2024
Advancing entity recognition in biomedicine via instruction tuning of large language models
Keloth, V.K., Hu, Y., Xie, Q., Peng, X., Wang, Y., Zheng, A., Selek, M., Raja, K., Wei, C.H., Jin, Q. Lu, Z., Chen, Q¶., and Xu, H¶
To appear in Bioinformatics
Genegpt: Augmenting large language models with domain tools for improved access to biomedical information
Jin, Q., Yang, Y., Chen, Q. and Lu, Z.
To appear in Bioinformatics
Improving large language models for clinical named entity recognition via prompt engineering.
Hu, Y., Chen, Q., Du, J., Peng, X., Keloth, V.K., Zuo, X., Zhou, Y., Li, Z., Jiang, X., Lu, Z., Roberts, K., and Xu., H.
To appear in Journal of the American Medical Informatics Association
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health.
Tian, S., Jin, Q., Yeganova, L., Lai, P.T., Zhu, Q., Chen, X., Yang, Y., Chen, Q., Kim, W., Comeau, D.C. , Islamaj, R. and Lu, Z.
To appear in Briefings in Bioinformatics.
2023
A deep network DeepOpacityNet for detection of cataracts from color fundus photographs
Elsawy, A*., Keenan, T.D*., Chen, Q*., Thavikulwat, A.T., Bhandari, S., Quek, T.C., Goh, J.H.L., Tham, Y.C., Cheng, C.Y., Chew, E.Y. and Lu, Z.
Nature Communications Medicine. 2023. See paper.
Large Language Models and the Retina: A Review of Current Applications and Future Directions
Gilson, A., Singer, M., Xu, H., Chen, Q¶., and Adelman, R.A¶.,
To appear in Retina-Vitreus/Journal of Retina-Vitreous
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval
Jin, Q., Kim, W., Chen, Q., Comeau, D.C., Yeganova, L., Wilbur, W.J. and Lu, Z.,
To appear in Bioinformatics
BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets
Lai, P.T., Wei, C.H., Luo, L., Chen, Q. and Lu, Z.
To appear in Journal of Biomedical Informatics.
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning
Luo, L., Wei, C.H., Lai, P.T., Leaman, R., Chen, Q. and Lu, Z
Bioinformatics. 2023. See paper.
Deep-GA-Net for Accurate and Explainable Detection of Geographic Atrophy on Optical Coherence Tomography Scans
Elsawy, A., Keenan, T.D., Chen, Q., Shi, X., Thavikulwat, A.T., Bhandari, S., Chew, E.Y. and Lu, Z.,
Ophthalmology Science. 2023. See paper.
Attention-based 3D convolutional networks for detection of geographic atrophy from optical coherence tomography scans
Elsawy, A., Kenan, T.D., Chen, Q., Shi, X., Chew, E.Y. and Lu, Z
In Medical Imaging 2023: Image Processing (Vol. 12464, pp. 751-755). SPIE. See paper.
From function to translation: Decoding genetic susceptibility to human diseases via artificial intelligence
Long, E., Wan, P., Chen, Q., Lu, Z. and Choi, J.,
Cell Genomics. 2023. See paper.
LitCovid in 2022: an information resource for the COVID-19 literature
Chen, Q., Allot, A., Leaman, R., Wei, C.H., Aghaarabi, E., Guerrerio, J.J., Xu, L. and Lu, Z
Nucleic Acids Research. 2023. See paper. See server.
Comprehensively identifying long Covid articles with human-in-the-loop machine learning
Leaman, R., Islamaj, R., Allot, A., Chen, Q., Wilbur, W.J. and Lu, Z.,
Cell Patterns. 2023. See paper.
Reticular Pseudodrusen Status, ARMS2/HTRA1 Genotype, and Geographic Atrophy Enlargement: Age-Related Eye Disease Study 2 Report 32
Agrón, E., Domalpally, A., Cukras, C.A., Clemons, T.E., Chen, Q., Swaroop, A., Lu, Z., Chew, E.Y. and Keenan, T.D
Ophthalmology. 2023. See paper.
2022
Automated and accessible diagnosis of age-related macular degeneration: a comparative analysis of the impact of machine learning models in clinical diagnostic workflows
Chen, Q., Keenan, T.D., Allot, A., Chiang, M., Hribar, M.R., Chew, E.Y., and Lu, Z
AMIA 2022 Annual Symposium - Stage 3 of AMIA 2022 Artificial Intelligence Evaluation Showcase, 2022. Poster.
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.
Chen, Q., Keenan, T.D., Agrón, E., Elsawy, A., Chew, E.Y., and Lu, Z.
AMIA 2022 Annual Symposium. Presentation.
Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework
Luo, L., Wei, C.H., Lai, P.T., Chen, Q., Doğan, R.I. and Lu, Z.
Database. See article.
LitMC-BERT: transformer-based multi-label classification of biomedical literature with an application on COVID-19 literature curation
Chen, Q., Du, J., Allot, A., and Lu, Z.
IEEE/ACM Transactions on Computational Biology and Bioinformatics. See article.
Robust convolutional neural networks against adversarial attacks on medical images
Shi, X., Peng, Y., Chen, Q., ..., Chew, E.Y., and Lu, Z.
Pattern Recognition. See article.
Reticular Pseudodrusen: the Third Macular Risk Feature for Progression to Late Age-related Macular Degeneration.
Agrón, E., Domalpally, A., Cukras, C.A., Clemons, T.E., Chen, Q., Lu, Z., Chew, E.Y. and Keenan, T.D.
Ophthalmology. See article.
Deep learning automated diagnosis and quantitative classification of cataract type and severity.
Keenan, T.D*., Chen, Q*., Agrón, E., Thavikulwat, A., Lu, Z., and Chew, E.
Ophthalmology. See article.
Automated and accessible diagnosis in age-related macular degeneration (AMD): a usability evaluation of diagnostic accuracy and efficiency assisted by machine learning model predictions
Chen, Q., Keenan, T.D., Allot, A., Chiang, M., Hribar, M.R., Chew, E.Y., and Lu, Z
AMIA 2022 Clinical Informatics Conference - Stage 2 of AMIA 2022 Artificial Intelligence Evaluation Showcase, 2022. Poster.
Benchmarking effectiveness and efficiency of deep-learning models for semantic textual similarity in the clinical domain.
Chen, Q., Rankie, A., Peng, Y., Arabi, E., and Lu, Z
JMIR Medical Informatics. See article. Top-ranked performance in the n2c2 challenge task.
Automated and accessible prediction of progression in age-related macular degeneration (AMD): external validation from the perspectives of methods, populations, and users.
Chen, Q., Keenan, T.D., Allot, A., Chiang, M., Hribar, M.R., Chew, E.Y., and Lu, Z
AMIA Informatics - Stage 1 of AMIA 2022 Artificial Intelligence Evaluation Showcase, 2022. Poster.
2021
Detecting Visually Significant Age-Related Cataract using Retinal Photograph-Based Deep Learning: Validation, and Comparison with Clinical Experts.
Tham, Y., Hui, J., Anees A., Rim. T., … Chen, Q., … Wong, T., Cheng, C.
Nature Aging. See article.
Seeing your Heart through your Eyes by Predicting Myocardial Infarction using Retinal Images and Demographic Data.
Diaz-Pinto, A., Attar, R., Ravikumar, N., … Chen, Q., … Plein, S., Frangi, A.
Nature Machine Intelligence. See article.
Overview of the BioCreative VII LitCovid Track: multi-label topic classification for COVID-19 literature annotation.
Chen, Q., Allot, A., Leaman, R., Islamaj R., and Lu, Z.
Proceedings of the 2021 BioCreative Challenge workshop. See article.
Long Covid: A Comprehensive Collection of Articles on Post-COVID Conditions
Leaman, R., Chen, Q., Allot, A., Islamaj R., and Lu, Z.
Proceedings of the 2021 BioCreative Challenge workshop. See article.
Improving Interpretability in Machine Diagnosis: Detection of Geographic Atrophy in Optical Coherence Tomography Scans
Shi, X., Keenan, T.D., Chen, Q., Silva, T.D., Thavikulwat, A.T., Broadhead, G., Bhandari, S., Cukras2, C., Chew, E.Y., Lu, Z
Ophthalmology Science. See article.
Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI
Zhu, Y., Wang, S., Chen, Q., Lee, S., ... Lu, Z. and Summers, R
Proceedings of the 12th Machine Learning in Medical Imaging workshop. See article.
Deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS
Ghahramani, G., Brendel, M., Lin, M., Chen, Q., Keenan, T.D., Chen, K., Chew, E.Y., Lu, Z., Peng, Y., Wang, F
AMIA 2021 Annual Symposium. See article.
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.
Chen, Q., Keenan, T.D., Lu, Z. and Chew, E.Y., 2021.
To appear in AMIA 2021 Annual Symposium. Presentation.
LitSuggest: A Web-based System for Literature Recommendation and Curation using Machine Learning
Allot, A*., Lee, K*., Chen, Q*., Luo, L., Wei, C.H., Yan, S. and Lu, Z.
Nucleic Acids Research. See article. See server.
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP)
Chen, Q*., Leaman, R*., Allot, A., Luo, L., Wei, C.H., Yan, S. and Lu, Z.
Annual Review of Biomedical Data Science. See article.
LitCovid: an open database of COVID-19 literature
Chen, Q*., Allot, A*. and Lu. Z.
Nucleic Acids Research. See article. See server.
2020
Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration
Chen, Q*., Keenan, T.D*., Allot, A., Peng, Y., Agrón, E., Domalpally, A., Klaver, C.C., Luttikhuizen, D.T., Colyer, M.H., Cukras, C.A., Wiley, H.E., Wong, W.T., Zhu, Y,, Chew, E.Y and Lu, Z.
Journal of the American Medical Informatics Association. See article.
Automatic recognition of abdominal lymph nodes from clinical text
Peng, Y., Lee, S., Elton, D.C., Shen, T., Tang, Y.X., Chen, Q., Wang, S., Zhu, Y., Summers, R. and Lu, Z.
In Proceedings of the 3rd Clinical Natural Language Processing Workshop. See article.
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view
Yeganova, L., Islamaj, R., Chen, Q., Leaman, R., Allot, A., Wei, C.H., Comeau, D.C., Kim, W., Peng, Y., Wilbur, W.J. and Lu, Z.
KDD (Health Day). See article.
Privacy concerns of the Australian My Health Record: Implications for other large-scale opt-out personal health records
Pang, P.C.I., McKay, D., Chang, S., Chen, Q., Zhang, X. and Cui, L., 2020. Privacy concerns of the Australian My Health Record: Implications for other large-scale opt-out personal health records.
Information Processing & Management. See article.
Better synonyms for enriching biomedical search
Yeganova, L., Kim S, Chen, Q., Wilbur, W. J., and Lu, Z.
Journal of the American Medical Informatics Association. See article.
Curation at Scale: Computational approaches to support curation in LitCovid
Chen, Q*., Allot, A*. and Lu. Z.
BioKDD workshop (Presentation)
Detection of reticular pseudodrusen using deep learning
Chen, Q., Keenan, T.D., Peng, Y., Agrón, E., Wong, W.T., Lu, Z. and Chew, E.Y.,
AMIA 2020 Annual Symposium (Presentation)
Deep representation of biomedical words, concepts, and sentences: models and applications
Chen, Q and Lu, Z., 2020.
Intelligent Systems for Molecular Biology (Poster)
Curation at Scale: Computational approaches to support curation in LitCovid
Chen, Q*., Allot, A*. and Lu. Z.
Intelligent Systems for Molecular Biology (Presentation and poster)
Predicting risk of late age-related macular degeneration using deep learning
Peng, Y., Keenan, T.D., Chen, Q., Agrón, E., Wong, W.T., Lu, Z. and Chew, E.Y.
To appear in npj Digital Medicine.
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Chen, Q¶., Britto, R., Erill, I., Jeffery, C.J., Liberzon, A., Magrane, M., Onami, J.I.,Robinson-Rechavi, M., Sponarova, J., Zobel, J¶. and Verspoor, K¶.,
Genomics, Proteomics & Bioinformatics. See article.
Deep learning automated detection of reticular pseudodrusen from fundus autofluorescence images or and color fundus photographs in AREDS2
Keenan, T.D*., Chen, Q*., Peng, Y., Agrón, E., Wong, W.T., Lu, Z. and Chew, E.Y.
Ophthalmology. See article.
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining
Peng, Y., Chen, Q., & Lu, Z. 2020.
ACL BioNLP workshop. See article.
Citation Cascade and the Evolution of Topic Relevance
Min, C*., Chen, Q*., Yan, E., Bu, Y., & Sun, J.
Journal of the Association for Information Science and Technology. See article. Github repository.
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale
Chen, Q., Lee, K., Yan, S., Kim, S., Wei, C.H. and Lu, Z.
PLOS Computational Biology. See article. Github repository.
Keep up with the latest coronavirus research
Chen, Q., Allot, A., & Lu, Z.
Nature (correspondence). See article. Website.
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records
Chen, Q., Du, J., Kim, S., Wilbur, W. J., & Lu, Z.
BMC Medical Informatics and Decision Making. See article. Top-ranked performance in the challenge task
2019
LitSense: making sense of biomedical literature at sentence level
Allot, A*., Chen, Q*., Kim, S*., Vera Alvarez, R., Comeau, D.C., Wilbur, W.J. and Lu, Z.
Nucleic acids research. See article. Web server.
BioSentVec: creating sentence embeddings for biomedical texts
Chen, Q*., Peng, Y*. and Lu, Z.
2019 IEEE International Conference on Healthcare Informatics. See article. Github repository.
A deep learning approach for automated detection of geographic atrophy from color fundus photographs.
Keenan, T.D., Dharssi, S., Peng, Y., Chen, Q., Agrón, E., Wong, W.T., Lu, Z. and Chew, E.Y
Ophthalmology. See article.
ML-Net: multi-label classification of biomedical texts with deep neural networks
Du, J., Chen, Q., Peng, Y., Xiang, Y., Tao, C. and Lu, Z., 2019.
Journal of the American Medical Informatics Association. See article. Github repository.
DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs
Peng, Y., Dharssi, S., Chen, Q., Keenan, T.D., Agrón, E., Wong, W.T., Chew, E.Y. and Lu, Z., 2019.
Ophthalmology. See article. Github repository.
Evaluation of Five Sentence Similarity Models on Electronic Medical Records
Chen, Q., Du, J., Kim, S., Wilbur, W.J. and Lu, Z.
ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. See article.
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine
Islamaj Doğan, R., Kim, S., Chatr-Aryamontri, A., Wei, C.H., Comeau, D.C., Antunes, R., Matos, S., Chen, Q., Elangovan, A., Panyam, N.C. and Verspoor, K., 2019.
Database. See article
Ensemble Deep Learning for Clinical Semantic Textual Similarity: NCBI at 2019 n2c2 Shared-Task Track 1
Chen, Q., Rankie, A., Peng, Y. and Lu, Z.
AMIA 2019 Annual Symposium. (Presentation). Top-ranked performance in the challenge task
Deep learning prediction of progression to late age-related macular degeneration in the Age-Related Eye Disease Study (AREDS) using deep feature extraction and survival analysis.
Keenan, T.D., Peng, Y., Chen, Q., Agron, E., Wong, W.T., Lu, Z. and Chew, E.Y.
Investigative Ophthalmology & Visual Science. (Presentation)
2018
Combining rich features and deep learning for finding similar sentences in electronic medical records
Chen, Q., Du, J., Kim, S., Wilbur, W.J. and Lu, Z.
Proceedings of the BioCreative/OHNLP Challenge. See article. Top-ranked performance in the challenge task.
Sentence similarity measures revisited: ranking sentences in PubMed documents
Chen, Q., Kim, S., Wilbur, W.J. and Lu, Z.
ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. See article.
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics
Chen, Q., Panyam, N.C., Elangovan, A. and Verspoor, K.
Database. See article. Top-ranked performance in the challenge task.
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions
Chen, Q¶., Zhang, X., Wan, Y., Zobel, J. and Verspoor, K.,
Journal of Computational Biology. See article.
Distributed Finite Time Consensus of Second-Order Multi-Agent Systems via Pinning Control
Zhou, Y., Jiang, G., Xu, F.Y. and Chen, Q.
IEEE Access. See article.
Biocuration: Distilling data into knowledge
International Society for Biocuration
PLOS Biology. See article.
Comparative analysis of sequence clustering methods for de-duplication of biological databases
Chen, Q., Wan, Y., Zhang, X., Lei, Y., Zobel, J. and Verspoor, K.
ACM Journal of Data and Information Quality. See article.
2017
Duplicates, redundancies, and inconsistencies in the primary nucleotide databases: a descriptive study
Chen, Q¶., Zobel, J. and Verspoor, K.
Database. See article.
Benchmarks for Measurement of Duplicate Detection Methods in Nucleotide Databases
Chen, Q., Zobel, J. and Verspoor, K.
Database. See article.
Sequence clustering methods and search completeness
Chen Q., Wan Y., Zhang X., Lei Y., Zobel J. and Verspoor K.
2017 IJCAI workshop on Advances in Bioinformatics and Artificial Intelligence. See article.
2016
Evaluation of CD-HIT for constructing non-redundant databases
Chen, Q., Wan, Y., Lei, Y., Zobel, J. and Verspoor, K.
In 2016 IEEE International Conference on Bioinformatics and Biomedicine. See article.
Supervised Learning for Detection of Duplicates in Genomic Sequence Databases
Chen, Q., Zobel, J., Zhang, X. and Verspoor, K.
PLOS ONE. See article.
Supervised learning enables detection of duplicates in biological databases
Chen.Q., Zobel, J., Zhang, X. and Verspoor, K.
Intelligent Systems for Molecular Biology. (Presentation and poster)
Benchmarks for measurement of duplicate detection methods for bioinformatics databases
Chen.Q., Zobel, J. and Verspoor, K.
The Ninth International Biocuration Conference. (Poster)
2015
Evaluation of a machine learning duplicate detection method for bioinformatics databases
Chen, Q., Zobel, J. and Verspoor, K.
ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics. See article.
2014
Integrating bdi agents into a matsim simulation
Padgham, L., Nagel, K., Singh, D. and Chen, Q.
The twenty-first European Conference on Artificial Intelligence. See article.
Adding BDI agents to MATSim traffic simulator
Chen, Q., Wilsher, A., Singh, D. and Padgham, L.
2014 international conference on Autonomous agents and multi-agent systems. See article.
Duplicate detection in bioinformatics databases
Chen.Q., Zobel, J. and Verspoor, K.
2014 Australian Bioinformatics Conference. (Poster)