Modeling of joint extraction of entity relationships in clinical electronic medical records

Abstract

The advancement of medical informatization necessitates extracting entities and their relationships from electronic medical records. Presently, research on electronic medical records predominantly concentrates on single-entity relationship extraction. However, clinical electronic medical records frequently exhibit overlapping complex entity relationships, thereby heightening the challenge of information extraction. To rectify the absence of a clinical medical relationship extraction dataset, this study utilizes electronic medical records from 584 patients in a hospital to create a compact clinical medical relationship extraction dataset. To address the pipelined relationship extraction model’s limitation in overlooking the one-to-many correlation problem between entities and relationships, this paper introduces a cascading relationship extraction model. This model integrates the MacBERT pre-training model, gated recurrent network, and multi-head self-attention mechanism to enhance the extraction of text features. Simultaneously, adversarial learning is incorporated to bolster the model’s robustness. In scenarios involving one-to-many relationships between entities, a two-phase task is employed. Initially, the main entity is predicted, followed by predicting the associated object and their correspondences. Employing this cascade-structured approach enables the model to flexibly manage intricate entity relationships, thereby enhancing extraction accuracy. Experimental results demonstrate the model’s efficiency, yielding F1-scores of 82.8%, 76.8%, and 88.2% for fulfilling relational extraction requirements and tasks on DuIE, CHIP-CDEE, and private datasets, respectively. These scores represent improvements over the benchmark model. The findings indicate the model’s applicability in practical domains, particularly in tasks such as biomedical information extraction.