Detecting duplicate biological entities using markov random field-based edit distance

Min Song; Alex Rudniy

doi:10.1109/BIBM.2008.34

Detecting duplicate biological entities using markov random field-based edit distance

Min Song, Alex Rudniy

Department of Library and Information Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

8 Citations (Scopus)

Abstract

Duplicate entities detection in biological data became a demanded research task [3,5,7,8,9]. In this paper, we propose a novel context-sensitive Markov Random Field-based Edit Distance (MRFED). We apply the Markov Random Field (MRF) theory to Needleman-Wunsch (NW) distance and combine MRFED with TFIDF, a token-based distance algorithm (SoftMRFED). We evaluate SoftMRFED and other distance algorithms (Levenstein, SoftTFIDF, and MongeElkan) at biological entity matching and synonym matching. The experiment results show SoftMRFED significantly outperforms other distance algorithms and its performance is superior to token-based distance algorithms in two matching tasks.

Original language	English
Title of host publication	Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages	457-460
Number of pages	4
DOIs	https://doi.org/10.1109/BIBM.2008.34
Publication status	Published - 2008
Event	2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States Duration: 2008 Nov 3 → 2008 Nov 5

Publication series

Name	Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Other

Other	2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Country/Territory	United States
City	Philadelphia, PA
Period	08/11/3 → 08/11/5

All Science Journal Classification (ASJC) codes

Molecular Biology
Information Systems
Biomedical Engineering

Access to Document

10.1109/BIBM.2008.34

Cite this

@inproceedings{839d3bdf014945aba647420fefbee63f,

title = "Detecting duplicate biological entities using markov random field-based edit distance",

abstract = "Duplicate entities detection in biological data became a demanded research task [3,5,7,8,9]. In this paper, we propose a novel context-sensitive Markov Random Field-based Edit Distance (MRFED). We apply the Markov Random Field (MRF) theory to Needleman-Wunsch (NW) distance and combine MRFED with TFIDF, a token-based distance algorithm (SoftMRFED). We evaluate SoftMRFED and other distance algorithms (Levenstein, SoftTFIDF, and MongeElkan) at biological entity matching and synonym matching. The experiment results show SoftMRFED significantly outperforms other distance algorithms and its performance is superior to token-based distance algorithms in two matching tasks.",

author = "Min Song and Alex Rudniy",

year = "2008",

doi = "10.1109/BIBM.2008.34",

language = "English",

isbn = "9780769534527",

series = "Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008",

pages = "457--460",

booktitle = "Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008",

note = "2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 ; Conference date: 03-11-2008 Through 05-11-2008",

}

Song, M & Rudniy, A 2008, Detecting duplicate biological entities using markov random field-based edit distance. in Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008., 4684939, Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, pp. 457-460, 2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, Philadelphia, PA, United States, 08/11/3. https://doi.org/10.1109/BIBM.2008.34

Detecting duplicate biological entities using markov random field-based edit distance. / Song, Min; Rudniy, Alex.
Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 457-460 4684939 (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - Detecting duplicate biological entities using markov random field-based edit distance

AU - Song, Min

AU - Rudniy, Alex

PY - 2008

Y1 - 2008

N2 - Duplicate entities detection in biological data became a demanded research task [3,5,7,8,9]. In this paper, we propose a novel context-sensitive Markov Random Field-based Edit Distance (MRFED). We apply the Markov Random Field (MRF) theory to Needleman-Wunsch (NW) distance and combine MRFED with TFIDF, a token-based distance algorithm (SoftMRFED). We evaluate SoftMRFED and other distance algorithms (Levenstein, SoftTFIDF, and MongeElkan) at biological entity matching and synonym matching. The experiment results show SoftMRFED significantly outperforms other distance algorithms and its performance is superior to token-based distance algorithms in two matching tasks.

AB - Duplicate entities detection in biological data became a demanded research task [3,5,7,8,9]. In this paper, we propose a novel context-sensitive Markov Random Field-based Edit Distance (MRFED). We apply the Markov Random Field (MRF) theory to Needleman-Wunsch (NW) distance and combine MRFED with TFIDF, a token-based distance algorithm (SoftMRFED). We evaluate SoftMRFED and other distance algorithms (Levenstein, SoftTFIDF, and MongeElkan) at biological entity matching and synonym matching. The experiment results show SoftMRFED significantly outperforms other distance algorithms and its performance is superior to token-based distance algorithms in two matching tasks.

UR - http://www.scopus.com/inward/record.url?scp=58049138671&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=58049138671&partnerID=8YFLogxK

U2 - 10.1109/BIBM.2008.34

DO - 10.1109/BIBM.2008.34

M3 - Conference contribution

AN - SCOPUS:58049138671

SN - 9780769534527

T3 - Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

SP - 457

EP - 460

BT - Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

T2 - 2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Y2 - 3 November 2008 through 5 November 2008

ER -

Detecting duplicate biological entities using markov random field-based edit distance

Abstract

Publication series

Other

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this