A graph kernel for protein-protein interaction extraction

Authors:
Antti Airola;Sampo Pyysalo;Jari Björne;Tapio Pahikkala;Filip Ginter;Tapio Salakoski
Affiliations:
University of Turku, Turku, Finland;University of Turku, Turku, Finland;University of Turku, Turku, Finland;University of Turku, Turku, Finland;University of Turku, Turku, Finland;University of Turku, Turku, Finland
Venue:
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Year:
2008

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Abstract

In this paper, we propose a graph kernel based approach for the automated extraction of protein-protein interactions (PPI) from scientific literature. In contrast to earlier approaches to PPI extraction, the introduced all-dependency-paths kernel has the capability to consider full, general dependency graphs. We evaluate the proposed method across five publicly available PPI corpora providing the most comprehensive evaluation done for a machine learning based PPI-extraction system. Our method is shown to achieve state-of-the-art performance with respect to comparable evaluations, achieving 56.4 F-score and 84.8 AUC on the AImed corpus. Further, we identify several pitfalls that can make evaluations of PPI-extraction systems incomparable, or even invalid. These include incorrect cross-validation strategies and problems related to comparing F-score results achieved on different evaluation resources.