Relation Extraction From Biomedical and Clinical Text: Unified Multitask Learning Framework

Abstract

MOTIVATION: To minimize the accelerating amount of time invested on the biomedical literature search, numerous approaches for automated knowledge extraction have been proposed. Relation extraction is one such task where semantic relations between the entities are identified from the free text. In the biomedical domain, extraction of regulatory pathways, metabolic processes, adverse drug reaction or disease models necessitates knowledge from the individual relations, for example, physical or regulatory interactions between genes, proteins, drugs, chemical, disease or phenotype. RESULTS: In this paper, we study the relation extraction task from three major biomedical and clinical tasks, namely drug-drug interaction, protein-protein interaction, and medical concept relation extraction. Towards this, we model the relation extraction problem in a multi-task learning (MTL)framework, and introduce for the first time the concept of structured self-attentive network complemented with the adversarial learning approach for the prediction of relationships from the biomedical and clinical text. The fundamental notion of MTL is to simultaneously learn multiple problems together by utilizing the concepts of the shared representation. Additionally, we also generate the highly efficient single task model which exploits the shortest dependency path embedding learned over the attentive gated recurrent unit to compare our proposed MTL models. The framework we propose significantly improves over all the baselines (deep learning techniques)and single-task models for predicting the relationships, without compromising on the performance of all the tasks.