Andrew Wen

According to our database, Andrew Wen authored at least 48 papers between 2017 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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, 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

J. Am. Medical Informatics Assoc., November, 2023

The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era.

Andrew Wen, Huan He, Sunyang Fu, Sijia Liu, Kurt Miller, Liwei Wang, Kirk E. Roberts, Steven Bedrick, William R. Hersh, Hongfang Liu

npj Digit. Medicine, 2023

MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks.

Rui Li, Andrew Wen, Jing Gao, Hongfang Liu

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022

Computational drug repurposing based on electronic health records: a scoping review.

Nansu Zong, Andrew Wen, Sungrim Moon, Sunyang Fu, Liwei Wang, Yiqing Zhao, Yue Yu, Ming Huang, Yanshan Wang, Gang Zheng, Michelle M. Mielke, James R. Cerhan, Hongfang Liu

npj Digit. Medicine, 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, Daniel J. Stone, David Knaack, Alanna M. Chamberlain, Emily R. Pfaff, Davera Gabriel, Christopher G. Chute, Nilay Shah, Guoqian Jiang

J. Biomed. Informatics, 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

MedTator: a serverless annotation tool for corpus development.

Huan He, Sunyang Fu, Liwei Wang, Sijia Liu, Andrew Wen, Hongfang Liu

Bioinform., 2022

BETA: a comprehensive benchmark for computational drug-target prediction.

Nansu Zong, Ning Li, Andrew Wen, Victoria Ngo, Yue Yu, Ming Huang, Shaika Chowdhury, Chao Jiang, Sunyang Fu, Richard Weinshilboum, Guoqian Jiang, Lawrence Hunter, Hongfang Liu

Briefings Bioinform., 2022

Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing.

Liwei Wang, Sunyang Fu, Andrew Wen, Xiaoyang Ruan, Huan He, Sijia Liu, Sungrim Moon, Michelle Mai, Irbaz Bin Riaz, Nan Wang, Ping Yang, Hua Xu, Jeremy L. Warner, Hongfang Liu

Proceedings of the 10th IEEE International Conference on Healthcare Informatics, 2022

MedTator: A Serverless Web-based Tool for Corpus Annotation.

Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Hongfang Liu

Proceedings of the 10th IEEE International Conference on Healthcare Informatics, 2022

Towards User-centered Corpus Development: Lessons Learnt from Designing and Developing MedTator.

Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Sungrim Moon, Kurt Miller, Hongfang Liu

Proceedings of the AMIA 2022, 2022

2021

An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses.

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

J. Biomed. Informatics, 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, Yue Yu, Ming Huang, Sijia Liu, Hongfang Liu, Qian Shi, Guoqian Jiang

Int. J. Medical Informatics, 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, 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

CoRR, 2021

Leveraging a Joint of Phenotypic and Genetic Features on Cancer Patient Subgrouping.

David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen

CoRR, 2021

Comparisons of Graph Neural Networks on Cancer Classification Leveraging a Joint of Phenotypic and Genetic Features.

David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen

CoRR, 2021

Drug-target prediction utilizing heterogeneous bio-linked network embeddings.

Nansu Zong, Rachael Sze Nga Wong, Yue Yu, Andrew Wen, Ming Huang, Ning Li

Briefings Bioinform., 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, Hongfang Liu

Proceedings of the MEDINFO 2021: One World, One Health - Global Partnership for Digital Innovation, 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, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Yuan Luo, Fei Wang, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR.

Daniel J. Stone, Sijia Liu, Yuan Luo, Andrew Wen, Nansu Zong, Luke V. Rasmussen, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Fei Wang, Cui Tao, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Disparity analysis of patient portal messaging use for COVID-19 in urban versus rural locality.

Ming Huang, Andrew Wen, Huan He, Liwei Wang, Sijia Liu, Yanshan Wang, Nansu Zong, Yue Yu, Julie E. Prigge, Brian Costello, Nilay D. Shah, Henry Ting, Chyke Doubeni, Jungwei Fan, Hongfang Liu, Christi A. Patten

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

COVID-19 Dashboard: Visual Exploration of the Regional Pandemic Trend.

Huan He, Liwei Wang, Andrew Wen, Ming Huang, Yanshan Wang, Hongfang Liu

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Patient Asynchronous Response to Coronavirus Disease 2019 (COVID-19): A Retrospective Analysis of Patient Portal Messages.

Ming Huang, Aditya Khurana, George M. Mastorakos, Andrew Wen, Huan He, Liwei Wang, Sijia Liu, Yanshan Wang, Julie E. Prigge, Brian Costello, Nilay D. Shah, Henry Ting, Christi A. Patten, Jungwei Fan, Hongfang Liu

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020

Clinical concept extraction: A methodology review.

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

J. Biomed. Informatics, 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, Hongfang Liu, William R. Hersh

Proceedings of the ACM WSDM 2020 Health Search and Data Mining Workshop, 2020

A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation.

Andrew Wen, Feichen Shen, Sungrim Moon, Hongfang Liu, Jungwei Fan

Proceedings of the 33rd IEEE International Symposium on Computer-Based Medical Systems, 2020

Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings.

Feichen Shen, Andrew Wen, Hongfang Liu

Proceedings of the 33rd IEEE International Symposium on Computer-Based Medical Systems, 2020

Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System.

Feichen Shen, Andrew Wen, Hongfang Liu

Proceedings of the 33rd IEEE International Symposium on Computer-Based Medical Systems, 2020

Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery.

Andrew Wen, Sunyang Fu, Feichen Shen, Hongfang Liu

Proceedings of the AMIA 2020, 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

Proceedings of the AMIA 2020, 2020

Predicting Section Location of Clinical Sentences using BERT Encoder - A Pilot Study.

Sijia Liu, Sunyang Fu, Sungrim Moon, Andrew Wen, Hongfang Liu

Proceedings of the AMIA 2020, 2020

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, Sunghwan Sohn, Hongfang Liu, Jungwei Fan

npj Digit. Medicine, 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

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology.

Feichen Shen, Suyuan Peng, Yadan Fan, Andrew Wen, Sijia Liu, Yanshan Wang, Liwei Wang, Hongfang Liu

J. Biomed. Informatics, 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, Yuan Luo, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang

J. Biomed. Informatics, 2019

Adapting and evaluating a deep learning language model for clinical why-question answering.

Andrew Wen, Mohamed Y. Elwazir, Sungrim Moon, Jungwei Fan

CoRR, 2019

Development of Clinical Concept Extraction Applications: A Methodology Review.

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

CoRR, 2019

Cross-lingual Data Transformation and Combination for Text Classification.

Jun Jiang, Shumao Pang, Xia Zhao, Liwei Wang, Andrew Wen, Hongfang Liu, Qianjin Feng

CoRR, 2019

CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model.

Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William R. Hersh, Hongfang Liu

CoRR, 2019

Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices.

Andrew Wen, Yanshan Wang, Vinod C. Kaggal, Sijia Liu, Hongfang Liu, Jungwei Fan

Proceedings of the 2019 IEEE International Conference on Big Data (IEEE BigData), 2019

Clinical Use of an Information Retrieval Framework for Cohort Discovery from Electronic Health Records.

Yanshan Wang, Andrew Wen, Sijia Liu, Jennifer L. St. Sauver, Adil E. Bharucha, Chunhua Weng, Hongfang Liu

Proceedings of the AMIA 2019, 2019

2018

MayoNLPTeam at the TREC 2018 Precision Medicine Track: Simple Information Retrieval Approach Is the Best.

Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu

Proceedings of the Twenty-Seventh Text REtrieval Conference, 2018

Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement.

Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Andrew Wen, Andrew H. Limper, Hongfang Liu

Proceedings of the IEEE International Conference on Healthcare Informatics Workshops, 2018

Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome.

Su-Yuan Peng, Yadan Fan, Liwei Wang, Andrew Wen, Xusheng Liu, Hongfang Liu, Feichen Shen

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

EMIRS: An Electronic Medical Information Retrieval System by Leveraging both Structured and Unstructured Electronic Health Records.

Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu

Proceedings of the AMIA 2018, 2018

Developing a RadLex-based Name Entity Recognition Tool for Mining Free-Text Radiology Reports.

Shintaro Tsuji, Andrew Wen, Guoqian Jiang

Proceedings of the AMIA 2018, 2018

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

Proceedings of the AMIA 2018, 2018

2017

Aligned-Layer Text Search in Clinical Notes.

Stephen T. Wu, Andrew Wen, Yanshan Wang, Sijia Liu, Hongfang Liu

Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017