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Hong Yu PhD, MA, MS

TitleAdjunct Professor
InstitutionUMass Chan Medical School
AddressUMass Chan Medical School
55 Lake Avenue North AC7-059
Worcester MA 01655
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DivisionCardiovascular Medicine

    InstitutionUMass Chan 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,Physiology & Molecular Biophys
    Columbia University, New York, NY, United StatesPHDBiomedical Informatics

    Collapse Overview 
    Collapse overview


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


    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


    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    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.
      Citations:    Fields:    Translation:Humans
    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.
      Citations: 2     Fields:    
    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.
      Citations: 6     Fields:    Translation:Humans
    4. Agarwal S, Yu H, Kohane I. BioN?T: a searchable database of biomedical negated sentences. BMC Bioinformatics. 2011 Oct 27; 12:420. PMID: 22032181.
      Citations: 10     Fields:    Translation:Humans
    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.
      Citations:    Fields:    Translation:Humans
    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.
      Citations: 4     Fields:    Translation:Humans
    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.
      Citations: 12     Fields:    Translation:Humans
    8. Liu F, Tur G, Hakkani-T?r 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.
      Citations: 6     Fields:    Translation:Humans
    9. Kim D, Ramesh BP, Yu H. Automatic figure classification in bioscience literature. J Biomed Inform. 2011 Oct; 44(5):848-58. PMID: 21645638.
      Citations: 4     Fields:    
    10. Agarwal S, Yu H. Figure summarizer browser extensions for PubMed Central. Bioinformatics. 2011 Jun 15; 27(12):1723-4. PMID: 21493658.
      Citations: 1     Fields:    
    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.
      Citations:    Fields:    
    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.
      Citations: 43     Fields:    
    13. Kim D, Yu H. Figure text extraction in biomedical literature. PLoS One. 2011 Jan 13; 6(1):e15338. PMID: 21249186.
      Citations: 3     Fields:    
    14. Ramesh BP, Yu H. Identifying discourse connectives in biomedical text. AMIA Annu Symp Proc. 2010 Nov 13; 2010:657-61. PMID: 21347060.
      Citations: 3     Fields:    Translation:Humans
    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.
      Citations: 7     Fields:    Translation:Humans
    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.
      Citations: 26     Fields:    Translation:Humans
    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.
      Citations: 10     Fields:    
    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.
      Citations: 24     Fields:    Translation:Humans
    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.
      Citations: 13     Fields:    
    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.
      Citations: 11     Fields:    
    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.
      Citations: 3     Fields:    
    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.
      Citations: 12     Fields:    
    23. Kim D, Yu H. Hierarchical image classification in the bioscience literature. AMIA Annu Symp Proc. 2009 Nov 14; 2009:327-31. PMID: 20351874.
      Citations: 4     Fields:    
    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 01; 1-4 Nov(2009):308-313. PMID: 21170175.
    25. Agarwal S, Yu H. Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion. Bioinformatics. 2009 Dec 01; 25(23):3174-80. PMID: 19783830.
      Citations: 20     Fields:    
    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 Jan 06; 4:1. PMID: 19126221.
    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.
      Citations: 17     Fields:    
    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.
      Citations: 26     Fields:    Translation:Humans
    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.
      Citations: 6     Fields:    Translation:Humans
    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.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    31. Yu H, Lee M. Accessing bioscience images from abstract sentences. Bioinformatics. 2006 Jul 15; 22(14):e547-56. PMID: 16873519.
      Citations: 21     Fields:    
    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.
      Citations: 11     Fields:    
    33. Lee M, Wang W, Yu H. Exploring supervised and unsupervised methods to detect topics in biomedical text. BMC Bioinformatics. 2006 Mar 16; 7:140. PMID: 16539745.
      Citations: 10     Fields:    Translation:Humans
    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.
      Citations: 16     Fields:    
    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.
      Citations: 12     Fields:    Translation:Humans
    36. Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Dubou? 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.
      Citations: 87     Fields:    Translation:Cells
    37. Yu H, Agichtein E. Extracting synonymous gene and protein terms from biological literature. Bioinformatics. 2003; 19 Suppl 1:i340-9. PMID: 12855479.
      Citations: 17     Fields:    
    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.
      Citations: 5     Fields:    
    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.
      Citations: 26     Fields:    
    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.
      Citations: 13     Fields:    
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