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Disease name recognition and normalization, which is generally called biomedical entity linking, is a fundamental process in biomedical text mining. Recently, neural joint learning of both tasks has been proposed to utilize the mutual benefits. While this approach achieves high performance, disease concepts that do not appear in the training dataset cannot be accurately predicted. This study introduces a novel end-to-end approach that combines span representations with dictionary-matching features to address this problem. Our model handles unseen concepts by referring to a dictionary while maintaining the performance of neural network-based models, in an end-to-end fashion. Experiments using two major datasets demonstrate that our model achieved competitive results with strong baselines, especially for unseen concepts during training.
We introduce BioCoM, a contrastive learning framework for biomedical entity linking that uses only two resources: a small-sized dictionary and a large number of raw biomedical articles. Specifically, we build the training instances from raw PubMed ar
We present ELQ, a fast end-to-end entity linking model for questions, which uses a biencoder to jointly perform mention detection and linking in one pass. Evaluated on WebQSP and GraphQuestions with extended annotations that cover multiple entities p
Entity linking - connecting entity mentions in a natural language utterance to knowledge graph (KG) entities is a crucial step for question answering over KGs. It is often based on measuring the string similarity between the entity label and its ment
Named entity recognition (NER) is a critical step in modern search query understanding. In the domain of eCommerce, identifying the key entities, such as brand and product type, can help a search engine retrieve relevant products and therefore offer
We present a graph-based Tree Adjoining Grammar (TAG) parser that uses BiLSTMs, highway connections, and character-level CNNs. Our best end-to-end parser, which jointly performs supertagging, POS tagging, and parsing, outperforms the previously repor