Loading...
Header Logo
Keywords
Last Name
Institution

Hong Yu PhD

TitleAdjunct Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentMedicine
AddressUniversity of Massachusetts Medical School
55 Lake Avenue North, AC7-059
Worcester MA 01655
Phone508-856-3474
vCardDownload vCard
    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentMedicine
    DivisionCardiovascular Medicine

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentBioinformatics and Computational Biology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentClinical Population Health Research

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentMasters in Clinical Investigation

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionUMMS - Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology


    Collapse Biography 
    Collapse education and training
    Huazhong University of Science and Technology, Wuhan, , ChinaBSBiomedical Engineering
    Beijing Normal University, Haidian, , ChinaMSPhysiology
    Columbia University, New York, NY, United StatesMABiomedical Informatics
    Columbia University, New York, NY, United StatesMPHILPhysiology & Molecular Biophys
    Columbia University, New York, NY, United StatesPHDBiomedical Informatics

    Collapse Overview 
    Collapse overview

    Interests

    Information retrieval, extraction, natural language processing, summarization, human-computer interaction, with a focus on biomedical applications.

    Biography

    Ph.D. Biomedical Informatics, Columbia University, New York; MA and MPh, Physiology and Cellular Biophysics, Columbia University, New York; MS, Physiology, Beijing University, China; BS, Biomedical Engineering, Huazhong University of Science and Technology, China

    Research

    Professor Yu's research interests are in the areas of information retrieval, extraction, natural language processing, summarization, human-computer interaction, with a focus on biomedical applications. She has led the development of many systems, including the biomedical question answering system AskHERMES (http://www.askhermes.org), the adverse drug event pharmacovigilance system (http://www.ADErepository.org), the innovative biomedical figure search system (http://figuresearch.askhermes.org), and the NoteAid systems that help patients comprehend electronic medical records (http://ClinicalNotesAid.org).

    Awards & Activities

    Professor Yu has served as co-Chair in the biomedical natural language processing sections of the Pacific Symposium of Biocomputing and IEEE International Conference on Bioinformatics & Biomedicine. She is a member of the editorial board of the Journal of Biomedical Informatics, and is the PI of several National Institutes of Health funded projects. She was a recipient of the National Library of Medicine (NLM) pre-doctoral training grant to Columbia University and is one of the six “star trainees” selected by NLM on its celebration of 175th anniversary. Her first paper in biomedical informatics was nominated as one of the best papers in the American Medical Informatics Association Fall Symposium of 1999. Her work is included as best paper in IMIA Yearbook of Medical Informatics 2011, described in “Translational Bioinformatics 2012 Year in Review” by Russ Altman, and featured in Science, Nature, BioInform, the Pulitzer-winning Milwaukee Journal Sentinel, and the Milwaukee Public Radio.




    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Liu F, Moosavinasab S, Houston TK, Yu H. MedTxting: learning based and knowledge rich SMS-style medical text contraction. AMIA Annu Symp Proc. 2012; 2012:558-67. PMID: 23304328.
      View in: PubMed
    2. Bockhorst JP, Conroy JM, Agarwal S, O'Leary DP, Yu H. Beyond captions: linking figures with abstract sentences in biomedical articles. PLoS One. 2012; 7(7):e39618. PMID: 22815711.
      View in: PubMed
    3. Ramesh BP, Prasad R, Miller T, Harrington B, Yu H. Automatic discourse connective detection in biomedical text. J Am Med Inform Assoc. 2012 Sep-Oct; 19(5):800-8. PMID: 22744958.
      View in: PubMed
    4. Agarwal S, Yu H, Kohane I. BioNØT: a searchable database of biomedical negated sentences. BMC Bioinformatics. 2011 Oct 27; 12:420. PMID: 22032181.
      View in: PubMed
    5. Miller T, Ravvaz K, Cimino JJ, Yu H. An investigation into the feasibility of spoken clinical question answering. AMIA Annu Symp Proc. 2011; 2011:954-9. PMID: 22195154.
      View in: PubMed
    6. Agarwal S, Liu F, Yu H. Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. BMC Bioinformatics. 2011 Oct 03; 12 Suppl 8:S10. PMID: 22151701.
      View in: PubMed
    7. Liu F, Antieau LD, Yu H. Toward automated consumer question answering: automatically separating consumer questions from professional questions in the healthcare domain. J Biomed Inform. 2011 Dec; 44(6):1032-8. PMID: 21856442.
      View in: PubMed
    8. Liu F, Tur G, Hakkani-Tür D, Yu H. Towards spoken clinical-question answering: evaluating and adapting automatic speech-recognition systems for spoken clinical questions. J Am Med Inform Assoc. 2011 Sep-Oct; 18(5):625-30. PMID: 21705457.
      View in: PubMed
    9. Kim D, Ramesh BP, Yu H. Automatic figure classification in bioscience literature. J Biomed Inform. 2011 Oct; 44(5):848-58. PMID: 21645638.
      View in: PubMed
    10. Agarwal S, Yu H. Figure summarizer browser extensions for PubMed Central. Bioinformatics. 2011 Jun 15; 27(12):1723-4. PMID: 21493658.
      View in: PubMed
    11. Zhang Q, Cao YG, Yu H. Parsing citations in biomedical articles using conditional random fields. Comput Biol Med. 2011 Apr; 41(4):190-4. PMID: 21419403.
      View in: PubMed
    12. Cao Y, Liu F, Simpson P, Antieau L, Bennett A, Cimino JJ, Ely J, Yu H. AskHERMES: An online question answering system for complex clinical questions. J Biomed Inform. 2011 Apr; 44(2):277-88. PMID: 21256977.
      View in: PubMed
    13. Kim D, Yu H. Figure text extraction in biomedical literature. PLoS One. 2011 Jan 13; 6(1):e15338. PMID: 21249186.
      View in: PubMed
    14. Ramesh BP, Yu H. Identifying discourse connectives in biomedical text. AMIA Annu Symp Proc. 2010 Nov 13; 2010:657-61. PMID: 21347060.
      View in: PubMed
    15. Agarwal S, Choubey L, Yu H. Automatically classifying the role of citations in biomedical articles. AMIA Annu Symp Proc. 2010 Nov 13; 2010:11-5. PMID: 21346931.
      View in: PubMed
    16. Agarwal S, Yu H. Biomedical negation scope detection with conditional random fields. J Am Med Inform Assoc. 2010 Nov-Dec; 17(6):696-701. PMID: 20962133.
      View in: PubMed
    17. Yu H, Liu F, Ramesh BP. Automatic figure ranking and user interfacing for intelligent figure search. PLoS One. 2010 Oct 07; 5(10):e12983. PMID: 20949102.
      View in: PubMed
    18. Li Z, Liu F, Antieau L, Cao Y, Yu H. Lancet: a high precision medication event extraction system for clinical text. J Am Med Inform Assoc. 2010 Sep-Oct; 17(5):563-7. PMID: 20819865.
      View in: PubMed
    19. Agarwal S, Yu H. Detecting hedge cues and their scope in biomedical text with conditional random fields. J Biomed Inform. 2010 Dec; 43(6):953-61. PMID: 20709188.
      View in: PubMed
    20. Cao YG, Cimino JJ, Ely J, Yu H. Automatically extracting information needs from complex clinical questions. J Biomed Inform. 2010 Dec; 43(6):962-71. PMID: 20670693.
      View in: PubMed
    21. Cao Y, Li Z, Liu F, Agarwal S, Zhang Q, Yu H. An IR-aided machine learning framework for the BioCreative II.5 Challenge. IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep; 7(3):454-61. PMID: 20671317.
      View in: PubMed
    22. Agarwal S, Yu H. FigSum: automatically generating structured text summaries for figures in biomedical literature. AMIA Annu Symp Proc. 2009 Nov 14; 2009:6-10. PMID: 20351812.
      View in: PubMed
    23. Kim D, Yu H. Hierarchical image classification in the bioscience literature. AMIA Annu Symp Proc. 2009 Nov 14; 2009:327-31. PMID: 20351874.
      View in: PubMed
    24. Yu H, Agarwal S, Frid N. Investigating and Annotating the Role of Citation in Biomedical Full-Text Articles. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2009 Nov 1; 1-4 Nov(2009):308-313. PMID: 21170175.
      View in: PubMed
    25. Agarwal S, Yu H. Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion. Bioinformatics. 2009 Dec 1; 25(23):3174-80. PMID: 19783830.
      View in: PubMed
    26. Yu H, Agarwal S, Johnston M, Cohen A. Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension. J Biomed Discov Collab. 2009; 4:1. PMID: 19126221.
      View in: PubMed
    27. Yu H, Cao YG. Automatically extracting information needs from Ad Hoc clinical questions. AMIA Annu Symp Proc. 2008 Nov 06; 96-100. PMID: 18999100.
      View in: PubMed
    28. Yu H, Lee M, Kaufman D, Ely J, Osheroff JA, Hripcsak G, Cimino J. Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians. J Biomed Inform. 2007 Jun; 40(3):236-51. PMID: 17462961.
      View in: PubMed
    29. Yu H, Kaufman D. A cognitive evaluation of four online search engines for answering definitional questions posed by physicians. Pac Symp Biocomput. 2007; 328-39. PMID: 17990503.
      View in: PubMed
    30. Tulipano PK, Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier YA, Friedman C. Natural language processing and visualization in the molecular imaging domain. J Biomed Inform. 2007 Jun; 40(3):270-81. PMID: 17084109.
      View in: PubMed
    31. Yu H, Lee M. Accessing bioscience images from abstract sentences. Bioinformatics. 2006 Jul 15; 22(14):e547-56. PMID: 16873519.
      View in: PubMed
    32. Yu H, Kim W, Hatzivassiloglou V, Wilbur WJ. Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. J Biomed Inform. 2007 Apr; 40(2):150-9. PMID: 16843731.
      View in: PubMed
    33. Lee M, Wang W, Yu H. Exploring supervised and unsupervised methods to detect topics in biomedical text. BMC Bioinformatics. 2006; 7:140. PMID: 16539745.
      View in: PubMed
    34. Yu H. Towards answering biological questions with experimental evidence: automatically identifying text that summarize image content in full-text articles. AMIA Annu Symp Proc. 2006; 834-8. PMID: 17238458.
      View in: PubMed
    35. Lee M, Cimino J, Zhu HR, Sable C, Shanker V, Ely J, Yu H. Beyond information retrieval--medical question answering. AMIA Annu Symp Proc. 2006; 469-73. PMID: 17238385.
      View in: PubMed
    36. Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 2004 Feb; 37(1):43-53. PMID: 15016385.
      View in: PubMed
    37. Yu H, Agichtein E. Extracting synonymous gene and protein terms from biological literature. Bioinformatics. 2003; 19 Suppl 1:i340-9. PMID: 12855479.
      View in: PubMed
    38. Yu H, Hatzivassiloglou V, Rzhetsky A, Wilbur WJ. Automatically identifying gene/protein terms in MEDLINE abstracts. J Biomed Inform. 2002 Oct-Dec; 35(5-6):322-30. PMID: 12968781.
      View in: PubMed
    39. Yu H, Hripcsak G, Friedman C. Mapping abbreviations to full forms in biomedical articles. J Am Med Inform Assoc. 2002 May-Jun; 9(3):262-72. PMID: 11971887.
      View in: PubMed
    40. Yu H, Hatzivassiloglou V, Friedman C, Rzhetsky A, Wilbur WJ. Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. Proc AMIA Symp. 2002; 919-23. PMID: 12463959.
      View in: PubMed
    For assistance with using Profiles, please refer to the online tutorials or contact UMMS Help Desk or call 508-856-8643.
    Yu's Networks
    Click the "See All" links for more information and interactive visualizations!
    Concepts Expand Description
    _
    Co-Authors Expand Description
    _
    Similar People Expand Description
    _
    Same Department Expand Description
    Physical Neighbors Expand Description
    _