Improving distantly supervised extraction of drug-drug and protein-protein interactions

Authors:
Tamara Bobić;Roman Klinger;Philippe Thomas;Martin Hofmann-Apitius
Affiliations:
Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany and Bonn-Aachen Center for Information Technology, Bonn, Germany;Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany;Humboldt-Universität, Berlin, Germany;Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany and Bonn-Aachen Center for Information Technology, Bonn, Germany
Venue:
ROBUS-UNSUP '12 Proceedings of the Joint Workshop on Unsupervised and Semi-Supervised Learning in NLP
Year:
2012

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Abstract

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.