The importance of graph databases and graph learning for clinical applications

Abstract

The increasing amount and complexity of clinical data require an appropriate way of storing and analyzing those data. Traditional approaches use a tabular structure (relational databases) for storing data and thereby complicate storing and retrieving interlinked data from the clinical domain. Graph databases provide a great solution for this by storing data in a graph as nodes (vertices) that are connected by edges (links). The underlying graph structure can be used for the subsequent data analysis (graph learning). Graph learning consists of two parts: graph representation learning and graph analytics. Graph representation learning aims to reduce high-dimensional input graphs to low-dimensional representations. Then, graph analytics uses the obtained representations for analytical tasks like visualization, classification, link prediction and clustering which can be used to solve domain-specific problems. In this survey, we review current state-of-the-art graph database management systems, graph learning algorithms and a variety of graph applications in the clinical domain. Furthermore, we provide a comprehensive use case for a clearer understanding of complex graph learning algorithms. Graphical abstract

Microbiome modeling: a beginner's guide

“…However, methods for graph analysis can be applied to any model that incorporates a network structure (e.g., generalized Lotka-Volterra models, Section 8.1 or genome-scale metabolic reconstructions, Section 9). The flexible structure of graphs also allows for storage and analysis of data in graph databases and knowledge graphs (Santos et al, 2022 ; Walke et al, 2023 ).…”

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“…However, methods for graph analysis can be applied to any model that incorporates a network structure (e.g., generalized Lotka-Volterra models, Section 8.1 or genome-scale metabolic reconstructions, Section 9). The flexible structure of graphs also allows for storage and analysis of data in graph databases and knowledge graphs (Santos et al, 2022;Walke et al, 2023).…”