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Generative pre-trained transformer (GPT) models have shown promise in clinical entity and relation extraction tasks because of their precise extraction and contextual understanding capability. In this work, we further leverage the Unified…

Objective: Our study aimed to construct an exhaustive Complementary and Integrative Health (CIH) Lexicon (CIHLex) to better represent the often underrepresented physical and psychological CIH approaches in standard terminologies. We also…

Large language models (LLMs), including zero-shot and few-shot paradigms, have shown promising capabilities in clinical text generation. However, real-world applications face two key challenges: (1) patient data is highly unstructured,…

The injection of domain-specific knowledge is crucial for adapting language models (LMs) to specialized fields such as biomedicine. While most current approaches rely on unstructured text corpora, this study explores two complementary…

Clinical decision-making requires synthesizing heterogeneous evidence, including patient histories, clinical guidelines, and trajectories of comparable cases. While large language models (LLMs) offer strong reasoning capabilities, they…

We used MetaMap and YTEX as a basis for the construc- tion of two separate systems to participate in the 2013 ShARe/CLEF eHealth Task 1[9], the recognition of clinical concepts. No modifications were directly made to these systems, but…

Clinicians are increasingly looking towards machine learning to gain insights about patient evolutions. We propose a novel approach named Multi-Modal UMLS Graph Learning (MMUGL) for learning meaningful representations of medical concepts…

Electronic health records (EHR) contain large volumes of unstructured text, requiring the application of Information Extraction (IE) technologies to enable clinical analysis. We present the open-source Medical Concept Annotation Toolkit…

Background: Widespread adoption of electronic health records (EHRs) has enabled secondary use of EHR data for clinical research and healthcare delivery. Natural language processing (NLP) techniques have shown promise in their capability to…

Intensive Care Units (ICU) require comprehensive patient data integration for enhanced clinical outcome predictions, crucial for assessing patient conditions. Recent deep learning advances have utilized patient time series data, and fusion…

Automated knowledge curation for biomedical ontologies is key to ensure that they remain comprehensive, high-quality and up-to-date. In the era of foundational language models, this study compares and analyzes three NLP paradigms for…

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called \textbf{MedGraphRAG}, aimed at enhancing Large Language Model (LLM) capabilities for generating…

Despite the remarkable progress of Large Language Models (LLMs), their performance in question answering (QA) remains limited by the lack of domain-specific and up-to-date knowledge. Retrieval-Augmented Generation (RAG) addresses this…

Contextual word embedding models, such as BioBERT and Bio_ClinicalBERT, have achieved state-of-the-art results in biomedical natural language processing tasks by focusing their pre-training process on domain-specific corpora. However, such…

Query Processing (QP) is optimized by a Cloud-based cache by storing the frequently accessed data closer to users. Nevertheless, the lack of focus on user intention type in queries affected the efficiency of QP in prevailing works. Thus, by…

Machine Unlearning (MU) has recently attracted considerable attention as a solution to privacy and copyright issues in large language models (LLMs). Existing MU methods aim to remove specific target sentences from an LLM while minimizing…

Automated annotation of clinical text with standardized medical concepts is critical for enabling structured data extraction and decision support. SNOMED CT provides a rich ontology for labeling clinical entities, but manual annotation is…

Large language models (LLMs) offer new opportunities for constructing knowledge graphs (KGs) from unstructured clinical narratives. However, existing approaches often rely on structured inputs and lack robust validation of factual accuracy…

Effective data-driven biomedical discovery requires data curation: a time-consuming process of finding, organizing, distilling, integrating, interpreting, annotating, and validating diverse information into a structured form suitable for…

The effectiveness of artificial intelligence (AI) in healthcare is significantly hindered by unstructured clinical documentation, which results in noisy, inconsistent, and logically fragmented training data. To address this challenge, we…