Related papers: Leveraging Semantic Type Dependencies for Clinical…

Named entity recognition (NER) is a fundamental part of extracting information from documents in biomedical applications. A notable advantage of NER is its consistency in extracting biomedical entities in a document context. Although…

Learning representations for knowledge base entities and concepts is becoming increasingly important for NLP applications. However, recent entity embedding methods have relied on structured resources that are expensive to create for new…

The success of pretrained word embeddings has motivated their use in the biomedical domain, with contextualized embeddings yielding remarkable results in several biomedical NLP tasks. However, there is a lack of research on quantifying…

Clinical notes contain an extensive record of a patient's health status, such as smoking status or the presence of heart conditions. However, this detail is not replicated within the structured data of electronic health systems.…

Natural language processing (NLP) of clinical trial documents can be useful in new trial design. Here we identify entity types relevant to clinical trial design and propose a framework called CT-BERT for information extraction from clinical…

Crucial information about the practice of healthcare is recorded only in free-form text, which creates an enormous opportunity for high-impact NLP. However, annotated healthcare datasets tend to be small and expensive to obtain, which…

In recent years, Deep Learning (DL) models are becoming important due to their demonstrated success at overcoming complex learning problems. DL models have been applied effectively for different Natural Language Processing (NLP) tasks such…

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…

Monitoring the administration of drugs and adverse drug reactions are key parts of pharmacovigilance. In this paper, we explore the extraction of drug mentions and drug-related information (reason for taking a drug, route, frequency,…

Biomedical named entity recognition (BNER) serves as the foundation for numerous biomedical text mining tasks. Unlike general NER, BNER require a comprehensive grasp of the domain, and incorporating external knowledge beyond training data…

Named entity recognition (NER) systems that perform well require task-related and manually annotated datasets. However, they are expensive to develop, and are thus limited in size. As there already exists a large number of NER datasets that…

Named Entity Recognition seeks to extract substrings within a text that name real-world objects and to determine their type (for example, whether they refer to persons or organizations). In this survey, we first present an overview of…

Clinical notes often describe important aspects of a patient's stay and are therefore critical to medical research. Clinical concept extraction (CCE) of named entities - such as problems, tests, and treatments - aids in forming an…

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…

Named entity recognition (NER) is the task to detect and classify the entity spans in the text. When entity spans overlap between each other, this problem is named as nested NER. Span-based methods have been widely used to tackle the nested…

We investigate the incorporation of character-based word representations into a standard CNN-based relation extraction model. We experiment with two common neural architectures, CNN and LSTM, to learn word vector representations from…

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…

The linking of clinical entities is a crucial part of extracting structured information from clinical texts. It is the process of assigning a code from a medical ontology or classification to a phrase in the text. The International…

Language Models (LMs) such as BERT, have been shown to perform well on the task of identifying Named Entities (NE) in text. A BERT LM is typically used as a classifier to classify individual tokens in the input text, or to classify spans of…

Biomedical named entity recognition (NER) is a fundamental task in text mining of medical documents and has many applications. Deep learning based approaches to this task have been gaining increasing attention in recent years as their…