Yonghui Wu - RankMe

135 papers A* 1B 2Misc 26Journal 74Unranked 32

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	A topic modeling analysis of stigma dimensions, social, and related behavioral circumstances in clinical notes among patients with HIV. Int. J. Medical Informatics Ziyi Chen, Yiyang Liu, Mattia Prosperi, Krishna Vaddiparti, Robert L. Cook, Jiang Bian, Yi Guo, Yonghui Wu
2026	J	`jnl`	Expert Threshold Routing for Autoregressive Language Modeling with Dynamic Computation Allocation and Load Balancing. CoRR Hanchi Sun, Yixin Liu, Yonghui Wu, Lichao Sun
2026	J	`jnl`	Improving Automatic Summarization of Radiology Reports through Mid-Training of Large Language Models. CoRR Mengxian Lyu, Cheng Peng, Ziyi Chen, Mengyuan Zhang, Jieting Li Lu, Yonghui Wu
2026	J	`jnl`	MedGPT-oss: Training a General-Purpose Vision-Language Model for Biomedicine. CoRR Kai Zhang, Zhengqing Yuan, Cheng Peng, Songlin Zhao, Mengxian Lyu, Ziyi Chen, Yanfang Ye, Wei Liu, Ying Zhang, Kaleb E. Smith, Lifang He, Lichao Sun, Yonghui Wu
2026	J	`jnl`	Multi-site analysis of COVID-19 and new-onset diabetes reveals need for improved sensitivity of EHR-based COVID-19 phenotypes - a DiCAYA Network analysis. J. Am. Medical Informatics Assoc. Lorna E. Thorpe, Jasmin Divers, Annemarie Hirsch, Brian S. Schwartz, Bo Cai, Jihad S. Obeid, Angela Liese, Tessa Crume, Anna Bellatorre, Jiang Bian, Yi Guo, Sarah Bost, Tianchen Lyu, Matthew T. Mefford, Matt Zhou, Eva Lustigova, Levon H. Utidjian, Mitchell Maltenfort, Patrick Hanley, Meda E. Pavkov, Marc B. Rosenman, Andrea R. Titus, Charles Bailey, Christopher B. Forrest, Levon Utidjian, Mitch Maltenfort, Amy Shah, Eneida A. Mendonça, G. Todd Alonso, Sara J. Deakyne Davies, H. Timothy Bunnell, Anne Kazak, Melody Kitzmiller, Manmohan Kamboj, Dimitri A. Christakis, Daksha Ranade, Annemarie G. Hirsch, Joseph J. Dewalle, H. Lester Kirchner, Meredith Lewis, Dione G. Mercer, Cara M. Nordberg, Amy Poissant, Brian E. Dixon, Shaun J. Grannis, Katie S. Allen, Anna Roberts, Nimish Valvi, Jeff Warvel, Ashley Wiensch, Tamara S. Hannon, Kristi Reynolds, John Chang, Don McCarthy, Rong Wei, Hui Zhou, Marc Rosenman, Lu Zhang, George Lales, Anthony Wong, Allison Zelinski, Yuan Luo, Mark Weiner, Pedro Rivera, Thomas Carton, Elizabeth Nauman, Harold P. Lehmann, Meredith Akerman, Rebecca Anthopolos, Stefanie Bendik, Sarah Conderino, Andrew Fair, Jessica Guillaume, Shahidul Islam, Alan Jacobson, David C. Lee, Chinyere Okpara, Anand Rajan, Andrea Titus, Dana Dabelea, Theresa Anderson, Rebecca Conway, Toan Ong, Jack Pattee, Shawna Burgett, Hui Shao, Elizabeth A. Shenkman, Sarah J. Bost, William T. Donahoo, William R. Hogan, Piaopiao Li, Mattia Prosperi, Yonghui Wu, Angela D. Liese, Lisa Knight, Caroline Rudisill, Jessica Stucker, Deborah Bowlby, Elaine Apperson, Alex Ewing, Giuseppina Imperatore, Deborah Rolka, Hui Xie, Ibrahim Zaganjor
2026	J	`jnl`	Natural language generation in healthcare: A review of methods and applications. J. Biomed. Informatics Mengxian Lyu, Xiaohan Li, Ziyi Chen, Jinqian Pan, Cheng Peng, Sankalp Talankar, Yonghui Wu
2025	J	`jnl`	A Study of Large Language Models for Patient Information Extraction: Model Architecture, Fine-Tuning Strategy, and Multi-task Instruction Tuning. CoRR Cheng Peng, Xinyu Dong, Mengxian Lyu, Daniel Paredes, Yaoyun Zhang, Yonghui Wu
2025	J	`jnl`	A Topic Modeling Analysis of Stigma Dimensions, Social, and Related Behavioral Circumstances in Clinical Notes Among Patients with HIV. CoRR Ziyi Chen, Yiyang Liu, Mattia Prosperi, Krishna Vaddiparti, Robert L. Cook, Jiang Bian, Yi Guo, Yonghui Wu
2025	J	`jnl`	Agentic AutoSurvey: Let LLMs Survey LLMs. CoRR Yixin Liu, Yonghui Wu, Denghui Zhang, Lichao Sun
2025	—	`conf`	Comparative Evaluation of Clinical Large Language Models and Machine Learning to Predict Antimicrobial Resistance in Hospital-Onset Sepsis. AIME (1) Scott A. Cohen, Ziyi Chen, Jiang Bian, Christina Boucher, Yonghui Wu, Mattia Prosperi
2025	—	`conf`	Improving Medical Visual Instruction Tuning with Labeled Datasets. MedAGI Amin Dada, Amanda Butler Contreras, Constantin Seibold, Osman Alperen Koras, Julius Keyl, Aokun Chen, Cheng Peng, Alexander Brehmer, Kaleb E. Smith, Jiang Bian, Yonghui Wu, Jens Kleesiek
2025	J	`jnl`	Leveraging undecided cases in chart-reviewed phenotypes to enhance EHR-based association studies. J. Biomed. Informatics Xinyao Jian, Dazheng Zhang, Zehao Yu, Hua Xu, Jiang Bian, Yonghui Wu, Jiayi Tong, Yong Chen
2025	A*	`conf`	MAP: Low-compute Model Merging with Amortized Pareto Fronts via Quadratic Approximation. ICLR Lu Li, Tianyu Zhang, Zhiqi Bu, Suyuchen Wang, Huan He, Jie Fu, Yonghui Wu, Jiang Bian, Yong Chen, Yoshua Bengio
2025	J	`jnl`	Medical foundation large language models for comprehensive text analysis and beyond. npj Digit. Medicine Qianqian Xie, Qingyu Chen, Aokun Chen, Cheng Peng, Yan Hu, Fongci Lin, Xueqing Peng, Jimin Huang, Jeffrey Zhang, Vipina Kuttichi Keloth, Xinyu Zhou, Lingfei Qian, Huan He, Dennis L. Shung, Lucila Ohno-Machado, Yonghui Wu, Hua Xu, Jiang Bian
2025	J	`jnl`	Scaling Up Biomedical Vision-Language Models: Fine-Tuning, Instruction Tuning, and Multi-Modal Learning. CoRR Cheng Peng, Kai Zhang, Mengxian Lyu, Hongfang Liu, Lichao Sun, Yonghui Wu
2025	J	`jnl`	Scaling up biomedical vision-language models: Fine-tuning, instruction tuning, and multi-modal learning. J. Biomed. Informatics Cheng Peng, Kai Zhang, Mengxian Lyu, Hongfang Liu, Lichao Sun, Yonghui Wu
2024	J	`jnl`	Automatic Summarization of Doctor-Patient Encounter Dialogues Using Large Language Model through Prompt Tuning. CoRR Mengxian Lyu, Cheng Peng, Xiaohan Li, Patrick Balian, Jiang Bian, Yonghui Wu
2024	—	`conf`	Comprehensive Study on German Language Models for Clinical and Biomedical Text Understanding. LREC/COLING Ahmad Idrissi-Yaghir, Amin Dada, Henning Schäfer, Kamyar Arzideh, Giulia Baldini, Jan Trienes, Max Hasin, Jeanette Bewersdorff, Cynthia S. Schmidt, Marie Bauer, Kaleb E. Smith, Jiang Bian, Yonghui Wu, Jörg Schlötterer, Torsten Zesch, Peter A. Horn, Christin Seifert, Felix Nensa, Jens Kleesiek, Christoph M. Friedrich
2024	J	`jnl`	Comprehensive Study on German Language Models for Clinical and Biomedical Text Understanding. CoRR Ahmad Idrissi-Yaghir, Amin Dada, Henning Schäfer, Kamyar Arzideh, Giulia Baldini, Jan Trienes, Max Hasin, Jeanette Bewersdorff, Cynthia S. Schmidt, Marie Bauer, Kaleb E. Smith, Jiang Bian, Yonghui Wu, Jörg Schlötterer, Torsten Zesch, Peter A. Horn, Christin Seifert, Felix Nensa, Jens Kleesiek, Christoph M. Friedrich
2024	J	`jnl`	Deep learning for identifying personal and family history of suicidal thoughts and behaviors from EHRs. npj Digit. Medicine Prakash Adekkanattu, Al'ona Furmanchuk, Yonghui Wu, Aman Pathak, Braja Gopal Patra, Sarah Bost, Destinee Morrow, Grace Hsin-Min Wang, Yuyang Yang, Noah James Forrest, Yuan Luo, Theresa L. Walunas, Wei-Hsuan Lo-Ciganic, Walid Gelad, Jiang Bian, Yuhua Bao, Mark G. Weiner, David W. Oslin, Jyotishman Pathak
2024	J	`jnl`	Extracting Pulmonary Nodules and Nodule Characteristics from Radiology Reports of Lung Cancer Screening Patients Using Transformer Models. J. Heal. Informatics Res. Shuang Yang, Xi Yang, Tianchen Lyu, James L. Huang, Aokun Chen, Xing He, Dejana Braithwaite, Hiren J. Mehta, Yonghui Wu, Yi Guo, Jiang Bian
2024	J	`jnl`	Feasibility of Identifying Factors Related to Alzheimer's Disease and Related Dementia in Real-World Data. CoRR Aokun Chen, Qian Li, Yu Huang, Yongqiu Li, Yu-Neng Chuang, Xia Hu, Serena Guo, Yonghui Wu, Yi Guo, Jiang Bian
2024	J	`jnl`	Generative large language models are all-purpose text analytics engines: text-to-text learning is all your need. J. Am. Medical Informatics Assoc. Cheng Peng, Xi Yang, Aokun Chen, Zehao Yu, Kaleb E. Smith, Anthony B. Costa, Mona G. Flores, Jiang Bian, Yonghui Wu
2024	—	`conf`	Identifying Symptoms of Delirium from Clinical Narratives Using Natural Language Processing. ICHI Aokun Chen, Daniel Paredes, Zehao Yu, Xiwei Lou, Roberta Brunson, Jamie N. Thomas, Kimberly A. Martinez, Robert J. Lucero, Tanja Magoc, Laurence M. Solberg, Urszula Alina Snigurska, Sarah E. Ser, Mattia Prosperi, Jiang Bian, Ragnhildur I. Bjarnadottir, Yonghui Wu
2024	J	`jnl`	Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias. J. Biomed. Informatics Zehao Yu, Cheng Peng, Xi Yang, Chong Dang, Prakash Adekkanattu, Braja Gopal Patra, Yifan Peng, Jyotishman Pathak, Debbie L. Wilson, Ching-Yuan Chang, Wei-Hsuan Lo-Ciganic, Thomas J. George, William R. Hogan, Yi Guo, Jiang Bian, Yonghui Wu
2024	J	`jnl`	Improving Generalizability of Extracting Social Determinants of Health Using Large Language Models through Prompt-tuning. CoRR Cheng Peng, Zehao Yu, Kaleb E. Smith, Wei-Hsuan Lo-Ciganic, Jiang Bian, Yonghui Wu
2024	J	`jnl`	MAP: Low-compute Model Merging with Amortized Pareto Fronts via Quadratic Approximation. CoRR Lu Li, Tianyu Zhang, Zhiqi Bu, Suyuchen Wang, Huan He, Jie Fu, Yonghui Wu, Jiang Bian, Yong Chen, Yoshua Bengio
2024	J	`jnl`	Me LLaMA: Foundation Large Language Models for Medical Applications. CoRR Qianqian Xie, Qingyu Chen, Aokun Chen, Cheng Peng, Yan Hu, Fongci Lin, Xueqing Peng, Jimin Huang, Jeffrey Zhang, Vipina Kuttichi Keloth, Xingyu Zhou, Huan He, Lucila Ohno-Machado, Yonghui Wu, Hua Xu, Jiang Bian
2024	J	`jnl`	Model tuning or prompt Tuning? a study of large language models for clinical concept and relation extraction. J. Biomed. Informatics Cheng Peng, Xi Yang, Kaleb E. Smith, Zehao Yu, Aokun Chen, Jiang Bian, Yonghui Wu
2024	J	`jnl`	Narrative Feature or Structured Feature? A Study of Large Language Models to Identify Cancer Patients at Risk of Heart Failure. CoRR Ziyi Chen, Mengyuan Zhang, Mustafa Mohammed Ahmed, Yi Guo, Thomas J. George, Jiang Bian, Yonghui Wu
2024	—	`conf`	UF-HOBI at "Discharge Me!": A Hybrid Solution for Discharge Summary Generation Through Prompt-based Tuning of GatorTronGPT Models. BioNLP@ACL Mengxian Lyu, Cheng Peng, Daniel Paredes, Ziyi Chen, Aokun Chen, Jiang Bian, Yonghui Wu
2024	J	`jnl`	UF-HOBI at "Discharge Me!": A Hybrid Solution for Discharge Summary Generation Through Prompt-based Tuning of GatorTronGPT Models. CoRR Mengxian Lyu, Cheng Peng, Daniel Paredes, Ziyi Chen, Aokun Chen, Jiang Bian, Yonghui Wu
2024	—	`conf`	Unveiling Fall Risk Factors: Nurse-Driven Corpus Development for Natural Language Processing. Nursing Informatics Ragnhildur I. Bjarnadottir, Yonghui Wu, Urszula Alina Snigurska, Sarah E. Ser, Laurence M. Solberg, Kimberly A. Martinez, Summer Bolin, Shannon E. Dwarica, Elizabeth Dunn, Laurie J. D. Duckworth, Xiwei Lou, Daniel Paredes, Zehao Yu, Robert J. Lucero
2024	J	`jnl`	Use of natural language processing to extract and classify papillary thyroid cancer features from surgical pathology reports. CoRR Ricardo Loor-Torres, Yuqi Wu, Esteban Cabezas, Mariana Borras, David Toro-Tobon, Mayra Durán, Misk Al Zahidy, Maria Mateo Chavez, Cristian Soto Jacome, Jungwei W. Fan, Naykky M. Singh Ospina, Yonghui Wu, Juan P. Brito
2023	J	`jnl`	A Study of Generative Large Language Model for Medical Research and Healthcare. CoRR Cheng Peng, Xi Yang, Aokun Chen, Kaleb E. Smith, Nima M. Pournejatian, Anthony B. Costa, Cheryl Martin, Mona G. Flores, Ying Zhang, Tanja Magoc, Gloria P. Lipori, Duane A. Mitchell, Naykky Singh Ospina, Mustafa M. Ahmed, William R. Hogan, Elizabeth Shenkman, Yi Guo, Jiang Bian, Yonghui Wu
2023	J	`jnl`	A study of generative large language model for medical research and healthcare. npj Digit. Medicine Cheng Peng, Xi Yang, Aokun Chen, Kaleb E. Smith, Nima M. Pournejatian, Anthony B. Costa, Cheryl Martin, Mona G. Flores, Ying Zhang, Tanja Magoc, Gloria P. Lipori, Duane A. Mitchell, Naykky Singh Ospina, Mustafa M. Ahmed, William R. Hogan, Elizabeth A. Shenkman, Yi Guo, Jiang Bian, Yonghui Wu
2023	J	`jnl`	Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer's disease and related dementias. Int. J. Medical Informatics Zhaoyi Chen, Hansi Zhang, Xi Yang, Songzi Wu, Xing He, Jie Xu, Jingchuan Guo, Mattia Prosperi, Fei Wang, Hua Xu, Yong Chen, Hui Hu, Steven DeKosky, Matthew Farrer, Yi Guo, Yonghui Wu, Jiang Bian
2023	J	`jnl`	Clinical Concept and Relation Extraction Using Prompt-based Machine Reading Comprehension. CoRR Cheng Peng, Xi Yang, Zehao Yu, Jiang Bian, William R. Hogan, Yonghui Wu
2023	J	`jnl`	Clinical concept and relation extraction using prompt-based machine reading comprehension. J. Am. Medical Informatics Assoc. Cheng Peng, Xi Yang, Zehao Yu, Jiang Bian, William R. Hogan, Yonghui Wu
2023	J	`jnl`	Contextualized Medication Information Extraction Using Transformer-based Deep Learning Architectures. CoRR Aokun Chen, Zehao Yu, Xi Yang, Yi Guo, Jiang Bian, Yonghui Wu
2023	J	`jnl`	Contextualized medication information extraction using Transformer-based deep learning architectures. J. Biomed. Informatics Aokun Chen, Zehao Yu, Xi Yang, Yi Guo, Jiang Bian, Yonghui Wu
2023	—	`conf`	Exploring the Effect of Eligibility Criteria on AD Severity and Severe Adverse Event in Eligible Patients. ICHI Aokun Chen, Qian Li, Elizabeth Shenkman, Yonghui Wu, Yi Guo, Jiang Bian
2023	J	`jnl`	Extracting Thyroid Nodules Characteristics from Ultrasound Reports Using Transformer-based Natural Language Processing Methods. CoRR Aman Pathak, Zehao Yu, Daniel Paredes, Elio Paul Monsour, Andrea Ortiz Rocha, Juan P. Brito, Naykky Singh Ospina, Yonghui Wu
2023	J	`jnl`	Generative Large Language Models Are All-purpose Text Analytics Engines: Text-to-text Learning Is All Your Need. CoRR Cheng Peng, Xi Yang, Aokun Chen, Zehao Yu, Kaleb E. Smith, Anthony B. Costa, Mona G. Flores, Jiang Bian, Yonghui Wu
2023	J	`jnl`	Identifying Symptoms of Delirium from Clinical Narratives Using Natural Language Processing. CoRR Aokun Chen, Daniel Paredes, Zehao Yu, Xiwei Lou, Roberta Brunson, Jamie N. Thomas, Kimberly A. Martinez, Robert J. Lucero, Tanja Magoc, Laurence M. Solberg, Urszula Alina Snigurska, Sarah E. Ser, Mattia Prosperi, Jiang Bian, Ragnhildur I. Bjarnadottir, Yonghui Wu
2023	J	`jnl`	Leveraging natural language processing to identify eligible lung cancer screening patients with the electronic health record. Int. J. Medical Informatics Siru Liu, Allison B. McCoy, Melinda C. Aldrich, Kim L. Sandler, Thomas J. Reese, Bryan D. Steitz, Jiang Bian, Yonghui Wu, Elise M. Russo, Adam Wright
2023	J	`jnl`	Model Tuning or Prompt Tuning? A Study of Large Language Models for Clinical Concept and Relation Extraction. CoRR Cheng Peng, Xi Yang, Kaleb E. Smith, Zehao Yu, Aokun Chen, Jiang Bian, Yonghui Wu
2023	—	`conf`	On the Impact of Cross-Domain Data on German Language Models. EMNLP (Findings) Amin Dada, Aokun Chen, Cheng Peng, Kaleb E. Smith, Ahmad Idrissi-Yaghir, Constantin Seibold, Jianning Li, Lars Heiliger, Christoph M. Friedrich, Daniel Truhn, Jan Egger, Jiang Bian, Jens Kleesiek, Yonghui Wu
2023	J	`jnl`	On the Impact of Cross-Domain Data on German Language Models. CoRR Amin Dada, Aokun Chen, Cheng Peng, Kaleb E. Smith, Ahmad Idrissi-Yaghir, Constantin Marc Seibold, Jianning Li, Lars Heiliger, Xi Yang, Christoph M. Friedrich, Daniel Truhn, Jan Egger, Jiang Bian, Jens Kleesiek, Yonghui Wu
2023	—	`conf`	Real-World Effectiveness of Lung Cancer Screening Using Deep Learning-Based Counterfactual Prediction. MedInfo Zheng Feng, Zhaoyi Chen, Yi Guo, Mattia Prosperi, Hiren J. Mehta, Dejana Braithwaite, Yonghui Wu, Jiang Bian
2023	J	`jnl`	The role of health system penetration rate in estimating the prevalence of type 1 diabetes in children and adolescents using electronic health records. J. Am. Medical Informatics Assoc. Piaopiao Li, Tianchen Lyu, Khalid Alkhuzam, Eliot Spector, William T. Donahoo, Sarah Bost, Yonghui Wu, William R. Hogan, Mattia Prosperi, Desmond A. Schatz, Mark A. Atkinson, Michael J. Haller, Elizabeth A. Shenkman, Yi Guo, Jiang Bian, Hui Shao
2022	—	`conf`	A Preliminary Study of Extracting Pulmonary Nodules and Nodule Characteristics from Radiology Reports Using Natural Language Processing. ICHI Shuang Yang, Xi Yang, Tianchen Lyu, Xing He, Dejana Braithwaite, Hiren J. Mehta, Yi Guo, Yonghui Wu, Jiang Bian
2022	J	`jnl`	A large language model for electronic health records. npj Digit. Medicine Xi Yang, Aokun Chen, Nima M. Pournejatian, Hoo Chang Shin, Kaleb E. Smith, Christopher Parisien, Colin Compas, Cheryl Martin, Anthony B. Costa, Mona G. Flores, Ying Zhang, Tanja Magoc, Christopher A. Harle, Gloria P. Lipori, Duane A. Mitchell, William R. Hogan, Elizabeth A. Shenkman, Jiang Bian, Yonghui Wu
2022	J	`jnl`	Biases in using social media data for public health surveillance: A scoping review. Int. J. Medical Informatics Yunpeng Zhao, Xing He, Zheng Feng, Sarah Bost, Mattia Prosperi, Yonghui Wu, Yi Guo, Jiang Bian
2022	J	`jnl`	GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records. CoRR Xi Yang, Nima M. Pournejatian, Hoo Chang Shin, Kaleb E. Smith, Christopher Parisien, Colin Compas, Cheryl Martin, Mona G. Flores, Ying Zhang, Tanja Magoc, Christopher A. Harle, Gloria P. Lipori, Duane A. Mitchell, William R. Hogan, Elizabeth A. Shenkman, Jiang Bian, Yonghui Wu
2022	—	`conf`	Identify Cancer Patients at Risk for Heart Failure using Electronic Health Record and Genetic Data. ICHI Zehao Yu, Xi Yang, Yiqing Chen, Ruogu Fang, William R. Hogan, Yan Gong, Yonghui Wu
2022	J	`jnl`	Identify diabetic retinopathy-related clinical concepts and their attributes using transformer-based natural language processing methods. BMC Medical Informatics Decis. Mak. Zehao Yu, Xi Yang, Gianna L. Sweeting, Yinghan Ma, Skylar E. Stolte, Ruogu Fang, Yonghui Wu
2022	J	`jnl`	SODA: A Natural Language Processing Package to Extract Social Determinants of Health for Cancer Studies. CoRR Zehao Yu, Xi Yang, Chong Dang, Prakash Adekkanattu, Braja Gopal Patra, Yifan Peng, Jyotishman Pathak, Debbie L. Wilson, Ching-Yuan Chang, Wei-Hsuan Lo-Ciganic, Thomas J. George, William R. Hogan, Yi Guo, Jiang Bian, Yonghui Wu
2021	Misc	`conf`	A Study of Social and Behavioral Determinants of Health in Lung Cancer Patients Using Transformers-based Natural Language Processing Models. AMIA Zehao Yu, Xi Yang, Chong Dang, Songzi Wu, Prakash Adekkanattu, Jyotishman Pathak, Thomas J. George, William R. Hogan, Yi Guo, Jiang Bian, Yonghui Wu
2021	J	`jnl`	A Study of Social and Behavioral Determinants of Health in Lung Cancer Patients Using Transformers-based Natural Language Processing Models. CoRR Zehao Yu, Xi Yang, Chong Dang, Songzi Wu, Prakash Adekkanattu, Jyotishman Pathak, Thomas J. George, William R. Hogan, Yi Guo, Jiang Bian, Yonghui Wu
2021	J	`jnl`	Clinical Relation Extraction Using Transformer-based Models. CoRR Xi Yang, Zehao Yu, Yi Guo, Jiang Bian, Yonghui Wu
2021	Misc	`conf`	Data and Model Biases in Social Media Analyses: A Case Study of COVID-19 Tweets. AMIA Yunpeng Zhao, Pengfei Yin, Yongqiu Li, Xing He, Jingcheng Du, Cui Tao, Yi Guo, Mattia Prosperi, Pierangelo Veltri, Xi Yang, Yonghui Wu, Jiang Bian
2021	Misc	`conf`	Developing an Ontology for Social and Behavioral Determinants of Health. AMIA Hansi Zhang, Xi Yang, Thomas J. George, William R. Hogan, Jiang Bian, Yonghui Wu
2021	J	`jnl`	Extracting social determinants of health from electronic health records using natural language processing: a systematic review. J. Am. Medical Informatics Assoc. Braja Gopal Patra, Mohit Manoj Sharma, Veer Vekaria, Prakash Adekkanattu, Olga V. Patterson, Benjamin S. Glicksberg, Lauren A. Lepow, Euijung Ryu, Joanna M. Biernacka, Al'ona Furmanchuk, Thomas J. George, William R. Hogan, Yonghui Wu, Xi Yang, Jiang Bian, Myrna Weissman, Priya Wickramaratne, J. John Mann, Mark Olfson, Thomas R. Campion Jr., Mark G. Weiner, Jyotishman Pathak
2021	—	`conf`	Identify Diabetic Retinopathy-related Clinical Concepts Using Transformer-based Natural Language Processing Methods. ICHI Zehao Yu, Xi Yang, Gianna L. Sweeting, Yinghan Ma, Skylar E. Stolte, Ruogu Fang, Yonghui Wu
2021	—	`conf`	Transformer-based named entity recognition for parsing clinical trial eligibility criteria. BCB Shubo Tian, Arslan Erdengasileng, Xi Yang, Yi Guo, Yonghui Wu, Jinfeng Zhang, Jiang Bian, Zhe He
2020	—	`conf`	A Natural Language Processing Tool to Extract Quantitative Smoking Status from Clinical Narratives. ICHI Xi Yang, Hanyuan Yang, Tianchen Lyu, Shuang Yang, Yi Guo, Jiang Bian, Hua Xu, Yonghui Wu
2020	J	`jnl`	Assessing mental health signals among sexual and gender minorities using Twitter data. Health Informatics J. Yunpeng Zhao, Yi Guo, Xing He, Yonghui Wu, Xi Yang, Mattia Prosperi, Yanghua Jin, Jiang Bian
2020	J	`jnl`	Assessing the practice of data quality evaluation in a national clinical data research network through a systematic scoping review in the era of real-world data. J. Am. Medical Informatics Assoc. Jiang Bian, Tianchen Lyu, Alexander T. Loiacono, Tonatiuh Mendoza Viramontes, Gloria P. Lipori, Yi Guo, Yonghui Wu, Mattia Prosperi, Thomas J. George, Christopher A. Harle, Elizabeth A. Shenkman, William R. Hogan
2020	J	`jnl`	Clinical concept extraction using transformers. J. Am. Medical Informatics Assoc. Xi Yang, Jiang Bian, William R. Hogan, Yonghui Wu
2020	Misc	`conf`	Developing and Validating a Computable Phenotype for the Identification of Transgender and Gender Nonconforming Individuals and Subgroups. AMIA Yi Guo, Xing He, Tianchen Lyu, Hansi Zhang, Yonghui Wu, Xi Yang, Zhaoyi Chen, Merry J. Markham, François Modave, Mengjun Xie, William R. Hogan, Christopher A. Harle, Elizabeth Shenkman, Jiang Bian
2020	J	`jnl`	Identification of important factors in an inpatient fall risk prediction model to improve the quality of care using EHR and electronic administrative data: A machine-learning approach. Int. J. Medical Informatics David S. Lindberg, Mattia Prosperi, Ragnhildur I. Bjarnadottir, Jaime Thomas, Marsha Crane, Zhaoyi Chen, Kristen Shear, Laurence M. Solberg, Urszula Alina Snigurska, Yonghui Wu, Yunpeng Xia, Robert J. Lucero
2020	J	`jnl`	Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting. J. Am. Medical Informatics Assoc. Xi Yang, Jiang Bian, Ruogu Fang, Ragnhildur I. Bjarnadottir, William R. Hogan, Yonghui Wu
2019	—	`conf`	A Study of Deep Learning Methods for De-identification of Clinical Notes at Cross Institute Settings. ICHI Xi Yang, Tianchen Lyu, Chih-Yin Lee, Jiang Bian, William R. Hogan, Yonghui Wu
2019	J	`jnl`	A study of deep learning methods for de-identification of clinical notes in cross-institute settings. BMC Medical Informatics Decis. Mak. Xi Yang, Tianchen Lyu, Qian Li, Chih-Yin Lee, Jiang Bian, William R. Hogan, Yonghui Wu
2019	J	`jnl`	Applying a deep learning-based sequence labeling approach to detect attributes of medical concepts in clinical text. BMC Medical Informatics Decis. Mak. Jun Xu, Zhiheng Li, Qiang Wei, Yonghui Wu, Yang Xiang, Hee-Jin Lee, Yaoyun Zhang, Stephen Wu, Hua Xu
2019	—	`conf`	Detect Attributes of Medical Concepts via Sequence Labeling. ICHI Jun Xu, Zhiheng Li, Qiang Wei, Yonghui Wu, Yang Xiang, Hee-Jin Lee, Yaoyun Zhang, Stephen Wu, Hua Xu
2019	Misc	`conf`	Identifying Cancer Patients at Risk for Heart Failure Using Machine Learning Methods. AMIA Xi Yang, Yan Gong, Nida Waheed, Keith March, Jiang Bian, William R. Hogan, Yonghui Wu
2019	J	`jnl`	Identifying Cancer Patients at Risk for Heart Failure Using Machine Learning Methods. CoRR Xi Yang, Yan Gong, Nida Waheed, Keith March, Jiang Bian, William R. Hogan, Yonghui Wu
2019	J	`jnl`	Time-sensitive clinical concept embeddings learned from large electronic health records. BMC Medical Informatics Decis. Mak. Yang Xiang, Jun Xu, Yuqi Si, Zhiheng Li, Laila Rasmy, Yujia Zhou, Firat Tiryaki, Fang Li, Yaoyun Zhang, Yonghui Wu, Xiaoqian Jiang, W. Jim Zheng, Degui Zhi, Cui Tao, Hua Xu
2018	J	`jnl`	A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. J. Biomed. Informatics Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, W. Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi
2018	—	`conf`	Assessing Mental Health Signals Among Sexual and Gender Minorities using Twitter Data. ICHI Workshops Yunpeng Zhao, Yi Guo, Xing He, Jinhai Huo, Yonghui Wu, Xi Yang, Jiang Bian
2018	J	`jnl`	CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines. J. Am. Medical Informatics Assoc. Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu
2018	Misc	`conf`	Combine Factual Medical Knowledge and Distributed Word Representation to Improve Clinical Named Entity Recognition. AMIA Yonghui Wu, Xi Yang, Jiang Bian, Yi Guo, Hua Xu, William R. Hogan
2018	Misc	`conf`	Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials. AMIA Hansi Zhang, Zhe He, Xing He, Yi Guo, David R. Nelson, François Modave, Yonghui Wu, William R. Hogan, Mattia Prosperi, Jiang Bian
2018	—	`conf`	Detecting Medications and Adverse Drug Events in Clinical Notes Using Recurrent Neural Networks. Medication and Adverse Drug Event Detection Xi Yang, Jiang Bian, Yonghui Wu
2018	J	`jnl`	Extraction of BI-RADS findings from breast ultrasound reports in Chinese using deep learning approaches. Int. J. Medical Informatics Shumei Miao, Tingyu Xu, Yonghui Wu, Hui Xie, Jingqi Wang, Shenqi Jing, Yaoyun Zhang, Xiaoliang Zhang, Yinshuang Yang, Xin Zhang, Tao Shan, Li Wang, Hua Xu, Shui Wang, Yun Liu
2018	J	`jnl`	PIE: A prior knowledge guided integrated likelihood estimation method for bias reduction in association studies using electronic health records data. J. Am. Medical Informatics Assoc. Jing Huang, Rui Duan, Rebecca A. Hubbard, Yonghui Wu, Jason H. Moore, Hua Xu, Yong Chen
2017	—	`conf`	A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records. CRI Hee-Jin Lee, Min Jiang, Yonghui Wu, Christian Shaffer, John H. Cleator, Eitan Friedman, Joshua P. Lewis, Dan M. Roden, Joshua C. Denny, Hua Xu
2017	J	`jnl`	A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). J. Am. Medical Informatics Assoc. Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Lulu Wang, Carmelo Blanquicett, Ergin Soysal, Jun Xu, Hua Xu
2017	Misc	`conf`	CLAMP - A User-Centric Clinical Natural Language Processing Toolkit. AMIA Hua Xu, Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu
2017	Misc	`conf`	Clinical Named Entity Recognition Using Deep Learning Models. AMIA Yonghui Wu, Min Jiang, Jun Xu, Degui Zhi, Hua Xu
2017	—	`conf`	Comparing Cancer Information Needs for Consumers in the US and China. MedInfo Zongcheng Ji, Yaoyun Zhang, Jun Xu, Xiaoling Chen, Yonghui Wu, Hua Xu
2017	Misc	`conf`	Detecting Body Location Modifiers of Disorders in Clinical Texts via Sequence Labeling. AMIA Jun Xu, Yonghui Wu, Yaoyun Zhang, Hua Xu
2017	Misc	`conf`	Detecting Contradictory and Consistent Citations in Biomedical Literature. AMIA Jun Xu, Yonghui Wu, Yaoyun Zhang, Qiang Wei, Hua Xu
2017	Misc	`conf`	Evaluating Word Embeddings from Multiple Domains for Symptom Recognition in Psychiatric Notes. AMIA Yaoyun Zhang, Hee-Jin Lee, Yonghui Wu, Hua Xu
2016	Misc	`conf`	An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies. AMIA Rui Duan, Ming Cao, Yonghui Wu, Jing Huang, Joshua C. Denny, Hua Xu, Yong Chen
2016	J	`jnl`	CD-REST: a system for extracting chemical-induced disease relation in literature. Database J. Biol. Databases Curation Jun Xu, Yonghui Wu, Yaoyun Zhang, Jingqi Wang, Hee-Jin Lee, Hua Xu
2016	J	`jnl`	Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. Database J. Biol. Databases Curation Yaoyun Zhang, Jun Xu, Hui Chen, Jingqi Wang, Yonghui Wu, Manu Prakasam, Hua Xu
2016	J	`jnl`	Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov. J. Am. Medical Informatics Assoc. Jun Xu, Hee-Jin Lee, Jia Zeng, Yonghui Wu, Yaoyun Zhang, Liang-Chin Huang, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Trevor Cohen, Funda Meric-Bernstam, Elmer V. Bernstam, Hua Xu
2016	—	`conf`	UTHealth at SemEval-2016 Task 12: an End-to-End System for Temporal Information Extraction from Clinical Notes. SemEval@NAACL-HLT Hee-Jin Lee, Hua Xu, Jingqi Wang, Yaoyun Zhang, Sungrim Moon, Jun Xu, Yonghui Wu
2016	Misc	`conf`	What Can Neural Networks Learn from Unlabeled Clinical Narratives? AMIA Yonghui Wu, Jun Xu, Yaoyun Zhang, Hua Xu
2015	Misc	`conf`	A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text. AMIA Yonghui Wu, Jun Xu, Min Jiang, Yaoyun Zhang, Hua Xu
2015	J	`jnl`	A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature. J. Cheminformatics Buzhou Tang, Yudong Feng, Xiaolong Wang, Yonghui Wu, Yaoyun Zhang, Min Jiang, Jingqi Wang, Hua Xu
2015	Misc	`conf`	Citation Sentiment Analysis in Clinical Trial Papers. AMIA Jun Xu, Yaoyun Zhang, Yonghui Wu, Jingqi Wang, Xiao Dong, Hua Xu
2015	—	`conf`	Clinical Abbreviation Disambiguation Using Neural Word Embeddings. BioNLP@IJCNLP Yonghui Wu, Jun Xu, Yaoyun Zhang, Hua Xu
2015	Misc	`conf`	Clinical Language Annotation, Modeling, and Processing Toolkit (CLAMP) - a user-centric NLP system. AMIA Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Hua Xu
2015	J	`jnl`	Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput. Biol. Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica A. Bowton, Dan M. Roden, Joshua C. Denny, Melinda C. Aldrich, Hua Xu, Zhongming Zhao
2015	—	`conf`	Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network. MedInfo Yonghui Wu, Min Jiang, Jianbo Lei, Hua Xu
2015	Misc	`conf`	Recognizing Disjoint Clinical Concepts in Clinical Text Using Machine Learning-based Methods. AMIA Buzhou Tang, Qingcai Chen, Xiaolong Wang, Yonghui Wu, Yaoyun Zhang, Jingqi Wang, Hua Xu
2015	—	`conf`	UTH-CCB: The Participation of the SemEval 2015 Challenge - Task 14. SemEval@NAACL-HLT Jun Xu, Yaoyun Zhang, Jingqi Wang, Yonghui Wu, Min Jiang, Ergin Soysal, Hua Xu
2014	Misc	`conf`	Development of a Unified Computable Problem-Medication Knowledge base. AMIA Yonghui Wu, Adam Wright, Hua Xu, Allison B. McCoy, Dean F. Sittig
2014	Misc	`conf`	Domain Adaptation for Semantic Role Labeling of Clinical Text. AMIA Yaoyun Zhang, Buzhou Tang, Min Jiang, Jingqi Wang, Yonghui Wu, Hua Xu
2014	—	`conf`	UTH_CCB: A report for SemEval 2014 - Task 7 Analysis of Clinical Text. SemEval@COLING Yaoyun Zhang, Jingqi Wang, Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Hua Xu
2013	J	`jnl`	A hybrid system for temporal information extraction from clinical text. J. Am. Medical Informatics Assoc. Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Joshua C. Denny, Hua Xu
2013	—	`conf`	A prototype application for real-time recognition and disambiguation of clinical abbreviations. DTMBIO Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Min Song, Hua Xu
2013	—	`conf`	Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages. MedInfo Yonghui Wu, Jianbo Lei, Wei-Qi Wei, Buzhou Tang, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Kai Zheng, Hua Xu
2013	Misc	`conf`	Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries. AMIA Yonghui Wu, S. Trent Rosenbloom, Joshua C. Denny, Randolph A. Miller, Dario A. Giuse, Hua Xu
2013	—	`conf`	Clinical Acronym/Abbreviation Normalization using a Hybrid Approach. CLEF (Working Notes) Yonghui Wu, Buzhou Tang, Min Jiang, Sungrim Moon, Joshua C. Denny, Hua Xu
2013	—	`conf`	Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model. CLEF (Working Notes) Buzhou Tang, Yonghui Wu, Min Jiang, Joshua C. Denny, Hua Xu
2013	J	`jnl`	Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features. BMC Medical Informatics Decis. Mak. Buzhou Tang, Hongxin Cao, Yonghui Wu, Min Jiang, Hua Xu
2012	Misc	`conf`	A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. AMIA Yonghui Wu, Joshua C. Denny, Samuel Rosenbloom, Randolph A. Miller, Dario A. Giuse, Hua Xu
2012	J	`jnl`	A new clustering method for detecting rare senses of abbreviations in clinical notes. J. Biomed. Informatics Hua Xu, Yonghui Wu, Noemie Elhadad, Peter D. Stetson, Carol Friedman
2012	Misc	`conf`	Clinical Entity Recognition Using Structural Support Vector Machines. AMIA Buzhou Tang, Yonghui Wu, Min Jiang, Hua Xu
2012	—	`conf`	Clinical entity recognition using structural support vector machines with rich features. DTMBIO@CIKM Buzhou Tang, Hongxin Cao, Yonghui Wu, Min Jiang, Hua Xu
2012	J	`jnl`	DTome: a web-based tool for drug-target interactome construction. BMC Bioinform. Jingchun Sun, Yonghui Wu, Hua Xu, Zhongming Zhao
2012	—	`conf`	Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data. HISB Mei Liu, Michael E. Matheny, Yonghui Wu, Eugenia R. McPeek Hinz, Joshua C. Denny, Jonathan S. Schildcrout, Randolph A. Miller, Hua Xu
2012	J	`jnl`	Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J. Am. Medical Informatics Assoc. Mei Liu, Yonghui Wu, Yukun Chen, Jingchun Sun, Zhongming Zhao, Xue-wen Chen, Michael E. Matheny, Hua Xu
2012	Misc	`conf`	MedEx-UIMA - An Open-Source System for Medication Information Extraction from Clinical Text. AMIA Anushi Shah, Min Jiang, Yonghui Wu, Joshua C. Denny, Hua Xu
2012	Misc	`conf`	Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation. Pacific Symposium on Biocomputing Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, Hua Xu
2010	J	`jnl`	On-line Hot Topic Recommendation Using Tolerance Rough Set Based Topic Clustering. J. Comput. Yonghui Wu, Yuxin Ding, Xiaolong Wang, Jun Xu
2010	—	`conf`	Topic Detection by Topic Model Induced Distance Using Biased Initiation. AST/UCMA/ISA/ACN Yonghui Wu, Yuxin Ding, Xiaolong Wang, Jun Xu
2010	Misc	`conf`	Topic based automatic news recommendation using topic model and affinity propagation. ICMLC Yonghui Wu, Yuxin Ding, Xiaolong Wang, Jun Xu
2009	B	`conf`	STRank: A SiteRank Algorithm Using Semantic Relevance and Time Frequency. SMC Hongzhi Guo, Qingcai Chen, Xiaolong Wang, Zhiyong Wang, Yonghui Wu
2008	B	`conf`	Genre identification of Chinese finance text using machine learning method. SMC Jun Xu, Yuxin Ding, Xiaolong Wang, Yonghui Wu