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Training a neural network-based biomedical named entity recognition (BioNER) model usually requires extensive and costly human annotations. While several studies have employed multi-task learning with multiple BioNER datasets to reduce…

Building real-world complex Named Entity Recognition (NER) systems is a challenging task. This is due to the complexity and ambiguity of named entities that appear in various contexts such as short input sentences, emerging entities, and…

General-purpose multilingual vector representations, used in retrieval, regression and classification, are traditionally obtained from bidirectional encoder models. Despite their wide applicability, encoders have been recently overshadowed…

Diagnostic or procedural coding of clinical notes aims to derive a coded summary of disease-related information about patients. Such coding is usually done manually in hospitals but could potentially be automated to improve the efficiency…

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…

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and…

The rapid growth of biomedical literature poses a significant challenge for curation and interpretation. This has become more evident during the COVID-19 pandemic. LitCovid, a literature database of COVID-19 related papers in PubMed, has…

Recent advancements for large-scale pre-training with neural signals such as electroencephalogram (EEG) have shown promising results, significantly boosting the development of brain-computer interfaces (BCIs) and healthcare. However, these…

Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity…

Understanding brain disorders is crucial for accurate clinical diagnosis and treatment. Recent advances in Multimodal Large Language Models (MLLMs) offer a promising approach to interpreting medical images with the support of text…

In this paper, we propose a multilingual encoder-decoder architecture capable of obtaining multilingual sentence representations by means of incorporating an intermediate {\em attention bridge} that is shared across all languages. That is,…

We introduce ColaCare, a framework that enhances Electronic Health Record (EHR) modeling through multi-agent collaboration driven by Large Language Models (LLMs). Our approach seamlessly integrates domain-specific expert models with LLMs to…

Medical coding is essential for standardizing clinical data and communication but is often time-consuming and prone to errors. Traditional Natural Language Processing (NLP) methods struggle with automating coding due to the large label…

Large language models (LLMs) show promising performance on small-scale graph reasoning tasks but fail when handling real-world graphs with complex queries. This phenomenon arises from LLMs' working memory constraints, which result in their…

Healthcare models are transitioning from unimodal prediction toward multimodal reasoning over heterogeneous diagnostic inputs. In computational pathology, for complex tumor subtypes where morphology alone can be challenging to distinguish,…

Medical imaging technologies, including computed tomography (CT) or chest X-Ray (CXR), are largely employed to facilitate the diagnosis of the COVID-19. Since manual report writing is usually too time-consuming, a more intelligent auxiliary…

Safe and reliable natural language inference is critical for extracting insights from clinical trial reports but poses challenges due to biases in large pre-trained language models. This paper presents a novel data augmentation technique to…

The application of large language models (LLMs) to healthcare information extraction has emerged as a promising approach. This study evaluates the classification performance of five open-source LLMs: GEMMA-3-27B-IT, LLAMA3-70B, LLAMA4-109B,…

The HeartBert model is introduced with three primary objectives: reducing the need for labeled data, minimizing computational resources, and simultaneously improving performance in machine learning systems that analyze Electrocardiogram…

Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data. While large language models (LLMs) have shown strong performance in biomedical NLP,…