Related papers: CliNER 2.0: Accessible and Accurate Clinical Conce…

Traditional text classification techniques in clinical domain have heavily relied on the manually extracted textual cues. This paper proposes a generally supervised machine learning method that is equally hassle-free and does not use…

Background Medical and life science research generates millions of publications, and it is a great challenge for researchers to utilize this information in full since its scale and complexity greatly surpasses human reading capabilities.…

Traditional named entity recognition (NER) aims to identify text mentions into pre-defined entity types. Continual Named Entity Recognition (CNER) is introduced since entity categories are continuously increasing in various real-world…

Clinical notes are an efficient way to record patient information but are notoriously hard to decipher for non-experts. Automatically simplifying medical text can empower patients with valuable information about their health, while saving…

Named Entity Recognition (NER) is a challenging and widely studied task that involves detecting and typing entities in text. So far,NER still approaches entity typing as a task of classification into universal classes (e.g. date, person, or…

Clinical notes are often stored in unstructured or semi-structured formats after extraction from electronic medical record (EMR) systems, which complicates their use for secondary analysis and downstream clinical applications. Reliable…

Electronic Health Records (EHR) store clinical documentation as base64 encoded attachments in FHIR DocumentReference resources, which makes semantic question answering difficult. Traditional vector database methods often miss nuanced…

Clinical notes are a rich source of information about patient state. However, using them to predict clinical events with machine learning models is challenging. They are very high dimensional, sparse and have complex structure. Furthermore,…

Extracting medical history entities (MHEs) related to a patient's chief complaint (CC), history of present illness (HPI), and past, family, and social history (PFSH) helps structure free-text clinical notes into standardized EHRs,…

Clinical trials (CTs) often fail due to inadequate patient recruitment. This paper tackles the challenges of CT retrieval by presenting an approach that addresses the patient-to-trials paradigm. Our approach involves two key components in a…

Health systems are rapidly deploying large language models (LLMs) that use clinical notes for clinical decision support applications. However, modern documentation practices rely heavily on templates, copy--paste shortcuts, and…

Document-level Relation Extraction (DocRE) involves identifying relations between entities across multiple sentences in a document. Evidence sentences, crucial for precise entity pair relationships identification, enhance focus on essential…

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…

There is a growing interest in creating tools to assist in clinical note generation using the audio of provider-patient encounters. Motivated by this goal and with the help of providers and medical scribes, we developed an annotation scheme…

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…

Medical concept extraction from electronic health records underpins many downstream applications, yet remains challenging because medically meaningful concepts are frequently implied rather than explicitly stated in medical narratives.…

The challenge of recognizing named entities in a given text has been a very dynamic field in recent years. This is due to the advances in neural network architectures, increase of computing power and the availability of diverse labeled…

Here we present the training and evaluation of NanoNER, a Named Entity Recognition (NER) model for Nanobiology. NER consists in the identification of specific entities in spans of unstructured texts and is often a primary task in Natural…

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) is essential in various Natural Language Processing (NLP) applications. Traditional NER models are effective but limited to a set of predefined entity types. In contrast, Large Language Models (LLMs) can…