| 2026 | WWW | PairSem: LLM-Guided Pairwise Semantic Matching for Scientific Document Retrieval. | Wonbin Kweon, Runchu Tian, Seongku Kang, Pengcheng Jiang, Zhiyong Lu, Jiawei Han, Hwanjo Yu |
| 2025 | ACL | MedCite: Can Language Models Generate Verifiable Text for Medicine? | Xiao Wang, Mengjue Tan, Qiao Jin, Guangzhi Xiong, Yu Hu, Aidong Zhang, Zhiyong Lu, Minjia Zhang |
| 2025 | HCI | Research on the Design of Community Two-Wheeled Electric Vehicle Parking Facilities Based on Kano-QFD and FBS-TRIZ Models. | Junnan Ye, Zhiyong Lu |
| 2024 | ACL | Benchmarking Retrieval-Augmented Generation for Medicine. | Guangzhi Xiong, Qiao Jin, Zhiyong Lu, Aidong Zhang |
| 2023 | MICCAI | Utilizing Longitudinal Chest X-Rays and Reports to Pre-fill Radiology Reports. | Qingqing Zhu, Tejas Sudharshan Mathai, Pritam Mukherjee, Yifan Peng, Ronald M. Summers, Zhiyong Lu |
| 2023 | SIGIR | LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search. | Qiao Jin, Andrew Shin, Zhiyong Lu |
| 2022 | AMIA | Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows. | 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 E. 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 |
| 2022 | AMIA | 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. | Qingyu Chen, Tiarnan D. Keenan, Elvira Agrn, Amr S. Elsawy, Emily Y. Chew, Zhiyong Lu |
| 2022 | AMIA | BioRED: A Comprehensive Biomedical Relation Extraction Dataset. | Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu |
| 2022 | AMIA | PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. | Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, Zhiyong Lu |
| 2022 | MICCAI | Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning. | Junghwan Lee, Tingyi Wanyan, Qingyu Chen, Tiarnan D. L. Keenan, Benjamin S. Glicksberg, Emily Y. Chew, Zhiyong Lu, Fei Wang, Yifan Peng |
| 2021 | AMIA | AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation. | Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu |
| 2021 | AMIA | 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. | Qingyu Chen, Tiarnan D. Keenan, Emily Y. Chew, Zhiyong Lu |
| 2021 | AMIA | Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS. | Gregory C. Ghahramani, Matthew Brendel, Mingquan Lin, Qingyu Chen, Tiarnan D. Keenan, Kun Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Fei Wang |
| 2021 | AMIA | TeamTat: A Collaborative Text Annotation Tool for Creating Gold-Standard Corpora. | Rezarta Islamaj, Dongseop Kwon, Sun Kim, Zhiyong Lu |
| 2021 | AMIA | NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in PubMed Full Text Literature. | Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Dorothy Trinh, Deborah Whitman, Keiko Sekiya, Zhiyong Lu |
| 2021 | AMIA | Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors. | Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu |
| 2021 | AMIA | Informatics-izing the National Institutes of Health. | Clement J. McDonald, Patricia Flatley Brennan, Michael F. Chiang, Joshua C. Denny, Zhiyong Lu |
| 2021 | AMIA | Improving PubMed Retrieval by Integrating Abstract and Full Text Search. | Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu |
| 2021 | MICCAI | Detection of Lymph Nodes in T2 MRI Using Neural Network Ensembles. | Tejas Sudharshan Mathai, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers |
| 2021 | MICCAI | Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI. | Yingying Zhu, Shuai Wang, Qingyu Chen, Sungwon Lee, Thomas C. Shen, Daniel C. Elton, Zhiyong Lu, Ronald M. Summers |
| 2020 | AMIA | Detection of reticular pseudodrusen using deep learning. | Qingyu Chen, Tiarnan D. Keenan, Yifan Peng, Elvira Agrn, Christopher Hwang, Alisa T. Thavikulwat, Debora Lee, Wai T. Wong, Emily Y. Chew, Zhiyong Lu |
| 2020 | EMNLP | A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2. | Robert Leaman, Zhiyong Lu |
| 2020 | MICCAI | COMe-SEE: Cross-modality Semantic Embedding Ensemble for Generalized Zero-Shot Diagnosis of Chest Radiographs. | Angshuman Paul, Thomas C. Shen, Niranjan Balachandar, Yuxing Tang, Yifan Peng, Zhiyong Lu, Ronald M. Summers |
| 2019 | AMIA | A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs. | Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrn, Wai T. Wong, Emily Y. Chew, Zhiyong Lu |
| 2019 | CVPR | Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning From Radiology Reports and Label Ontology. | Ke Yan, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers |
| 2019 | MICCAI | MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation. | Ke Yan, Youbao Tang, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers |
| 2019 | PSB | Text Mining and Machine Learning for Precision Medicine. | Graciela Gonzalez, Zhiyong Lu, Robert Leaman, Davy Weissenbacher, Mary Regina Boland, Yong Chen, Jingcheng Du, Juliane Fluck, Casey S. Greene, John H. Holmes, Aditya Kashyap, Rikke Linnemann Nielsen, Zhengqing Ouyang, Sebastian Schaaf, Jaclyn N. Taroni, Cui Tao, Yuping Zhang, Hongfang Liu |
| 2018 | AMIA | Online evaluation of PubMed's new relevance search algorithm. | Nicolas Fiorini, Zhiyong Lu |
| 2018 | AMIA | Experimenting new search and user interface in PubMed Labs. | Zhiyong Lu, Nicolas Fiorini |
| 2018 | CVPR | TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-Rays. | Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers |
| 2018 | NAACL | Personalized neural language models for real-world query auto completion. | Nicolas Fiorini, Zhiyong Lu |
| 2018 | WWW | A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. | Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu |
| 2017 | AMIA | New Relevance Search Algorithm for PubMed. | Nicolas Fiorini, Zhiyong Lu |
| 2017 | AMIA | Text Mining Radiology Reports for Deep Learning Radiology Images. | Yifan Peng, Xiaosong Wang, Le Lu, Mohammadhadi Bagheri, Ronald M. Summers, Zhiyong Lu |
| 2017 | CVPR | ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases. | Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers |
| 2015 | PSB | Session Introduction. | Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu |
| 2014 | AMIA | Automatic Extraction of Drug Indications from FDA Drug Labels. | Ritu Khare, Chih-Hsuan Wei, Zhiyong Lu |
| 2014 | PSB | Session Introduction. | S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte |
| 2013 | AMIA | NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization. | Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu |
| 2013 | AMIA | DNorm: A New Method and Online Tool for Disease Name Normalization. | Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu |
| 2013 | AMIA | Predicting clicks of PubMed articles. | Yuqing Mao, Zhiyong Lu |
| 2013 | AMIA | A systematic comparison of current sources of disease knowledge. | Aurlie Nvol, Bastien Rance, Zhiyong Lu |
| 2013 | PSB | Session Introduction. | Zhiyong Lu, Pankaj Agarwal, Atul J. Butte |
| 2010 | COLING | Learning to Annotate Scientific Publications. | Minlie Huang, Zhiyong Lu |
| 2010 | ICMLA | A Textual Representation Scheme for Identifying Clinical Relationships in Patient Records. | Rezarta Islamaj Dogan, Aurlie Nvol, Zhiyong Lu |
| 2009 | AMIA | Finding Query Suggestions for PubMed. | Zhiyong Lu, W. John Wilbur, Johanna R. McEntyre, Alexey Iskhakov, Lee Szilagyi |
| 2008 | AMIA | Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. | Zhiyong Lu, Won Kim, W. John Wilbur |
| 2007 | PSB | Generif Quality Assurance as Summary Revision. | Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter |
| 2006 | PSB | Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. | Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter |
| 2006 | PSB | Finding GeneRIFs via Gene Ontology Annotations. | Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter |
| 2005 | PSB | GO Molecular Function Terms Are Predictive of Subcellular Localization. | Zhiyong Lu, Lawrence Hunter |
| 2003 | PAKDD | Automatic Extraction of Clusters from Hierarchical Clustering Representations. | Jrg Sander, Xuejie Qin, Zhiyong Lu, Nan Niu, Alex Kovarsky |