Multistage gene normalization and SVM-based ranking for protein interactor extraction in full-text articles

Hong Jie Dai, Po Ting Lai, Richard Tzong Han Tsai

研究成果: 雜誌貢獻期刊論文同行評審

22 引文 斯高帕斯(Scopus)

摘要

The interactor normalization task (INT) is to identify genes that play the interactor role in protein-protein interactions (PPIs), to map these genes to unique IDs, and to rank them according to their normalized confidence. INT has two subtasks: gene normalization (GN) and interactor ranking. The main difficulties of INT GN are identifying genes across species and using full papers instead of abstracts. To tackle these problems, we developed a multistage GN algorithm and a ranking method, which exploit information in different parts of a paper. Our system achieved a promising AUC of 0.43471. Using the multistage GN algorithm, we have been able to improve system performance (AUC) by 1.719 percent compared to a one-stage GN algorithm. Our experimental results also show that with full text, versus abstract only, INT AUC performance was 22.6 percent higher.

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文章編號5467043
頁(從 - 到)412-420
頁數9
期刊IEEE/ACM Transactions on Computational Biology and Bioinformatics
7
發行號3
DOIs
出版狀態已出版 - 2010

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