Combine Factual Medical Knowledge and Distributed Word Representation to Improve Clinical Named Entity Recognition. - Yonghui Wu; Xi Yang 015; Jiang Bian 001; Yi Guo 005; Hua Xu 001; William R. Hogan (AMIA, 2018)

Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. - Xing He 003; Rui Zhang 028; Rubina F. Rizvi; Jake Vasilakes; Xi Yang 015; Yi Guo 005; Zhe He 001; Mattia Prosperi; Jiang Bian 001 (BIBM, 2018)

Assessing Mental Health Signals Among Sexual and Gender Minorities using Twitter Data. - Yunpeng Zhao; Yi Guo 005; Xing He 003; Jinhai Huo; Yonghui Wu; Xi Yang 015; Jiang Bian 001 (ICHI Workshops, 2018)

Detecting Medications and Adverse Drug Events in Clinical Notes Using Recurrent Neural Networks. - Xi Yang 015; Jiang Bian 001; Yonghui Wu (Medication and Adverse Drug Event Detection, 2018)

OC-2-KB: integrating crowdsourcing into an obesity and cancer knowledge base curation system. - Juan Antonio Lossio-Ventura; William R. Hogan; François Modave; Yi Guo 005; Zhe He 001; Xi Yang 015; Hansi Zhang; Jiang Bian 001 (BMC Medical Informatics Decis. Mak., 2018)

Identifying Cancer Patients at Risk for Heart Failure Using Machine Learning Methods. - Xi Yang 015; Yan Gong; Nida Waheed; Keith March; Jiang Bian 001; William R. Hogan; Yonghui Wu (AMIA, 2019)

STAT: A Web-based Semantic Text Annotation Tool to Assist Building Mental Health Knowledge Base. - Xing He 003; Hansi Zhang; Xi Yang 015; Yi Guo 005; Jiang Bian 001 (ICHI, 2019)

A Study of Deep Learning Methods for De-identification of Clinical Notes at Cross Institute Settings. - Xi Yang 015; Tianchen Lyu; Chih-Yin Lee; Jiang Bian 001; William R. Hogan; Yonghui Wu (ICHI, 2019)

ALOHA: developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design. - Xing He 003; Rui Zhang 028; Rubina F. Rizvi; Jake Vasilakes; Xi Yang 015; Yi Guo 005; Zhe He 001; Mattia Prosperi; Jinhai Huo; Jordan Alpert; Jiang Bian 001 (BMC Medical Informatics Decis. Mak., 2019)

A study of deep learning methods for de-identification of clinical notes in cross-institute settings. - Xi Yang 015; Tianchen Lyu; Qian Li 034; Chih-Yin Lee; Jiang Bian 001; William R. Hogan; Yonghui Wu (BMC Medical Informatics Decis. Mak., 2019)

Developing and Validating a Computable Phenotype for the Identification of Transgender and Gender Nonconforming Individuals and Subgroups. - Yi Guo 005; Xing He 003; Tianchen Lyu; Hansi Zhang; Yonghui Wu; Xi Yang 015; Zhaoyi Chen; Merry J. Markham; François Modave; Mengjun Xie; William R. Hogan; Christopher A. Harle; et al. (AMIA, 2020)

A Natural Language Processing Tool to Extract Quantitative Smoking Status from Clinical Narratives. - Xi Yang 015; Hanyuan Yang; Tianchen Lyu; Shuang Yang; Yi Guo 005; Jiang Bian 001; Hua Xu 001; Yonghui Wu (ICHI, 2020)

Assessing mental health signals among sexual and gender minorities using Twitter data. - Yunpeng Zhao; Yi Guo 005; Xing He 003; Yonghui Wu; Xi Yang 015; Mattia Prosperi; Yanghua Jin; Jiang Bian 001 (Health Informatics J., 2020)

Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting. - Xi Yang 015; Jiang Bian 001; Ruogu Fang; Ragnhildur I. Bjarnadottir; William R. Hogan; Yonghui Wu (J. Am. Medical Informatics Assoc., 2020)

Clinical concept extraction using transformers. - Xi Yang 015; Jiang Bian 001; William R. Hogan; Yonghui Wu (J. Am. Medical Informatics Assoc., 2020)

A Study of Social and Behavioral Determinants of Health in Lung Cancer Patients Using Transformers-based Natural Language Processing Models. - Zehao Yu 001; Xi Yang 015; Chong Dang; Songzi Wu; Prakash Adekkanattu; Jyotishman Pathak; Thomas J. George; William R. Hogan; Yi Guo 005; Jiang Bian 001; Yonghui Wu (AMIA, 2021)

Developing an Ontology for Social and Behavioral Determinants of Health. - Hansi Zhang; Xi Yang 015; Thomas J. George; William R. Hogan; Jiang Bian 001; Yonghui Wu (AMIA, 2021)

Data and Model Biases in Social Media Analyses: A Case Study of COVID-19 Tweets. - Yunpeng Zhao; Pengfei Yin; Yongqiu Li; Xing He 003; Jingcheng Du; Cui Tao; Yi Guo 005; Mattia Prosperi; Pierangelo Veltri; Xi Yang 015; Yonghui Wu; Jiang Bian 001 (AMIA, 2021)

Transformer-based named entity recognition for parsing clinical trial eligibility criteria. - Shubo Tian; Arslan Erdengasileng; Xi Yang 015; Yi Guo 005; Yonghui Wu; Jinfeng Zhang; Jiang Bian 001; Zhe He 001 (BCB, 2021)

Identify Diabetic Retinopathy-related Clinical Concepts Using Transformer-based Natural Language Processing Methods. - Zehao Yu 001; Xi Yang 015; Gianna L. Sweeting; Yinghan Ma; Skylar E. Stolte; Ruogu Fang; Yonghui Wu (ICHI, 2021)

Clinical Relation Extraction Using Transformer-based Models. - Xi Yang 015; Zehao Yu 001; Yi Guo 005; Jiang Bian 001; Yonghui Wu (CoRR, 2021)

Extracting social determinants of health from electronic health records using natural language processing: a systematic review. - 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; et al. (J. Am. Medical Informatics Assoc., 2021)

A Preliminary Study of Extracting Pulmonary Nodules and Nodule Characteristics from Radiology Reports Using Natural Language Processing. - Shuang Yang; Xi Yang 015; Tianchen Lyu; Xing He 003; Dejana Braithwaite; Hiren J. Mehta; Yi Guo 005; Yonghui Wu; Jiang Bian 001 (ICHI, 2022)

Identify Cancer Patients at Risk for Heart Failure using Electronic Health Record and Genetic Data. - Zehao Yu 001; Xi Yang 015; Yiqing Chen; Ruogu Fang; William R. Hogan; Yan Gong; Yonghui Wu (ICHI, 2022)

GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records. - Xi Yang 015; Nima M. Pournejatian; Hoo Chang Shin; Kaleb E. Smith; Christopher Parisien; Colin Compas; Cheryl Martin 002; Mona G. Flores; Ying Zhang; Tanja Magoc; Christopher A. Harle; Gloria P. Lipori; et al. (CoRR, 2022)

SODA: A Natural Language Processing Package to Extract Social Determinants of Health for Cancer Studies. - Zehao Yu 001; Xi Yang 015; Chong Dang; Prakash Adekkanattu; Braja Gopal Patra; Yifan Peng 002; Jyotishman Pathak; Debbie L. Wilson; Ching-Yuan Chang; Wei-Hsuan Lo-Ciganic; Thomas J. George; William R. Hogan; et al. (CoRR, 2022)

Identify diabetic retinopathy-related clinical concepts and their attributes using transformer-based natural language processing methods. - Zehao Yu 001; Xi Yang 015; Gianna L. Sweeting; Yinghan Ma; Skylar E. Stolte; Ruogu Fang; Yonghui Wu (BMC Medical Informatics Decis. Mak., 2022)

A large language model for electronic health records. - Xi Yang 015; Aokun Chen; Nima M. Pournejatian; Hoo Chang Shin; Kaleb E. Smith; Christopher Parisien; Colin Compas; Cheryl Martin 002; Anthony B. Costa; Mona G. Flores; Ying Zhang; Tanja Magoc; et al. (npj Digit. Medicine, 2022)

On the Impact of Cross-Domain Data on German Language Models. - Amin Dada; Aokun Chen; Cheng Peng 009; Kaleb E. Smith; Ahmad Idrissi-Yaghir; Constantin Marc Seibold; Jianning Li 002; Lars Heiliger; Xi Yang 015; Christoph M. Friedrich; Daniel Truhn; Jan Egger; et al. (CoRR, 2023)

Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer's disease and related dementias. - Zhaoyi Chen; Hansi Zhang; Xi Yang 015; Songzi Wu; Xing He 003; Jie Xu 012; Jingchuan Guo; Mattia Prosperi; Fei Wang 001; Hua Xu 001; Yong Chen 016; Hui Hu; et al. (Int. J. Medical Informatics, 2023)

A study of generative large language model for medical research and healthcare. - Cheng Peng 009; Xi Yang 015; Aokun Chen; Kaleb E. Smith; Nima M. Pournejatian; Anthony B. Costa; Cheryl Martin 002; Mona G. Flores; Ying Zhang; Tanja Magoc; Gloria P. Lipori; Duane A. Mitchell; et al. (npj Digit. Medicine, 2023)

Contextualized medication information extraction using Transformer-based deep learning architectures. - Aokun Chen; Zehao Yu 001; Xi Yang 015; Yi Guo 005; Jiang Bian 001; Yonghui Wu (J. Biomed. Informatics, 2023)

Clinical concept and relation extraction using prompt-based machine reading comprehension. - Cheng Peng 009; Xi Yang 015; Zehao Yu 001; Jiang Bian 001; William R. Hogan; Yonghui Wu (J. Am. Medical Informatics Assoc., 2023)

Generative large language models are all-purpose text analytics engines: text-to-text learning is all your need. - Cheng Peng 009; Xi Yang 015; Aokun Chen; Zehao Yu 001; Kaleb E. Smith; Anthony B. Costa; Mona G. Flores; Jiang Bian 001; Yonghui Wu (J. Am. Medical Informatics Assoc., 2024)

Model tuning or prompt Tuning? a study of large language models for clinical concept and relation extraction. - Cheng Peng 009; Xi Yang 015; Kaleb E. Smith; Zehao Yu 001; Aokun Chen; Jiang Bian 001; Yonghui Wu (J. Biomed. Informatics, 2024)

Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias. - Zehao Yu 001; Cheng Peng 009; Xi Yang 015; Chong Dang; Prakash Adekkanattu; Braja Gopal Patra; Yifan Peng 002; Jyotishman Pathak; Debbie L. Wilson; Ching-Yuan Chang; Wei-Hsuan Lo-Ciganic; Thomas J. George; et al. (J. Biomed. Informatics, 2024)

Extracting Pulmonary Nodules and Nodule Characteristics from Radiology Reports of Lung Cancer Screening Patients Using Transformer Models. - Shuang Yang; Xi Yang 015; Tianchen Lyu; James L. Huang; Aokun Chen; Xing He 003; Dejana Braithwaite; Hiren J. Mehta; Yonghui Wu; Yi Guo 005; Jiang Bian 001 (J. Heal. Informatics Res., 2024)