Related papers: LLM-Augmented Computational Phenotyping of Long Co…

Large language models (LLMs) show promise for extracting clinically meaningful information from unstructured health records, yet their translation into real-world settings is constrained by the lack of scalable and trustworthy validation…

Understanding the interactions between biomarkers among brain regions during neurodegenerative disease is essential for unravelling the mechanisms underlying disease progression. For example, pathophysiological models of Alzheimer's Disease…

The vast amount of biomedical information available today presents a significant challenge for investigators seeking to digest, process, and understand these findings effectively. Large Language Models (LLMs) have emerged as powerful tools…

Long-horizon clinical simulation -- predicting how a patient's physiology evolves over years under specified interventions -- is central to chronic-disease care, yet existing electronic health record (EHR) models are predominantly…

Social media user-generated content (UGC) provides real-time, self-reported indicators of mental health conditions such as depression, offering a valuable source for predictive analytics. While prior studies integrate medical knowledge to…

Background: Several studies show that large language models (LLMs) struggle with phenotype-driven gene prioritization for rare diseases. These studies typically use Human Phenotype Ontology (HPO) terms to prompt foundation models like GPT…

The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from…

Current knowledge graph (KG) construction methods are confirmatory, focusing on recovering known relationships rather than identifying novel or context-dependent nodes. This paper proposes a phenotype-driven and evidence-governed framework…

Large Language Models (LLMs) face significant limitations when applied to large-scale graphs, struggling with context constraints and inflexible reasoning. We present GraphChain, a framework that enables LLMs to analyze complex graphs…

Rare disease diagnosis requires matching variant-bearing genes to complex patient phenotypes across large and heterogeneous evidence sources. This process remains time-intensive in current clinical interpretation pipelines. To overcome…

Fine-tuning for large language models (LLMs) typically requires substantial amounts of high-quality supervised data, which is both costly and labor-intensive to acquire. While synthetic data generation has emerged as a promising solution,…

Following the global COVID-19 pandemic, the number of scientific papers studying the virus has grown massively, leading to increased interest in automated literate review. We present a clinical text mining system that improves on previous…

Large language models (LLMs) have presented significant opportunities to enhance various machine learning applications, including graph neural networks (GNNs). By leveraging the vast open-world knowledge within LLMs, we can more effectively…

Rare diseases affect hundreds of millions worldwide, yet diagnosis often spans years. Convectional pipelines decouple noisy evidence extraction from downstream inferential diagnosis, and general/medical large language models (LLMs) face…

Identifying disease phenotypes from electronic health records (EHRs) is critical for numerous secondary uses. Manually encoding physician knowledge into rules is particularly challenging for rare diseases due to inadequate EHR coding,…

Modern scientific discovery faces growing challenges in integrating vast and heterogeneous knowledge critical to breakthroughs in biomedicine and drug development. Traditional hypothesis-driven research, though effective, is constrained by…

In-context learning (ICL) enhances large language models (LLMs) by incorporating demonstration examples, yet its effectiveness heavily depends on the quality of selected examples. Current methods typically use text embeddings to measure…

Large Language Models (LLMs) have demonstrated remarkable capabilities in text generation and understanding, yet their reliance on implicit, unstructured knowledge often leads to factual inaccuracies and limited interpretability. Knowledge…

Interpreting quantitative CT biomarkers, such as organ volume and tissue attenuation, requires large-scale healthy reference distributions. However, creating these is challenging because clinical datasets are often heavily enriched with…

Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling…