Related papers: Improving Large Language Models for Clinical Named…

[Context]: Companies are increasingly recognizing the importance of automating Requirements Engineering (RE) tasks due to their resource-intensive nature. The advent of GenAI has made these tasks more amenable to automation, thanks to its…

Background: The potential of large language models (LLMs) to automate and support pharmacoepidemiologic study design is an emerging area of interest, yet their reliability remains insufficiently characterized. General-purpose LLMs often…

Background: Identifying relationships between clinical events and temporal expressions is a key challenge in meaningfully analyzing clinical text for use in advanced AI applications. While previous studies exist, the state-of-the-art…

This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical…

Objective To develop soft prompt-based learning algorithms for large language models (LLMs), examine the shape of prompts, prompt-tuning using frozen/unfrozen LLMs, transfer learning, and few-shot learning abilities. Methods We developed a…

This study investigated the application of Large Language Models (LLMs) for simplifying biomedical texts to enhance health literacy. Using a public dataset, which included plain language adaptations of biomedical abstracts, we developed and…

Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical…

Entity matching is the task of deciding whether two entity descriptions refer to the same real-world entity. Entity matching is a central step in most data integration pipelines. Many state-of-the-art entity matching methods rely on…

Popular solutions to Named Entity Recognition (NER) include conditional random fields, sequence-to-sequence models, or utilizing the question-answering framework. However, they are not suitable for nested and overlapping spans with large…

Named entity recognition (NER) has been one of the essential preliminary steps in modern NLP applications. This report focuses on implementing the NER task on finetuning two pretrained models: (i) an encoder-only model (BERT) with a simple…

Recent advances in large language models (LLMs) have shown impressive ability in biomedical question-answering, but have not been adequately investigated for more specific biomedical applications. This study investigates the performance of…

Objective: To investigate GPT-3.5 in generating and coding medical documents with ICD-10 codes for data augmentation on low-resources labels. Materials and Methods: Employing GPT-3.5 we generated and coded 9,606 discharge summaries based on…

Automating data extraction from full-text randomised controlled trials (RCTs) for meta-analysis remains a significant challenge. This study evaluates the practical performance of three LLMs (Gemini-2.0-flash, Grok-3, GPT-4o-mini) across…

Named entity recognition (NER) is a fundamental part of extracting information from documents in biomedical applications. A notable advantage of NER is its consistency in extracting biomedical entities in a document context. Although…

Recent advances in natural language processing (NLP) can be largely attributed to the advent of pre-trained language models such as BERT and RoBERTa. While these models demonstrate remarkable performance on general datasets, they can…

Pre-trained language models have shown excellent results in few-shot learning scenarios using in-context learning. Although it is impressive, the size of language models can be prohibitive to make them usable in on-device applications, such…

Objective: To develop a natural language processing system that solves both clinical concept extraction and relation extraction in a unified prompt-based machine reading comprehension (MRC) architecture with good generalizability for…

Background: Machine learning methods for clinical named entity recognition and entity normalization systems can utilize both labeled corpora and Knowledge Graphs (KGs) for learning. However, infrequently occurring concepts may have few…

There are a few challenges related to the task of biomedical named entity recognition, which are: the existing methods consider a fewer number of biomedical entities (e.g., disease, symptom, proteins, genes); and these methods do not…

Currently, the most widespread neural network architecture for training language models is the so called BERT which led to improvements in various Natural Language Processing (NLP) tasks. In general, the larger the number of parameters in a…