Document-level Biomedical Relation Extraction Based on Multi-Dimensional Fusion Information and Multi-Granularity Logical Reasoning

Abstract

Document-level biomedical relation extraction (Bio-DocuRE) is an important branch of biomedical text mining that aims to automatically extract all relation facts from the biomedical text. Since there are a considerable number of relations in biomedical documents that need to be judged by other existing relations, logical reasoning has become a research hotspot in the past two years. However, current models with reasoning are single-granularity only based on one element information, ignoring the complementary fact of different granularity reasoning information. In addition, obtaining rich document information is a prerequisite for logical reasoning, but most of the previous models cannot sufficiently utilize document information, which limits the reasoning ability of the model. In this paper, we propose a novel Bio-DocuRE model called FILR, based on Multi-Dimensional Fusion Information and Multi-Granularity Logical Reasoning. Specifically, FILR presents a multi-dimensional information fusion module MDIF to extract sufficient global document information. Then FILR proposes a multi-granularity reasoning module MGLR to obtain rich inference information through the reasoning of both entity-pairs and mention-pairs. We evaluate our FILR model on two widely used biomedical corpora CDR and GDA. Experimental results show that FILR achieves state-of-the-art performance.