Andrew Wen

Andrew Wen

Sr. Data Science Analyst at the Department of AI & Informatics Research, Mayo Clinic

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I am a Senior Data Science Analyst currently at the Mayo Clinic, where I have the great privilege of being mentored by Dr. Hongfang Liu. My research focuses on clinical natural language processing methodology development using big data, the usage of clinical NLP to enhance information extraction and retrieval, as well as its applicability to digital health applications.

I obtained my MSc in Biomedical Informatics from the Oregon Health & Sciences University, where I was advised by Dr. Stephen Wu. Prior to that, I obtained my BS in Computer Science from the Portland State University.

Selected Peer-Reviewed Publications

  • Wen A, He H, Fu S, Liu S, Miller K, Wang L, Roberts KE, Bedrick SD, Hersh WR, Liu H, The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era. npj Digit. Med. 6, 132 (2023). https://doi.org/10.1038/s41746-023-00878-9
  • Wen A, Wang L, He H, Liu S, Fu S, Sohn S, Kugel JA, Kaggal VC, Huang M, Wang Y, Shen F, Fan J, Liu H. An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. J Biomed Inform. 2020 Dec 13; 113:103660 [Epub ahead of print] PMID: 33321199 PMCID: 7832634 DOI: 10.1016/j.jbi.2020.103660
  • Wen A, Shen F, Moon S, Liu H, Fan J. A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, 2020, pp. 546-551, doi: 10.1109/CBMS49503.2020.00109.
  • Wen A, Wang Y, Kaggal V, Liu S, Liu H, Fan J. Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices. Proceedings of the 2019 IEEE International Conference on Big Data (Big Data). 2019; 2800-2807. Epub 2020 Feb 24.
  • Wen A, El Wazir M, Moon S, Fan J. Adapting and evaluating a deep learning language model for clinical why-question answering. JAMIA Open. 2020 Feb 04. DOI: 10.1093/jamiaopen/ooz072
  • Wen A, Fu S, Moon S, El Wazir M, Rosenbaum A, Kaggal VC, Liu S, Sohn S, Liu H, Fan J. Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation. NPJ Digit Med. 2019; 2:130 Epub 2019 Dec 17 PMID: 31872069 PMCID: 6917754 DOI: 10.1038/s41746-019-0208-8

Book Chapters

  • Fu S, Wen A, Liu, H. (2023). Clinical Natural Language Processing in Secondary Use of EHR for Research. In: Richesson RL, Andrews JE, Fultz Hollis, K (eds) Clinical Research Informatics. Health Informatics. Springer, Cham. https://doi.org/10.1007/978-3-031-27173-1_21

Full Bibliography (Peer Reviewed, Grouped by Topic)

Clinical Information Retrieval Leveraging NLP

  • Wen A, He H, Fu S, Liu S, Miller K, Wang L, Roberts KE, Bedrick SD, Hersh WR, Liu H, The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era. npj Digit. Med. 6, 132 (2023). https://doi.org/10.1038/s41746-023-00878-9
  • Liu S, Wang Y,Wen A, Wang L, Hong N, Shen F, Bedrick S, Hersh W, Liu H. Implementation of a Cohort Retrieval System for Clinical Data Repositories Using the Observational Medical Outcomes Partnership Common Data Model: Proof-of-Concept System Validation. JMIR Med Inform. 2020 Oct 6; 8 (10):e17376 Epub 2020 Oct 06 PMID: 33021486 PMCID: 7576539 DOI: 10.2196/17376
  • Chamberlin SR, Bedrick SD, Cohen AM, Wang Y, Wen A, Liu S, Liu H, Hersh WR. Evaluation of patient-level retrieval from electronic health record data for a cohort discovery task. JAMIA Open. 2020 Oct; 3 (3):395-404 Epub 2020 July 26 PMID: 33215074 PMCID: 7660955
  • Wen A, Wang Y, Kaggal V, Liu S, Liu H, Fan J. Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices. Proceedings of the 2019 IEEE International Conference on Big Data (Big Data). 2019; 2800-2807. Epub 2020 Feb 24.
  • Wen A, El Wazir M, Moon S, Fan J. Adapting and evaluating a deep learning language model for clinical why-question answering. JAMIA Open. 2020 Feb 04. DOI: 10.1093/jamiaopen/ooz072
  • Chamberlin SR, Bedrick SD, Cohen AM, Wang Y, Wen A, Liu S, Liu H, Hersh WR. A query taxonomy describes performance of patient-level retrieval from electronic health record data CEUR Workshop Proceedings. 2020; 2551:27-33
  • Wang Y, Wen A, Liu S, Hersh W, Bedrick S, Liu H. Test collections for electronic health record-based clinical information retrieval. JAMIA Open. 2019 Oct; 2 (3):360-368 Epub 2019 June 04 PMID: 31709390 PMCID: 6824517 DOI: 10.1093/jamiaopen/ooz016
  • Wang Y, Wen A, Liu S, Liu H. MayoNLPTeam at the TREC 2018 Precision Medicine Track: Simple Information Retrieval Approach Is the Best Text REtrieval Conference (TREC) - Precision Medicine Track. 2018
  • Wu S, Wen A, Wang Y, Liu S, Liu H. Aligned-Layer Text Search in Clinical Notes. Stud Health Technol Inform. 2017; 245:629-633 PMID: 29295172

Clinical Information Extraction and its Applications

  • Fu S, Wen A, Liu, H. (2023). Clinical Natural Language Processing in Secondary Use of EHR for Research. In: Richesson RL, Andrews JE, Fultz Hollis, K (eds) Clinical Research Informatics. Health Informatics. Springer, Cham. https://doi.org/10.1007/978-3-031-27173-1_21
  • Huang M, Wen A, He H, Wang L, Liu S, Wang Y, Zong N, Yu Y, Prigge JE, Costello BA, Shah ND, Ting HH, Doubeni C, Fan JW, Liu H, Patten CA. Midwest rural-urban disparities in use of patient online services for COVID-19. J Rural Health. 2022 Sep; 38 (4):908-915 Epub 2022 Mar 08 PMID: 35261092 PMCID: 9115171 DOI: 10.1111/jrh.12657
  • Wang L, Fu S, Wen A, Ruan X, He H, Liu S, Moon S, Mai M, Riaz IB, Wang N, Yang P, Xu H, Warner JL, Liu H. Assessment of Electronic Health Record for Cancer Research and Patient Care Through a Scoping Review of Cancer Natural Language Processing. JCO Clin Cancer Inform. 2022 Jul; 6:e2200006 PMID: 35917480 PMCID: 9470142 DOI: 10.1200/CCI.22.00006
  • Huang M, Khurana A, Mastorakos G, Wen A, He H, Wang L, Liu S, Wang Y, Zong N, Prigge J, Costello B, Shah N, Ting H, Fan J, Patten C, Liu H. Patient Portal Messaging for Asynchronous Virtual Care During the COVID-19 Pandemic: Retrospective Analysis. JMIR Hum Factors. 2022 May 5; 9 (2):e35187 Epub 2022 May 05 PMID: 35171108 PMCID: 9084445 DOI: 10.2196/35187
  • Fu S, Thorsteinsdottir B, Zhang X, Lopes GS, Pagali SR, LeBrasseur NK, Wen A, Liu H, Rocca WA, Olson JE, Sauver JS, Sohn S. A hybrid model to identify fall occurrence from electronic health records. Int J Med Inform. 2022 Mar 7; 162:104736 Epub 2022 Mar 07 PMID: 35316697 PMCID: 9448825 DOI: 10.1016/j.ijmedinf.2022.104736
  • Fu S, Lopes GS, Pagali SR, Thorsteinsdottir B, LeBrasseur NK, Wen A, Liu H, Rocca WA, Olson JE, St Sauver J, Sohn S. Ascertainment of Delirium Status Using Natural Language Processing From Electronic Health Records. J Gerontol A Biol Sci Med Sci. 2022 Mar 3; 77 (3):522-528 PMID: 33125037 PMCID: 8893184 DOI: 10.1093/gerona/glaa275
  • Huang M , Khurana A , Mastorakos G , Wen A , He H , Wang L , Liu S , Wang Y , Zong N , Prigge J , Costello B , Shah N , Ting H , Fan J , Patten C , Liu H . Patient portal messaging for asynchronous virtual care during the COVID-19 pandemic: retrospective analysis. JMIR Human Factors. 2022; 9 (2):e35187
  • Wang L , Fu S , Wen A , Ruan X , He H , Liu S , Moon S , Mai M , Riaz I , Wang N , Yang P , Xu H , Warner JL , Liu H . Evaluation of mCODE coverage in EHR: a scoping review of cancer natural language processing. Proceedings - 2022 IEEE 10th International Conference on Healthcare Informatics, ICHI 2022. 2022; 517-8
  • Tsuji S, Wen A, Takahashi N, Zhang H, Ogasawara K, Jiang G. Developing a RadLex-Based Named Entity Recognition Tool for Mining Textual Radiology Reports: Development and Performance Evaluation Study. J Med Internet Res. 2021 Oct 29; 23 (10):e25378 PMID: 34714247 DOI: 10.2196/25378
  • Wen A, Wang L, He H, Liu S, Fu S, Sohn S, Kugel JA, Kaggal VC, Huang M, Wang Y, Shen F, Fan J, Liu H. An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. J Biomed Inform. 2020 Dec 13; 113:103660 [Epub ahead of print] PMID: 33321199 PMCID: 7832634 DOI: 10.1016/j.jbi.2020.103660
  • Fu S, Lopes GS, Pagali SR, Thorsteinsdottir B, LeBrasseur NK, Wen A, Liu H, Rocca WA, Olson JE, St Sauver J, Sohn S. Ascertainment of delirium status using natural language processing from electronic health records. J Gerontol A Biol Sci Med Sci. 2020 Oct 30 [Epub ahead of print] PMID: 33125037 DOI: 10.1093/gerona/glaa275
  • Fu S, Chen D, He H, Liu S, Moon S, Peterson KJ, Shen F, Wang L, Wang Y, Wen A, Zhao Y, Sohn S, Liu H. Clinical Concept Extraction: a Methodology Review. J Biomed Inform. 2020 Aug 5; 103526 Epub 2020 Aug 05 PMID: 32768446 DOI: 10.1016/j.jbi.2020.103526
  • Fan Y, Wen A, Shen F, Sohn S, Liu H, Wang L. Evaluating the Impact of Dictionary Updates on Automatic Annotations Based on Clinical NLP Systems. AMIA Jt Summits Transl Sci Proc. 2019; 2019:714-721 Epub 2019 May 06 PMID: 31259028 PMCID: 6568114

Digital Health Development Tools/Infrastructure

  • He H , Fu S , Wang L , Wen A , Liu S , Liu H. MedTator: a serverless web-based tool for corpus annotation. Proceedings - 2022 IEEE 10th International Conference on Healthcare Informatics, ICHI 2022. 2022; 530-1
  • Wen A, Fu S, Moon S, El Wazir M, Rosenbaum A, Kaggal VC, Liu S, Sohn S, Liu H, Fan J. Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation. NPJ Digit Med. 2019; 2:130 Epub 2019 Dec 17 PMID: 31872069 PMCID: 6917754 DOI: 10.1038/s41746-019-0208-8

NLP and Standards (Particularly HL7 FHIR and the OHDSI CDM)

  • Yu Y, Zong N, Wen A, Liu S, Stone DJ, Knaack D, Chamberlain AM, Pfaff E, Gabriel D, Chute CG, Shah N, Jiang G. Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration. J Biomed Inform. 2022 Mar; 127:104002. Epub 2022 Jan 22. PMID: 35077901 PMCID: 8791245 DOI: 10.1016/j.jbi.2022.104002
  • Liu S, Luo Y, Stone D, Zong N, Wen A, Yu Y, Rasmussen LV, Wang F, Pathak J, Liu H, Jiang G. Integration of NLP2FHIR Representation with Deep Learning Models for EHR Phenotyping: A Pilot Study on Obesity Datasets AMIA Jt Summits Transl Sci Proc. 2021 (in press). 2021.
  • Wen A, Rasmussen LV, Stone D, Liu S, Kiefer R, Adekkanattu P, Brandt PS, Pacheco JA, Luo Y, Wang F, Pathak J, Liu H, Jiang G. CQL4NLP: Development and Integration of FHIR NLP Extensions in Clinical Quality Language for EHR-driven Phenotyping AMIA Jt Summits Transl Sci Proc. 2021 (in press). 2021.
  • Zong N, Stone DJ, Sharma DK,Wen A, Wang C, Yu Y, Huang M, Liu S, Liu H, Shi Q, Jiang G. Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. Int J Med Inform. 2021 Jan; 145:104308 Epub 2020 Oct 22
  • Yu Y, Ruddy KJ, Mansfield A, Zong N, Wen A, Tsuji S, Huang M, Liu H, Shah N, Jiang G. Detecting and Filtering Immune-Related Adverse Events Signal Based on Text Mining and Observational Health Data Sciences and Informatics Common Data Model: Framework Development Study. JMIR Med Inform. 2020 Jun 12; 8 (6):e17353 Epub 2020 June 12 PMID: 32530430 PMCID: 7320306 DOI: 10.2196/17353
  • Yu Y, Ruddy KJ, Wen A, Zong N, Tsuji S, Chen J, Shah ND, Jiang G. Integrating Electronic Health Record Data into the ADEpedia-on-OHDSI Platform for Improved Signal Detection: A Case Study of Immune-related Adverse Events. AMIA Jt Summits Transl Sci Proc. 2020; 2020:710-719 Epub 2020 May 30 PMID: 32477694 PMCID: 7233056
  • Zong N, Wen A, Stone DJ, Sharma DK, Wang C, Yu Y, Liu H, Shi Q, Jiang G. Developing an FHIR-Based Computational Pipeline for Automatic Population of Case Report Forms for Colorectal Cancer Clinical Trials Using Electronic Health Records. JCO Clin Cancer Inform. 2020 Mar; 4:201-209 PMID: 32134686 DOI: 10.1200/CCI.19.00116
  • Hong N, Wen A, Shen F, Sohn S, Wang C, Liu H, Jiang G. Developing a scalable FHIR-based clinical data normalization pipeline for standardizing and integrating unstructured and structured electronic health record data. JAMIA Open. 2019 Dec; 2 (4):570-579 Epub 2019 Oct 18 PMID: 32025655 PMCID: 6993992 DOI: 10.1093/jamiaopen/ooz056
  • Hong N, Wen A, Stone DJ, Tsuji S, Kingsbury PR, Rasmussen LV, Pacheco JA, Adekkanattu P, Wang F, Luo Y, Pathak J, Liu H, Jiang G. Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. J Biomed Inform. 2019 Nov; 99:103310 Epub 2019 Oct 14 PMID: 31622801 PMCID: 6990976 DOI: 10.1016/j.jbi.2019.103310
  • Yu Y, Ruddy KJ, Hong N, Tsuji S, Wen A, Shah ND, Jiang G. ADEpedia-on-OHDSI: A next generation pharmacovigilance signal detection platform using the OHDSI common data model. J Biomed Inform. 2019 Mar; 91:103119 Epub 2019 Feb 07 PMID: 30738946 PMCID: 6432939 DOI: 10.1016/j.jbi.2019.103119
  • Hong N, Wen A, Mojarad MR, Sohn S, Liu H, Jiang G. Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP. AMIA Annu Symp Proc. 2018; 2018:574-583 Epub 2018 Dec 05 PMID: 30815098 PMCID: 6371380
  • Hong N, Wen A, Shen F, Sohn S, Liu S, Liu H, Jiang G. Integrating Structured and Unstructured EHR Data Using an FHIR-based Type System: A Case Study with Medication Data. AMIA Jt Summits Transl Sci Proc. 2018; 2017:74-83 Epub 2018 May 18 PMID: 29888045 PMCID: 5961797

Patient Representations and Finding Like Patients

  • Li R, Wen A, Gao G, Liu H. MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks. In Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB ‘23). Association for Computing Machinery, New York, NY, USA, Article 11, 1–10. https://doi.org/10.1145/3584371.3612967
  • Wen A, Shen F, Moon S, Liu H, Fan J. A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, 2020, pp. 546-551, doi: 10.1109/CBMS49503.2020.00109.
  • Shen F, Wen A, Liu H, “Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System,” 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, 2020, pp. 37-40
  • Shen F, Wen A, Liu H, “Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings,” 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, 2020, pp. 169-172, doi: 10.1109/CBMS49503.2020.00039.
  • Shen F, Peng S, Fan Y, Wen A, Liu S, Wang Y, Wang L, Liu H. HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. J Biomed Inform. 2019 Aug; 96:103246 Epub 2019 June 27 PMID: 31255713 PMCID: 6710011 DOI: 10.1016/j.jbi.2019.103246
  • Shen F, Liu S, Wang Y, Wen A, Wang L, Liu H. Utilization of Electronic Medical Records and Biomedical Literature to Support the Diagnosis of Rare Diseases Using Data Fusion and Collaborative Filtering Approaches. JMIR Med Inform. 2018 Oct 10; 6 (4):e11301 PMID: 30305261 PMCID: 6231873 DOI: 10.2196/11301
  • Shen F, Liu S, Wang Y, Wang L, Wen A, Limper A, Liu H. Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement IEEE International Conference on Healthcare Informatics Workshop (ICHI-W). 2018; 29-33.

Other/Miscellaneous

  • Zong N, Li N, Wen A, Ngo V, Yu Y, Huang M, Chowdhury S, Jiang C, Fu S, Weinshilboum R, Jiang G, Hunter L, Liu H. BETA: a comprehensive benchmark for computational drug-target prediction. Brief Bioinform. 2022 Jul 18; 23 (4) PMID: 35649342 PMCID: 9294420 DOI: 10.1093/bib/bbac199
  • Zong N, Wen A, Moon S, Fu S, Wang L, Zhao Y, Yu Y, Huang M, Wang Y, Zheng G, Mielke MM, Cerhan JR, Liu H. Computational drug repurposing based on electronic health records: a scoping review. NPJ Digit Med. 2022 Jun 14; 5 (1):77 Epub 2022 June 14 PMID: 35701544 PMCID: 9198008 DOI: 10.1038/s41746-022-00617-6
  • Fu S, Wen A, Pagali S, Zong N, St Sauver J, Sohn S, Fan J, Liu H. The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records. Stud Health Technol Inform. 2022 Jun 6; 290:173-177 PMID: 35672994 DOI: 10.3233/SHTI220055
  • Fu S, Wen A, Schaeferle GM, Wilson PM, Demuth G, Ruan X, Liu S, Storlie C, Liu H. Assessment of Data Quality Variability across Two EHR Systems through a Case Study of Post-Surgical Complications. AMIA Annu Symp Proc. 2022; 2022:196-205 Epub 2022 May 23 PMID: 35854735 PMCID: 9285181
  • Zong N, Ngo V, Stone DJ, Wen A, Zhao Y, Yu Y, Liu S, Huang M, Wang C, Jiang G. Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study. JMIR Med Inform. 2021 May 25; 9 (5):e23586 PMID: 34032581 PMCID: 8188315 DOI: 10.2196/23586
  • Zong N, Wong RSN, Yu Y, Wen A, Huang M, Li N. Drug-target prediction utilizing heterogeneous bio-linked network embeddings. Brief Bioinform. 2021 Jan 18; 22 (1):568-580 PMID: 31885036 DOI: 10.1093/bib/bbz147
  • Zong N, Wong RSN, Yu Y, Wen A, Huang M, Li N. Drug-target prediction utilizing heterogeneous bio-linked network embeddings. Brief Bioinform. 2019 Dec 27 [Epub ahead of print] PMID: 31885036 DOI: 10.1093/bib/bbz147
  • Peng S, Shen F, Wen A, Wang L, Fan Y, Liu X, Liu H. Detecting Lifestyle Risk Factors for Chronic Kidney Disease With Comorbidities: Association Rule Mining Analysis of Web-Based Survey Data. J Med Internet Res. 2019 Dec 10; 21 (12):e14204 PMID: 31821152 PMCID: 6930505 DOI: 10.2196/14204
  • Peng S, Fan Y, Wang L, Wen A, Liu X, Liu H, Shen F. Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2018; 1302-1309.

Conference Presentations and Organized Workshops

  • Workshop: On Clinical Information Extraction for Collaborative EHR-based Clinical Research. Workshop Co-Organizer. Oct 31, 2021; 2021 AMIA Annual Symposium
  • Podium Presentation: Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. Nov 18, 2020; 2020 AMIA Annual Symposium
  • Paper Presentation: A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. Jul 29, 2020; IEEE 33rd International Symposium on Computer-Based Medical Systems
  • Podium Presentation: Visualizing Clinical Assessment Variation for Quality Improvement: An Example in Preoperative Physical Status Classification. Mar 23, 2020; 2020 AMIA Informatics Summit
  • Paper Presentation: Enhancing Clinical Information Retrieval through Contextual Queries and Indices. Dec 10, 2019; 2019 IEEE International Conference on Big Data