All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning

Background: Automated extraction of protein-protein interactions (PPI) is an important and widely studied task in biomedical text mining. We propose a graph kernel based approach for this task. In contrast to earlier approaches to PPI extraction, the introduced all-paths graph kernel has the capability to make use of full, general dependency graphs representing the sentence structure. Results: We evaluate the proposed method on five publicly available PPI corpora, providing the most comprehensive evaluation done for a machine learning based PPI-extraction system. We additionally perform a detailed evaluation of the effects of training and testing on different resources, providing insight into the challenges involved in applying a system beyond the data it was trained on. Our method is shown to achieve state-of-the-art performance with respect to comparable evaluations, with 56.4 F-score and 84.8 AUC on the AImed corpus. Conclusion: We show that the graph kernel approach performs on st...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski
• Keywords: BMCBI 2008, Graph Kernel, Kernel Based Approach, PPI Extraction