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Register a new userFast and Effective Biomedical Entity Linking Using a Dual Encoder
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Added by
Rajarshi Bhowmik
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a retrieve and rerank paradigm, where the candidate entities are first selected using a retriever model, and then the retrieved candidates are ranked by a reranker model. While this paradigm produces state-of-the-art results, they are slow both at training and test time as they can process only one mention at a time. To mitigate these issues, we propose a BERT-based dual encoder model that resolves multiple mentions in a document in one shot. We show that our proposed model is multiple times faster than existing BERT-based models while being competitive in accuracy for biomedical entity linking. Additionally, we modify our dual encoder model for end-to-end biomedical entity linking that performs both mention span detection and entity disambiguation and out-performs two recently proposed models.
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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.
Entity Linking has two main open areas of research: 1) generate candidate entities without using alias tables and 2) generate more contextual representations for both mentions and entities. Recently, a solution has been proposed for the former as a dual-encoder entity retrieval system (Gillick et al., 2019) that learns mention and entity representations in the same space, and performs linking by selecting the nearest entity to the mention in this space. In this work, we use this retrieval system solely for generating candidate entities. We then rerank the entities by using a cross-attention encoder over the target mention and each of the candidate entities. Whereas a dual encoder approach forces all information to be contained in the small, fixed set of vector dimensions used to represent mentions and entities, a crossattention model allows for the use of detailed information (read: features) from the entirety of each <mention, context, candidate entity> tuple. We experiment with features used in the reranker including different ways of incorporating document-level context. We achieve state-of-the-art results on TACKBP-2010 dataset, with 92.05% accuracy. Furthermore, we show how the rescoring model generalizes well when trained on the larger CoNLL-2003 dataset and evaluated on TACKBP-2010.
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.
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.
Entity linking (or Normalization) is an essential task in text mining that maps the entity mentions in the medical text to standard entities in a given Knowledge Base (KB). This task is of great importance in the medical domain. It can also be used for merging different medical and clinical ontologies. In this paper, we center around the problem of disease linking or normalization. This task is executed in two phases: candidate generation and candidate scoring. In this paper, we present an approach to rank the candidate Knowledge Base entries based on their similarity with disease mention. We make use of the Triplet Network for candidate ranking. While the existing methods have used carefully generated sieves and external resources for candidate generation, we introduce a robust and portable candidate generation scheme that does not make use of the hand-crafted rules. Experimental results on the standard benchmark NCBI disease dataset demonstrate that our system outperforms the prior methods by a significant margin.
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