JCBIE: a joint continual learning neural network for biomedical information extraction

Abstract

Extracting knowledge from heterogeneous data sources is fundamental for the construction of structured biomedical knowledge graphs (BKGs), where entities and relations are represented as nodes and edges in the graphs, respectively. Previous biomedical knowledge extraction methods simply considered limited entity types and relations by using a task-specific training set, which is insufficient for large-scale BKGs development and downstream task applications in different scenarios. To alleviate this issue, we propose a joint continual learning biomedical information extraction (JCBIE) network to extract entities and relations from different biomedical information datasets. By empirically studying different joint learning and continual learning strategies, the proposed JCBIE can learn and expand different types of entities and relations from different datasets. JCBIE uses two separated encoders in joint-feature extraction, hence can effectively avoid the feature confusion problem comparing with using one hard-parameter sharing encoder. Specifically, it allows us to adopt entity augmented inputs to establish the interaction between named entity recognition and relation extraction. Finally, a novel evaluation mechanism is proposed for measuring cross-corpus generalization errors, which was ignored by traditional evaluation methods. Our empirical studies show that JCBIE achieves promising performance when continual learning strategy is adopted with multiple corpora.