Related papers: OEMA: Ontology-Enhanced Multi-Agent Collaboration …

Recently, neural methods have achieved state-of-the-art (SOTA) results in Named Entity Recognition (NER) tasks for many languages without the need for manually crafted features. However, these models still require manually annotated…

Weak supervision has shown promising results in many natural language processing tasks, such as Named Entity Recognition (NER). Existing work mainly focuses on learning deep NER models only with weak supervision, i.e., without any human…

Named Entity Recognition (NER) or the extraction of concepts from clinical text is the task of identifying entities in text and slotting them into categories such as problems, treatments, tests, clinical departments, occurrences (such as…

Electronic Health Records (EHRs) are digital records of patient information, often containing unstructured clinical text. Named Entity Recognition (NER) is essential in EHRs for extracting key medical entities like problems, tests, and…

A significant shortcoming of current state-of-the-art (SOTA) named-entity recognition (NER) systems is their lack of generalization to unseen domains, which poses a major problem since obtaining labeled data for NER in a new domain is…

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…

Integrating novel medical concepts and relationships into existing ontologies can significantly enhance their coverage and utility for both biomedical research and clinical applications. Clinical notes, as unstructured documents rich with…

Fine-grained entity typing (FET) is the task of identifying specific entity types at a fine-grained level for entity mentions based on their contextual information. Conventional methods for FET require extensive human annotation, which is…

Large language models (LLMs) have demonstrated dominating performance in many NLP tasks, especially on generative tasks. However, they often fall short in some information extraction tasks, particularly those requiring domain-specific…

Ontology matching (OM) plays an essential role in enabling semantic interoperability and integration across heterogeneous knowledge sources, particularly in the biomedical domain which contains numerous complex concepts related to diseases…

Large Language Models (LLMs) have revolutionized various sectors, including healthcare where they are employed in diverse applications. Their utility is particularly significant in the context of rare diseases, where data scarcity,…

Named-entity recognition (NER) is fundamental to extracting structured information from the >80% of healthcare data that resides in unstructured clinical notes and biomedical literature. Despite recent advances with large language models,…

Many previous models of named entity recognition (NER) suffer from the problem of Out-of-Entity (OOE), i.e., the tokens in the entity mentions of the test samples have not appeared in the training samples, which hinders the achievement of…

Matching patients to clinical trials is a key unsolved challenge in bringing new drugs to market. Today, identifying patients who meet a trial's eligibility criteria is highly manual, taking up to 1 hour per patient. Automated screening is…

Entity Matching (EM) is a core data cleaning task, aiming to identify different mentions of the same real-world entity. Active learning is one way to address the challenge of scarce labeled data in practice, by dynamically collecting the…

Medical entity retrieval is an integral component for understanding and communicating information across various health systems. Current approaches tend to work well on specific medical domains but generalize poorly to unseen…

Objective: Develop a cost-effective, large language model (LLM)-based pipeline for automatically extracting Review of Systems (ROS) entities from clinical notes. Materials and Methods: The pipeline extracts ROS section from the clinical…

We study clinical Named Entity Recognition (NER) on the CADEC corpus and compare three families of approaches: (i) BERT-style encoders (BERT Base, BioClinicalBERT, RoBERTa-large), (ii) GPT-4o used with few-shot in-context learning (ICL)…

This study is dedicated to exploring the application of prompt learning methods to advance Named Entity Recognition (NER) within the medical domain. In recent years, the emergence of large-scale models has driven significant progress in NER…

Entity matching (EM) is the problem of determining whether two records refer to same real-world entity, which is crucial in data integration, e.g., for product catalogs or address databases. A major drawback of many EM approaches is their…