Related papers: Large Language Models with Retrieval-Augmented Gen…

The versatility of large language models (LLMs) has been explored across various sectors, but their application in healthcare poses challenges, particularly in the domain of pharmaceutical contraindications where accurate and reliable…

Genes, proteins and other biological entities influence one another via causal molecular networks. Causal relationships in such networks are mediated by complex and diverse mechanisms, through latent variables, and are often specific to…

Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…

Large Language Models (LLMs) have demonstrated remarkable adaptability, showcasing their capacity to excel in tasks for which they were not explicitly trained. However, despite their impressive natural language processing (NLP)…

Traditional diagnosis of chronic diseases involves in-person consultations with physicians to identify the disease. However, there is a lack of research focused on predicting and developing application systems using clinical notes and blood…

Recent advancements in language models (LMs) have led to the emergence of powerful models such as Small LMs (e.g., T5) and Large LMs (e.g., GPT-4). These models have demonstrated exceptional capabilities across a wide range of tasks, such…

The malicious usage of large language models (LLMs) has motivated the detection of LLM-generated texts. Previous work in topological data analysis shows that the persistent homology dimension (PHD) of text embeddings can serve as a more…

This exploratory pilot study investigated the potential of combining a domain-specific model, BERN2, with large language models (LLMs) to enhance automated disease phenotyping from research survey data. Motivated by the need for efficient…

Background: Large language models (LLMs) show promise in medicine, but their deployment in hospitals is limited by restricted access to electronic health record (EHR) systems. The Model Context Protocol (MCP) enables integration between…

The automatic construction of knowledge graphs (KGs) is an important research area in medicine, with far-reaching applications spanning drug discovery and clinical trial design. These applications hinge on the accurate identification of…

Automating code documentation through explanatory text can prove highly beneficial in code understanding. Large Language Models (LLMs) have made remarkable strides in Natural Language Processing, especially within software engineering tasks…

This study represents the first integration of large language models (LLMs) with non-negative matrix factorization (NMF), marking a novel advancement in the source separation field. The LLM is employed in two unique ways: enhancing the…

Accurate survival prediction in radiotherapy (RT) is critical for optimizing treatment decisions. This study developed and validated the RT-Surv framework, which integrates general-domain, open-source large language models (LLMs) to…

Alzheimer's disease (AD) is the fifth-leading cause of death among Americans aged 65 and older. Screening and early detection of AD and related dementias (ADRD) are critical for timely intervention and for identifying clinical trial…

Biomedical question answering (QA) poses significant challenges due to the need for precise interpretation of specialized knowledge drawn from a vast, complex, and rapidly evolving corpus. In this work, we explore how large language models…

Creation and curation of knowledge graphs can accelerate disease discovery and analysis in real-world data. While disease ontologies aid in biological data annotation, codified categories (SNOMED-CT, ICD10, CPT) may not capture patient…

Exploring the application of powerful large language models (LLMs) on the named entity recognition (NER) task has drawn much attention recently. This work pushes the performance boundary of zero-shot NER with LLMs by proposing a…

We evaluate the ability of large language models (LLMs) to infer causal relations from natural language. Compared to traditional natural language processing and deep learning techniques, LLMs show competitive performance in a benchmark of…

Large Language Models (LLMs) are increasingly being integrated into various components of Ontology Matching pipelines. This paper investigates the capability of LLMs to perform ontology matching directly on ontology modules and generate the…

Large Language Models (LLMs) have demonstrated potential in predicting mental health outcomes from online text, yet traditional classification methods often lack interpretability and robustness. This study evaluates structured reasoning…