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Background: Semantic resources such as knowledge bases contains high-qualitystructured knowledge and therefore require significant effort from domain experts. Using the resources to reinforce the information retrieval from the unstructured text may further exploit the potentials of such unstructured text resources and their curated knowledge. Results: The paper proposes a novel method that uses a deep neural network model adopting the prior knowledge to improve performance in the automated extraction of biological semantic relations from the scientific literature. The model is based on a recurrent neural network combining the attention mechanism with the semantic resources, i.e., UniProt and BioModels. Our method is evaluated on the BioNLP and BioCreative corpus, a set of manually annotated biological text. The experiments demonstrate that the method outperforms the current state-of-the-art models, and the structured semantic information could improve the result of biotext-mining. Conclusion: The experiment results show that our approach can effectively make use of the external prior knowledge information and improve the performance in the protein-protein interaction extraction task. The method should be able to be generalized for other types of data, although it is validated on biomedical texts.

Natural languages display a trade-off among different strategies to convey syntactic structure, such as word order or inflection. This trade-off, however, has not appeared in recent simulations of iterated language learning with neural network agents (Chaabouni et al., 2019b). We re-evaluate this result in light of three factors that play an important role in comparable experiments from the Language Evolution field: (i) speaker bias towards efficient messaging, (ii) non systematic input languages, and (iii) learning bottleneck. Our simulations show that neural agents mainly strive to maintain the utterance type distribution observed during learning, instead of developing a more efficient or systematic language.

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