Cross-Corpus Training with TreeLSTM for the Extraction of Biomedical Relationships from Text

Legrand Joël, Yannick Toussaint, Chedy Raïssi, Adrien Coulet

Abstract: A bottleneck problem in machine learning-based relationship extraction (RE) algorithms, and particularly of deep learning-based ones, is the availability of training data in the form of annotated corpora. For specific domains, such as biomedicine, the long time and high expertise required for the development of manually annotated corpora explain that most of the existing one are relatively small (i.e., hundreds of sentences). Beside, larger corpora focusing on general or domain-specific relationships (such as citizenship or drug-drug interactions) have been developed. In this paper, we study how large annotated corpora developed for alternative tasks may improve the performances on biomedicine related tasks, for which few annotated resources are available. We experiment two deep learning-based models to extract relationships from biomedical texts with high performance. The first one combine locally extracted features using a Convolutional Neural Network (CNN) model, while the second exploit the syntactic structure of sentences using a Recursive Neural Network (RNN) architecture. Our experiments show that, contrary to the former, the latter benefits from a cross-corpus learning strategy to improve the performance of relationship extraction tasks. Indeed our approach leads to the best published performances for two biomedical RE tasks, and to state-of-the-art results for two other biomedical RE tasks, for which few annotated resources are available (less than 400 manually annotated sentences). This may be particularly impactful in specialized domains in which training resources are scarce, because they would benefit from the training data of other domains for which large annotated corpora does exist.

Keywords: Relationships Extraction, Deep Learning, TreeLSTM, NLP