Scalable network estimation with L 0 penalty

Stat Anal Data Min. 2021 Feb;14(1):18-30. doi: 10.1002/sam.11483. Epub 2020 Oct 21.

Abstract

With the advent of high-throughput sequencing, an efficient computing strategy is required to deal with large genomic data sets. The challenge of estimating a large precision matrix has garnered substantial research attention for its direct application to discriminant analyses and graphical models. Most existing methods either use a lasso-type penalty that may lead to biased estimators or are computationally intensive, which prevents their applications to very large graphs. We propose using an L 0 penalty to estimate an ultra-large precision matrix (scalnetL0). We apply scalnetL0 to RNA-seq data from breast cancer patients represented in The Cancer Genome Atlas and find improved accuracy of classifications for survival times. The estimated precision matrix provides information about a large-scale co-expression network in breast cancer. Simulation studies demonstrate that scalnetL0 provides more accurate and efficient estimators, yielding shorter CPU time and less Frobenius loss on sparse learning for large-scale precision matrix estimation.

Keywords: L0 penalty; genomics; network; scalable.