Recognition of medication information from discharge summaries using ensembles of classifiers

BMC Medical Informatics and Decision Making

Volumn 12, Issue 1, 2012, Pages

  Doan, Son ^a   Collier, Nigel ^a   Xu, Hua ^b   Duy, Pham Hoang ^c   Phuong, Tu Minh ^c  

^a NATIONAL INSTITUTE OF INFORMATICS   (Japan)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c POSTS AND TELECOMMUNICATIONS INSTITUTE OF TECHNOLOGY   (Viet Nam)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; COMPUTER PROGRAM; DECISION SUPPORT SYSTEM; FEMALE; HOSPITAL DISCHARGE; HOSPITAL ORGANIZATION; HUMAN; INFORMATION RETRIEVAL; MALE; MANAGEMENT; METHODOLOGY; NATURAL LANGUAGE PROCESSING; REPRODUCIBILITY; SEMANTICS; SUPPORT VECTOR MACHINE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; DECISION SUPPORT TECHNIQUES; FEMALE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INSTITUTIONAL MANAGEMENT TEAMS; MALE; MEDICATION SYSTEMS; NATURAL LANGUAGE PROCESSING; PATIENT DISCHARGE; PATTERN RECOGNITION, AUTOMATED; PHARMACEUTICAL PREPARATIONS; REPRODUCIBILITY OF RESULTS; SEMANTICS; SOFTWARE DESIGN; SUPPORT VECTOR MACHINES;

EID: 84860595742     PISSN: None     EISSN: 14726947     Source Type: Journal    
DOI: 10.1186/1472-6947-12-36     Document Type: Article

References (28)

1. Rutabaga by any other name: extracting biological names. Hirschman L, Morgan AA, Yeh AS, J Biomed Inform 2002 35 247 259 10.1016/S1532-0464(03)00014-5 12755519
2. Term identification in the biomedical literature. Krauthammer M, Nenadic G, J Biomed Inform 2004 37 512 526 10.1016/j.jbi.2004.08.004 15542023
3. Tuning Support Vector Machines for biomedical named entity recognition. Kazama J, Makino T, Ohta Y, Tsujii T, Proceedings of the ACL-02 Workshop on Natural Language Processing in the Biomedical Domain 2002 1 8
4. Overview of BioCreative II gene mention recognition. Smith L, Tanabe L, Ando R, Kuo C, Chung I, Hsu C, Lin Y, Klinger R, Friedrich C, Ganchev K, Torii M, Liu H, Haddow B, Struble C, Povinelli R, Vlachos A, Baumgartner W, Hunter L, Carpenter B, Tsai R, Dai H, Liu F, Chen Y, Sun C, Katrenko S, Adriaans P, Blaschke C, Torres R, Neves M, Nakov P, Divoli M, Mana-Lopez A, Mata-Vazquez J, Wilbur W, Genome Biol 2008 9 Suppl 2 2 10.1186/gb-2008-9-s2-s2 18834493
5. Bio-medical entity extraction using Support Vector Machines. Takeuchi K, Collier N, Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine 2003 57 64
6. BioTagger-GM: a gene/protein name recognition system. Torii M, Hu Z, Wu CH, Liu H, J Am Med Inform Assoc 2009 16 247 255 10.1197/jamia.M2844 19074302
7. Protein name tagging for biomedical annotation in text. Yamamoto K, Kudo T, Konagaya A, Matsumoto Y, Proceedings of ACL,workshop on Natural Language Processing in Biomedicine 2003 65 72
8. Recognition of protein/gene names from text using an ensemble of classifiers. Zhou G, Shen D, Zhang J, Su J, Tan S, BMC Bioinformatics 2005 6 Suppl 1 7 10.1186/1471-2105-6-S1-S7 16351756
9. Extracting medication information from clinical text. Uzuner Ö Solti I, Cadag E, J Am Med Inform Assoc 2010 17 5 514 518 10.1136/jamia.2010.003947 20819854
10. High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge. Patrick J, Li M, J Am Med Inform Assoc 2010 17 5 524 527 10.1136/jamia.2010.003939 20819856
11. Integrating existing natural language processing tools for medication extraction from discharge summaries. Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H, J Am Med Inform Assoc 2010 17 5 528 531 10.1136/jamia.2010.003855 20819857
12. Statistical extraction of medication information from clinical records. Halgrim S, Xia F, Solti I, Cadag E, Uzuner Ö Proceedings of AMIA Summit on Translational Bioinformatics 2010 10 12
13. A cascade of classifiers for extracting medication information from discharge summaries. Halgrim S, Xia F, Solti I, Cadag E, Uzuner Ö Journal of Biomedical Semantics 2011 2 Suppl 3 2 10.1186/2041-1480-2-S3-S2 22166595
14. Recognizing medication related entities in hospital discharge summaries using support vector machine. Doan S, Xu H, Proceedings of the 23th Conference on Computational Linguistics 2010 259 266
15. Community annotation experiment for ground truth generation for the i2b2 medication challenge. Uzuner Ö Solti I, Xia F, Cadag E, J Am Med Inform Assoc 2010 17 5 519 523 10.1136/jamia.2010.004200 20819855
16. MedEx: a medication information extraction system for clinical narratives. Xu H, Stenner SP, Doan S, Johnson KB, Waitman LR, Denny JC, J Am Med Inform Assoc 2010 17 1 19 24 10.1197/jamia.M3378 20064797
17. Biomedical named entity recognition using conditional random fields and rich feature sets. Settles B, Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP) 2004 104 107
18. A Tutorial on support vector machines for pattern recognition. Burges CJC, Data Mining and Knowledge Discovery 1998 2 2 121 167 10.1023/A: 1009715923555
19. Vapnik VN, The Nature of Statistical Learning Springer 1995
20. TinySVM toolkit, [ http://chasen.org/∼taku/software/TinySVM/ ]
21. Yamcha toolkit, [ http://chasen.org/∼taku/software/YamCha/ ]
22. Lancet: a high precision medication event extraction system for clinical text. Li Z, Liu F, Antieau L, Cao Y, Yu H, J Am Med Inform Assoc 2010 17 5 563 567 10.1136/jamia.2010.004077 20819865
23. CRF++ toolkit [ http://crfpp.sourceforge.net/ ]
24. NLTK package [ www.nltk.org ]
25. Extracting the names of genes and gene products with a hidden Markov model. Collier N, Nobata C, Tsujii J, Proceedings of the 18th Conference on Computational Linguistics 2000 201 207
26. Bagging predictors. Breiman L, Machine Learning 1996 24 123 140
27. Schapire RE, Singer Y, Improved boosting algorithms using confidence-rated predictions. Proceedings of the 11th Annual ACM Conference on Computational Learning Theory 1998 80 91
28. ConllEval evaluation script [ http://www.cnts.ua.ac.be/conll2002/ner/bin/ conlleval.txt ]