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
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.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
2020
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., April, 2020
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.
PLoS Comput. Biol., 2020
npj Digit. Medicine, 2020
J. Am. Medical Informatics Assoc., 2020
Privacy concerns of the Australian My Health Record: Implications for other large-scale opt-out personal health records.
Inf. Process. Manag., 2020
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases.
Genom. Proteom. Bioinform., 2020
Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration.
CoRR, 2020
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP).
CoRR, 2020
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view.
CoRR, 2020
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing, 2020
Proceedings of the AMIA 2020, 2020
Proceedings of the 3rd Clinical Natural Language Processing Workshop, 2020
2019
Nucleic Acids Res., 2019
J. Comput. Biol., 2019
J. Am. Medical Informatics Assoc., 2019
A deep learning approach for automated detection of geographic atrophy from color fundus photographs.
CoRR, 2019
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.
Database J. Biol. Databases Curation, 2019
Proceedings of the 2019 IEEE International Conference on Healthcare Informatics, 2019
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs.
Proceedings of the AMIA 2019, 2019
2018
Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases.
ACM J. Data Inf. Qual., 2018
A multi-task deep learning model for the classification of Age-related Macular Degeneration.
CoRR, 2018
DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs.
CoRR, 2018
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics.
Database J. Biol. Databases Curation, 2018
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
2017
PhD thesis, 2017
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.
Database J. Biol. Databases Curation, 2017
Proceedings of the Workshop on Advances in Bioinformatics and Artificial Intelligence: Bridging the Gap co-located with 26th International Joint Conference on Artificial Intelligence (IJCAI 2017), 2017
2016
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016
2015
Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases.
Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics, 2015