Answering clinical questions with knowledge-based and statistical techniques

Computational Linguistics

Volumn 33, Issue 1, 2007, Pages 63-103

  Demner Fushman, Dina ^a,b   Lin, Jimmy ^a  

^a UNIVERSITY OF MARYLAND   (United States)

^b Institute for Advanced Computer Studies   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTING; CLINICAL RESEARCH; KNOWLEDGE BASED SYSTEMS; NATURAL LANGUAGE PROCESSING SYSTEMS; SEMANTICS;

CLINICAL MEDICINE; COMPLEX QUESTIONS; EVIDENCE-BASED MEDICINE; KNOWLEDGE BASED; MEDICAL DOMAINS; QUESTION ANSWERING; SEMANTIC PROCESSING; STATISTICAL TECHNIQUES;

DATA MINING;

EID: 34047168718     PISSN: 08912017     EISSN: 15309312     Source Type: Journal    
DOI: 10.1162/coli.2007.33.1.63     Document Type: Article

References (59)

1. Ad Hoc Working Group for Critical Appraisal of the Medical Literature. 1987. A proposal for more informative abstracts of clinical articles. Annals of Internal Medicine, 106:595-604.
2. Aronson, Alan R. 2001. Effective mapping of biomedical text to the UMLS Metathesaurus: The MetaMap program. In Proceeding of the 2001 Annual Symposium of the American Medical Informatics Association (AMIA 2001), pages 17-21, Portland, OR.
3. Aronson, Alan R., James G. Mork, Clifford W. Gay, Susanne M. Humphrey, and Willie J. Rogers. 2004. The NLM Indexing Initiative's Medical Text Indexer. In Proceedings of the 11th World Congress on Medical Informatics (MEDINFO 2004), pages 268-272, San Francisco, CA.
4. Aronson, Alan R., Thomas C. Rindflesch, and Allen C. Browne. 1994. Exploiting a large thesaurus for information retrieval. In Proceedings of RIAO 1994: Intelligent Multimedia Information Retrieval Systems and Management, pages 197-216, New York.
5. Baeza-Yates, Ricardo and Berthier Ribeiro-Neto. 1999. Modern Information Retrieval. ACM Press, New York.
6. Barry, Carol and Linda Schamber. 1998. Users' criteria for relevance evaluation: A cross-situational comparison. Information Processing and Management, 34(2/3):219-236.
7. Booth, Andrew. 2000. Formulating the question. In Andrew Booth and Graham Walton, editors, Managing Knowledge in Health Services. Library Association Publishing, London, England.
8. Chambliss, M. Lee and Jennifer Conley. 1996. Answering clinical questions. The Journal of Family Practice, 43:140-144.
9. Cogdill, Keith W. and Margaret E. Moore. 1997. First-year medical students' information needs and resource selection: Responses to a clinical scenario. Bulletin of the Medical Library Association, 85(1)51-54.
10. Covell, David G., Gwen C. Uman, and Phil R. Manning. 1985. Information needs in office practice: Are they being met? Annals of Internal Medicine, 103(4):596-599.
11. De Groote, Sandra L. and Josephine L. Dorsch. 2003. Measuring use patterns of online journals and databases. Journal of the Medical Library Association, 91(2):231-240.
12. Demner-Fushman, Dina, Barbara Few, Susan E. Hauser, and George Thoma. 2006. Automatically identifying health outcome information in MEDLINE records. Journal of the American Medical Informatics Association, 13(1):52-60.
13. Demner-Fushman, Dina and Jimmy Lin. 2005. Knowledge extraction for clinical question answering: Preliminary results. In Proceedings of the AAAI-05 Workshop on Question Answering in Restricted Domains, pages 1-10, Pittsburgh, PA.
14. Demner-Fushman, Dina and Jimmy Lin. 2006. Answer extraction, semantic clustering, and extractive summarization for clinical question answering. In Proceedings of the 21st International Conference on Computational Linguistics and 44th Annual Meeting of the Association for Computational Linguistics (COLING/ACL 2006), pages 841-848, Sydney, Australia.
15. Ebell, Mark H., Jay Siwek, Barry D. Weiss, Steven H. Woolf, Jeffrey Susman, Bernard Ewigman, and Marjorie Bowman. 2004. Strength of Recommendation Taxonomy (SORT): A patient-centered approach to grading evidence in the medical literature. The Journal of the American Board of Family Practice, 17(1)59-67.
16. Elhadad, Noemie, Min-Yen Kan, Judith Klavans, and Kathleen McKeown. 2005. Customization in a unified framework for summarizing medical literature. Journal of Artificial Intelligence in Medicine, 33(2):179-198.
17. Ely, John W., Jerome A. Osheroff, Mark H. Ebell, George R. Bergus, Barcey T. Levy, M. Lee Chambliss, and Eric R. Evans. 1999. Analysis of questions asked by family doctors regarding patient care. BMJ, 319:358-361.
18. Ely, John W., Jerome A. Osheroff, M. Lee Chambliss, Mark H. Ebell, and Marcy E. Rosenbaum. 2005. Answering physicians' clinical questions: Obstacles and potential solutions. Journal of the American Medical Informatics Association, 12(2):217-224.
19. Fiszman, Marcelo, Thomas C. Rindflesch, and Halil Kilicoglu. 2004. Abstraction summarization for managing the biomedical research literature. In Proceedings of the HLT/NAACL 2004 Workshop on Computational Lexical Semantics, pages 76-83, Boston, MA.
20. Gorman, Paul N., Joan S. Ash, and Leslie W. Wykoff. 1994. Can primary care physicians' questions be answered using the medical journal literature? Bulletin of the Medical Library Association, 82(2):140-146.
21. Haynes, R. Brian, Nancy Wilczynski, K. Ann McKibbon, Cynthia J. Walker, and John C. Sinclair. 1994. Developing optimal search strategies for detecting clinically sound studies in MEDLINE. Journal of the American Medical Informatics Association, 1(6):447-458.
22. Hearst, Marti A. 1996. Improving full-text precision on short queries using simple constraints. In Proceedings of the Fifth Annual Symposium on Document Analysis and Information Retrieval (SDAIR 1996), pages 217-232, Las Vegas, NV.
23. Hersh, William, Ravi Teja Bhupatiraju, and Sarah Corley. 2004. Enhancing access to the bibliome: The TREC genomics track. In Proceedings of the 11th World Congress on Medical Informatics (MEDINFO 2004), pages 773-777, San Francisco, CA.
24. Hersh, William, Aaron Cohen, Jianji Yang, Ravi Teja Bhupatirajul, Phoebe Roberts, and Marti Hearst. 2005. TREC 2005 genomics track overview. In Proceedings of the Fourteenth Text REtrieval Conference (TREC 2005), Gaithersburg, MD.
25. Hildebrandt, Wesley, Boris Katz, and Jimmy Lin. 2004. Answering definition questions with multiple knowledge sources. In Proceedings of the 2004 Human Language Technology Conference and the North American Chapter of the Association for Computational Linguistics Annual Meeting (HLT/NAACL 2004), pages 49-56, Boston, MA.
26. Hirschman, Lynette and Robert Gaizauskas. 2001. Natural language question answering: The view from here. Natural Language Engineering, 7(4):275-300.
27. Huang, Xiaoli, Jimmy Lin, and Dina Demner-Fushman. 2006. Evaluation of PICO as a knowledge representation for clinical questions. In Proceeding of the 2006 Annual Symposium of the American Medical Informatics Association (AMIA 2006), pages 359-363, Washington, D.C.
28. Ingwersen, Peter. 1999. Cognitive information retrieval. Annual Review of Information Science and Technology, 34:3-52.
29. Jacquemart, Pierre and Pierre Zweigenbaum. 2003. Towards a medical question-answering system: A feasibility study. In Robert Baud, Marius Fieschi, Pierre Le Beux, and Patrick Ruch, editors, The New Navigators: From Professionals to Patients, volume 95 of Actes Medical Informatics Europe, Studies in Health Technology and Informatics. IOS Press, Amsterdam, pages 463-468.
30. Kauffman, Ralph E., L. A. Sawyer, and M. L. Scheinbaum. 1992. Antipyretic efficacy of ibuprofen vs acetaminophen. American Journal of Diseases of Children, 146(5):622-625.
31. Light, Marc, Xin Ying Qiu, and Padmini Srinivasan. 2004. The language of bioscience: Facts, speculations, and statements in between. In Proceedings of the BioLink 2004 Workshop at HLT/NAACL 2004, pages 17-24, Boston, MA.
32. Lin, Jimmy and Dina Demner-Fushman. 2005a. Automatically evaluating answers to definition questions. In Proceedings of the 2005 Human Language Technology Conference and Conference on Empirical Methods in Natural Language Processing (HLT/EMNLP 2005), pages 931-938, Vancouver, Canada.
33. Lin, Jimmy and Dina Demner-Fushman. 2005b. Evaluating summaries and answers: Two sides of the same coin? In Proceedings of the ACL 2005 Workshop on Intrinsic and Extrinsic Evaluation Measures for MT and/or Summarization, pages 41-48, Ann Arbor, MI.
34. Lin, Jimmy and Dina Demner-Fushman. 2006a. The role of knowledge in conceptual retrieval: A study in the domain of clinical medicine. In Proceedings of the 29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2006), pages 99-106, Seattle, WA.
35. Lin, Jimmy and Dina Demner-Fushman. 2006b. Will pyramids built of nuggets topple over? In Proceedings of the 2006 Human Language Technology Conference and North American Chapter of the Association for Computational Linguistics Annual Meeting (HLT/NAACL 2006), pages 383-390, New York.
36. Lin, Jimmy, Damianos Karakos, Dina Demner-Fushman, and Sanjeev Khudanpur. 2006. Generative content models for structural analysis of medical abstracts. In Proceedings of the HLT/NAACL 2006 Workshop on Biomedical Natural Language Processing (BioNLP'06), pages 65-72, New York.
37. Lin, Jimmy, Dennis Quan, Vineet Sinha, Karun Bakshi, David Huynh, Boris Katz, and David R. Karger. 2003. What makes a good answer? The role of context in question answering. In Proceedings of the Ninth IFIP TC13 International Conference on Human-Computer Interaction (INTERACT 2003), pages 25-32, Zürich, Switzerland.
38. Lindberg, Donald A., Betsy L. Humphreys, and Alexa T. McCray. 1993. The Unified Medical Language System. Methods of Information in Medicine, 32(4):281-291.
39. McCray, Alexa T., Anita Burgun, and Olivier Bodenreider. 2001. Aggregating UMLS semantic types for reducing conceptual complexity. In Proceedings of 10th World Congress on Medical Informatics (MEDINFO 2001), pages 216-220, London, England.
40. McKeown, Kathleen, Noemie Elhadad, and Vasileios Hatzivassiloglou. 2003. Leveraging a common representation for personalized search and summarization in a medical digital library. In Proceedings of the 3rd ACM/IEEE Joint Conference on Digital Libraries (JCDL 2003), pages 159-170, Houston, TX.
41. McKnight, Larry and Padmini Srinivasan. 2003. Categorization of sentence types in medical abstracts. In Proceeding of the 2003 Annual Symposium of the American Medical Informatics Association (AMIA 2003), pages 440-144, Washington, D.C.
42. Meadow, Charles T., Barbara A. Cerny, Christine L. Borgman, and Donald O. Case. 1989. Online access to knowledge: System design. Journal of the American Society for Information Science, 40(2):86-98.
43. Mendonça, Eneida A. and James J. Cimino. 2001. Building a knowledge base to support a digital library. In Proceedings of 10th World Congress on Medical Informatics (MEDINFO 2001), pages 222-225, London, England.
44. Mladenic, Dunja and Marko Grobelnik. 1999. Feature selection for unbalanced class distribution and Naïve Bayes. In Proceedings of the Sixteenth International Conference on Machine Learning (ICML 1999), pages 258-267, Bled, Slovenia.
45. Nenkova, Ani and Rebecca Passonneau. 2004. Evaluating content selection in summarization: The pyramid method. In Proceedings of the 2004 Human Language Technology Conference and the North American Chapter of the Association for Computational Linguistics Annual Meeting (HLT/NAACL 2004), pages 145-152, Boston, MA.
46. Niu, Yun and Graeme Hirst. 2004. Analysis of semantic classes in medical text for question answering. In Proceedings of the ACL 2004 Workshop on Question Answering in Restricted Domains, pages 54-61, Barcelona, Spain.
47. Pratt, Wanda and Meliha Yetisgen-Yildiz. 2003. A study of biomedical concept identification: MetaMap vs. people. In Proceeding of the 2003 Annual Symposium of the American Medical Informatics Association (AMIA 2003), pages 529-533, Washington, D.C.
48. Richardson, W. Scott, Mark C. Wilson, James Nishikawa, and Robert S. Hayward. 1995. The well-built clinical question: A key to evidence-based decisions. American College of Physicians Journal Club, 123(3):A12-A13.
49. Rinaldi, Fabio, James Dowdall, Gerold Schneider, and Andreas Persidis. 2004. Answering questions in the genomics domain. In Proceedings of the ACL 2004 Workshop on Question Answering in Restricted Domains, pages 46-53, Barcelona, Spain.
50. Rindflesch, Thomas C. and Marcelo Fiszman. 2003. The interaction of domain knowledge and linguistic structure in natural language processing: Interpreting hypernymic propositions in biomedical text. Journal of Biomedical Informatics, 36(6):462-477.
51. Sackett, David L., Sharon E. Straus, W. Scott Richardson, William Rosenberg, and R. Brian Haynes. 2000. Evidence-Based Medicine: How to Practice and Teach EBM, second edition. Churchill Livingstone, Edinburgh, Scotland.
52. Saracevic, Tefko. 1975. Relevance: A review of and a framework for thinking on the notion in information science. Journal of the American Society for Information Science, 26(6):321-343.
53. Sneiderman, Charles, Dina Demner-Fushman, Marcelo Fiszman, and Thomas C. Rindflesch. 2005. Semantic characteristics of MEDLINE citations useful for therapeutic decision-making. In Proceeding of the 2005 Annual Symposium of the American Medical Informatics Association (AMIA 2005), page 1117, Washington, D.C.
54. Tbahriti, Imad, Christine Chichester, Frédérique Lisacek, and Patrick Ruch. 2006. Using argumentation to retrieve articles with similar citations: An inquiry into improving related articles search in the MEDLINE digital library. International Journal of Medical Informatics, 75(6):488-495.
55. Ting, Kai Ming and Ian H. Witten. 1999. Issues in stacked generalization. Journal of Artificial Intelligence Research, 10:271-289.
56. Voorhees, Ellen M. 2003. Overview of the TREC 2003 question answering track. In Proceedings of the Twelfth Text REtrieval Conference (TREC 2003), pages 54-68, Gaithersburg, MD.
57. Voorhees, Ellen M. and Dawn M. Tice. 1999. The TREC-8 question answering track evaluation. In Proceedings of the Eighth Text REtrieval Conference (TREC-8), pages 83-106, Gaithersburg, MD.
58. Wilczynski, Nancy, K. Ann McKibbon, and R. Brian Haynes. 2001. Enhancing retrieval of best evidence for health care from bibliographic databases: Calibration of the hand search of the literature. In Proceedings of 10th World Congress on Medical Informatics (MEDINFO 2001), pages 390-393, London, England.
59. Yang, Yiming and Jan O. Pedersen. 1997. A comparative study on feature selection in text categorization. In Proceedings of the Fourteenth International Conference on Machine Learning (ICML 1997), pages 412-120, Nashville, TN.