Extraction of Gene Regulatory Relation Using BioBERT

Relation Extraction (RE) is a critical task typically carried out after Named Entity recognition for identifying gene-gene association from scientific publication. Current state-of the-art tools have limited capacity as most of them only extract entity relations from abstract texts. The retrieved gene-gene relations typically do not cover gene regulatory relations. There still exists a lot of room for improvement. In this work, we propose GeREx, a transformer based RE tool for identifying gene regulatory relations from full texts by incorporating labeling from pathway figures. GeREx achieved an F1-Score of 83.45% when evaluated on an independent test dataset.