Extracting biomedical concepts from fulltext by relative importance in a graph model

Min Song, Said Bleik, Hwanjo Yu, Wook Shin Han

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Extracting concepts from fulltext data collections is a daunting task in that many different concepts and themes are intertwined and ample term variation exists in fulltext. Concepts represent topics or themes of a article and are helpful means of managing and searching large document collections. In addition, automatically extracting and assigning concepts play a pivotal role in indexing electronic documents and building digital libraries. In this paper we propose a novel approach to biomedical concept extraction by adopting a ranking algorithm of relative importance in concept graphs. The proposed consists of two major steps: First, we represent full-text documents by graphs whose nodes and edges are determined by named entity recognition and UMLS Semantic Network. Second, we rank concepts with relative importance algorithms. We evaluate our technique with a set of biomedical full-texts and compare it to various different key-phrase extraction and graph ranking techniques. The experimental results show that our technique achieves the best performance over other compared algorithms.

Original languageEnglish
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages586-593
Number of pages8
DOIs
Publication statusPublished - 2011 Dec 1
Event2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: 2011 Nov 122011 Nov 15

Publication series

Name2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Other

Other2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
CountryUnited States
CityAtlanta, GA
Period11/11/1211/11/15

Fingerprint

Unified Medical Language System
Digital Libraries
Digital libraries
Semantics

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Song, M., Bleik, S., Yu, H., & Han, W. S. (2011). Extracting biomedical concepts from fulltext by relative importance in a graph model. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 586-593). [6112433] (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112433
Song, Min ; Bleik, Said ; Yu, Hwanjo ; Han, Wook Shin. / Extracting biomedical concepts from fulltext by relative importance in a graph model. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. pp. 586-593 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).
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Song, M, Bleik, S, Yu, H & Han, WS 2011, Extracting biomedical concepts from fulltext by relative importance in a graph model. in 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011., 6112433, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, pp. 586-593, 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 11/11/12. https://doi.org/10.1109/BIBMW.2011.6112433

Extracting biomedical concepts from fulltext by relative importance in a graph model. / Song, Min; Bleik, Said; Yu, Hwanjo; Han, Wook Shin.

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 586-593 6112433 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Song M, Bleik S, Yu H, Han WS. Extracting biomedical concepts from fulltext by relative importance in a graph model. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 586-593. 6112433. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112433