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Bioinformatics. 2019 Jan 1;35(1):112-118. doi: 10.1093/bioinformatics/bty513.

Tightly integrated genomic and epigenomic data mining using tensor decomposition.

Author information

1
Computational & Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, USA.

Abstract

Motivation:

Complex diseases such as cancers often involve multiple types of genomic and/or epigenomic abnormalities. Rapid accumulation of multiple types of omics data demands methods for integrating the multidimensional data in order to elucidate complex relationships among different types of genomic and epigenomic abnormalities.

Results:

In the present study, we propose a tightly integrated approach based on tensor decomposition. Multiple types of data, including mRNA, methylation, copy number variations and somatic mutations, are merged into a high-order tensor which is used to develop predictive models for overall survival. The weight tensors of the models are constrained using CANDECOMP/PARAFAC (CP) tensor decomposition and learned using support tensor machine regression (STR) and ridge tensor regression (RTR). The results demonstrate that the tensor decomposition based approaches can achieve better performance than the models based individual data type and the concatenation approach.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
29939222
PMCID:
PMC6298052
[Available on 2020-01-01]
DOI:
10.1093/bioinformatics/bty513

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