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A Graph Kernel for Protein-Protein Interaction Extraction

Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski, A Graph Kernel for Protein-Protein Interaction Extraction. In: Sophia Ananiadou K. Bretonnel Cohen John Pestian Jun'ichi Tsujii Dina Demner-Fushman, Bonnie Webber (Eds.), Proceedings of ACL-08: HLT BioNLP 2008 Workshop: Current Trends in Biomedical Natural Language Processing, 1–9, The Association for Computational Linguistics, 2008.

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.

Files:

Abstract in PDF-format

BibTeX entry:

@INPROCEEDINGS{inpAiPyBjPaGiSa08a,
  title = {A Graph Kernel for Protein-Protein Interaction Extraction},
  booktitle = {Proceedings of ACL-08: HLT BioNLP 2008 Workshop: Current Trends in Biomedical Natural Language Processing},
  author = {Airola, Antti and Pyysalo, Sampo and Björne, Jari and Pahikkala, Tapio and Ginter, Filip and Salakoski, Tapio},
  editor = {Dina Demner-Fushman, Sophia Ananiadou K. Bretonnel Cohen John Pestian Jun'ichi Tsujii and Bonnie Webber},
  publisher = {The Association for Computational Linguistics},
  pages = {1–9},
  year = {2008},
  keywords = {BioNLP, Information Extraction, Kernel Methods, Machine Learning},
}

Belongs to TUCS Research Unit(s): Algorithmics and Computational Intelligence Group (ACI), Turku BioNLP Group

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