Predicting gene disease associations with knowledge graph embeddings for diseases with curtailed information

Gualdi, Francesco; Oliva Miguel, Baldomero; Piñero González, Janet, 1977-

doi:http://dx.doi.org/10.1093/nargab/lqae049

Predicting gene disease associations with knowledge graph embeddings for diseases with curtailed information

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Gualdi F, Oliva B, Piñero J. Predicting gene disease associations with knowledge graph embeddings for diseases with curtailed information. NAR Genom Bioinform. 2024 May 14;6(2):lqae049. DOI: 10.1093/nargab/lqae049

Abstract

Knowledge graph embeddings (KGE) are a powerful technique used in the biomedical domain to represent biological knowledge in a low dimensional space. However, a deep understanding of these methods is still missing, and, in particular, regarding their applications to prioritize genes associated with complex diseases with reduced genetic information. In this contribution, we built a knowledge graph (KG) by integrating heterogeneous biomedical data and generated KGE by implementing state-of-the-art methods, and two novel algorithms: Dlemb and BioKG2vec. Extensive testing of the embeddings with unsupervised clustering and supervised methods showed that KGE can be successfully implemented to predict genes associated with diseases and that our novel approaches outperform most existing algorithms in both scenarios. Our findings underscore the significance of data quality, preprocessing, and integration in achieving accurate predictions. Additionally, we applied KGE to predict genes linked to Intervertebral Disc Degeneration (IDD) and illustrated that functions pertinent to the disease are enriched within the prioritized gene set.