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Performance Enhancement of Tree Kernel-based Protein-Protein Interaction Extraction by Parse Tree Pruning and Decay Factor Adjustment  

Choi, Sung-Pil (한국과학기술정보연구원 정보기술연구실)
Choi, Yun-Soo (한국과학기술정보연구원 정보기술연구실)
Jeong, Chang-Hoo (한국과학기술정보연구원 정보기술연구실)
Myaeng, Sung-Hyon (한국과학기술원 전산학과)
Publication Information
Journal of KIISE:Software and Applications / v.37, no.2, 2010 , pp. 85-94 More about this Journal
Abstract
This paper introduces a novel way to leverage convolution parse tree kernel to extract the interaction information between two proteins in a sentence without multiple features, clues and complicated kernels. Our approach needs only the parse tree alone of a candidate sentence including pairs of protein names which is potential to have interaction information. The main contribution of this paper is two folds. First, we show that for the PPI, it is imperative to execute parse tree pruning removing unnecessary context information in deciding whether the current sentence imposes interaction information between proteins by comparing with the latest existing approaches' performance. Secondly, this paper presents that tree kernel decay factor can play an pivotal role in improving the extraction performance with the identical learning conditions. Consequently, we could witness that it is not always the case that multiple kernels with multiple parsers perform better than each kernels alone for PPI extraction, which has been argued in the previous research by presenting our out-performed experimental results compared to the two existing methods by 19.8% and 14% respectively.
Keywords
Protein-Protein Interaction Extraction; Kernel Methods; Convolution Parse Tree Kernel; Information Extraction; Relation Extraction;
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