Publications

1. Seligson ND, Warner JL, Dalton WS, Martin D, Miller RS, Patt D, Kehl KL, Palchuk MB, Alterovitz G, Wiley LK, Huang M, Shen F, Wang Y, Nguyen KA, Wong AF, Meric-Bernstam F, Bernstam EV, Chen JL. Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity. J Am Med Inform Assoc. 2020 Sep 4 Epub 2020 Sept 04
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2. 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 6; 109:103526 Epub 2020 Aug 06
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3. Wang Y, Zhao Y, Therneau TM, Atkinson EJ, Tafti AP, Zhang N, Amin S, Limper AH, Khosla S, Liu H. Unsupervised machine learning for the discovery of latent disease clusters and patient subgroups using electronic health records. J Biomed Inform. 2020 Feb; 102:103364 Epub 2019 Dec 28
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4. Fu S, Carlson LA, Peterson KJ, Wang N, Zhou X, Peng S, Jiang J, Wang Y, Sauver JS, Liu H. Natural Language Processing for the Evaluation of Methodological Standards and Best Practices of EHR-based Clinical Research. AMIA Jt Summits Transl Sci Proc. 2020; 2020:171-180 Epub 2020 May 30
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5. 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.
   
6. Wang L, Luo L, Wang Y, Wampfler J, Yang P, Liu H. Natural language processing for populating lung cancer clinical research data. BMC Med Inform Decis Mak. 2019 Dec 5; 19 (Suppl 5):239 Epub 2019 Dec 05
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7. Wang Y, Xu H, Uzuner O. Editorial: The second international workshop on health natural language processing (HealthNLP 2019). BMC Med Inform Decis Mak. 2019 Dec 5; 19 (Suppl 5):233 Epub 2019 Dec 05
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8. Wyles CC, Tibbo ME, Fu S, Wang Y, Sohn S, Kremers WK, Berry DJ, Lewallen DG, Maradit-Kremers H. Use of Natural Language Processing Algorithms to Identify Common Data Elements in Operative Notes for Total Hip Arthroplasty. J Bone Joint Surg Am. 2019 Nov 6; 101 (21):1931-1938
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9. Zhou X, Wang Y, Sohn S, Therneau TM, Liu H, Knopman DS. Automatic extraction and assessment of lifestyle exposures for Alzheimer's disease using natural language processing. Int J Med Inform. 2019 Oct; 130:103943 Epub 2019 Aug 06
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10. 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
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11. 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
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12. Wang Y, Tafti AP, Sohn S, Zhang R. Applications of Natural Language Processing in Clinical Research and Practice Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics. 2019.
    
13. Wang L, Luo L, Wang Y, Wampfler JA, Yang P, Liu H. Information Extraction for Populating Lung Cancer Clinical Research Data. IEEE Int Conf Healthc Inform. 2019 Jun; 2019 Epub 2019 Nov 21
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14. Tafti AP, Wang Y, Shen F, Sagheb E, Kingsbury P, Liu H. Integrating word embedding neural networks with PubMed abstracts to extract keyword proximity of chronic diseases 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). 2019.
    
15. Fu S, Leung LY, Wang Y, Raulli AO, Kallmes DF, Kinsman KA, Nelson KB, Clark MS, Luetmer PH, Kingsbury PR, Kent DM, Liu H. Natural Language Processing for the Identification of Silent Brain Infarcts From Neuroimaging Reports. JMIR Med Inform. 2019 Apr 21; 7 (2):e12109
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16. Wang Y, Mehrabi S, Sohn S, Atkinson EJ, Amin S, Liu H. Natural language processing of radiology reports for identification of skeletal site-specific fractures. BMC Med Inform Decis Mak. 2019 Apr 4; 19 (Suppl 3):73 Epub 2019 Apr 04
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17. Wang L, Wang Y, Shen F, Rastegar-Mojarad M, Liu H. Discovering associations between problem list and practice setting. BMC Med Inform Decis Mak. 2019 Apr 4; 19 (Suppl 3):69 Epub 2019 Apr 04
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18. Shen F, Zhao Y, Wang L, Mojarad MR, Wang Y, Liu S, Liu H. Rare disease knowledge enrichment through a data-driven approach. BMC Med Inform Decis Mak. 2019 Feb 14; 19 (1):32
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19. Wang Y, Sohn S, Liu S, Shen F, Wang L, Atkinson EJ, Amin S, Liu H. A clinical text classification paradigm using weak supervision and deep representation. BMC Med Inform Decis Mak. 2019 Jan 7; 19 (1):1 Epub 2019 Jan 07
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20. Islamaj Dogan R, Kim S, Chatr-Aryamontri A, Wei CH, Comeau DC, Antunes R, Matos S, Chen Q, Elangovan A, Panyam NC, Verspoor K, Liu H, Wang Y, Liu Z, Altinel B, Husunbeyi ZM, Ozgur A, Fergadis A, Wang CK, Dai HJ, Tran T, Kavuluru R, Luo L, Steppi A, Zhang J, Qu J, Lu Z. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database (Oxford). 2019 Jan 1; 2019 Epub 2019 Jan 01
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21. Moon S, Liu S, Chen D, Wang Y, Wood DL, Chaudhry R, Liu H, Kingsbury P. Salience of Medical Concepts of Inside Clinical Texts and Outside Medical Records for Referred Cardiovascular Patients Journal of Healthcare Informatics Research. 2019; 1-20.
    
22. Zhao Y, Wang Y, Wang H, Yan B, Shen F, Peterson KJ, Rocca WA, St Sauver J, Liu H. Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2018.
    
23. Wang Y, Liu S, Afzal N, Rastegar-Mojarad M, Wang L, Shen F, Kingsbury P, Liu H. A comparison of word embeddings for the biomedical natural language processing. J Biomed Inform. 2018 Nov; 87:12-20 Epub 2018 Sept 12
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24. 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
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25. Zhou X, Liu H, Wang Y. A Comparison of Lifestyle Interventions for Alzheimer's Disease Extracted from Clinical Notes and Literature IEEE International Conference on Healthcare Informatics Workshop (ICHI-W). 2018; 74-75.
    
26. McRoy S, Rastegar-Mojarad M, Wang Y, Ruddy KJ, Haddad TC, Liu H. Assessing Unmet Information Needs of Breast Cancer Survivors: Exploratory Study of Online Health Forums Using Text Classification and Retrieval. JMIR Cancer. 2018 May 15; 4 (1):e10
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27. Sohn S, Wang Y, Wi CI, Krusemark EA, Ryu E, Ali MH, Juhn YJ, Liu H. Clinical documentation variations and NLP system portability: a case study in asthma birth cohorts across institutions. J Am Med Inform Assoc. 2018 Mar 1; 25 (3):353-359
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28. Wang Y, Mehrabi S, Sohn S, Atkinson E, Amin S, Liu H. Automatic extraction of major osteoporotic fractures from radiology reports using natural language processing Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. 2018; 64-5
    
29. Wang L, Rastegar-Mojarad M, Komandur Elayavilli R, Wang Y, Liu H. Identification of genetic causality statements in Medline abstracts leveraging distant supervision Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. 2018; 1-8. Epub 1900 Jan 01.
    
30. Liu S, Shen F, Komandur Elayavilli R, Wang Y, Rastegar-Mojarad M, Chaudhary V, Liu H. Extracting chemical-protein relations using attention-based neural networks. Database (Oxford). 2018 Jan 1; 2018 Epub 2018 Jan 01
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31. Wang L, Rastegar-Mojarad M, Ji Z, Liu S, Liu K, Moon S, Shen F, Wang Y, Yao L, Davis Iii JM, Liu H. Detecting Pharmacovigilance Signals Combining Electronic Medical Records With Spontaneous Reports: A Case Study of Conventional Disease-Modifying Antirheumatic Drugs for Rheumatoid Arthritis. Front Pharmacol. 2018; 9:875 Epub 2018 Aug 07
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32. Wang Y, Wang L, Rastegar-Mojarad M, Moon S, Shen F, Afzal N, Liu S, Zeng Y, Mehrabi S, Sohn S, Liu H. Clinical information extraction applications: A literature review. J Biomed Inform. 2018 Jan; 77:34-49 Epub 2017 Nov 21
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33. Wang Y, Afzal N, Fu S, Wang L, Shen F, Rastegar-Mojarad M, Liu H. MedSTS: a resource for clinical semantic textual similarity Language Resources and Evaluation. 2018; 1-6.
    
34. Wang L, Wang Y, Shen F, Rastegar-Mojarad M, Liu H. Predicting practice setting using topic modeling Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. 2018; 62-3. Epub 1900 Jan 01.
    
35. Moon S, Liu S, Kingsbury P, Chen D, Wang Y, Shen F, Chaudhry R, Liu H. Medical concept intersection between outside medical records and consultant notes: A case study in transferred cardiovascular patients 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2017; 1495-1500.
    
36. Zeng Y, Liu X, Wang Y, Shen F, Liu S, Rastegar-Mojarad M, Wang L, Liu H. Recommending Education Materials for Diabetic Questions Using Information Retrieval Approaches. J Med Internet Res. 2017 Oct 16; 19 (10):e342
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37. Liu S, Wang Y, Hong N, Shen F, Wu S, Hersh W, Liu H. On Mapping Textual Queries to a Common Data Model 2017 IEEE International Conference on Healthcare Informatics. 2017.
    
38. Wang Y, Choi I, Liu H. Generalized Ensemble Model for Document Ranking in Information Retrieval Computer Science & Information Systems. 2017; 14(1):123-151.
    
39. Shen F, Liu S, Wang Y, Wang L, Afzal N, Liu H. Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. AMIA Annu Symp Proc. 2017; 2017:1554-1563 Epub 2018 Apr 16
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40. 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
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41. Wang Y, Wang L, Rastegar-Mojarad M, Liu S, Shen F, Liu H. Systematic Analysis of Free-Text Family History in Electronic Health Record. AMIA Jt Summits Transl Sci Proc. 2017; 2017:104-113 Epub 2017 July 26
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42. Wang Y, Liu S, Shen F, Liu H, Rastegar-Mojarad M, Liu F. Dependency and AMR embeddings for drug-drug interaction extraction from biomedical literature ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 2017; 36-43. Epub 1900 Jan 01.
    
43. Wu S, Liu S, Wang Y, Timmons T, Uppili H, Bedrick S, Hersh W, Liu H. Intrainstitutional EHR collections for patient-level information retrieval Journal of the Association for Information Science and Technology. 2017; 68 (11):2636-48
    
44. Zeng Y, Liu X, Wang L, Liu H, Wang Y. Answering diabetic patients' questions using expert-vetted online resources: A case study Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. 01/01/2017; 525-8.
    
45. Wang Y, Rastegar-Mojarad M, Komandur-Elayavilli R, Liu H. Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. Database (Oxford). 2017 Jan 1; 2017
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46. Wang Y, Wu S, Li D, Mehrabi S, Liu H. A Part-Of-Speech term weighting scheme for biomedical information retrieval. J Biomed Inform. 2016 Oct; 63:379-389 Epub 2016 Sept 01
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47. Wang Y, Lee J, Choi I. Indexing by Latent Dirichlet Allocation and Ensemble Model Journal of the American Society for Information Science and Technology. 2016; 67(7):1736-1750.
    
48. Li D, Liu S, Rastegar-Mojarad M, Wang Y, Chaudhary V, Therneau T, Liu H. A Topic-modeling Based Framework for Drug-drug Interaction Classification from Biomedical Text. AMIA Annu Symp Proc. 2016; 2016:789-798 Epub 2017 Feb 10
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49. Liu S, Wang Y, Mehrabi S, Li D, Liu H. MayoBMI at ImageCLEF 2016 handwritten document retrieval task CEUR Workshop Proceedings. 2016; 1609:347-55.
    
50. Wang Y, Wu S, Liu H. MayoNLPTeam at the 2016 CLEF eHealth information retrieval task 1 CEUR Workshop Proceedings. 2016; 1609:198-204.
    
51. Kaggal VC, Elayavilli RK, Mehrabi S, Pankratz JJ, Sohn S, Wang Y, Li D, Rastegar MM, Murphy SP, Ross JL, Chaudhry R, Buntrock JD, Liu H. Toward a Learning Health-care System - Knowledge Delivery at the Point of Care Empowered by Big Data and NLP. Biomed Inform Insights. 2016; 8 (Suppl 1):13-22 Epub 2016 June 23
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52. Mehrabi S, Wang Y, Ihrke D, Liu H. Exploring Gaps of Family History Documentation in EHR for Precision Medicine -A Case Study of Familial Hypercholesterolemia Ascertainment. AMIA Jt Summits Transl Sci Proc. 2016; 2016:160-6 Epub 2016 July 20
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53. Afzal N, Wang Y, Liu H. MayoNLP at SemEval-2016 task 1: Semantic textual similarity based on lexical semantic net and deep learning semantic model Proceedings of SemEval 2016 - 10th International Workshop on Semantic Evaluation. 2016.
    
54. Li D, Afzal N, Rastegar M, Komandur R, Liu S, Wang Y, Shen F, Liu H. Resolution of Chemical Disease Relations with Diverse Features and Rules Proceedings of the Fifth BioCreative Challenge Evaluation Workshop. 2015; 280-285.
    
55. Li D, Rastegar-Mojarad M, Elayavilli RK, Wang Y, Mehrabi S, Yu Y, Sohn S, Li Y, Afzal N, Liu H. A frequency-filtering strategy of obtaining PHI-free sentences from clinical data repository BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 2015; 315-24.
    
56. Wang Y, Mehrabi S, Mojarad MR, Li D, Liu H. Retrieval of semantically similar healthcare questions in healthcare forums Proceedings - 2015 IEEE International Conference on Healthcare Informatics, ICHI 2015. 2015; 517-8.
    
57. Wang Y. Market index and stock price direction prediction using machine learning techniques: An empirical study on the KOSPI and HSI International Journal of Business Intelligence and Data Mining. 2014; 9(2):145-160.
    
58. Wang Y. A novel soft keyboard for touch screen phones International Journal of Human Factors and Ergonomics. 2013; 2(4):246-261.
    
59. Wang Y, Choi I. A Text Classification Method Based on Latent Topics Proceedings of the 1st International Conference on Operations Research and Enterprise Systems (ICORES). 2012; 212-214.