Spot counting on fluorescence in situ hybridization in suspension images using Gaussian mixture model. - Sijia Liu 002; Ruhan Sa; Orla Maguire; Hans Minderman; Vipin Chaudhary (Image Processing, 2015)

A Topic-modeling Based Framework for Drug-drug Interaction Classification from Biomedical Text. - Dingcheng Li; Sijia Liu 002; Majid Rastegar-Mojarad; Yanshan Wang; Xiaodi Li; Vipin Chaudhary; Terry M. Therneau; Hongfang Liu (AMIA, 2016)

Drug-drug Interaction Detection with A Topic-modeling Based Framework Augmented with Distant-supervision. - Dingcheng Li; Sijia Liu 002; Majid Rastegar-Mojarad; Yanshan Wang; Xiaodi Li; Vipin Chaudhary; Terry M. Therneau; Hongfang Liu (AMIA, 2016)

MayoBMI at ImageCLEF 2016 Handwritten Document Retrieval Task. - Sijia Liu 002; Yanshan Wang; Saeed Mehrabi 003; Dingcheng Li; Hongfang Liu (CLEF (Working Notes), 2016)

An Infinite Mixture Model for Coreference Resolution in Clinical Notes. - Sijia Liu 002; Hongfang Liu; Vipin Chaudhary; Dingcheng Li (CRI, 2016)

LabLinker: Finding Links of Laboratory Test Results between Structured Records and Clinical Notes. - Sijia Liu 002; Vipin Chaudhary; Liwei Wang 010; Hongfang Liu (ICHI, 2016)

An Ensemble Model of Clinical Information Extraction and Information Retrieval for Clinical Decision Support. - Yanshan Wang; Majid Rastegar-Mojarad; Ravikumar Komandur Elayavilli; Sijia Liu 002; Hongfang Liu (TREC, 2016)

Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. - Feichen Shen; Sijia Liu 002; Yanshan Wang; Liwei Wang 010; Naveed Afzal; Hongfang Liu (AMIA, 2017)

Accelerating Rare Disease Diagnosis with Collaborative Filtering. - Feichen Shen; Sijia Liu 002; Yanshan Wang; Liwei Wang 010; Naveed Afzal; Hongfang Liu (AMIA, 2017)

Recommending education materials for diabetic questions using information retrieval approaches. - Yuqun Zeng; Yanshan Wang; Feichen Shen; Sijia Liu 002; Liwei Wang 010; Majid Rastegar-Mojarad; Xusheng Liu; Hongfang Liu (AMIA, 2017)

Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature. - Yanshan Wang; Sijia Liu 002; Majid Rastegar-Mojarad; Liwei Wang 010; Feichen Shen; Fei Liu 004; Hongfang Liu (BCB, 2017)

Medical concept intersection between outside medical records and consultant notes: A case study in transferred cardiovascular patients. - Sungrim Moon; Sijia Liu 002; Paul R. Kingsbury; David Chen 003; Yanshan Wang; Feichen Shen; Rajeev Chaudhry; Hongfang Liu (BIBM, 2017)

Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose. - Sijia Liu 002; Liwei Wang 010; Donna M. Ihrke; Vipin Chaudhary; Cui Tao; Chunhua Weng; Hongfang Liu (CRI, 2017)

Populating Physician Biographical Pages Based on EMR Data. - Feichen Shen; Sunghwan Sohn; Majid Rastegar-Mojarad; Sijia Liu 002; Joshua J. Pankratz; Michael Hatton; Nancy Sowada; Om Shrestha; Shawna Shurson; Hongfang Liu (CRI, 2017)

Content Analysis of Free-Text Family History. - Yanshan Wang; Liwei Wang 010; Majid Rastegar-Mojarad; Sijia Liu 002; Feichen Shen; Hongfang Liu (CRI, 2017)

On Mapping Textual Queries to a Common Data Model. - Sijia Liu 002; Yanshan Wang; Na Hong; Feichen Shen; Stephen T. Wu; William R. Hersh; Hongfang Liu (ICHI, 2017)

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

MayoNLP at SemEval 2017 Task 10: Word Embedding Distance Pattern for Keyphrase Classification in Scientific Publications. - Sijia Liu 002; Feichen Shen; Vipin Chaudhary; Hongfang Liu (SemEval@ACL, 2017)

Intrainstitutional EHR collections for patient-level information retrieval. - Stephen T. Wu; Sijia Liu 002; Yanshan Wang; Tamara Timmons; Harsha Uppili; Steven Bedrick; William R. Hersh; Hongfang Liu (J. Assoc. Inf. Sci. Technol., 2017)

ARETA: A Corpus for Asthma Related Event Temporal Association. - Sijia Liu 002; Liwei Wang 010; Sunghwan Sohn; Liping Xia; Hongfang Liu (AMIA, 2018)

Leveraging Electronic Health Records for Identification of Features Associated with Sudden Death for Hypertrophic Cardiomyopathy Patients. - Sungrim Moon; Sijia Liu 002; Sujith Samudrala; Jane L. Shellum; Jeffrey B. Geske; Peter A. Noseworthy; Steve Ommen; Rajeev Chaudhry; Rick Nishimura; Hongfang Liu; Adelaide M. Arruda-Olson (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)

BioCreative/OHNLP Challenge 2018. - Majid Rastegar-Mojarad; Sijia Liu 002; Yanshan Wang; Naveed Afzal; Liwei Wang 010; Feichen Shen; Sunyang Fu; Hongfang Liu (BCB, 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)

Extracting chemical-protein relations using attention-based neural networks. - Sijia Liu 002; Feichen Shen; Ravikumar Komandur Elayavilli; Yanshan Wang; Majid Rastegar-Mojarad; Vipin Chaudhary; Hongfang Liu (Database J. Biol. Databases Curation, 2018)

A Deep Representation Empowered Distant Supervision Paradigm for Clinical Information Extraction. - Yanshan Wang; Sunghwan Sohn; Sijia Liu 002; Feichen Shen; Liwei Wang 010; Elizabeth J. Atkinson; Shreyasee Amin; Hongfang Liu (CoRR, 2018)

A comparison of word embeddings for the biomedical natural language processing. - Yanshan Wang; Sijia Liu 002; Naveed Afzal; Majid Rastegar-Mojarad; Liwei Wang 010; Feichen Shen; Paul R. Kingsbury; Hongfang Liu (J. Biomed. Informatics, 2018)

Clinical information extraction applications: A literature review. - Yanshan Wang; Liwei Wang 010; Majid Rastegar-Mojarad; Sungrim Moon; Feichen Shen; Naveed Afzal; Sijia Liu 002; Yuqun Zeng; Saeed Mehrabi 003; Sunghwan Sohn; Hongfang Liu (J. Biomed. Informatics, 2018)

Modeling asynchronous event sequences with RNNs. - Stephen T. Wu; Sijia Liu 002; Sunghwan Sohn; Sungrim Moon; Chung-Il Wi; Young J. Juhn; Hongfang Liu (J. Biomed. Informatics, 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)

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)

Automated extraction of sudden cardiac death risk factors in hypertrophic cardiomyopathy patients by natural language processing. - Sungrim Moon; Sijia Liu 002; Christopher Scott; Sujith Samudrala; Mohamed M. Abidian; Jeffrey B. Geske; Peter A. Noseworthy; Jane L. Shellum; Rajeev Chaudhry; Steve Ommen; Rick Nishimura; Hongfang Liu; et al. (Int. J. Medical 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)

Salience of Medical Concepts of Inside Clinical Texts and Outside Medical Records for Referred Cardiovascular Patients. - Sungrim Moon; Sijia Liu 002; David Chen 003; Yanshan Wang; Douglas L. Wood; Rajeev Chaudhry; Hongfang Liu; Paul R. Kingsbury (J. Heal. Informatics Res., 2019)

Rare disease knowledge enrichment through a data-driven approach. - Feichen Shen; Yiqing Zhao; Liwei Wang 010; Majid Rastegar-Mojarad; Yanshan Wang; Sijia Liu 002; Hongfang Liu (BMC Medical Informatics Decis. Mak., 2019)

A clinical text classification paradigm using weak supervision and deep representation. - Yanshan Wang; Sunghwan Sohn; Sijia Liu 002; Feichen Shen; Liwei Wang 010; Elizabeth J. Atkinson; Shreyasee Amin; Hongfang Liu (BMC Medical Informatics Decis. Mak., 2019)

Deep learning and alternative learning strategies for retrospective real-world clinical data. - David Chen 003; Sijia Liu 002; Paul R. Kingsbury; Sunghwan Sohn; Curtis B. Storlie; Elizabeth B. Habermann; James M. Naessens; David W. Larson; Hongfang Liu (npj Digit. Medicine, 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 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)

Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. - Fang Li 011; Jingcheng Du; Yongqun He; Hsing-yi Song; Mohcine Madkour; Guozheng Rao; Yang Xiang 003; Yi Luo; Henry W. Chen; Sijia Liu 002; Liwei Wang 010; Hongfang Liu; et al. (J. Am. Medical Informatics Assoc., 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)

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)

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)

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

The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP models. - Yao Yan; Thomas Yu; Kathleen Muenzen; Sijia Liu 002; Connor Boyle; George Koslowski; Jiaxin Zheng; Nicholas J. Dobbins; Clement Essien; Hongfang Liu; Larsson Omberg; Meliha Yestigen; et al. (CoRR, 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)

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)