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	Predicting gene-disease associations using a heterogeneous graph neural network</div>

Sidorenko Denis A. , Shalyto Anatoly A.

2024 , VOLUME 24, NUMBER 4 ( may-june )

ISSN 2226-1494 (print), ISSN 2500-0373 (online)

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Editor-in-Chief

Nikiforov
Vladimir O.
D.Sc., Prof.

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doi: 10.17586/2226-1494-2024-24-4-594-601

Predicting gene-disease associations using a heterogeneous graph neural network

D. A. Sidorenko, A. A. Shalyto

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Article in Russian

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Sidorenko D.A., Shalyto A.A. Predicting gene-disease associations using a heterogeneous graph neural network. Scientific and Technical Journal of Information Technologies, Mechanics and Optics, 2024, vol. 24, no. 4, pp. 594–601 (in Russian). doi: 10.17586/2226-1494-2024-24-4-594-601

Abstract

The research presents the development of a heterogeneous graph neural network model for predicting gene-disease using existing genomic and medical data. The novelty of the approach is in integrating the principles of graph neural networks and heterogeneous information networks for efficient processing of structured data and consideration of complex genepathology interactions. The solution proposed is a heterogeneous graph neural network which utilizes a heterogeneous graph structure for representing genes, diseases, and their relationships. The performance of the developed model was evaluated on the DisGeNET, LASTFM, YELP datasets. On these datasets, a comparison was made with current SOTA models. The comparison results demonstrated that the proposed model outperforms other models in terms of Average Precision (AP), F1-measure (F1@S), Hit@k, Area Under Receiver Operating Characteristic curve (AUROC) in predicting “gene-disease” associations. The model developed serves as a tool for bioinformatics analysis and can aid researchers and doctors in studying genetic diseases. This could expedite the discovery of new drug targets and the advancement of personalized medicine.

Keywords: machine learning, graph neural networks, heterogeneous information networks, bioinformatics, genetics, “gene-disease” prediction associations

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