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Register a new userEnd-to-end Biomedical Entity Linking with Span-based Dictionary Matching
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Added by
Shogo Ujiie
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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.
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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 articles by dictionary matching and use them to train a context-aware entity linking model with contrastive learning. We predict the normalized biomedical entity at inference time through a nearest-neighbor search. Results found that BioCoM substantially outperforms state-of-the-art models, especially in low-resource settings, by effectively using the context of the entities.
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 per question, ELQ outperforms the previous state of the art by a large margin of +12.7% and +19.6% F1, respectively. With a very fast inference time (1.57 examples/s on a single CPU), ELQ can be useful for downstream question answering systems. In a proof-of-concept experiment, we demonstrate that using ELQ significantly improves the downstream QA performance of GraphRetriever (arXiv:1911.03868). Code and data available at https://github.com/facebookresearch/BLINK/tree/master/elq
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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 reported best results by more than 2.2 LAS and UAS points. The graph-based parsing architecture allows for global inference and rich feature representations for TAG parsing, alleviating the fundamental trade-off between transition-based and graph-based parsing systems. We also demonstrate that the proposed parser achieves state-of-the-art performance in the downstream tasks of Parsing Evaluation using Textual Entailments (PETE) and Unbounded Dependency Recovery. This provides further support for the claim that TAG is a viable formalism for problems that require rich structural analysis of sentences.
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