Discovering drug-target interaction knowledge from biomedical literature.

MOTIVATION: The interaction between drugs and targets (DTI) in human body plays a crucial role in biomedical science and applications. As millions of papers come out every year in the biomedical domain, automatically discovering DTI knowledge from biomedical literature, which are usually triplets about drugs, targets and their interaction, becomes an urgent demand in the industry. Existing methods of discovering biological knowledge are mainly extractive approaches that often require detailed annotations (e.g. all mentions of biological entities, relations between every two entity mentions, etc.). However, it is difficult and costly to obtain sufficient annotations due to the requirement of expert knowledge from biomedical domains. RESULTS: To overcome these difficulties, we explore an end-to-end solution for this task by using generative approaches. We regard the DTI triplets as a sequence and use a Transformer-based model to directly generate them without using the detailed annotations of entities and relations. Further, we propose a semi-supervised method, which leverages the aforementioned end-to-end model to filter unlabeled literature and label them. Experimental results show that our method significantly outperforms extractive baselines on DTI discovery. We also create a dataset, KD-DTI, to advance this task and release it to the community. AVAILABILITY AND IMPLEMENTATION: Our code and data are available at https://github.com/bert-nmt/BERT-DTI. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

FewJoint: few-shot learning for joint dialogue understanding.

Few-shot learning (FSL) is one of the key future steps in machine learning and raises a lot of attention. In this paper, we focus on the FSL problem of dialogue understanding, which contains two closely related tasks: intent detection and slot filling. Dialogue understanding has been proven to benefit a lot from jointly learning the two sub-tasks. However, such joint learning becomes challenging in the few-shot scenarios: on the one hand, the sparsity of samples greatly magnifies the difficulty of modeling the connection between the two tasks; on the other hand, how to jointly learn multiple tasks in the few-shot setting is still less investigated. In response to this, we introduce FewJoint, the first FSL benchmark for joint dialogue understanding. FewJoint provides a new corpus with 59 different dialogue domains from real industrial API and a code platform to ease FSL experiment set-up, which are expected to advance the research of this field. Further, we find that insufficient performance of the few-shot setting often leads to noisy sharing between two sub-task and disturbs joint learning. To tackle this, we guide slot with explicit intent information and propose a novel trust gating mechanism that blocks low-confidence intent information to ensure high quality sharing. Besides, we introduce a Reptile-based meta-learning strategy to achieve better generalization in unseen few-shot domains. In the experiments, the proposed method brings significant improvements on two datasets and achieve new state-of-the-art performance.