Andrew Wen

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 52

Top Topics

Information Retrieval

Natural Language

Clinical Trials

Top Venues

J. Biomed. Informatics

J. Am. Medical Informatics Assoc.

Publications

Shaika Chowdhury, Yongbin Chen, Pengyang Li, Sivaraman Rajaganapathy, Andrew Wen, Xiao Ma, Qiying Dai, Yue Yu, Sunyang Fu, Xiaoqian Jiang, Zhe He, Sunghwan Sohn, Xiaoke Liu, Suzette J. Bielinski, Alanna M. Chamberlain, James R. Cerhan, Nansu Zong
Stratifying heart failure patients with graph neural network and transformer using Electronic Health Records to optimize drug response prediction. J. Am. Medical Informatics Assoc. 31 (8) (2024)
Qiuhao Lu, Rui Li, Andrew Wen, Jinlian Wang, Liwei Wang, Hongfang Liu
Large Language Models Struggle in Token-Level Clinical Named Entity Recognition. CoRR (2024)
Sunyang Fu, Heling Jia, Maria Vassilaki, Vipina Kuttichi Keloth, Yifang Dang, Yujia Zhou, Muskan Garg, Ronald C. Petersen, Jennifer St Sauver, Sungrim Moon, Liwei Wang, Andrew Wen, Fang Li, Hua Xu, Cui Tao, Jungwei Fan, Hongfang Liu, Sunghwan Sohn
FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. J. Biomed. Informatics 152 (2024)
Sunyang Fu, Liwei Wang, Huan He, Andrew Wen, Nansu Zong, Anamika Kumari, Feifan Liu, Sicheng Zhou, Rui Zhang, Chenyu Li, Yanshan Wang, Jennifer St Sauver, Hongfang Liu, Sunghwan Sohn
A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction. J. Am. Medical Informatics Assoc. 31 (7) (2024)
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)
Rui Li, Andrew Wen, Jing Gao, Hongfang Liu
MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks. BCB (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)
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
Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing. ICHI (2022)
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
A hybrid model to identify fall occurrence from electronic health records. Int. J. Medical Informatics 162 (2022)
Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Sungrim Moon, Kurt Miller, Hongfang Liu
Towards User-centered Corpus Development: Lessons Learnt from Designing and Developing MedTator. AMIA (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)
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
Computational drug repurposing based on electronic health records: a scoping review. npj Digit. Medicine 5 (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)
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
BETA: a comprehensive benchmark for computational drug-target prediction. Briefings Bioinform. 23 (4) (2022)
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
On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. AMIA (2021)
David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen
Comparisons of Graph Neural Networks on Cancer Classification Leveraging a Joint of Phenotypic and Genetic Features. CoRR (2021)
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)
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
FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. AMIA (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)
Sunyang Fu, Andrew Wen, Sandeep R. Pagali, Nansu Zong, Jennifer St Sauver, Sunghwan Sohn, Jungwei Fan, Hongfang Liu
The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records. MedInfo (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)
Nansu Zong, Rachael Sze Nga Wong, Yue Yu, Andrew Wen, Ming Huang, Ning Li
Drug-target prediction utilizing heterogeneous bio-linked network embeddings. Briefings Bioinform. 22 (1) (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)
David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen
Leveraging a Joint of Phenotypic and Genetic Features on Cancer Patient Subgrouping. CoRR (2021)
Huan He, Liwei Wang, Andrew Wen, Ming Huang, Yanshan Wang, Hongfang Liu
COVID-19 Dashboard: Visual Exploration of the Regional Pandemic Trend. AMIA (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)
Feichen Shen, Andrew Wen, Hongfang Liu
Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings. CBMS (2020)
Mohamed Y. Elwazir, Andrew Wen, Sungrim Moon, Jungwei Fan
A Perturbation Approach to Assessing BERT Robustness for Different Linguistic Aspects in Medical Question-Answering. AMIA (2020)
Andrew Wen, Sunyang Fu, Feichen Shen, Hongfang Liu
Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. AMIA (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)
Feichen Shen, Andrew Wen, Hongfang Liu
Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System. CBMS (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)
Andrew Wen, Feichen Shen, Sungrim Moon, Hongfang Liu, Jungwei Fan
A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. CBMS (2020)
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)
Andrew Wen, Mohamed Y. Elwazir, Sungrim Moon, Jungwei Fan
Adapting and evaluating a deep learning language model for clinical why-question answering. CoRR (2019)
Jun Jiang, Shumao Pang, Xia Zhao, Liwei Wang, Andrew Wen, Hongfang Liu, Qianjin Feng
Cross-lingual Data Transformation and Combination for Text Classification. CoRR (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)
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
Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. J. Biomed. Informatics 99 (2019)
Yue Yu, Kathryn J. Ruddy, Na Hong, Shintaro Tsuji, Andrew Wen, Nilay D. Shah, Guoqian Jiang
ADEpedia-on-OHDSI: A next generation pharmacovigilance signal detection platform using the OHDSI common data model. J. Biomed. Informatics 91 (2019)
Na Hong, Andrew Wen, Majid Rastegar-Mojarad, Sunghwan Sohn, Hongfang Liu, Guoqian Jiang
Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP. AMIA (2018)
Su-Yuan Peng, Yadan Fan, Liwei Wang, Andrew Wen, Xusheng Liu, Hongfang Liu, Feichen Shen
Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome. BIBM (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)
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)
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)
Shintaro Tsuji, Andrew Wen, Guoqian Jiang
Developing a RadLex-based Name Entity Recognition Tool for Mining Free-Text Radiology Reports. AMIA (2018)
Stephen T. Wu, Andrew Wen, Yanshan Wang, Sijia Liu, Hongfang Liu
Aligned-Layer Text Search in Clinical Notes. MedInfo (2017)