Combining multiple evidence for gene symbol disambiguation. - Hua Xu 001; Jungwei Fan 001; Carol Friedman (BioNLP@ACL, 2007)

Using Distributional Analysis to Semantically Classify UMLS Concepts. - Jungwei Fan 001; Hua Xu 001; Carol Friedman (MedInfo, 2007)

Gene symbol disambiguation using knowledge-based profiles. - Hua Xu 001; Jungwei Fan 001; George Hripcsak; Eneida A. Mendonça; Marianthi Markatou; Carol Friedman (Bioinform., 2007)

Using contextual and lexical features to restructure and validate the classification of biomedical concepts. - Jungwei Fan 001; Hua Xu 001; Carol Friedman (BMC Bioinform., 2007)

A review of auditing methods applied to the content of controlled biomedical terminologies. - Xinxin Zhu; Jungwei Fan 001; David M. Baorto; Chunhua Weng; James J. Cimino (J. Biomed. Informatics, 2009)

An initial study of full parsing of clinical text using the Stanford Parser. - Hua Xu 001; Samir AbdelRahman; Min Jiang 007; Jungwei Fan 001; Yang Huang 008 (BIBM Workshops, 2011)

Disorder Concept Identification from Clinical Notes: an Experience with the ShARe/CLEF 2013 Challenge. - Jungwei Fan 001; Navdeep Sood; Yang Huang 008 (CLEF (Working Notes), 2013)

Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. - Jungwei Fan 001; Elly W. Yang; Min Jiang 007; Rashmi Prasad; Richard M. Loomis; Daniel Zisook; Joshua C. Denny; Hua Xu 001; Yang Huang 008 (J. Am. Medical Informatics Assoc., 2013)

Building a Treebank of hospital discharge summaries. - Yang Huang 008; Jungwei Fan 001; Elly W. Yang; Hua Xu 001 (AMIA, 2014)

Finding Difficult-to-Disambiguate Words: Towards an Efficient Workflow to Implement Word Sense Disambiguation. - Manabu Torii; Jungwei Fan 001; Daniel S. Zisook (ICHI, 2015)

Risk factor detection for heart disease by applying text analytics in electronic medical records. - Manabu Torii; Jungwei Fan 001; Weili Yang; Theodore Lee; Matthew T. Wiley; Daniel S. Zisook; Yang Huang 008 (J. Biomed. Informatics, 2015)

Parsing clinical text: how good are the state-of-the-art parsers? - Min Jiang 007; Yang Huang 008; Jungwei Fan 001; Buzhou Tang; Joshua C. Denny; Hua Xu 001 (BMC Medical Informatics Decis. Mak., 2015)

Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices. - Andrew Wen; Yanshan Wang; Vinod C. Kaggal; Sijia Liu 002; Hongfang Liu; Jungwei Fan 001 (IEEE BigData, 2019)

Adapting and evaluating a deep learning language model for clinical why-question answering. - Andrew Wen; Mohamed Y. Elwazir; Sungrim Moon; Jungwei Fan 001 (CoRR, 2019)

Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation. - Andrew Wen; Sunyang Fu; Sungrim Moon; Mohamed El Wazir; Andrew Rosenbaum; Vinod C. Kaggal; Sijia Liu 002; Sunghwan Sohn; Hongfang Liu; Jungwei Fan 001 (npj Digit. Medicine, 2019)

How You Ask Matters: The Effect of Paraphrastic Questions to BERT Performance on a Clinical SQuAD Dataset. - Sungrim Moon; Jungwei Fan 001 (ClinicalNLP@EMNLP, 2020)

Deep Semantic Embeddings and Clustering to Facilitate Identification of Transportation Barriers in Patient Portal Messages. - Ming Huang 006; Jungwei Fan 001 (AMIA, 2020)

Annotating Chronic Pain Episodes in EHR Text: Guideline Development and Corpus Analysis. - Luke A. Carlson; Molly M. Jeffery; Sunyang Fu; Huan He; Rozalina G. McCoy; Yanshan Wang; W. M. Hooten; Jennifer L. St. Sauver; Hongfang Liu; Jungwei Fan 001 (AMIA, 2020)

Big Impact from Small Data: Unsupervised Machine Learning Approaches for Chronic Pain Patient Subgrouping. - Luke A. Carlson; Jennifer St. Sauver; Sunyang Fu; Ahmad P. Tafti; Jungwei Fan 001; Molly M. Jeffery; Rozalina G. McCoy; Hongfang Liu; Yanshan Wang (AMIA, 2020)

A Perturbation Approach to Assessing BERT Robustness for Different Linguistic Aspects in Medical Question-Answering. - Mohamed Y. Elwazir; Andrew Wen; Sungrim Moon; Jungwei Fan 001 (AMIA, 2020)

A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. - Andrew Wen; Feichen Shen; Sungrim Moon; Hongfang Liu; Jungwei Fan 001 (CBMS, 2020)

A review of auditing techniques for the Unified Medical Language System. - Ling Zheng; Zhe He 001; Duo Helen Wei; Vipina Kuttichi Keloth; Jungwei Fan 001; Luke Lindemann; Xinxin Zhu; James J. Cimino; Yehoshua Perl (J. Am. Medical Informatics Assoc., 2020)

Patient Asynchronous Response to Coronavirus Disease 2019 (COVID-19): A Retrospective Analysis of Patient Portal Messages. - Ming Huang 006; Aditya Khurana; George M. Mastorakos; Andrew Wen; Huan He; Liwei Wang 010; Sijia Liu 002; Yanshan Wang; Julie E. Prigge; Brian Costello; Nilay D. Shah; Henry Ting; et al. (AMIA, 2021)

Disparity analysis of patient portal messaging use for COVID-19 in urban versus rural locality. - Ming Huang 006; Andrew Wen; Huan He; Liwei Wang 010; Sijia Liu 002; Yanshan Wang; Nansu Zong; Yue Yu; Julie E. Prigge; Brian Costello; Nilay D. Shah; Henry Ting; et al. (AMIA, 2021)

Development of a Clinical Question-Answering Corpus with Realistic Multi-Answer Challenges. - Sungrim Moon; Huan He; Jungwei Fan 001 (AMIA, 2021)

A Scoping Review of Informatics Research for Clinical Practice Variation. - Sunghwan Sohn; Sungrim Moon; Larry J. Prokop; Victor M. Montori; Jungwei Fan 001 (AMIA, 2021)

Identification of Transportation Barriers in Patient Portal Messages via Deep Semantic Embeddings and Clustering. - Ming Huang 006; Aditya Khurana; George M. Mastorakos; Jungwei Fan 001 (MedInfo, 2021)

The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records. - Sunyang Fu; Andrew Wen; Sandeep R. Pagali; Nansu Zong; Jennifer St Sauver; Sunghwan Sohn; Jungwei Fan 001; Hongfang Liu (MedInfo, 2021)

An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. - Andrew Wen; Liwei Wang 010; Huan He; Sijia Liu 002; Sunyang Fu; Sunghwan Sohn; Jacob A. Kugel; Vinod C. Kaggal; Ming Huang 006; Yanshan Wang; Feichen Shen; Jungwei Fan 001; et al. (J. Biomed. Informatics, 2021)

Quality Assessment of Functional Status Documentation in EHR Across Institutions. - Sunyang Fu; Maria Vassilaki; Omar A. Ibrahim; Ronald C. Petersen; Jennifer St. Sauver; Liwei Wang 010; Jungwei Fan 001; Hongfang Liu; Sunghwan Sohn (AMIA, 2022)

Effects of Information Masking in the Task-Specific Finetuning of a Transformers-Based Clinical Question-Answering Framework. - Sungrim Moon; Huan He; Jungwei Fan 001 (ICHI, 2022)

Mining Transportation Issues from Patient Portal Messages. - Nan Wang; Ming Huang 006; Jungwei Fan 001 (ICHI, 2022)

RxWhyQA: a clinical question-answering dataset with the challenge of multi-answer questions. - Sungrim Moon; Huan He; Hongfang Liu; Jungwei Fan 001 (CoRR, 2022)

Quality assessment of functional status documentation in EHRs across different healthcare institutions. - Sunyang Fu; Maria Vassilaki; Omar A. Ibrahim; Ronald C. Petersen; Sandeep R. Pagali; Jennifer St Sauver; Sungrim Moon; Liwei Wang 010; Jungwei Fan 001; Hongfang Liu; Sunghwan Sohn (Frontiers Digit. Health, 2022)

Classification of Patient Portal Messages with BERT-based Language Models. - Yang Ren; Dezhi Wu; Aditya Khurana; George M. Mastorakos; Sunyang Fu; Nansu Zong; Jungwei Fan 001; Hongfang Liu; Ming Huang 006 (ICHI, 2023)

Retrospective content analysis of consumer product reviews related to chronic pain. - Jungwei Fan 001; Wanjing Wang; Ming Huang 006; Hongfang Liu; W. M. Hooten (Frontiers Digit. Health, 2023)

Use of natural language processing to extract and classify papillary thyroid cancer features from surgical pathology reports. - 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 001; Naykky M. Singh Ospina; Yonghui Wu; et al. (CoRR, 2024)

Explainable Diagnosis Prediction through Neuro-Symbolic Integration. - Qiuhao Lu; Rui Li; Elham Sagheb; Andrew Wen; Jinlian Wang; Liwei Wang 010; Jungwei W. Fan 001; Hongfang Liu (CoRR, 2024)

Environment Scan of Generative AI Infrastructure for Clinical and Translational Science. - Betina Idnay; Zihan Xu; William G. Adams; Mohammad Adibuzzaman; Nicholas R. Anderson 001; Neil Bahroos; Douglas S. Bell; Cody Bumgardner; Thomas R. Campion Jr.; Victor M. Castro; James J. Cimino; I. Glenn Cohen; et al. (CoRR, 2024)

Automatic uncovering of patient primary concerns in portal messages using a fusion framework of pretrained language models. - Yang Ren; Yuqi Wu; Jungwei W. Fan 001; Aditya Khurana; Sunyang Fu; Dezhi Wu; Hongfang Liu; Ming Huang 006 (J. Am. Medical Informatics Assoc., 2024)

FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. - Sunyang Fu; Heling Jia; Maria Vassilaki; Vipina Kuttichi Keloth; Yifang Dang; Yujia Zhou 003; Muskan Garg; Ronald C. Petersen; Jennifer St Sauver; Sungrim Moon; Liwei Wang 010; Andrew Wen; et al. (J. Biomed. Informatics, 2024)

Developing and sustaining inclusive language in biomedical informatics communications: an AMIA Board of Directors endorsed paper on the Inclusive Language and Context Style Guidelines. - Oliver J. Bear Don't Walk IV; Shefali Haldar; Duo Helen Wei; Hu Huang 004; Rebecca L. Rivera; Jungwei W. Fan 001; Vipina Kuttichi Keloth; Tiffany I. Leung; Pooja M. Desai; Diane M. Korngiebel; Lisa Grossman Liu; Adrienne Pichon; et al. (J. Am. Medical Informatics Assoc., 2025)

Social determinants of health extraction from clinical notes across institutions using large language models. - Vipina Kuttichi Keloth; Salih Selek; Qingyu Chen 001; Christopher Gilman; Sunyang Fu; Yifang Dang; Xinghan Chen; Xinyue Hu 002; Yujia Zhou 003; Huan He; Jungwei W. Fan 001; Karen Wang; et al. (npj Digit. Medicine, 2025)