Eztract interaction detection methods from the biological literature
Background: Considerable efforts have been made to extract protein-protein interactions from the biological literature, but little work has been clone on the extraction of interaction detection methods. It is crucial to annotate the detection methods in the literature, since different detection methods shed different degrees of reliability on the reported interactions.However, the diversity of method mentions in the literature makes the automatic extraction quite challenging.Results: In this article, we develop a generative topic model, the Correlated Method-Word model (CMW model) to extract the detection methods from the literature. In the CMW model, we formulate the correlation between the different methods and related words in a probabilistic framework in order to infer the potential methods from the given document. By applying the model on a corpus of 5319 full text documents annotated by the MINT and IntAct databases, we observe promising results, which outperform the best result reported in the BioCreative Ⅱchallenge evaluation.Conclusions: From the promising experiment results, we can see that the CMW model overcomes the issues caused by the diversity in the method mentions and properly captures the in-depth correlations between the detection methods and related words. The performance outperforming the baseline methods confirms that the dependence assumptions of the model are reasonable and the model is competent for the practical processing.
Hongning Wang Minlie Huang Xiaoyan Zhu
State Key Laboratory of Intelligent Technology and Systems, Tsinghua National Laboratory for Information Science and Technology, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
国际会议
The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)
北京
英文
631-643
2009-01-01（万方平台首次上网日期，不代表论文的发表时间）