RDscan: Extracting RNA-disease relationship from the literature based on pre-training model

Abstract

With the rapid advancements in molecular biology and genomics, a multitude of connections between RNA and diseases has been unveiled, making the efficient and accurate extraction of RNA-disease (RD) relationships from extensive biomedical literature crucial for advancing research in this field. This study introduces RDscan, a novel text mining method developed based on the pre-training and fine-tuning strategy, aimed at automatically extracting RD-related information from a vast corpus of literature using pre-trained biomedical large language models (LLM). Initially, we constructed a dedicated RD corpus by manually curating from literature, comprising 2,082 positive and 2,000 negative sentences, alongside an independent test dataset (comprising 500 positive and 500 negative sentences) for training and evaluating RDscan. Subsequently, by fine-tuning the Bioformer and BioBERT pre-trained models, RDscan demonstrated exceptional performance in text classification and named entity recognition (NER) tasks. In 5-fold cross-validation, RDscan significantly outperformed traditional machine learning methods (Support Vector Machine, Logistic Regression and Random Forest). In addition, we have developed an accessible webserver that assists users in extracting RD relationships from text. In summary, RDscan represents the first text mining tool specifically designed for RD relationship extraction, and is poised to emerge as an invaluable tool for researchers dedicated to exploring the intricate interactions between RNA and diseases. Webserver of RDscan is free available at https://cellknowledge.com.cn/RDscan/.