BioRel: A LargeScale Dataset for Biomedical Relation Extraction Valuable biomedical knowledge usually exists in the form of electronic publications and literature, which is growing at an enormous rate. Relation extraction plays a critical role in discovering such knowledge and transform them into structural form. Previous relation extraction datasets in biomedical domain are mainly humanannotated, whose scales are usually limited due to their laborintensive and timeconsuming nature. In this paper, we present BioRel, a largescale dataset constructed by using Unified Medical Language System (UMLS) as knowledge base and Medline as corpus. Entities in sentences of Medline are identified and linked to UMLS by Metamap. Relation label for each sentence is recognized using distant supervision. We adapt both stateoftheart deep learning and statistical machine learning methods as baseline models and conduct comprehensive experiments on BioRel. Experimental results show that BioRel is suitable for training and evaluating relation extraction models for both deep learning and statistical methods by providing both reasonable baseline performance and many remaining challenges.

A neural networkbased joint learning approach for biomedical entity and relation extraction from biomedical literature Abstract   Recently joint modeling methods of entity and relation exhibit more promising results than traditional pipelined methods in general domain. However, they are inappropriate for the biomedical domain due to numerous overlapping relations in biomedical text. To alleviate the problem, we propose a neural networkbased joint learning approach for biomedical entity and relation extraction. In this approach, a novel tagging scheme that takes into account overlapping relations is proposed. Then the AttBiLSTMCRF model is built to jointly extract the entities and their relations with our extraction rules. Moreover, the contextualized ELMo representations pretrained on biomedical text are used to further improve the performance. Experimental results on biomedical corpora show that our method can significantly improve the performance of overlapping relation extraction and achieves the stateoftheart performance.