메뉴 건너뛰기




Volumn 45, Issue 1, 2012, Pages 129-140

Enhancing clinical concept extraction with distributional semantics

Author keywords

Clinical informatics; Distributional semantics; Information extraction; NER; NLP

Indexed keywords

BOOTSTRAP RESAMPLING; CLINICAL INFORMATICS; CLINICAL TRIAL; CONCEPT EXTRACTION; CONDITIONAL RANDOM FIELD; DICTIONARY MATCHING; DISCRIMINATIVE CLASSIFIERS; DISEASE PROGRESSION; ENABLING TECHNOLOGIES; EXTRACTING CONCEPT; F-SCORE; FEATURE WORDS; INFORMATION EXTRACTION; INTELLIGENT ANALYSIS; MEDLINE; NER; NLP; PART-OF-SPEECH TAGS; SEMANTIC FEATURES; SEMANTIC RELATEDNESS; SEQUENCE CLASSIFICATION; SEQUENCE LABELING; SLIDING WINDOW; SUPERVISED MACHINE LEARNING; TRAINING AND TESTING; TRAINING DATA; TRAINING SETS; UNANNOTATED TEXTS; VECTOR REPRESENTATIONS; VECTOR SPACE MODELS;

EID: 84856376731     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2011.10.007     Document Type: Article
Times cited : (93)

References (68)
  • 1
    • 50649122567 scopus 로고    scopus 로고
    • Extracting information from textual documents in the electronic health record: a review of recent research
    • Meystre S.M., Savova G.K., Kipper-Schuler K.C., Hurdle J.F. Extracting information from textual documents in the electronic health record: a review of recent research. Yearbook Med Informat 2008, 128-144.
    • (2008) Yearbook Med Informat , pp. 128-144
    • Meystre, S.M.1    Savova, G.K.2    Kipper-Schuler, K.C.3    Hurdle, J.F.4
  • 2
    • 84916627188 scopus 로고    scopus 로고
    • BioCreative II gene mention tagging system at IBM Watson
    • Proceedings of the second biocreative challenge;
    • Ando RK. BioCreative II gene mention tagging system at IBM Watson. In: Proceedings of the second biocreative challenge; 2007.
    • (2007)
    • Ando, R.K.1
  • 3
    • 84860513891 scopus 로고    scopus 로고
    • Learning predictive structures for semantic role labeling of NomBank
    • Proceedings of the 45th annual meeting of the association of computational linguistics. Prague (Czech Republic): Association for Computational Linguistics;
    • Liu C, Ng HT. Learning predictive structures for semantic role labeling of NomBank. In: Proceedings of the 45th annual meeting of the association of computational linguistics. Prague (Czech Republic): Association for Computational Linguistics; 2007. p. 208-15.
    • (2007) , pp. 208-15
    • Liu, C.1    Ng, H.T.2
  • 4
    • 23144460953 scopus 로고    scopus 로고
    • Random indexing of text samples for latent semantic analysis.
    • Proceedings of the 22nd annual conference of the cognitive science society, Citeseer;
    • Kanerva P, Kristofersson J, Holst A. Random indexing of text samples for latent semantic analysis. In: Proceedings of the 22nd annual conference of the cognitive science society, Citeseer; 2000. p. 1036.
    • (2000) , pp. 1036
    • Kanerva, P.1    Kristofersson, J.2    Holst, A.3
  • 5
    • 0012532696 scopus 로고
    • Extracting company names from text
    • Seventh IEEE conference on artificial intelligence applications
    • Rau LF, Res GE, Center D, Schenectady NY. Extracting company names from text. In: Seventh IEEE conference on artificial intelligence applications; 1991. p. 1.
    • (1991) , pp. 1
    • Rau, L.F.1    Res, G.E.2    Center, D.3    Schenectady, N.Y.4
  • 6
    • 33845563164 scopus 로고    scopus 로고
    • Discriminative models, not discriminative training. Microsoft Research (MSR-TR-2005-144)
    • Minka T. Discriminative models, not discriminative training. Microsoft Research (MSR-TR-2005-144); 2005.
    • (2005)
    • Minka, T.1
  • 8
    • 85026967968 scopus 로고
    • From text to structured information: automatic processing of medical reports.
    • Proceedings of the national computer conference and exposition. New York NY, (USA)
    • Hirschman L, Grishman R, Sager N. From text to structured information: automatic processing of medical reports. In: Proceedings of the national computer conference and exposition. New York NY, (USA); 1976. p. 267.
    • (1976) , pp. 267
    • Hirschman, L.1    Grishman, R.2    Sager, N.3
  • 9
    • 0016428140 scopus 로고
    • Sublanguage grammers in science information processing
    • Sager N. Sublanguage grammers in science information processing. J Am Soc Inform Sci 1975, 26:10-16.
    • (1975) J Am Soc Inform Sci , vol.26 , pp. 10-16
    • Sager, N.1
  • 10
    • 0347210450 scopus 로고    scopus 로고
    • Towards a comprehensive medical language processing system: methods and issues. In: AMIA;
    • Friedman C. Towards a comprehensive medical language processing system: methods and issues. In: AMIA; 1997.
    • (1997)
    • Friedman, C.1
  • 11
    • 0035752429 scopus 로고    scopus 로고
    • Effective mapping of biomedical text to the UMLS Metathesaurus
    • the MetaMap program. In: AMIA;
    • Aronson AR. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. In: AMIA; 2001.
    • (2001)
    • Aronson, A.R.1
  • 12
    • 33748073236 scopus 로고    scopus 로고
    • Evaluation of medical problem extraction from electronic clinical documents using MetaMap Transfer (MMTx)
    • Meystre S., Haug P.J. Evaluation of medical problem extraction from electronic clinical documents using MetaMap Transfer (MMTx). Stud Health Technol Informat 2005, 116:823.
    • (2005) Stud Health Technol Informat , vol.116 , pp. 823
    • Meystre, S.1    Haug, P.J.2
  • 13
    • 33748046130 scopus 로고    scopus 로고
    • Extracting principal diagnosis, co-morbidity and smoking status for asthma research
    • evaluation of a natural language processing system, BMC Med Inform Decis Mak;
    • Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus R. Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system, vol. 6. BMC Med Inform Decis Mak; 2006. p. 30.
    • (2006) , vol.6 , pp. 30
    • Zeng, Q.T.1    Goryachev, S.2    Weiss, S.3    Sordo, M.4    Murphy, S.N.5    Lazarus, R.6
  • 15
    • 0036370590 scopus 로고    scopus 로고
    • A comparison of the Charlson comorbidities derived from medical language processing and administrative data
    • AMIA Symposium;
    • Chuang J-H, Friedman C, Hripcsak G. A comparison of the Charlson comorbidities derived from medical language processing and administrative data. In: AMIA Symposium; 2002. p. 160-64.
    • (2002) , pp. 160-64
    • Chuang, J.-H.1    Friedman, C.2    Hripcsak, G.3
  • 16
    • 0033258535 scopus 로고    scopus 로고
    • Automatic identification of pneumonia related concepts on chest X-ray reports
    • AMIA;
    • Fiszman M, Chapman WW, Evans SR, Haug PJ. Automatic identification of pneumonia related concepts on chest X-ray reports. In AMIA; 1999. p. 67-71.
    • (1999) , pp. 67-71
    • Fiszman, M.1    Chapman, W.W.2    Evans, S.R.3    Haug, P.J.4
  • 18
    • 0025056759 scopus 로고
    • Computerized extraction of coded findings from free-text radiologic reports. Work in progress
    • Haug P.J., Ranum D.L., Frederick P.R. Computerized extraction of coded findings from free-text radiologic reports. Work in progress. Radiology 1990, 174:543-548.
    • (1990) Radiology , vol.174 , pp. 543-548
    • Haug, P.J.1    Ranum, D.L.2    Frederick, P.R.3
  • 19
    • 24944470272 scopus 로고    scopus 로고
    • Automation of a problem list using natural language processing
    • Meystre S., Haug P.J. Automation of a problem list using natural language processing. BMC Med Inform Decis Mak 2005, 5:30.
    • (2005) BMC Med Inform Decis Mak , vol.5 , pp. 30
    • Meystre, S.1    Haug, P.J.2
  • 20
    • 33750722813 scopus 로고    scopus 로고
    • Natural language processing to extract medical problems from electronic clinical documents: performance evaluation
    • Meystre S., Haug P.J. Natural language processing to extract medical problems from electronic clinical documents: performance evaluation. J Biomed Inform 2006, 39:589-599.
    • (2006) J Biomed Inform , vol.39 , pp. 589-599
    • Meystre, S.1    Haug, P.J.2
  • 21
    • 16544373807 scopus 로고    scopus 로고
    • Extracting structured information from free text pathology reports
    • Schadow G., McDonald C.J. Extracting structured information from free text pathology reports. AMIA Annu Symp Proc 2003, 584-588.
    • (2003) AMIA Annu Symp Proc , pp. 584-588
    • Schadow, G.1    McDonald, C.J.2
  • 22
    • 0033258434 scopus 로고    scopus 로고
    • A statistical natural language processor for medical reports
    • Taira R.K., Soderland S.G. A statistical natural language processor for medical reports. Proc AMIA Symp 1999, 970-974.
    • (1999) Proc AMIA Symp , pp. 970-974
    • Taira, R.K.1    Soderland, S.G.2
  • 23
    • 36749066006 scopus 로고    scopus 로고
    • Using implicit information to identify smoking status in smoke-blind medical discharge summaries
    • Wicentowski R., Sydes M.R. Using implicit information to identify smoking status in smoke-blind medical discharge summaries. J Am Med Inform Assoc 2008, 15:29-31.
    • (2008) J Am Med Inform Assoc , vol.15 , pp. 29-31
    • Wicentowski, R.1    Sydes, M.R.2
  • 24
    • 16544382055 scopus 로고    scopus 로고
    • Facilitating research in pathology using natural language processing
    • Xu H., Friedman C. Facilitating research in pathology using natural language processing. AMIA Annu Symp Proc 2003, 1057.
    • (2003) AMIA Annu Symp Proc , pp. 1057
    • Xu, H.1    Friedman, C.2
  • 26
    • 61949432274 scopus 로고    scopus 로고
    • Empirical distributional semantics: methods and biomedical applications
    • Cohen T., Widdows D. Empirical distributional semantics: methods and biomedical applications. J Biomed Informat 2009, 42:390-405.
    • (2009) J Biomed Informat , vol.42 , pp. 390-405
    • Cohen, T.1    Widdows, D.2
  • 27
    • 84862285546 scopus 로고    scopus 로고
    • Word representations: a simple and general method for semi-supervised learning
    • ACL
    • Turian J, Opérationnelle R, Ratinov L, Bengio Y. Word representations: a simple and general method for semi-supervised learning. In: ACL, vol. 51; 2010. p. 61801.
    • (2010) , vol.51 , pp. 61801
    • Turian, J.1    Opérationnelle, R.2    Ratinov, L.3    Bengio, Y.4
  • 29
    • 0003424374 scopus 로고    scopus 로고
    • Numerical linear algebra.
    • Society for industrial mathematics;
    • Trefethen LN, Bau D. Numerical linear algebra. Society for industrial mathematics; 1997.
    • (1997)
    • Trefethen, L.N.1    Bau, D.2
  • 30
    • 77952700189 scopus 로고    scopus 로고
    • From frequency to meaning: vector space models of semantics
    • Turney P.D., Pantel P. From frequency to meaning: vector space models of semantics. J Artif Intellig Res 2010, 37:141-188.
    • (2010) J Artif Intellig Res , vol.37 , pp. 141-188
    • Turney, P.D.1    Pantel, P.2
  • 31
    • 0016572913 scopus 로고
    • A vector space model for automatic indexing
    • Salton G., Wong A., Yang C.S. A vector space model for automatic indexing. Commun ACM 1975, 18:613-620.
    • (1975) Commun ACM , vol.18 , pp. 613-620
    • Salton, G.1    Wong, A.2    Yang, C.S.3
  • 33
    • 0000600219 scopus 로고    scopus 로고
    • A solution to Plato's problem: the latent semantic analysis theory of acquisition, induction, and representation of knowledge
    • Landauer T.K., Dumais S.T. A solution to Plato's problem: the latent semantic analysis theory of acquisition, induction, and representation of knowledge. Psychol Rev 1997, 104:211-240.
    • (1997) Psychol Rev , vol.104 , pp. 211-240
    • Landauer, T.K.1    Dumais, S.T.2
  • 34
    • 0142161367 scopus 로고
    • Word space.
    • Advances in neural information processing systems 5 (NIPS conference)
    • Schütze H. Word space. In: Advances in neural information processing systems 5 (NIPS conference); 1992. p. 895-902.
    • (1992) , pp. 895-902
    • Schütze, H.1
  • 35
    • 78650453776 scopus 로고    scopus 로고
    • Hyperspace analog to language (HAL): a general model of semantic representation
    • Lund K., Burgess C. Hyperspace analog to language (HAL): a general model of semantic representation. Lang Cognit Process 1996.
    • (1996) Lang Cognit Process
    • Lund, K.1    Burgess, C.2
  • 36
    • 85143523004 scopus 로고    scopus 로고
    • Automatic retrieval and clustering of similar words
    • Proceedings of the 17th international conference on computational linguistics - Montreal, Quebec, Canada;
    • Lin D. Automatic retrieval and clustering of similar words. In: Proceedings of the 17th international conference on computational linguistics - Montreal, Quebec, Canada; 1998. p. 768-74.
    • (1998) , pp. 768-74
    • Lin, D.1
  • 37
    • 0034818212 scopus 로고    scopus 로고
    • Unsupervised learning by probabilistic latent semantic analysis
    • Hofmann T. Unsupervised learning by probabilistic latent semantic analysis. Mach Learn 2001, 42:177-196.
    • (2001) Mach Learn , vol.42 , pp. 177-196
    • Hofmann, T.1
  • 38
    • 6344225887 scopus 로고    scopus 로고
    • Mining the web for synonyms: PMI-IR versus LSA on TOEFL.
    • Proceedings of the twelfth European conference on machine learning;
    • Turney P. Mining the web for synonyms: PMI-IR versus LSA on TOEFL. In: Proceedings of the twelfth European conference on machine learning; 2001.
    • (2001)
    • Turney, P.1
  • 40
    • 23144460953 scopus 로고    scopus 로고
    • Random indexing of text samples for latent semantic analysis
    • Proceedings of the 22nd annual conference of the cognitive science society;
    • Kanerva P, Kristoferson J, Holst A. Random indexing of text samples for latent semantic analysis. In: Proceedings of the 22nd annual conference of the cognitive science society; 2000. p. 1036.
    • (2000) , pp. 1036
    • Kanerva, P.1    Kristoferson, J.2    Holst, A.3
  • 42
    • 34347357484 scopus 로고    scopus 로고
    • Dependency-based construction of semantic space models
    • Padó S., Lapata M. Dependency-based construction of semantic space models. Comput Linguist 2007, 33:161-199.
    • (2007) Comput Linguist , vol.33 , pp. 161-199
    • Padó, S.1    Lapata, M.2
  • 43
    • 0001654702 scopus 로고
    • Extensions of Lipschitz mappings into a Hilbert space
    • Johnson W.B., Lindenstrauss J. Extensions of Lipschitz mappings into a Hilbert space. Contemp Math 1984, 189-206.
    • (1984) Contemp Math , pp. 189-206
    • Johnson, W.B.1    Lindenstrauss, J.2
  • 44
    • 0033337021 scopus 로고    scopus 로고
    • Fisher discriminant analysis with kernels. In: Neural networks for signal processing IX:
    • proceedings of the 1999 IEEE signal processing society workshop (Cat. No. 98TH8468). Madison, WI, USA
    • Mika S, Ratsch G, Weston J, Scholkopf B, Mullers KR. Fisher discriminant analysis with kernels. In: Neural networks for signal processing IX: proceedings of the 1999 IEEE signal processing society workshop (Cat. No. 98TH8468). Madison, WI, USA. p. 41-8.
    • Mika, S.1    Ratsch, G.2    Weston, J.3    Scholkopf, B.4    Mullers, K.R.5
  • 45
    • 70450271895 scopus 로고    scopus 로고
    • Permutations as a means to encode order in word space
    • Proceedings of the 30th annual meeting of the cognitive science society
    • Sahlgren M, Holst A, Kanerva P. Permutations as a means to encode order in word space. In: Proceedings of the 30th annual meeting of the cognitive science society; 2008. p. 23-6.
    • (2008) , pp. 23-6
    • Sahlgren, M.1    Holst, A.2    Kanerva, P.3
  • 46
    • 35048882582 scopus 로고    scopus 로고
    • The computation of word associations: comparing syntagmatic and paradigmatic approaches
    • Proceedings of the 19th international conference on computational linguistics, Association for computational linguistics;
    • Rapp R. The computation of word associations: comparing syntagmatic and paradigmatic approaches. In: Proceedings of the 19th international conference on computational linguistics, vol. 1. Association for computational linguistics; 2002. p. 7.
    • (2002) , vol.1 , pp. 7
    • Rapp, R.1
  • 48
    • 84856370238 scopus 로고    scopus 로고
    • The word-space model;
    • Sahlgren M. The word-space model; 2006.
    • (2006)
    • Sahlgren, M.1
  • 49
    • 33846292907 scopus 로고    scopus 로고
    • Representing word meaning and order information in a composite holographic lexicon
    • Jones M.N., Mewhort D.J.K. Representing word meaning and order information in a composite holographic lexicon. Psychol Rev 2007, 114:1-37.
    • (2007) Psychol Rev , vol.114 , pp. 1-37
    • Jones, M.N.1    Mewhort, D.J.K.2
  • 50
    • 0029310084 scopus 로고    scopus 로고
    • Holographic reduced representations
    • Neural networks, IEEE transactions on
    • Plate TA. Holographic reduced representations. In: Neural networks, IEEE transactions on 2002, vol. 6. p. 623-641.
    • (2002) , vol.6 , pp. 623-641
    • Plate, T.A.1
  • 51
    • 79960133907 scopus 로고    scopus 로고
    • Semantic oscillations: encoding context and structure in complex valued holographic vectors
    • AAAI fall symposium series; 2010.
    • De Vine L, Bruza P. Semantic oscillations: encoding context and structure in complex valued holographic vectors. In: 2010 AAAI fall symposium series; 2010.
    • (2010)
    • De Vine, L.1    Bruza, P.2
  • 53
    • 0036706501 scopus 로고    scopus 로고
    • Two biomedical sublanguages: a description based on the theories of Zellig Harris
    • Friedman C., Kra P., Rzhetsky A. Two biomedical sublanguages: a description based on the theories of Zellig Harris. J Biomed Informat 2002, 35:222-235.
    • (2002) J Biomed Informat , vol.35 , pp. 222-235
    • Friedman, C.1    Kra, P.2    Rzhetsky, A.3
  • 54
    • 79952051431 scopus 로고    scopus 로고
    • The Semantic vectors package: new algorithms and public tools for distributional semantics
    • Fourth IEEE international conference on semantic computing,
    • Widdows D, Cohen T. The Semantic vectors package: new algorithms and public tools for distributional semantics. In: Fourth IEEE international conference on semantic computing, vol. 1. 2010. p. 43.
    • (2010) , vol.1 , pp. 43
    • Widdows, D.1    Cohen, T.2
  • 55
    • 85006332590 scopus 로고    scopus 로고
    • Semantic vectors: a scalable open source package and online technology management application
    • Sixth international conference on language resources and evaluation;
    • Widdows D, Ferraro K. Semantic vectors: a scalable open source package and online technology management application. In: Sixth international conference on language resources and evaluation; 2008.
    • (2008)
    • Widdows, D.1    Ferraro, K.2
  • 56
    • 40549140499 scopus 로고    scopus 로고
    • BANNER: an executable survey of advances in biomedical named entity recognition
    • Pacific symposium in bioinformatics;
    • Leaman R, Gonzalez G. BANNER: an executable survey of advances in biomedical named entity recognition. In: Pacific symposium in bioinformatics; 2008.
    • (2008)
    • Leaman, R.1    Gonzalez, G.2
  • 57
    • 84856376979 scopus 로고    scopus 로고
    • MALLET: a machine learning for language toolkit .
    • MALLET: a machine learning for language toolkit http://mallet.cs.umass.edu.
  • 58
    • 80053292637 scopus 로고    scopus 로고
    • 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text
    • Uzuner O., South B.R., Shen S., Duvall S.L. 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. J Am Med Inform Assoc 2011.
    • (2011) J Am Med Inform Assoc
    • Uzuner, O.1    South, B.R.2    Shen, S.3    Duvall, S.L.4
  • 59
    • 84856370239 scopus 로고    scopus 로고
    • Apache Lucene .
    • Apache Lucene http://lucene.apache.org.
  • 61
    • 40749116424 scopus 로고    scopus 로고
    • BioCreative 2 gene mention task
    • Proceedings of the second biocreative challenge workshop;
    • Wilbur J, Smith L, Tanabe T. BioCreative 2 gene mention task. In: Proceedings of the second biocreative challenge workshop; 2007. p. 7-16.
    • (2007) , pp. 7-16
    • Wilbur, J.1    Smith, L.2    Tanabe, T.3
  • 62
    • 85099019865 scopus 로고    scopus 로고
    • Introduction to the CoNLL-2003 shared task
    • Proceedings of the seventh conference on natural language learning. Edmonton, Canada
    • Tjong Kim Sang EF, De Meulder F. Introduction to the CoNLL-2003 shared task. In: Proceedings of the seventh conference on natural language learning. Edmonton, Canada; 2003. p. 142-47.
    • (2003) , pp. 142-47
    • Tjong Kim Sang, E.F.1    De Meulder, F.2
  • 63
    • 84856370235 scopus 로고    scopus 로고
    • An effective approach to biomedical information extraction with limited training data.
    • PhD Dissertation, Arizona State University;
    • Jonnalagadda S. An effective approach to biomedical information extraction with limited training data. PhD Dissertation, Arizona State University; 2011.
    • (2011)
    • Jonnalagadda, S.1
  • 64
    • 68649115793 scopus 로고    scopus 로고
    • A realistic assessment of methods for extracting gene/protein interactions from free text
    • Kabiljo R., Clegg A.B., Shepherd A.J. A realistic assessment of methods for extracting gene/protein interactions from free text. BMC Bioinformat 2009, 10:233.
    • (2009) BMC Bioinformat , vol.10 , pp. 233
    • Kabiljo, R.1    Clegg, A.B.2    Shepherd, A.J.3
  • 66
    • 84856403312 scopus 로고    scopus 로고
    • Event detection in blogs using temporal random indexing.
    • Proceedings of the workshop on events in emerging text types. Stroudsburg, PA (USA): Association for Computational Linguistics;
    • Jurgens D, Stevens K. Event detection in blogs using temporal random indexing. In: Proceedings of the workshop on events in emerging text types. Stroudsburg, PA (USA): Association for Computational Linguistics; 2009. p. 9-16.
    • (2009) , pp. 9-16
    • Jurgens, D.1    Stevens, K.2
  • 67
    • 78649497264 scopus 로고    scopus 로고
    • The trajectory of scientific discovery: concept co-occurrence and converging semantic distance
    • Cohen T., Schvaneveldt R.W. The trajectory of scientific discovery: concept co-occurrence and converging semantic distance. Stud Health Technol Inform 2010, 160:661-665.
    • (2010) Stud Health Technol Inform , vol.160 , pp. 661-665
    • Cohen, T.1    Schvaneveldt, R.W.2
  • 68
    • 46249118461 scopus 로고    scopus 로고
    • Clinical ontologies for discovery applications
    • Springer, C.J.O. Baker, K.-H. Cheung (Eds.)
    • Lussier Y.A., Bodenreider O. Clinical ontologies for discovery applications. Semantic web 2007, 101-119. Springer. C.J.O. Baker, K.-H. Cheung (Eds.).
    • (2007) Semantic web , pp. 101-119
    • Lussier, Y.A.1    Bodenreider, O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.