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A Bidirectional Tree Tagging Scheme for Joint Medical Relation Extraction

Joint medical relation extraction refers to extracting triples, composed of entities and relations, from the medical text with a single model. One of the solutions is to convert this task into a sequential tagging task. However, in the existing works, the methods of representing and tagging the triples in a linear way failed to the overlapping triples, and the methods of organizing the triples as a graph faced the challenge of large computational effort. In this paper, inspired by the tree-like relation structures in the medical text, we propose a novel scheme called Bidirectional Tree Tagging (BiTT) to form the medical relation triples into two two binary trees and convert the trees into a word-level tags sequence. Based on BiTT scheme, we develop a joint relation extraction model to predict the BiTT tags and further extract medical triples efficiently. Our model outperforms the best baselines by 2.0\% and 2.5\% in F1 score on two medical datasets. What's more, the models with our BiTT scheme also obtain promising results in three public datasets of other domains.