All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning.
In: BMC Bioinformatics, Jg. 9 (2008-01-12), S. 1-12
Online
academicJournal
Zugriff:
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 state-of-the-art level in PPI extraction, and note the possible extension to the task of extracting complex interactions. Cross-corpus results provide further insight into how the learning generalizes beyond individual corpora. 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. Recommendations for avoiding these pitfalls are provided. [ABSTRACT FROM AUTHOR]
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All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning.
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Autor/in / Beteiligte Person: | Airola, Antti ; Pyysalo, Sampo ; Björne, Jari ; Pahikkala, Tapio ; Ginter, Filip ; Salakoski, Tapio |
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Zeitschrift: | BMC Bioinformatics, Jg. 9 (2008-01-12), S. 1-12 |
Veröffentlichung: | 2008 |
Medientyp: | academicJournal |
ISSN: | 1471-2105 (print) |
DOI: | 10.1186/1471-2105-9-S11-S2 |
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