Related papers: Clustering-based Inference for Biomedical Entity L…

Previous work has shown promising results in performing entity linking by measuring not only the affinities between mentions and entities but also those amongst mentions. In this paper, we present novel training and inference procedures…

Entity linking involves aligning textual mentions of named entities to their corresponding entries in a knowledge base. Entity linking systems often exploit relations between textual mentions in a document (e.g., coreference) to decide if…

Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate…

Understanding the meaning of text often involves reasoning about entities and their relationships. This requires identifying textual mentions of entities, linking them to a canonical concept, and discerning their relationships. These tasks…

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…

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…

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,…

Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…

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…

Clinical text is rich in information, with mentions of treatment, medication and anatomy among many other clinical terms. Multiple terms can refer to the same core concepts which can be referred as a clinical entity. Ontologies like the…

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot…

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…

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…

The increasing amount of data on the Web, in particular of Linked Data, has led to a diverse landscape of datasets, which make entity retrieval a challenging task. Explicit cross-dataset links, for instance to indicate co-references or…

Existing work on Entity Linking mostly assumes that the reference knowledge base is complete, and therefore all mentions can be linked. In practice this is hardly ever the case, as knowledge bases are incomplete and because novel concepts…

Automatically locating named entities in natural language text - named entity recognition - is an important task in the biomedical domain. Many named entity mentions are ambiguous between several bioconcept types, however, causing text…

Fine-grained entity typing is a challenging problem since it usually involves a relatively large tag set and may require to understand the context of the entity mention. In this paper, we use entity linking to help with the fine-grained…

Currently, data-driven discovery in biological sciences resides in finding segmentation strategies in multivariate data that produce sensible descriptions of the data. Clustering is but one of several approaches and sometimes falls short…

Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a…

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…