Aligned-Layer Text Search in Clinical Notes. - Stephen T. Wu; Andrew Wen; Yanshan Wang; Sijia Liu 002; Hongfang Liu (MedInfo, 2017)

Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP. - Na Hong; Andrew Wen; Majid Rastegar-Mojarad; Sunghwan Sohn; Hongfang Liu; Guoqian Jiang (AMIA, 2018)

Developing a RadLex-based Name Entity Recognition Tool for Mining Free-Text Radiology Reports. - Shintaro Tsuji; Andrew Wen; Guoqian Jiang (AMIA, 2018)

EMIRS: An Electronic Medical Information Retrieval System by Leveraging both Structured and Unstructured Electronic Health Records. - Yanshan Wang; Andrew Wen; Sijia Liu 002; Hongfang Liu (AMIA, 2018)

Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome. - Su-Yuan Peng; Yadan Fan; Liwei Wang 010; Andrew Wen; Xusheng Liu; Hongfang Liu; Feichen Shen (BIBM, 2018)

Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. - Feichen Shen; Sijia Liu 002; Yanshan Wang; Liwei Wang 010; Andrew Wen; Andrew H. Limper; Hongfang Liu (ICHI Workshops, 2018)

MayoNLPTeam at the TREC 2018 Precision Medicine Track: Simple Information Retrieval Approach Is the Best. - Yanshan Wang; Andrew Wen; Sijia Liu 002; Hongfang Liu (TREC, 2018)

Clinical Use of an Information Retrieval Framework for Cohort Discovery from Electronic Health Records. - Yanshan Wang; Andrew Wen; Sijia Liu 002; Jennifer L. St. Sauver; Adil E. Bharucha; Chunhua Weng; Hongfang Liu (AMIA, 2019)

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)

CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model. - Sijia Liu 002; Yanshan Wang; Andrew Wen; Liwei Wang 010; Na Hong; Feichen Shen; Steven Bedrick; William R. Hersh; Hongfang Liu (CoRR, 2019)

Cross-lingual Data Transformation and Combination for Text Classification. - Jun Jiang; Shumao Pang; Xia Zhao; Liwei Wang 010; Andrew Wen; Hongfang Liu; Qianjin Feng (CoRR, 2019)

Development of Clinical Concept Extraction Applications: A Methodology Review. - Sunyang Fu; David Chen 003; Sijia Liu 002; Sungrim Moon; Kevin J. Peterson; Feichen Shen; Yanshan Wang; Liwei Wang 010; Andrew Wen; Yiqing Zhao; Sunghwan Sohn; Hongfang Liu (CoRR, 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)

Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. - Na Hong; Andrew Wen; Daniel J. Stone; Shintaro Tsuji; Paul R. Kingsbury; Luke V. Rasmussen; Jennifer A. Pacheco; Prakash Adekkanattu; Fei Wang 001; Yuan Luo 001; Jyotishman Pathak; Hongfang Liu; et al. (J. Biomed. Informatics, 2019)

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. - Feichen Shen; Suyuan Peng; Yadan Fan; Andrew Wen; Sijia Liu 002; Yanshan Wang; Liwei Wang 010; Hongfang Liu (J. Biomed. Informatics, 2019)

ADEpedia-on-OHDSI: A next generation pharmacovigilance signal detection platform using the OHDSI common data model. - Yue Yu; Kathryn J. Ruddy; Na Hong; Shintaro Tsuji; Andrew Wen; Nilay D. Shah; Guoqian Jiang (J. Biomed. Informatics, 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)

Predicting Section Location of Clinical Sentences using BERT Encoder - A Pilot Study. - Sijia Liu 002; Sunyang Fu; Sungrim Moon; Andrew Wen; Hongfang Liu (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)

Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. - Andrew Wen; Sunyang Fu; Feichen Shen; Hongfang Liu (AMIA, 2020)

Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System. - Feichen Shen; Andrew Wen; Hongfang Liu (CBMS, 2020)

Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings. - Feichen Shen; Andrew Wen; Hongfang Liu (CBMS, 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 Query Taxonomy Describes Performance of Patient-Level Retrieval from Electronic Health Record Data. - Steve Chamberlin; Steven Bedrick; Aaron M. Cohen; Yanshan Wang; Andrew Wen; Sijia Liu 002; Hongfang Liu; William R. Hersh (HSDM@WSDM, 2020)

Clinical concept extraction: A methodology review. - Sunyang Fu; David Chen 003; Huan He; Sijia Liu 002; Sungrim Moon; Kevin J. Peterson; Feichen Shen; Liwei Wang 010; Yanshan Wang; Andrew Wen; Yiqing Zhao; Sunghwan Sohn; et al. (J. Biomed. Informatics, 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)

COVID-19 Dashboard: Visual Exploration of the Regional Pandemic Trend. - Huan He; Liwei Wang 010; Andrew Wen; Ming Huang 006; Yanshan Wang; Hongfang Liu (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)

FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. - Daniel J. Stone; Sijia Liu 002; Yuan Luo 001; Andrew Wen; Nansu Zong; Luke V. Rasmussen; Prakash Adekkanattu; Pascal S. Brandt; Jennifer A. Pacheco; Fei Wang 001; Cui Tao; Jyotishman Pathak; et al. (AMIA, 2021)

On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. - Andrew Wen; Luke V. Rasmussen; Daniel J. Stone; Sijia Liu 002; Prakash Adekkanattu; Pascal S. Brandt; Jennifer A. Pacheco; Yuan Luo 001; Fei Wang 001; Jyotishman Pathak; Hongfang Liu; Guoqian Jiang (AMIA, 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)

Drug-target prediction utilizing heterogeneous bio-linked network embeddings. - Nansu Zong; Rachael Sze Nga Wong; Yue Yu; Andrew Wen; Ming Huang 006; Ning Li (Briefings Bioinform., 2021)

Comparisons of Graph Neural Networks on Cancer Classification Leveraging a Joint of Phenotypic and Genetic Features. - David Oniani; Chen Wang 001; Yiqing Zhao; Andrew Wen; Hongfang Liu; Feichen Shen (CoRR, 2021)

Leveraging a Joint of Phenotypic and Genetic Features on Cancer Patient Subgrouping. - David Oniani; Chen Wang 001; Yiqing Zhao; Andrew Wen; Hongfang Liu; Feichen Shen (CoRR, 2021)

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). - Sijia Liu 002; Andrew Wen; Liwei Wang 010; Huan He; Sunyang Fu; Robert T. Miller; Andrew E. Williams; Daniel R. Harris; Ramakanth Kavuluru; Mei Liu; Noor Abu-El-Rub; Rui Zhang 028; et al. (CoRR, 2021)

Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. - Nansu Zong; Daniel J. Stone; Deepak K. Sharma; Andrew Wen; Chen Wang 001; Yue Yu; Ming Huang 006; Sijia Liu 002; Hongfang Liu; Qian Shi; Guoqian Jiang (Int. J. Medical Informatics, 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)

Towards User-centered Corpus Development: Lessons Learnt from Designing and Developing MedTator. - Huan He; Sunyang Fu; Liwei Wang 010; Andrew Wen; Sijia Liu 002; Sungrim Moon; Kurt Miller; Hongfang Liu (AMIA, 2022)

MedTator: A Serverless Web-based Tool for Corpus Annotation. - Huan He; Sunyang Fu; Liwei Wang 010; Andrew Wen; Sijia Liu 002; Hongfang Liu (ICHI, 2022)

Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing. - Liwei Wang 010; Sunyang Fu; Andrew Wen; Xiaoyang Ruan; Huan He; Sijia Liu 002; Sungrim Moon; Michelle Mai; Irbaz Bin Riaz; Nan Wang; Ping Yang; Hua Xu 001; et al. (ICHI, 2022)

BETA: a comprehensive benchmark for computational drug-target prediction. - Nansu Zong; Ning Li; Andrew Wen; Victoria Ngo; Yue Yu; Ming Huang 006; Shaika Chowdhury; Chao Jiang 002; Sunyang Fu; Richard Weinshilboum; Guoqian Jiang; Lawrence Hunter; et al. (Briefings Bioinform., 2022)

MedTator: a serverless annotation tool for corpus development. - Huan He; Sunyang Fu; Liwei Wang 010; Sijia Liu 002; Andrew Wen; Hongfang Liu (Bioinform., 2022)

A hybrid model to identify fall occurrence from electronic health records. - Sunyang Fu; Bjoerg Thorsteinsdottir; Xin Zhang; Guilherme S. Lopes; Sandeep R. Pagali; Nathan K. LeBrasseur; Andrew Wen; Hongfang Liu; Walter A. Rocca; Janet E. Olson; Jennifer St. Sauver; Sunghwan Sohn (Int. J. Medical Informatics, 2022)

Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration. - Yue Yu; Nansu Zong; Andrew Wen; Sijia Liu 002; Daniel J. Stone; David Knaack; Alanna M. Chamberlain; Emily R. Pfaff; Davera Gabriel; Christopher G. Chute; Nilay Shah; Guoqian Jiang (J. Biomed. Informatics, 2022)

Computational drug repurposing based on electronic health records: a scoping review. - Nansu Zong; Andrew Wen; Sungrim Moon; Sunyang Fu; Liwei Wang 010; Yiqing Zhao; Yue Yu; Ming Huang 006; Yanshan Wang; Gang Zheng; Michelle M. Mielke; James R. Cerhan; et al. (npj Digit. Medicine, 2022)

MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks. - Rui Li; Andrew Wen; Jing Gao 004; Hongfang Liu (BCB, 2023)

The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era. - Andrew Wen; Huan He; Sunyang Fu; Sijia Liu 002; Kurt Miller; Liwei Wang 010; Kirk E. Roberts; Steven Bedrick; William R. Hersh; Hongfang Liu (npj Digit. Medicine, 2023)

An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). - Sijia Liu 002; Andrew Wen; Liwei Wang 010; Huan He; Sunyang Fu; Robert T. Miller; Andrew E. Williams; Daniel R. Harris; Ramakanth Kavuluru; Mei Liu; Noor Abu-El-Rub; Dalton Schutte; et al. (J. Am. Medical Informatics Assoc., 2023)

Large Language Models Struggle in Token-Level Clinical Named Entity Recognition. - Qiuhao Lu; Rui Li; Andrew Wen; Jinlian Wang; Liwei Wang 010; Hongfang Liu (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)

Stratifying heart failure patients with graph neural network and transformer using Electronic Health Records to optimize drug response prediction. - Shaika Chowdhury; Yongbin Chen; Pengyang Li; Sivaraman Rajaganapathy; Andrew Wen; Xiao Ma 019; Qiying Dai; Yue Yu; Sunyang Fu; Xiaoqian Jiang; Zhe He 001; Sunghwan Sohn; et al. (J. Am. Medical Informatics Assoc., 2024)

A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction. - Sunyang Fu; Liwei Wang 010; Huan He; Andrew Wen; Nansu Zong; Anamika Kumari; Feifan Liu; Sicheng Zhou; Rui Zhang 028; Chenyu Li; Yanshan Wang; Jennifer St Sauver; et al. (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)

ReasonerRank: Redefining Language Model Evaluation with Ground-Truth-Free Ranking Frameworks. - Jiamu Zhang; Jiayi Yuan 001; Andrew Wen; Hoang Anh Duy Le; Yu-Neng Chuang; Soo-Hyun Choi; Rui Chen 012; Xia Hu 001 (ACL (Findings), 2025)

Dynamic few-shot prompting for clinical note section classification using lightweight, open-source large language models. - Kurt Miller; Steven Bedrick; Qiuhao Lu; Andrew Wen; William R. Hersh; Kirk Roberts; Hongfang Liu (J. Am. Medical Informatics Assoc., 2025)

A scoping review of OMOP CDM adoption for cancer research using real world data. - Liwei Wang 010; Andrew Wen; Sunyang Fu; Xiaoyang Ruan; Ming Huang 006; Rui Li; Qiuhao Lu; Heather Lyu; Andrew E. Williams; Hongfang Liu (npj Digit. Medicine, 2025)

Stop Overthinking: A Survey on Efficient Reasoning for Large Language Models. - Yang Sui; Yu-Neng Chuang; Guanchu Wang; Jiamu Zhang; Tianyi Zhang; Jiayi Yuan 001; Hongyi Liu; Andrew Wen; Shaochen Zhong; Na Zou 001; Hanjie Chen; Xia Hu 001 (Trans. Mach. Learn. Res., 2025)

The Science of Evaluating Foundation Models. - Jiayi Yuan 001; Jiamu Zhang; Andrew Wen; Xia Hu 001 (CoRR, 2025)

Stop Overthinking: A Survey on Efficient Reasoning for Large Language Models. - Yang Sui; Yu-Neng Chuang; Guanchu Wang; Jiamu Zhang; Tianyi Zhang; Jiayi Yuan 001; Hongyi Liu; Andrew Wen; Shaochen Zhong; Hanjie Chen; Xia Ben Hu (CoRR, 2025)

Multi-Label Classification with Generative AI Models in Healthcare: A Case Study of Suicidality and Risk Factors. - Ming Huang 006; Zehan Li; Yan Hu; Wanjing Wang; Andrew Wen; Scott Lane; Salih Selek; Lokesh Shahani; Rodrigo Machado-Vieira; Jair Soares; Hua Xu 001; Hongfang Liu (CoRR, 2025)