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We evaluate four state-of-the-art instruction-tuned large language models (LLMs) -- ChatGPT, Flan-T5 UL2, Tk-Instruct, and Alpaca -- on a set of 13 real-world clinical and biomedical natural language processing (NLP) tasks in English, such…

Pre-training large-scale neural language models on raw texts has made a significant contribution to improving transfer learning in natural language processing (NLP). With the introduction of transformer-based language models, such as…

Recent work explored the potential of large-scale Transformer-based pre-trained models, especially Pre-trained Language Models (PLMs) in natural language processing. This raises many concerns from various perspectives, e.g., financial costs…

State-of-the-art language models are becoming increasingly large in an effort to achieve the highest performance on large corpora of available textual data. However, the sheer size of the Transformer architectures makes it difficult to…

Large language models (LLMs) have demonstrated remarkable success in NLP tasks. However, there is a paucity of studies that attempt to evaluate their performances on social media-based health-related natural language processing tasks, which…

Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical…

Transformer language models (TLMs) are critical for most NLP tasks, but they are difficult to create for low-resource languages because of how much pretraining data they require. In this work, we investigate two techniques for training…

The process of matching patients with suitable clinical trials is essential for advancing medical research and providing optimal care. However, current approaches face challenges such as data standardization, ethical considerations, and a…

Deep learning (DL) based predictive models from electronic health records (EHR) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required to achieve high accuracy, hindering the adoption of…

Europe's healthcare systems require enhanced interoperability and digitalization, driving a demand for innovative solutions to process legacy clinical data. This paper presents the results of our project, which aims to leverage Large…

Background: Clinical documentation represents a significant burden for healthcare providers, with physicians spending up to 2 hours daily on administrative tasks. Recent advances in large language models (LLMs) offer promising solutions,…

Large Language Models (LLMs) have remarkable capabilities across NLP tasks. However, their performance in multilingual contexts, especially within the mental health domain, has not been thoroughly explored. In this paper, we evaluate…

High-throughput phenotyping, the automated mapping of patient signs and symptoms to standardized ontology concepts, is essential to gaining value from electronic health records (EHR) in the support of precision medicine. Despite…

We hypothesize that large language models (LLMs) based on the transformer architecture can enable automated detection of clinical phenotype terms, including terms not documented in the HPO. In this study, we developed two types of models:…

Large language models (LLMs) have shown promise in safety-critical applications such as healthcare, yet the ability to quantify performance has lagged. An example of this challenge is in evaluating a summary of the patient's medical record.…

Radiology reports are critical for clinical decision-making but often lack a standardized format, limiting both human interpretability and machine learning (ML) applications. While large language models (LLMs) have shown strong capabilities…

Recently, Large Language Models (LLM) have demonstrated impressive capability to solve a wide range of tasks. However, despite their success across various tasks, no prior work has investigated their capability in the biomedical domain yet.…

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…

NLP is currently dominated by general-purpose pretrained language models like RoBERTa, which achieve strong performance on NLU tasks through pretraining on billions of words. But what exact knowledge or skills do Transformer LMs learn from…

Large language models (LLMs) perform remarkably well on tabular datasets in zero- and few-shot settings, since they can extract meaning from natural language column headers that describe features and labels. Similarly, TabPFN, a recent…