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ForgeNet: a graph deep neural network model using tree-based ensemble classifiers for feature graph construction.

ABSTRACT:

Motivation

A unique challenge in predictive model building for omics data has been the small number of samples (n) versus the large amount of features (p). This 'n≪p' property brings difficulties for disease outcome classification using deep learning techniques. Sparse learning by incorporating known functional relationships between the biological units, such as the graph-embedded deep feedforward network (GEDFN) model, has been a solution to this issue. However, such methods require an existing feature graph, and potential mis-specification of the feature graph can be harmful on classification and feature selection.

Results

To address this limitation and develop a robust classification model without relying on external knowledge, we propose a forest graph-embedded deep feedforward network (forgeNet) model, to integrate the GEDFN architecture with a forest feature graph extractor, so that the feature graph can be learned in a supervised manner and specifically constructed for a given prediction task. To validate the method's capability, we experimented the forgeNet model with both synthetic and real datasets. The resulting high classification accuracy suggests that the method is a valuable addition to sparse deep learning models for omics data.

Availability and implementation

The method is available at https://github.com/yunchuankong/forgeNet.

Contact

tianwei.yu@emory.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Kong Y

PROVIDER: S-EPMC7267822 | biostudies-literature |

REPOSITORIES: biostudies-literature

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