Sentence Simplification Aids Protein-Protein Interaction Extraction

TL;DR

This paper demonstrates that automatic sentence simplification significantly improves the recall of protein-protein interaction extraction systems from biomedical literature, aiding biomedical research.

Contribution

It introduces the impact of sentence simplification on PPI extraction performance, showing a notable recall improvement without harming precision.

Findings

Recall increased by 8% with sentence simplification

No significant change in precision observed

Simplification enhances extraction system effectiveness

Abstract

Accurate systems for extracting Protein-Protein Interactions (PPIs) automatically from biomedical articles can help accelerate biomedical research. Biomedical Informatics researchers are collaborating to provide metaservices and advance the state-of-art in PPI extraction. One problem often neglected by current Natural Language Processing systems is the characteristic complexity of the sentences in biomedical literature. In this paper, we report on the impact that automatic simplification of sentences has on the performance of a state-of-art PPI extraction system, showing a substantial improvement in recall (8%) when the sentence simplification method is applied, without significant impact to precision.