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Biomedical entity linking (BioEL) has achieved remarkable progress with the help of pre-trained language models. However, existing BioEL methods usually struggle to handle rare and difficult entities due to long-tailed distribution. To…

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…

A conventional approach to entity linking is to first find mentions in a given document and then infer their underlying entities in the knowledge base. A well-known limitation of this approach is that it requires finding mentions without…

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base. It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as…

Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names,…

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base (KB). A popular approach to the task are name-based methods, i.e. those identifying the most appropriate name in the KB for a given mention, either…

Biomedical entity linking maps textual mentions to concepts in structured knowledge bases such as UMLS or SNOMED CT. Most existing systems link each mention independently, using only the mention or its surrounding sentence. This ignores…

Some Question Answering (QA) systems rely on knowledge bases (KBs) to provide accurate answers. Entity Linking (EL) plays a critical role in linking natural language mentions to KB entries. However, most existing EL methods are designed for…

Linking biomedical entities is an essential aspect in biomedical natural language processing tasks, such as text mining and question answering. However, a difficulty of linking the biomedical entities using current large language models…

Despite recent progress, Biomedical Entity Linking (BEL) with large language models (LLMs) remains computationally inefficient and challenging to deploy in practical settings. In this work, we demonstrate that instruction-tuning of…

Entity linking (EL) is the computational process of connecting textual mentions to corresponding entities. Like many areas of natural language processing, the EL field has greatly benefited from deep learning, leading to significant…

Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable…

Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using…

Community Question Answering (CQA) platforms contain plenty of CQA texts (i.e., questions and answers corresponding to the question) where named entities appear ubiquitously. In this paper, we define a new task of CQA entity linking (CQAEL)…

Entity disambiguation (ED), which links the mentions of ambiguous entities to their referent entities in a knowledge base, serves as a core component in entity linking (EL). Existing generative approaches demonstrate improved accuracy…

Entity linking (mapping ambiguous mentions in text to entities in a knowledge base) is a foundational step in tasks such as knowledge graph construction, question-answering, and information extraction. Our method, LELA, is a modular…

Biomedical question-answering (QA) has gained increased attention for its capability to provide users with high-quality information from a vast scientific literature. Although an increasing number of biomedical QA datasets has been recently…

Cross-lingual biomedical entity linking (BEL) maps mentions in any language to unique identifiers in a biomedical knowledge base (KB), supporting clinical and biomedical NLP applications. However, expert-annotated training data for BEL are…

Entity linking (EL) is the process of linking entity mentions appearing in web text with their corresponding entities in a knowledge base. EL plays an important role in the fields of knowledge engineering and data mining, underlying a…

Medical entity linking is the task of identifying and standardizing medical concepts referred to in an unstructured text. Most of the existing methods adopt a three-step approach of (1) detecting mentions, (2) generating a list of candidate…