Literature Based Discovery (LBD): Towards Hypothesis Generation and Knowledge Discovery in Biomedical Text Mining

TL;DR

This paper reviews Literature Based Discovery in biomedical text mining, highlighting its methods, resources, recent deep learning applications, key discoveries, limitations, and future directions in hypothesis generation from scientific literature.

Contribution

It provides a comprehensive overview of LBD approaches, resources, and recent deep learning advancements, emphasizing its ongoing importance in biomedical knowledge discovery.

Findings

LBD effectively reduces discovery time for hidden biomedical associations.

Deep learning models like transformers enhance LBD performance.

Key biomedical discoveries have been made using LBD approaches.

Abstract

Biomedical knowledge is growing in an astounding pace with a majority of this knowledge is represented as scientific publications. Text mining tools and methods represents automatic approaches for extracting hidden patterns and trends from this semi structured and unstructured data. In Biomedical Text mining, Literature Based Discovery (LBD) is the process of automatically discovering novel associations between medical terms otherwise mentioned in disjoint literature sets. LBD approaches proven to be successfully reducing the discovery time of potential associations that are hidden in the vast amount of scientific literature. The process focuses on creating concept profiles for medical terms such as a disease or symptom and connecting it with a drug and treatment based on the statistical significance of the shared profiles. This knowledge discovery approach introduced in 1989 still remains as a core task in text mining. Currently the ABC principle based two approaches namely open discovery and closed discovery are mostly explored in LBD process. This review starts with general introduction about text mining followed by biomedical text mining and introduces various literature resources such as MEDLINE, UMLS, MESH, and SemMedDB. This is followed by brief introduction of the core ABC principle and its associated two approaches open discovery and closed discovery in LBD process. This review also discusses the deep learning applications in LBD by reviewing the role of transformer models and neural networks based LBD models and its future aspects. Finally, reviews the key biomedical discoveries generated through LBD approaches in biomedicine and conclude with the current limitations and future directions of LBD.