Protein-Protein Interaction Article Classification Using a Convolutional Recurrent Neural Network with Pre-trained Word Embeddings

Abstract

Curation of protein interactions from scientific articles is an important task, since interaction networks are essential for the understanding of biological processes associated with disease or pharmacological action for example. However, the increase in the number of publications that potentially contain relevant information turns this into a very challenging and expensive task. In this work we used a convolutional recurrent neural network for identifying relevant articles for extracting information regarding protein interactions. Using the BioCreative III Article Classification Task dataset, we achieved an area under the precision-recall curve of 0.715 and a Matthew’s correlation coefficient of 0.600, which represents an improvement over previous works.

Keywords

• literature retrieval
• protein-protein interactions
• machine learning
• recurrent neural networks
• word embeddings