2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
Predicting gene-disease associations from the
heterogeneous network using graph embedding
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Abstract-The discovery of gene-disease associations is
important for the prevention, diagnosis and treatment of diseases.
The studies on gene-disease associations have produced diverse
data, which can facilitate the gene-disease association prediction.
Integrating diverse information is critical for developing high-
accuracy prediction models. In this paper, we propose a
heterogeneous network-based method that enhances gene-disease
association prediction by using graph embedding and ensemble
learning, abbreviated as “HNEEM”. A heterogeneous network is
constructed based on gene-disease associations, gene-chemical
associations and disease-chemical associations, to combine diverse
information. The network uses genes, diseases and chemicals as
nodes, and uses their associations as edges. The graph embedding
methods are utilized to extract representation vectors of nodes in the
heterogeneous network, and the feature vectors of genes and
diseases are merged to represent gene-disease pairs, and the random
forest is employed to build the prediction model based on gene-
disease pairs. We consider six types of graph embedding methods,
and take the individual graph embedding method-generated features
to build prediction models and use them as base predictors, and then
combine base predictors to develop the ensemble learning model
HNEEM. We comprehensively compare different graph embedding
methods, and results demonstrate that the graph embedding methods
produce satisfying results in the gene-disease association prediction,
and integrating different graph embedding methods can make
further improvements. In computational experiments, HNEEM
produces better results compared to the state-of-the-art gene-disease
perdition methods, and HNEEM is robust to the data richness as well.
Moreover, the usefulness of the proposed method HNEEM is
validated by the case studies. In conclusion, HNEEM is a promising
method for predicting gene-disease associations.
Keywords: gene-disease association; heterogeneous network;
graph embedding
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