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Improving Distantly Supervised Extraction of Drug-Drug and Protein-Protein Interactions

: Bobic, T.; Klinger, R.; Thomas, P.; Hofmann-Apitius, M.

Volltext (PDF; )

Daelemans, W.:
Proceedings of ROBUS-UNSUP 2012: Joint Workshop on Unsupervised and Semi-Supervised Learning in NLP : 13th Conference of the European Chapter of the Association for Computational Linguistics, EACL 2012. April 23-27 2012, Avignon
Avignon, 2012
Joint Workshop on Unsupervised and Semi-Supervised Learning in NLP <2012, Avignon>
Konferenzbeitrag, Elektronische Publikation
Fraunhofer SCAI ()

Relation extraction is frequently and successfully addressed by machine learning methods. The downside of this approach is the need for annotated training data, typically generated in tedious manual, cost intensive work. Distantly supervised approaches make use of weakly annotated data, like automatically annotated corpora.
Recent work in the biomedical domain has applied distant supervision for protein-protein interaction (PPI) with reasonable results making use of the IntAct database. Such data is typically noisy and heuristics to filter the data are commonly applied. We propose a constraint to increase the quality of data used for training based on the assumption that no self-interaction of real-world
objects are described in sentences. In addition, we make use of the University of Kansas Proteomics Service (KUPS) database. These two steps show an increase of 7 percentage points (pp) for the PPI corpus AIMed. We demonstrate the broad applicability of our approach by using the same workflow for the analysis of drug-drug interactions, utilizing relationships available from the drug database DrugBank. We achieve 37.31%in F1 measure without manually annotated training data on an independent test set.