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Named entity recognition has been extensively studied on English news texts. However, the transfer to other domains and languages is still a challenging problem. In this paper, we describe the system with which we participated in the first subtrack of the PharmaCoNER competition of the BioNLP Open Shared Tasks 2019. Aiming at pharmacological entity detection in Spanish texts, the task provides a non-standard domain and language setting. However, we propose an architecture that requires neither language nor domain expertise. We treat the task as a sequence labeling task and experiment with attention-based embedding selection and the training on automatically annotated data to further improve our systems performance. Our system achieves promising results, especially by combining the different techniques, and reaches up to 88.6% F1 in the competition.
The recognition and normalization of clinical information, such as tumor morphology mentions, is an important, but complex process consisting of multiple subtasks. In this paper, we describe our system for the CANTEMIST shared task, which is able to
We formulate sequence to sequence transduction as a noisy channel decoding problem and use recurrent neural networks to parameterise the source and channel models. Unlike direct models which can suffer from explaining-away effects during training, no
Entity representations are useful in natural language tasks involving entities. In this paper, we propose new pretrained contextualized representations of words and entities based on the bidirectional transformer. The proposed model treats words and
Entity alignment typically suffers from the issues of structural heterogeneity and limited seed alignments. In this paper, we propose a novel Multi-channel Graph Neural Network model (MuGNN) to learn alignment-oriented knowledge graph (KG) embeddings
Previous work on neural noisy channel modeling relied on latent variable models that incrementally process the source and target sentence. This makes decoding decisions based on partial source prefixes even though the full source is available. We pur