Neural network-based approaches for biomedical relation classification: A review

Abstract

The explosive growth of biomedical literature has created a rich source of knowledge, such as that on protein-protein interactions (PPIs) and drug-drug interactions (DDIs), locked in unstructured free text. Biomedical relation classification aims to automatically detect and classify biomedical relations, which has great benefits for various biomedical research and applications. In the past decade, significant progress has been made in biomedical relation classification. With the advance of neural network methodology, neural network-based approaches have been applied in biomedical relation classification and achieved state-of-the-art performance for some public datasets and shared tasks. In this review, we describe the recent advancement of neural network-based approaches for classifying biomedical relations. We summarize the available corpora and introduce evaluation metrics. We present the general framework for neural network-based approaches in biomedical relation extraction and pretrained word embedding resources. We discuss neural network-based approaches, including convolutional neural networks (CNNs) and recurrent neural networks (RNNs). We conclude by describing the remaining challenges and outlining future directions.

Keywords: Biomedical literature; Biomedical relation classification; Deep learning; Natural language processing; Neural networks.