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Table 4 Area under ROC curve (AUROC) and Area under PR curve (AUPR) for gene Interaction Prediction

From: GNE: a deep learning framework for gene network inference by aggregating biological information

Methods

Yeast

E. coli

 

AUROC

AUPR

AUROC

AUPR

Correlation

0.582

0.579

0.537

0.557

Isomap

0.507

0.588

0.559

0.672

LINE

0.726

0.686

0.897

0.851

node2vec

0.739

0.708

0.912

0.862

Isomap+

0.653

0.652

0.644

0.649

LINE+

0.745

0.713

0.899

0.856

node2vec+

0.751

0.716

0.871

0.826

GNE (Topology)

0.787

0.784

0.930

0.931

GNE (our model)

0.825*

0.821*

0.940*

0.939*

  1. + indicates the concatenation of expression data with learned embeddings to create final representation. * denotes that GNE significantly outperforms node2vec at 0.01 level paired t-test. Note that method that achieves the best performance is bold faced
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BMC Systems Biology

ISSN: 1752-0509

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