Related papers: Harnessing Large Language Models for Biomedical Na…

Machine learning (ML) holds great promise for clinical applications but is often hindered by limited access to high-quality data due to privacy concerns, high costs, and long timelines associated with clinical trials. While large language…

Motivation: A perennial challenge for biomedical researchers and clinical practitioners is to stay abreast with the rapid growth of publications and medical notes. Natural language processing (NLP) has emerged as a promising direction for…

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,…

Although deep learning techniques have shown significant achievements, they frequently depend on extensive amounts of hand-labeled data and tend to perform inadequately in few-shot scenarios. The objective of this study is to devise a…

Open Named Entity Recognition (NER), which involves identifying arbitrary types of entities from arbitrary domains, remains challenging for Large Language Models (LLMs). Recent studies suggest that fine-tuning LLMs on extensive NER data can…

Background: Biomedical entity normalization is critical to biomedical research because the richness of free-text clinical data, such as progress notes, can often be fully leveraged only after translating words and phrases into structured…

Prediction tasks in digital pathology are challenging due to the massive size of whole-slide images (WSIs) and the weak nature of training signals. Advances in computing, data availability, and self-supervised learning (SSL) have paved the…

Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and…

Recent advances in large language models (LLMs) and biomedical foundation models (BioFMs) have achieved strong results in biological text reasoning, molecular modeling, and single-cell analysis, yet they remain siloed in disjoint embedding…

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general…

Extracting clinically relevant information from unstructured medical narratives such as admission notes, discharge summaries, and emergency case histories remains a challenge in clinical natural language processing (NLP). Medical Entity…

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…

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting…

Conversational agents such as Cortana, Alexa and Siri are continuously working on increasing their capabilities by adding new domains. The support of a new domain includes the design and development of a number of NLU components for domain…

Biomedical queries have become increasingly prevalent in web searches, reflecting the growing interest in accessing biomedical literature. Despite recent research on large-language models (LLMs) motivated by endeavours to attain generalized…

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…

Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named…

Large Language Models (LLMs) have provided a new pathway for Named Entity Recognition (NER) tasks. Compared with fine-tuning, LLM-powered prompting methods avoid the need for training, conserve substantial computational resources, and rely…

Motivation: The proliferation of Biomedical research articles has made the task of information retrieval more important than ever. Scientists and Researchers are having difficulty in finding articles that contain information relevant to…

We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER)…