Extracting protein-protein interaction sentences by applying rough set data analysis

: Ginter F, Pahikkala T, Pyysalo S, Boberg J, Jarvinen J, Salakoski T

: Tsumoto Husaku, Slowinski Roman, Komorowski Jan, Grzymala-Busse Jerzy W

: Fourth International Conference on Rough Sets and Current Trends in Computing

: 2004

: Lecture Notes in Computer Science

: Proceedings of the Fourth International Conference on Rough Sets and Current Trends in Computing

: ROUGH SETS AND CURRENT TRENDS IN COMPUTING

: LECT NOTES ARTIF INT

: 3066

: 780

: 785

: 6

: 3-540-22117-4

: 0302-9743

In this paper, we introduce away to apply rough set data analysis to the problem of extracting protein-protein interaction sentences in biomedical literature. Our approach builds on decision rules of protein names, interaction words, and their mutual positions in sentences. In order to broaden the set of potential interaction words, we develop a morphological model which generates spelling and inflection variants of the interaction words. We evaluate the performance of the proposed method on a hand-tagged dataset of 1894 sentences and show a precision-recall break-even performance of 79,8% by using leave-one-out cross-validation.