Publications

  1. George Mastorakos, Aditya Khurana, Ming Huang, Sunyang Fu, Ahmad P. Tafti, Jungwei Fan, Hongfang Liu. Probing Patient Messages Enhanced by Natural Language Processing: A Top-Down Message Corpus Analysis Health Data Science. 2021; Accepted.
  2. Fan J, Jeffery MM, Hooten WM, Shah ND, McCoy RG. Trends in Pain Medication Initiation Among Patients With Newly Diagnosed Diabetic Peripheral Neuropathy, 2014-2018. JAMA Netw Open. 2021 Jan 4; 4 (1):e2035632 Epub 2021 Jan 04
    View PubMed
  3. 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. 2021 Jan; 113:103660 Epub 2020 Dec 13
    View PubMed
  4. Moon S, Fan J. How You Ask Matters: The Effect of Paraphrastic Questions to BERT Performance on a Clinical SQuAD Dataset Proceedings of the 3rd Clinical Natural Language Processing Workshop. 2020.
  5. Carlson LA, Jeffery MM, Fu S, He H, McCoy RG, Wang Y, Hooten WM, St Sauver J, Liu H, Fan J. Characterizing Chronic Pain Episodes in Clinical Text at Two Health Care Systems: Comprehensive Annotation and Corpus Analysis. JMIR Med Inform. 2020 Nov 16; 8 (11):e18659
    View PubMed
  6. Zheng L, He Z, Wei D, Keloth V, Fan JW, Lindemann L, Zhu X, Cimino JJ, Perl Y. A review of auditing techniques for the Unified Medical Language System. J Am Med Inform Assoc. 2020 Oct 1; 27 (10):1625-1638
    View PubMed
  7. Wen A, Shen F, Moon S, Liu H, Fan J. A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation Proceedings of the IEEE International Symposium on Computer Based Medical Systems (CBMS). 2020; 549.
  8. Wen A, Elwazir MY, Moon S, Fan J. Adapting and evaluating a deep learning language model for clinical why-question answering. JAMIA Open. 2020 Apr; 3 (1):16-20 Epub 2020 Feb 04
    View PubMed
  9. 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.
  10. Fan J. Annotating and characterizing clinical sentences with explicit why-QA cues. Proceedings of the 2nd Clinical Natural Language Processing Workshop. 2019.
  11. Vitali F, Berghout J, Fan J, Li J, Li Q, Li H, Lussier YA. Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphisms. Proceedings of the Pacific Symposium on Biocomputing (PSB). 2019.
    View PubMed
  12. 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
    View PubMed
  13. Li H, Fan J, Berghout J, Aberasturi D, Li J, Wilson L, Chiu W, Pumajero M, Han J, Kenost C, Koripella PC, Pouladi N, Billheimer D, Bedrick EJ, Lussier YA. Novel disease syndromes unveiled by integrative multiscale network analysis of diseases sharing molecular effectors and comorbidities. BMC Medical Genomics. 2018; 11(Suppl 6):112.
    View PubMed
  14. Fan JW, Li J, Lussier YA. Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context. J Healthc Eng. 2017; 2017:3818302 Epub 2017 Aug 30
    View PubMed
  15. Fan JW, Lussier YA. Word-of-Mouth Innovation: Hypothesis Generation for Supplement Repurposing based on Consumer Reviews. AMIA Annu Symp Proc. 2017; 2017:689-695 Epub 2018 Apr 16
    View PubMed
  16. Torii M, Tilak SS, Doan S, Zisook DS, Fan JW. Mining Health-Related Issues in Consumer Product Reviews by Using Scalable Text Analytics. Biomed Inform Insights. 2016; 8 (Suppl 1):1-11 Epub 2016 June 20
    View PubMed
  17. Torii M, Fan JW, Yang WL, Lee T, Wiley MT, Zisook DS, Huang Y. Risk factor detection for heart disease by applying text analytics in electronic medical records. J Biomed Inform. 2015 Dec; 58 Suppl:S164-70 Epub 2015 Aug 14
    View PubMed
  18. Jiang M, Huang Y, Fan JW, Tang B, Denny J, Xu H. Parsing clinical text: how good are the state-of-the-art parsers? BMC Med Inform Decis Mak. 2015; 15 Suppl 1:S2 Epub 2015 May 20
    View PubMed
  19. Fan JW, Yang EW, Jiang M, Prasad R, Loomis RM, Zisook DS, Denny JC, Xu H, Huang Y. Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. J Am Med Inform Assoc. 2013 Nov-Dec; 20 (6):1168-77 Epub 2013 Aug 01
    View PubMed
  20. Xu H, AbdelRahman S, Jiang M, Fan JW, Huang Y. An initial study of full parsing of clinical text using the Stanford Parser. IEEE BIBM 2011 Workshop. 2011; 607-14.
  21. Fan JW, Friedman C. Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies. J Biomed Inform. 2011 Oct; 44 (5):805-14 Epub 2011 Apr 28
    View PubMed
  22. Fan JW, Prasad R, Yabut RM, Loomis RM, Zisook DS, Mattison JE, Huang Y. Part-of-speech tagging for clinical text: wall or bridge between institutions? AMIA Annu Symp Proc. 2011; 2011:382-91 Epub 2011 Oct 22
    View PubMed
  23. Fan JW, Friedman C. Generating quality word sense disambiguation test sets based on MeSH indexing. AMIA Annu Symp Proc. 2009 Nov 14; 2009:183-7
    View PubMed
  24. Zhu X, Fan JW, Baorto DM, Weng C, Cimino JJ. A review of auditing methods applied to the content of controlled biomedical terminologies. J Biomed Inform. 2009 Jun; 42 (3):413-25 Epub 2009 Mar 12
    View PubMed
  25. Fan JW, Friedman C. Word sense disambiguation via semantic type classification. AMIA Annu Symp Proc. 2008 Nov 6; 177-81 Epub 2008 Nov 06
    View PubMed
  26. Fan JW, Friedman C. Semantic reclassification of the UMLS concepts. Bioinformatics. 2008 Sep 1; 24 (17):1971-3 Epub 2008 July 13
    View PubMed
  27. Fan JW, Xu H, Friedman C. Using contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007 Jul 24; 8:264 Epub 2007 July 24
    View PubMed
  28. Fan JW, Friedman C. Semantic classification of biomedical concepts using distributional similarity. J Am Med Inform Assoc. 2007 Jul-Aug; 14 (4):467-77 Epub 2007 Apr 25
    View PubMed
  29. Xu H, Fan JW, Friedman C. Combining multiple evidence for gene symbol disambiguation. Proceedings of BioNLP. 2007; 41-8.
  30. Xu H, Fan JW, Hripcsak G, Mendonca EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics. 2007 Apr 15; 23 (8):1015-22 Epub 2007 Feb 21
    View PubMed
  31. Chen HH, Chiu TH, Fan JW. Educating knowledge management professionals in the era of knowledge economy. Journal of Information & Knowledge Management. 2002; 1(2):91-98.