Hong Yu

Summary

Affiliation: University of Wisconsin-Milwaukee
Country: USA

Publications

  1. pmc Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI 53201 0413, USA
    J Biomed Discov Collab 4:1. 2009
  2. pmc The biomedical discourse relation bank
    Rashmi Prasad
    Institute for Research in Cognitive Science, University of Pennsylvania, 3401 Walnut Street, Philadelphia, PA 19104, USA
    BMC Bioinformatics 12:188. 2011
  3. pmc Automatic figure ranking and user interfacing for intelligent figure search
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, United States of America
    PLoS ONE 5:e12983. 2010
  4. ncbi request reprint Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Enderis Hall 939, 2400 E Hartford Avenue, P O Box 413, Milwaukee, WI 53211, USA
    J Biomed Inform 40:236-51. 2007
  5. ncbi request reprint Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI 53211, USA
    J Biomed Inform 40:150-9. 2007
  6. pmc AskHERMES: An online question answering system for complex clinical questions
    Yonggang Cao
    Department of Health Sciences, University of Wisconsin Milwaukee, 2400 E Hartford Avenue, Milwaukee, WI 53211, USA
    J Biomed Inform 44:277-88. 2011
  7. pmc Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion
    Shashank Agarwal
    University of Wisconsin, Milwaukee, Milwaukee WI 53211, USA
    Bioinformatics 25:3174-80. 2009
  8. pmc Figure text extraction in biomedical literature
    Daehyun Kim
    Department of Health Science, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, United States of America
    PLoS ONE 6:e15338. 2011
  9. pmc Automatic figure classification in bioscience literature
    Daehyun Kim
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
    J Biomed Inform 44:848-58. 2011
  10. pmc Toward automated consumer question answering: automatically separating consumer questions from professional questions in the healthcare domain
    Feifan Liu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI 53211, United States
    J Biomed Inform 44:1032-8. 2011

Collaborators

Detail Information

Publications42

  1. pmc Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI 53201 0413, USA
    J Biomed Discov Collab 4:1. 2009
    ..As a crucial step, we studied the importance of associated text in biomedical figure comprehension...
  2. pmc The biomedical discourse relation bank
    Rashmi Prasad
    Institute for Research in Cognitive Science, University of Pennsylvania, 3401 Walnut Street, Philadelphia, PA 19104, USA
    BMC Bioinformatics 12:188. 2011
    ..A biomedical text corpus annotated with discourse relations would be very useful for developing and evaluating methods for biomedical discourse processing. However, little effort has been made to develop such an annotated resource...
  3. pmc Automatic figure ranking and user interfacing for intelligent figure search
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, United States of America
    PLoS ONE 5:e12983. 2010
    ..org). Existing research in figure search treats each figure equally, but we introduce a novel concept of "figure ranking": figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery...
  4. ncbi request reprint Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Enderis Hall 939, 2400 E Hartford Avenue, P O Box 413, Milwaukee, WI 53211, USA
    J Biomed Inform 40:236-51. 2007
    ....
  5. ncbi request reprint Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI 53211, USA
    J Biomed Inform 40:150-9. 2007
    ..We report up to 92% prediction precision and up to 91% coverage...
  6. pmc AskHERMES: An online question answering system for complex clinical questions
    Yonggang Cao
    Department of Health Sciences, University of Wisconsin Milwaukee, 2400 E Hartford Avenue, Milwaukee, WI 53211, USA
    J Biomed Inform 44:277-88. 2011
    ..We have built a clinical question answering system named AskHERMES to perform robust semantic analysis on complex clinical questions and output question-focused extractive summaries as answers...
  7. pmc Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion
    Shashank Agarwal
    University of Wisconsin, Milwaukee, Milwaukee WI 53211, USA
    Bioinformatics 25:3174-80. 2009
    ..95% accuracy and an average F-score of 91.55%, which is significantly higher than baseline systems. A web version of this system is available online at-http://wood.ims.uwm.edu/full_text_classifier/...
  8. pmc Figure text extraction in biomedical literature
    Daehyun Kim
    Department of Health Science, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, United States of America
    PLoS ONE 6:e15338. 2011
    ..Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures...
  9. pmc Automatic figure classification in bioscience literature
    Daehyun Kim
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
    J Biomed Inform 44:848-58. 2011
    ..7% F1-score for five-type classification. We demonstrated our system at http://figureclassification.askhermes.org/...
  10. pmc Toward automated consumer question answering: automatically separating consumer questions from professional questions in the healthcare domain
    Feifan Liu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI 53211, United States
    J Biomed Inform 44:1032-8. 2011
    ..In this paper, we propose that a first step toward answering the queries of different users is automatically classifying questions according to whether they were asked by healthcare professionals or consumers...
  11. pmc Lancet: a high precision medication event extraction system for clinical text
    Zuofeng Li
    College of Health Sciences, University of Wisconsin Milwaukee, Wisconsin, USA
    J Am Med Inform Assoc 17:563-7. 2010
    ....
  12. pmc Figure summarizer browser extensions for PubMed Central
    Shashank Agarwal
    Medical Informatics, College of Health Science, University of Wisconsin Milwaukee, Milwaukee, WI 53201 0413, USA
    Bioinformatics 27:1723-4. 2011
    ..askhermes.org/). In this article, we report on the development of web browser extensions for Mozilla Firefox, Google Chrome and Apple Safari to display summaries for figures in PubMed Central and NCBI Images...
  13. ncbi request reprint Accessing bioscience images from abstract sentences
    Hong Yu
    Department of Health Sciences, University of Wisconsin Milwaukee, Wisconsin, USA
    Bioinformatics 22:e547-56. 2006
    ..We further developed systems that explored hierarchical clustering algorithms to automatically identify abstract sentences that summarize the images. One of the systems achieves a precision of 100% that corresponds to a recall of 4.6%...
  14. pmc Automatically extracting information needs from complex clinical questions
    Yong gang Cao
    University of Wisconsin Milwaukee, 2400 Hartford Avenue, Milwaukee, WI 53201, USA
    J Biomed Inform 43:962-71. 2010
    ..Our study is motivated in the context of developing the larger clinical question answering system AskHERMES (Help clinicians to Extract and aRrticulate Multimedia information for answering clinical quEstionS)...
  15. doi request reprint An IR-aided machine learning framework for the BioCreative II.5 Challenge
    Yonggang Cao
    College of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI 53211, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:454-61. 2010
    ..The results demonstrated that our IR-based framework is efficient, robust, and potentially scalable...
  16. pmc Parsing citations in biomedical articles using conditional random fields
    Qing Zhang
    University of Wisconsin Milwaukee, Milwaukee, WI 53211, USA
    Comput Biol Med 41:190-4. 2011
    ..Author, Title, Journal, and Year). With a subset of html format open-access PubMed Central articles, we report an overall 97.95% F1-score. The citation parser can be accessed at: http://www.cs.uwm.edu/∼qing/projects/cithit/index.html...
  17. pmc An investigation into the feasibility of spoken clinical question answering
    Tim Miller
    College of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
    AMIA Annu Symp Proc 2011:954-9. 2011
    ..Our results suggest that the medical domain differs enough from the open domain to require additional work in automatic speech recognition adapted for the biomedical domain...
  18. pmc Automatic discourse connective detection in biomedical text
    Balaji Polepalli Ramesh
    Department of Electrical Engineering and Computer Science, University of Wisconsin Milwaukee, Milwaukee, Wisconsin 53211, USA
    J Am Med Inform Assoc 19:800-8. 2012
    ..In this study supervised machine-learning approaches were developed and evaluated for automatically identifying discourse connectives in biomedical text...
  19. pmc BioNØT: a searchable database of biomedical negated sentences
    Shashank Agarwal
    Medical Informatics, College of Engineering and Applied Sciences, University of Wisconsin Milwaukee, 3200 N, Cramer St, Milwaukee, WI 53201 0784, USA
    BMC Bioinformatics 12:420. 2011
    ..We report on the development of BioNØT, a database of negated sentences that can be used to extract such negated events...
  20. pmc Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions
    Shashank Agarwal
    Medical Informatics, College of Engineering and Applied Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
    BMC Bioinformatics 12:S10. 2011
    ....
  21. pmc Detecting hedge cues and their scope in biomedical text with conditional random fields
    Shashank Agarwal
    Medical Informatics, University of Wisconsin Milwaukee, Milwaukee, WI, USA
    J Biomed Inform 43:953-61. 2010
    ..Our objective was to develop an algorithm that would automatically detect hedge cues and their scope in biomedical literature...
  22. pmc FigSum: automatically generating structured text summaries for figures in biomedical literature
    Shashank Agarwal
    University of Wisconsin Milwaukee, Milwaukee, WI, USA
    AMIA Annu Symp Proc 2009:6-10. 2009
    ..Our evaluation shows that FigSum captures 53% of the sentences in the gold standard summaries annotated by biomedical scientists and achieves an average ROUGE-1 score of 0.70, which is higher than a baseline system...
  23. pmc Beyond captions: linking figures with abstract sentences in biomedical articles
    Joseph P Bockhorst
    Department of Computer Science, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, United States of America
    PLoS ONE 7:e39618. 2012
    ..82 fewer mouse clicks. A user evaluation shows that human users find our system beneficial. The system is available at http://FigureItOut.askHERMES.org...
  24. pmc Towards spoken clinical-question answering: evaluating and adapting automatic speech-recognition systems for spoken clinical questions
    Feifan Liu
    Department of Health Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
    J Am Med Inform Assoc 18:625-30. 2011
    ..To evaluate existing automatic speech-recognition (ASR) systems to measure their performance in interpreting spoken clinical questions and to adapt one ASR system to improve its performance on this task...
  25. pmc Hierarchical image classification in the bioscience literature
    Daehyun Kim
    Department of Health Science, University of Wisconsin Milwaukee, Milwaukee, WI, USA
    AMIA Annu Symp Proc 2009:327-31. 2009
    ..In particular, the recall of hierarchical image classification was greatly improved due to the high accuracy of the initial classification...
  26. pmc Biomedical negation scope detection with conditional random fields
    Shashank Agarwal
    Medical Informatics, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
    J Am Med Inform Assoc 17:696-701. 2010
    ..Text mining applications benefit from the detection of negation and its scope. However, due to the complexity of language, identifying the scope of negation in a sentence is not a trivial task...
  27. pmc Learning to rank figures within a biomedical article
    Feifan Liu
    Department of Computer Science, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, United States of America
    PLoS ONE 9:e61567. 2014
    ....
  28. ncbi request reprint CiteGraph: a citation network system for MEDLINE articles and analysis
    Qing Zhang
    Department of Electrical Engineering and Computer Science, University of Wisconsin Milwaukee, Milwaukee, WI, USA
    Stud Health Technol Inform 192:832-6. 2013
    ..CiteGraph can be a useful resource to both the biomedical community, and bibliometric research. ..
  29. pmc MedTxting: learning based and knowledge rich SMS-style medical text contraction
    Feifan Liu
    University of Wisconsin Milwaukee, Milwaukee, WI, USA
    AMIA Annu Symp Proc 2012:558-67. 2012
    ....
  30. pmc Automatically classifying the role of citations in biomedical articles
    Shashank Agarwal
    University of Wisconsin Milwaukee, Milwaukee, WI
    AMIA Annu Symp Proc 2010:11-5. 2010
    ..We annotated 1,710 sentences using the annotation schema and our trained classifier obtained an average F1-score of 76.5%. The classifier is available for free as a Java API from http://citation.askhermes.org...
  31. pmc Identifying discourse connectives in biomedical text
    Balaji Polepalli Ramesh
    University of Wisconsin Milwaukee, Milwaukee, WI
    AMIA Annu Symp Proc 2010:657-61. 2010
    ..69 F1-score, a much better performance despite a much smaller training size. Our preliminary analysis suggests the existence of domain-specific features, and we speculate that domain-adaption approaches may further improve performance...
  32. ncbi request reprint Natural language processing and visualization in the molecular imaging domain
    P Karina Tulipano
    Department of Biomedical Informatics, Columbia University, 622 West 168th Street, Vanderbilt Clinic Floor 5, NY 10032, USA
    J Biomed Inform 40:270-81. 2007
    ..74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information...
  33. ncbi request reprint Extracting synonymous gene and protein terms from biological literature
    Hong Yu
    Department of Computer Science, Columbia University, New York, NY, USA
    Bioinformatics 19:i340-9. 2003
    ..Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance...
  34. ncbi request reprint GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data
    Andrey Rzhetsky
    Columbia Genome Center, Columbia University, New York, NY 10032, USA
    J Biomed Inform 37:43-53. 2004
    ..GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information...
  35. pmc Exploring supervised and unsupervised methods to detect topics in biomedical text
    Minsuk Lee
    Department of Biomedical Informatics, Columbia University, 622West, 168th Street, VC 5, NY 10032, USA
    BMC Bioinformatics 7:140. 2006
    ....
  36. pmc Frontiers of biomedical text mining: current progress
    Pierre Zweigenbaum
    LIMSI CNRS, BP 133, 91403 Orsay Cedex, France
    Brief Bioinform 8:358-75. 2007
    ..In this article we review the current state of the art in biomedical text mining or 'BioNLP' in general, focusing primarily on papers published within the past year...
  37. ncbi request reprint Automatically identifying gene/protein terms in MEDLINE abstracts
    Hong Yu
    Department of Computer Science, Columbia University, 1214 Amsterdam Avenue, New York, NY 10027, USA
    J Biomed Inform 35:322-30. 2002
    ..We found that many of the pairs in our knowledge source do not appear in the current GenBank database. Therefore our methods may also be used for automatic lexicon generation...
  38. doi request reprint Right ventricular pacing is an independent predictor for ventricular tachycardia/ventricular fibrillation occurrence and heart failure events in patients with an implantable cardioverter-defibrillator
    Ajmal Gardiwal
    Department of Cardiovascular Medicine, Hannover Medical School, Carl Neuberg Str 1, 30625 Hannover, Germany
    Europace 10:358-63. 2008
    ....
  39. ncbi request reprint A draft sequence for the genome of the domesticated silkworm (Bombyx mori)
    Qingyou Xia
    Southwest Agricultural University, Chongqing Beibei, 400716, China
    Science 306:1937-40. 2004
    ..Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content...
  40. ncbi request reprint Nonlinear control for a class of hydraulic servo system
    Hong Yu
    School of Mechanical Engineering, Shanghai Jiaotong University, Shanghai 200030, China
    J Zhejiang Univ Sci 5:1413-7. 2004
    ..Compared with previously proposed robust controllers, this paper's robust controller based on backstepping recursive design method is easier to design, and is more suitable for implementation...
  41. pmc Hierarchical modularity of nested bow-ties in metabolic networks
    Jing Zhao
    School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
    BMC Bioinformatics 7:386. 2006
    ..Topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks...
  42. pmc Mapping abbreviations to full forms in biomedical articles
    Hong Yu
    Department of Medical Informatics, Columbia University, New York, New York 10032, USA
    J Am Med Inform Assoc 9:262-72. 2002
    ..To develop methods that automatically map abbreviations to their full forms in biomedical articles...

Research Grants1

  1. HERMES - Help physicians to Extract and aRticulate Multimedia information from li
    Hong Yu; Fiscal Year: 2009
    ..5) Design a usability study to measure efficacy, accuracy and perceived ease of use of HERMES and to compare HERMES with other information systems. ..