Related papers: Improving Large Language Models for Clinical Named…
Named Entity Recognition (NER) in the rare disease domain poses unique challenges due to limited labeled data, semantic ambiguity between entity types, and long-tail distributions. In this study, we evaluate the capabilities of GPT-4o for…
Named entity recognition (NER) is a fundamental task in numerous downstream applications. Recently, researchers have employed pre-trained language models (PLMs) and large language models (LLMs) to address this task. However, fully…
Biomedical literature and clinical narratives pose multifaceted challenges for natural language understanding, from precise entity extraction and document synthesis to multi-step diagnostic reasoning. This study extends a unified benchmark…
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…
This work presents our participation in the EvalLLM 2025 challenge on biomedical Named Entity Recognition (NER) and health event extraction in French (few-shot setting). For NER, we propose three approaches combining large language models…
Objective: Clinical trials are essential for advancing pharmaceutical interventions, but they face a bottleneck in selecting eligible participants. Although leveraging electronic health records (EHR) for recruitment has gained popularity,…
Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes…
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)…
Biomedical named entity recognition (NER) is a high-utility natural language processing (NLP) task, and large language models (LLMs) show promise particularly in few-shot settings (i.e., limited training data). In this article, we address…
This paper evaluates Few-Shot Prompting with Large Language Models for Named Entity Recognition (NER). Traditional NER systems rely on extensive labeled datasets, which are costly and time-consuming to obtain. Few-Shot Prompting or…
Introduction: Medication prescriptions are often in free text and include a mix of two languages, local brand names, and a wide range of idiosyncratic formats and abbreviations. Large language models (LLMs) have shown promising ability to…
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…
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…
Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and…
Deep neural network models have recently achieved state-of-the-art performance gains in a variety of natural language processing (NLP) tasks (Young, Hazarika, Poria, & Cambria, 2017). However, these gains rely on the availability of large…
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…
Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits 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…
Large language models (LLMs) have become the preferred solution for many natural language processing tasks. In low-resource environments such as specialized domains, their few-shot capabilities are expected to deliver high performance.…
Supervised models trained to predict properties from representations have been achieving high accuracy on a variety of tasks. For instance, the BERT family seems to work exceptionally well on the downstream task from NER tagging to the…