Automatic summarization of MEDLINE citations for evidence-based medical treatment: A topic-oriented evaluation

Journal of Biomedical Informatics

Volumn 42, Issue 5, 2009, Pages 801-813

  Fiszman, Marcelo ^a   Demner Fushman, Dina ^a   Kilicoglu, Halil ^a,b   Rindflesch, Thomas C ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b Gina Cody School of Engineering and Computer Science   (Canada)

Author keywords

Artificial intelligence; Automatic summarization; Evaluation; Evidence based medicine; Knowledge representation; Natural language processing; Semantic processing

Indexed keywords

AUTOMATIC SUMMARIZATION; EVALUATION; EVIDENCE-BASED MEDICINE; NATURAL LANGUAGE PROCESSING; SEMANTIC PROCESSING;

ARTIFICIAL INTELLIGENCE; COMPUTATIONAL LINGUISTICS; INFORMATION SERVICES; KNOWLEDGE REPRESENTATION; LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS; SEMANTICS; TECHNICAL WRITING;

MEDICINE;

ACETYLSALICYLIC ACID; ALPRAZOLAM; ALTEPLASE; ANCROD; ANTICOAGULANT AGENT; BENZODIAZEPINE; BUSPIRONE; CAPTOPRIL; CLONAZEPAM; DIGOXIN; DILTIAZEM; DIPEPTIDYL CARBOXYPEPTIDASE INHIBITOR; DONEPEZIL; FIBRINOLYTIC AGENT; FLUOXETINE; GINKGO BILOBA EXTRACT; HEPARIN; IMIPRAMINE; LISINOPRIL; LOW MOLECULAR WEIGHT HEPARIN; METOPROLOL; MONOAMINE OXIDASE INHIBITOR; RAMIPRIL; SEROTONIN UPTAKE INHIBITOR; SERTRALINE; STREPTOKINASE; THROMBIN; TRICYCLIC ANTIDEPRESSANT AGENT; UNINDEXED DRUG; VERAPAMIL;

ACCURACY; ACUTE HEART INFARCTION; ARTICLE; AUTOMATION; CEREBROVASCULAR ACCIDENT; CITATION ANALYSIS; DATA SYNTHESIS; DEMENTIA; DRUG INFORMATION; EVIDENCE BASED MEDICINE; HEART ATRIUM FIBRILLATION; HEART FAILURE; INFORMATION SYSTEM; LANGUAGE PROCESSING; MEDLINE; PANIC; PHYSICIAN; PRIORITY JOURNAL; REFERENCE DATABASE; SCORING SYSTEM; SEMANTICS; STANDARD; UNSTABLE ANGINA PECTORIS;

ARTIFICIAL INTELLIGENCE; AUTOMATIC DATA PROCESSING; DISEASE; DRUG THERAPY; EVIDENCE-BASED MEDICINE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MEDICAL INFORMATICS; MEDLINE; NATURAL LANGUAGE PROCESSING; SEMANTICS; USER-COMPUTER INTERFACE; VOCABULARY, CONTROLLED;

EID: 70349452436     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2008.10.002     Document Type: Article

References (48)

1. Wennberg J.E. Unwarranted variations in healthcare delivery: Implications for academic medical centers. Br Med J 325 7370 (2002) 961-964
2. McGlynn E.A., Asch S.M., Adams J., et al. The quality of health care delivered to adults in the United States. N Engl J Med 348 26 (2003) 2635-2645
3. Institute of Medicine, Committee on Quality Health Care in America. Crossing the quality chasm: A new health system for the 21st century. Washington, DC: National Academy Press; 2001.
4. Sackett D.L., Straus S.E., Richardson W.S., Rosenberg W., and Haynes R.B. Evidence-based medicine: how to practice and teach EBM (2000), Churchill Livingstone, Philadelphia, PA
5. Hersh W., Hickam D.H., Haynes R.B., et al. Evaluation of SAPHIRE: an automated approach to indexing and retrieving medical literature. Proc Annu Symp Comput Appl Med Care (1991) 808-812
6. Srinivasan P. Retrieval feedback in MEDLINE. J Am Med Inform Assoc 3 2 (1996) 157-167
7. Schardt C., Adams M.B., Owens T., et al. Utilization of the PICO framework to improve searching PubMed for clinical questions. BMC Med Inform Decis Mak 7 (2007) 16
8. Ide N.C., Loane R.F., and Demner-Fushman D. Essie: a concept-based search engine for structured biomedical text. J Am Med Inform Assoc 14 3 (2007) 253-263
9. Demner-Fushman D., and Lin J. Answering clinical questions with knowledge-based and statistical techniques. Comput Linguist 33 1 (2007) 63-103
10. Lin Y., Li W., Chen K., et al. A document clustering and ranking system for exploring MEDLINE citations. J Am Med Inform Assoc 14 5 (2007) 651-661
11. Mani I. Automatic summarization (2001), John Benjamins Publishing Co, Philadelphia, PA
12. Fiszman M, Rindflesch TC, Kilicoglu H. Abstraction summarization for managing the biomedical research literature. In: Proceedings of the HLT-NAACL workshop on computational lexical semantics 2004;76-83.
13. Clinical evidence concise. London: BMJ Publishing Group; 2004.
14. Physicians' Desk Reference. Montvale, NJ: Medical Economics Data; 2004.
15. Teufel S., and Moens M. Summarizing scientific articles-experiments with relevance and rhetorical status. Comput. Linguist. 28 4 (2002) 409-445
16. Kupiec J, Pedersen J, Chen F. A trainable document summarizer. In: Proceedings of the 18th annual international ACM SIGIR conference on research and development in information retrieval 1995;68-73.
17. McKeown K.R., Barzilay R., Evans D., et al. Tracking and summarizing news on a daily basis with Columbia's Newsblaster. Proc HLT-NAACL (2002) 280-285
18. Radev D. A Common theory of information fusion from multiple text sources, step one: cross-document structure. In: Proceedings of 1st ACL SIGDIAL workshop on discourse and dialogue 2000;74-83.
19. Daniel N, Radev Dr, Allison T. Sub-event based multi-document summarization. In: Proceedings of the HLT-NAACL workshop on text summarization 2003;9-16.
20. Grover C, Hachey B, Korycinski C. Summarising legal texts: sentential tense and argumentative roles. In: Proceedings of the HLT-NAACL workshop on text summarization 2003;33-40.
21. McKeown HR, Chang, SF, Cimino J, et al. PERSIVAL, a system for personalized search and summarization over multimedia healthcare information. In: Proceedings of the 1st ACM/IEEE-CS joint conference on digital libraries 2001;331-40.
22. Afantenos S., Karkaletsis V., and Stamatopoulos P. Summarization from medical documents: a survey. Artif Intell Med 33 2 (2005) 157-177
23. Lin CY, Hovy E. From single to multi-document summarization: a prototype system and its evaluation. In: Proceedings of the 40th annual meeting of the association for computational linguistics 2001;457-64.
24. Paice CD, Jones PA. The identification of important concepts in highly structured technical papers. In: Proceedings of the 16th annual international ACM SIGIR conference on research and development in information retrieval 1993;69-78.
25. McKeown K, Radev D. Generating summaries of multiple news articles. In: Proceedings of the 18th annual international ACM SIGIR conference on research and development in information retrieval 1995;74-82.
26. Elhadad N., Kan M.Y., Klavans J.L., and McKeown K.R. Customization in a unified framework for summarizing medical literature. Artif Intell Med 33 2 (2005) 179-198
27. Hahn U., and Mani I. The challenges of automatic summarization. Computer 33 11 (2000) 29-36
28. Rindflesch T.C., Fiszman M., and Libbus B. Semantic interpretation for the biomedical research literature. In: Chen H., Fuller S., Hersh W., and Friedman C. (Eds). Medical informatics: knowledge management and data mining in biomedicine (2005), Springer, New York 399-422
29. Rindflesch T.C., and Fiszman M. The interaction of domain knowledge and linguistic structure in natural language processing: Interpreting hypernymic propositions in biomedical text. J Biomed Inform 36 6 (2003) 462-477
30. Humphreys B.L., Lindberg D.A., Schoolman H.M., and Barnett G.O. The Unified Medical Language System: an informatics research collaboration. J Am Med Inform Assoc 5 1 (1998) 1-11
31. Hahn U., and Reimer U. Knowledge-based text summarization: salience and generalization operators for knowledge base abstraction. In: Mani I., and Maybury M.T. (Eds). Advances in automatic text summarization (1999), MIT Press, Cambridge 215-232
32. Jing H, Barzilay R, McKeown KR, et al. Summarization evaluation methods: Experiments and analysis. AAAI Symposium on Intelligent Summarization 1998;60-68.
33. Lin CY, Hovy E. Manual and automatic evaluation of summaries. In: Proceedings of the ACL workshop on automatic summarization 2002;45-51.
34. Radev D, Teufel S, Saigon H, et al. Evaluation challenges in large-scale document summarization. In: Proceedings of the 41st annual meeting on association for computational linguistics 2003;375-382.
35. Nenkova A, Passonneau R, McKeown K. The Pyramid Method: Incorporating human content selection variation in summarization evaluation. ACM Transactions on Speech and Language Processing 2007;4(2):4-es.
36. Mani I, House D, Klein G. The TIPSTER SUMMAC text summarization evaluation. In: Proceedings of the ninth conference on European chapter of the association for computational linguistics 1999;77-85.
37. Elhadad N., McKeown K., Kaufman D., and Jordan D. Facilitating physicians' access to information via tailored text summarization. AMIA Annu Symp Proc (2005) 226-230
38. McKeown H, Passonneau RJ, Elson DK, et al. Do summaries help? A task-based evaluation of multidocument summarization. In: Proceedings of the 28th annual international ACM SIGIR conference on research and development in information retrieval 2005;210-217.
39. Amigo E, Gonzalo J, Peinado V. An empirical study of information synthesis tasks. In: Proceedings of the 42nd annual meeting of the association for computational linguistics 2004;207-14.
40. Available from: .
41. Aronson A.R. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc AMIA Symp (2001) 17-21
42. Available from:
43. Bangalore A., Thorn K.E., Tilley C., and Peters L. The UMLS knowledge source server: an object model for delivering UMLS data. AMIA Annu Symp Proc (2003) 51-55
44. Available from: .
45. Zar J.H. Biostatistical analysis (1974), Prentice Hall Inc., EngleWood Cliffs, NJ
46. Haynes R.B., Wilczynski N., McKibbon K.A., et al. Developing optimal search strategies for detecting clinically sound studies in MEDLINE. J Am Med Inform Assoc 1 6 (1994) 447-458
47. Aphinyanaphongs Y., Tsamardinos I., Statnikov A., Hardin D., and Aliferis C.F. Text categorization models for high-quality article retrieval in internal medicine. J Am Med Inform Assoc 12 2 (2005) 207-216
48. Kilicoglu H, Demner-Fushman D, Rindflesch T, Wilczynski NL, Haynes RB. Towards automatic recognition of scientifically rigorous clinical Research Evidence. J Am Med Inform Assoc 2005; in press.