Sijia Liu

Publication Activity (10 Years)

Years Active: 2015-2023
Publications (10 Years): 58

Top Topics

Clinical Information

Natural Language

Information Retrieval

Disease Diagnosis

Top Venues

J. Biomed. Informatics

Publications

Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 30 (12) (2023)
Andrew Wen, Huan He, Sunyang Fu, Sijia Liu, Kurt Miller, Liwei Wang, Kirk E. Roberts, Steven Bedrick, William R. Hersh, Hongfang Liu
The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era. npj Digit. Medicine 6 (2023)
Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Hongfang Liu
MedTator: A Serverless Web-based Tool for Corpus Annotation. ICHI (2022)
Yue Yu, Nansu Zong, Andrew Wen, Sijia Liu, Daniel J. Stone, David Knaack, Alanna M. Chamberlain, Emily R. Pfaff, Davera Gabriel, Christopher G. Chute, Nilay Shah, Guoqian Jiang
Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration. J. Biomed. Informatics 127 (2022)
Yao Yan, Thomas Yu, Kathleen Muenzen, Sijia Liu, Connor Boyle, George Koslowski, Jiaxin Zheng, Nicholas J. Dobbins, Clement Essien, Hongfang Liu, Larsson Omberg, Meliha Yestigen, Bradley Taylor, James A. Eddy, Justin Guinney, Sean D. Mooney, Thomas Schaffter
The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP models. CoRR (2022)
Huan He, Sunyang Fu, Liwei Wang, Sijia Liu, Andrew Wen, Hongfang Liu
MedTator: a serverless annotation tool for corpus development. Bioinform. 38 (6) (2022)
Andrew Wen, Liwei Wang, Huan He, Sijia Liu, Sunyang Fu, Sunghwan Sohn, Jacob A. Kugel, Vinod C. Kaggal, Ming Huang, Yanshan Wang, Feichen Shen, Jungwei Fan, Hongfang Liu
An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. J. Biomed. Informatics 113 (2021)
Ming Huang, Andrew Wen, Huan He, Liwei Wang, Sijia Liu, Yanshan Wang, Nansu Zong, Yue Yu, Julie Prigge, Brian Costello, Nilay D. Shah, Henry Ting, Chyke Doubeni, Jungwei Fan, Hongfang Liu, Christi Patten
Disparity analysis of patient portal messaging use for COVID-19 in urban versus rural locality. AMIA (2021)
Nansu Zong, Daniel J. Stone, Deepak K. Sharma, Andrew Wen, Chen Wang, Yue Yu, Ming Huang, Sijia Liu, Hongfang Liu, Qian Shi, Guoqian Jiang
Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. Int. J. Medical Informatics 145 (2021)
Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Rui Zhang, John D. Osborne, Masoud Rouhizadeh, Yongqun He, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). CoRR (2021)
Ming Huang, Aditya Khurana, George M. Mastorakos, Andrew Wen, Huan He, Liwei Wang, Sijia Liu, Yanshan Wang, Julie Prigge, Brian Costello, Nilay D. Shah, Henry Ting, Christi Patten, Jungwei Fan, Hongfang Liu
Patient Asynchronous Response to Coronavirus Disease 2019 (COVID-19): A Retrospective Analysis of Patient Portal Messages. AMIA (2021)
Sijia Liu, Sunyang Fu, Sungrim Moon, Andrew Wen, Hongfang Liu
Predicting Section Location of Clinical Sentences using BERT Encoder - A Pilot Study. AMIA (2020)
Ioannis C. Tsaknakis, Mingyi Hong, Sijia Liu
Decentralized Min-Max Optimization: Formulations, Algorithms and Applications in Network Poisoning Attack. ICASSP (2020)
Fang Li, Jingcheng Du, Yongqun He, Hsing-yi Song, Mohcine Madkour, Guozheng Rao, Yang Xiang, Yi Luo, Henry W. Chen, Sijia Liu, Liwei Wang, Hongfang Liu, Hua Xu, Cui Tao
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. J. Am. Medical Informatics Assoc. 27 (7) (2020)
Steve Chamberlin, Steven Bedrick, Aaron M. Cohen, Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu, William R. Hersh
A Query Taxonomy Describes Performance of Patient-Level Retrieval from Electronic Health Record Data. HSDM@WSDM (2020)
Sunyang Fu, David Chen, Huan He, Sijia Liu, Sungrim Moon, Kevin J. Peterson, Feichen Shen, Liwei Wang, Yanshan Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu
Clinical concept extraction: A methodology review. J. Biomed. Informatics 109 (2020)
Feichen Shen, Yiqing Zhao, Liwei Wang, Majid Rastegar-Mojarad, Yanshan Wang, Sijia Liu, Hongfang Liu
Rare disease knowledge enrichment through a data-driven approach. BMC Medical Informatics Decis. Mak. 19 (1) (2019)
Feichen Shen, Suyuan Peng, Yadan Fan, Andrew Wen, Sijia Liu, Yanshan Wang, Liwei Wang, Hongfang Liu
HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. J. Biomed. Informatics 96 (2019)
Sungrim Moon, Sijia Liu, David Chen, Yanshan Wang, Douglas L. Wood, Rajeev Chaudhry, Hongfang Liu, Paul R. Kingsbury
Salience of Medical Concepts of Inside Clinical Texts and Outside Medical Records for Referred Cardiovascular Patients. J. Heal. Informatics Res. 3 (2) (2019)
Sungrim Moon, Sijia Liu, Christopher Scott, Sujith Samudrala, Mohamed M. Abidian, Jeffrey B. Geske, Peter A. Noseworthy, Jane L. Shellum, Rajeev Chaudhry, Steve Ommen, Rick Nishimura, Hongfang Liu, Adelaide M. Arruda-Olson
Automated extraction of sudden cardiac death risk factors in hypertrophic cardiomyopathy patients by natural language processing. Int. J. Medical Informatics 128 (2019)
Yanshan Wang, Sunghwan Sohn, Sijia Liu, Feichen Shen, Liwei Wang, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu
A clinical text classification paradigm using weak supervision and deep representation. BMC Medical Informatics Decis. Mak. 19 (1) (2019)
David Chen, Sijia Liu, Paul R. Kingsbury, Sunghwan Sohn, Curtis B. Storlie, Elizabeth B. Habermann, James M. Naessens, David W. Larson, Hongfang Liu
Deep learning and alternative learning strategies for retrospective real-world clinical data. npj Digit. Medicine 2 (2019)
Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William R. Hersh, Hongfang Liu
CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model. CoRR (2019)
Yanshan Wang, Andrew Wen, Sijia Liu, Jennifer L. St. Sauver, Adil E. Bharucha, Chunhua Weng, Hongfang Liu
Clinical Use of an Information Retrieval Framework for Cohort Discovery from Electronic Health Records. AMIA (2019)
Andrew Wen, Yanshan Wang, Vinod C. Kaggal, Sijia Liu, Hongfang Liu, Jungwei Fan
Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices. IEEE BigData (2019)
Sunyang Fu, David Chen, Sijia Liu, Sungrim Moon, Kevin J. Peterson, Feichen Shen, Yanshan Wang, Liwei Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu
Development of Clinical Concept Extraction Applications: A Methodology Review. CoRR (2019)
Andrew Wen, Sunyang Fu, Sungrim Moon, Mohamed El Wazir, Andrew Rosenbaum, Vinod C. Kaggal, Sijia Liu, Sunghwan Sohn, Hongfang Liu, Jungwei Fan
Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation. npj Digit. Medicine 2 (2019)
Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sungrim Moon, Feichen Shen, Naveed Afzal, Sijia Liu, Yuqun Zeng, Saeed Mehrabi, Sunghwan Sohn, Hongfang Liu
Clinical information extraction applications: A literature review. J. Biomed. Informatics 77 (2018)
Yanshan Wang, Sunghwan Sohn, Sijia Liu, Feichen Shen, Liwei Wang, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu
A Deep Representation Empowered Distant Supervision Paradigm for Clinical Information Extraction. CoRR (2018)
Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Paul R. Kingsbury, Hongfang Liu
A comparison of word embeddings for the biomedical natural language processing. J. Biomed. Informatics 87 (2018)
Stephen T. Wu, Sijia Liu, Sunghwan Sohn, Sungrim Moon, Chung-Il Wi, Young J. Juhn, Hongfang Liu
Modeling asynchronous event sequences with RNNs. J. Biomed. Informatics 83 (2018)
Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Paul R. Kingsbury, Hongfang Liu
A Comparison of Word Embeddings for the Biomedical Natural Language Processing. CoRR (2018)
Sijia Liu, Liwei Wang, Sunghwan Sohn, Liping Xia, Hongfang Liu
ARETA: A Corpus for Asthma Related Event Temporal Association. AMIA (2018)
Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Andrew Wen, Andrew H. Limper, Hongfang Liu
Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. ICHI Workshops (2018)
Sungrim Moon, Sijia Liu, Sujith Samudrala, Jane L. Shellum, Jeffrey B. Geske, Peter A. Noseworthy, Steve Ommen, Rajeev Chaudhry, Rick Nishimura, Hongfang Liu, Adelaide M. Arruda-Olson
Leveraging Electronic Health Records for Identification of Features Associated with Sudden Death for Hypertrophic Cardiomyopathy Patients. AMIA (2018)
Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu
MayoNLPTeam at the TREC 2018 Precision Medicine Track: Simple Information Retrieval Approach Is the Best. TREC (2018)
Majid Rastegar-Mojarad, Sijia Liu, Yanshan Wang, Naveed Afzal, Liwei Wang, Feichen Shen, Sunyang Fu, Hongfang Liu
BioCreative/OHNLP Challenge 2018. BCB (2018)
Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu
EMIRS: An Electronic Medical Information Retrieval System by Leveraging both Structured and Unstructured Electronic Health Records. AMIA (2018)
Sijia Liu, Feichen Shen, Ravikumar Komandur Elayavilli, Yanshan Wang, Majid Rastegar-Mojarad, Vipin Chaudhary, Hongfang Liu
Extracting chemical-protein relations using attention-based neural networks. Database J. Biol. Databases Curation 2018 (2018)
Sijia Liu, Yanshan Wang, Na Hong, Feichen Shen, Stephen T. Wu, William R. Hersh, Hongfang Liu
On Mapping Textual Queries to a Common Data Model. ICHI (2017)
Yanshan Wang, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Fei Liu, Hongfang Liu
Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature. BCB (2017)
Stephen T. Wu, Andrew Wen, Yanshan Wang, Sijia Liu, Hongfang Liu
Aligned-Layer Text Search in Clinical Notes. MedInfo (2017)
Sijia Liu, Feichen Shen, Vipin Chaudhary, Hongfang Liu
MayoNLP at SemEval 2017 Task 10: Word Embedding Distance Pattern for Keyphrase Classification in Scientific Publications. SemEval@ACL (2017)
Stephen T. Wu, Sijia Liu, Yanshan Wang, Tamara Timmons, Harsha Uppili, Steven Bedrick, William R. Hersh, Hongfang Liu
Intrainstitutional EHR collections for patient-level information retrieval. J. Assoc. Inf. Sci. Technol. 68 (11) (2017)
Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sijia Liu, Feichen Shen, Hongfang Liu
Content Analysis of Free-Text Family History. CRI (2017)
Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, Hongfang Liu
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. AMIA (2017)
Sungrim Moon, Sijia Liu, Paul R. Kingsbury, David Chen, Yanshan Wang, Feichen Shen, Rajeev Chaudhry, Hongfang Liu
Medical concept intersection between outside medical records and consultant notes: A case study in transferred cardiovascular patients. BIBM (2017)
Yuqun Zeng, Yanshan Wang, Feichen Shen, Sijia Liu, Liwei Wang, Majid Rastegar-Mojarad, Xusheng Liu, Hongfang Liu
Recommending education materials for diabetic questions using information retrieval approaches. AMIA (2017)
Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, Hongfang Liu
Accelerating Rare Disease Diagnosis with Collaborative Filtering. AMIA (2017)
Feichen Shen, Sunghwan Sohn, Majid Rastegar-Mojarad, Sijia Liu, Joshua J. Pankratz, Michael Hatton, Nancy Sowada, Om Shrestha, Shawna Shurson, Hongfang Liu
Populating Physician Biographical Pages Based on EMR Data. CRI (2017)
Sijia Liu, Liwei Wang, Donna M. Ihrke, Vipin Chaudhary, Cui Tao, Chunhua Weng, Hongfang Liu
Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose. CRI (2017)
Sijia Liu, Hongfang Liu, Vipin Chaudhary, Dingcheng Li
An Infinite Mixture Model for Coreference Resolution in Clinical Notes. CRI (2016)
Yanshan Wang, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Sijia Liu, Hongfang Liu
An Ensemble Model of Clinical Information Extraction and Information Retrieval for Clinical Decision Support. TREC (2016)
Sijia Liu, Vipin Chaudhary, Liwei Wang, Hongfang Liu
LabLinker: Finding Links of Laboratory Test Results between Structured Records and Clinical Notes. ICHI (2016)
Dingcheng Li, Sijia Liu, Majid Rastegar-Mojarad, Yanshan Wang, Xiaodi Li, Vipin Chaudhary, Terry M. Therneau, Hongfang Liu
A Topic-modeling Based Framework for Drug-drug Interaction Classification from Biomedical Text. AMIA (2016)
Sijia Liu, Yanshan Wang, Saeed Mehrabi, Dingcheng Li, Hongfang Liu
MayoBMI at ImageCLEF 2016 Handwritten Document Retrieval Task. CLEF (Working Notes) (2016)
Dingcheng Li, Sijia Liu, Majid Rastegar-Mojarad, Yanshan Wang, Xiaodi Li, Vipin Chaudhary, Terry M. Therneau, Hongfang Liu
Drug-drug Interaction Detection with A Topic-modeling Based Framework Augmented with Distant-supervision. AMIA (2016)
Sijia Liu, Ruhan Sa, Orla Maguire, Hans Minderman, Vipin Chaudhary
Spot counting on fluorescence in situ hybridization in suspension images using Gaussian mixture model. Medical Imaging: Image Processing (2015)