Related papers: Do LLMs Surpass Encoders for Biomedical NER?

Large Language Models (LLMs) are increasingly adopted for applications in healthcare, reaching the performance of domain experts on tasks such as question answering and document summarisation. Despite their success on these tasks, it is…

Backgrounds: Information extraction (IE) is critical in clinical natural language processing (NLP). While large language models (LLMs) excel on generative tasks, their performance on extractive tasks remains debated. Methods: We…

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…

Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the…

Despite their strong linguistic capabilities, Large Language Models (LLMs) are computationally demanding and require substantial resources for fine-tuning, which is unadapted to privacy and budget constraints of many healthcare settings. To…

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the…

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…

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,…

Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual…

Named entity recognition (NER) is evolving from a sequence labeling task into a generative paradigm with the rise of large language models (LLMs). We conduct a systematic evaluation of open-source LLMs on both flat and nested NER tasks. We…

Biomedical Named Entity Recognition (NER) is a fundamental task of Biomedical Natural Language Processing for extracting relevant information from biomedical texts, such as clinical records, scientific publications, and electronic health…

Prevalent solution for BioNER involves using representation learning techniques coupled with sequence labeling. However, such methods are inherently task-specific, demonstrate poor generalizability, and often require dedicated model for…

Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence…

Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment…

Recent advancements in language models (LMs) have led to the emergence of powerful models such as Small LMs (e.g., T5) and Large LMs (e.g., GPT-4). These models have demonstrated exceptional capabilities across a wide range of tasks, such…

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…

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…

Large language models (LLMs) excel at clinical information extraction but their computational demands limit practical deployment. Knowledge distillation--the process of transferring knowledge from larger to smaller models--offers a…

Clinical named entity recognition (NER) aims to retrieve important entities within clinical narratives. Recent works have demonstrated that large language models (LLMs) can achieve strong performance in this task. While previous works focus…

Recent years have witnessed a substantial increase in the use of deep learning to solve various natural language processing (NLP) problems. Early deep learning models were constrained by their sequential or unidirectional nature, such that…