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Register a new userLearning Domain-Specialised Representations for Cross-Lingual Biomedical Entity Linking
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Fangyu Liu
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Injecting external domain-specific knowledge (e.g., UMLS) into pretrained language models (LMs) advances their capability to handle specialised in-domain tasks such as biomedical entity linking (BEL). However, such abundant expert knowledge is available only for a handful of languages (e.g., English). In this work, by proposing a novel cross-lingual biomedical entity linking task (XL-BEL) and establishing a new XL-BEL benchmark spanning 10 typologically diverse languages, we first investigate the ability of standard knowledge-agnostic as well as knowledge-enhanced monolingual and multilingual LMs beyond the standard monolingual English BEL task. The scores indicate large gaps to English performance. We then address the challenge of transferring domain-specific knowledge in resource-rich languages to resource-poor ones. To this end, we propose and evaluate a series of cross-lingual transfer methods for the XL-BEL task, and demonstrate that general-domain bitext helps propagate the available English knowledge to languages with little to no in-domain data. Remarkably, we show that our proposed domain-specific transfer methods yield consistent gains across all target languages, sometimes up to 20 Precision@1 points, without any in-domain knowledge in the target language, and without any in-domain parallel data.
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Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.
Neural entity linking models are very powerful, but run the risk of overfitting to the domain they are trained in. For this problem, a domain is characterized not just by genre of text but even by factors as specific as the particular distribution of entities, as neural models tend to overfit by memorizing properties of frequent entities in a dataset. We tackle the problem of building robust entity linking models that generalize effectively and do not rely on labeled entity linking data with a specific entity distribution. Rather than predicting entities directly, our approach models fine-grained entity properties, which can help disambiguate between even closely related entities. We derive a large inventory of types (tens of thousands) from Wikipedia categories, and use hyperlinked mentions in Wikipedia to distantly label data and train an entity typing model. At test time, we classify a mention with this typing model and use soft type predictions to link the mention to the most similar candidate entity. We evaluate our entity linking system on the CoNLL-YAGO dataset (Hoffart et al., 2011) and show that our approach outperforms prior domain-independent entity linking systems. We also test our approach in a harder setting derived from the WikilinksNED dataset (Eshel et al., 2017) where all the mention-entity pairs are unseen during test time. Results indicate that our approach generalizes better than a state-of-the-art neural model on the dataset.
Cross-lingual Entity Linking (XEL) aims to ground entity mentions written in any language to an English Knowledge Base (KB), such as Wikipedia. XEL for most languages is challenging, owing to limited availability of resources as supervision. We address this challenge by developing the first XEL approach that combines supervision from multiple languages jointly. This enables our approach to: (a) augment the limited supervision in the target language with additional supervision from a high-resource language (like English), and (b) train a single entity linking model for multiple languages, improving upon individually trained models for each language. Extensive evaluation on three benchmark datasets across 8 languages shows that our approach significantly improves over the current state-of-the-art. We also provide analyses in two limited resource settings: (a) zero-shot setting, when no supervision in the target language is available, and in (b) low-resource setting, when some supervision in the target language is available. Our analysis provides insights into the limitations of zero-shot XEL approaches in realistic scenarios, and shows the value of joint supervision in low-resource settings.
Cross-language entity linking grounds mentions in multiple languages to a single-language knowledge base. We propose a neural ranking architecture for this task that uses multilingual BERT representations of the mention and the context in a neural network. We find that the multilingual ability of BERT leads to robust performance in monolingual and multilingual settings. Furthermore, we explore zero-shot language transfer and find surprisingly robust performance. We investigate the zero-shot degradation and find that it can be partially mitigated by a proposed auxiliary training objective, but that the remaining error can best be attributed to domain shift rather than language transfer.
Although over 100 languages are supported by strong off-the-shelf machine translation systems, only a subset of them possess large annotated corpora for named entity recognition. Motivated by this fact, we leverage machine translation to improve annotation-projection approaches to cross-lingual named entity recognition. We propose a system that improves over prior entity-projection methods by: (a) leveraging machine translation systems twice: first for translating sentences and subsequently for translating entities; (b) matching entities based on orthographic and phonetic similarity; and (c) identifying matches based on distributional statistics derived from the dataset. Our approach improves upon current state-of-the-art methods for cross-lingual named entity recognition on 5 diverse languages by an average of 4.1 points. Further, our method achieves state-of-the-art F_1 scores for Armenian, outperforming even a monolingual model trained on Armenian source data.
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