A survey of the recent trends in deep learning for literature based discovery in the biomedical domain

Abstract

Every day, enormous amounts of biomedical texts discussing various biomedical topics are produced. Revealing strong semantic connections hidden in those unstructured data is essential for many interesting applications such as knowledge base development for the biomedical domain as well as drug repurposing and drug–disease associations. Literature based discovery (LBD) is a well-known paradigm that refers to the issues of finding new hidden knowledge in scientific literature by connecting pieces of semantically-related information belonging to independent documents. This challenging research area has been extensively investigated by the research community and different proposals adopting natural language processing, text mining, machine learning and recently deep learning have been developed. This paper exploits a very focused task, it surveys a collection of research papers published in the recent years that have adopted Deep Learning for literature based discovery as an effective technique to discover new relationships between existing knowledge in biomedical domain. The study provides an analysis of the key characteristics of each work surveyed, including the Literature based discovery application area, the deep learning method used, the type of analyzed data, and the results obtained. Recognizing the significance of Pre-trained Language Models (PLMs), another primary aim of this paper is to offer an extensive overview of the latest developments in pre-trained language models within the field of biomedicine. This focus will primarily be on how they are applied to downstream tasks associated with Literature-Based Discovery in the biomedical domain. Additionally, the survey highlights the key drawbacks of the current state-of-the-art proposals, as well as the challenges that require further study by the research community.