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Complex harmonic regularization with differential evolution in a memetic framework for biomarker selection.
- Source :
- PLoS ONE; 2/14/2019, Vol. 14 Issue 2, p1-21, 21p
- Publication Year :
- 2019
-
Abstract
- For studying cancer and genetic diseases, the issue of identifying high correlation genes from high-dimensional data is an important problem. It is a great challenge to select relevant biomarkers from gene expression data that contains some important correlation structures, and some of the genes can be divided into different groups with a common biological function, chromosomal location or regulation. In this paper, we propose a penalized accelerated failure time model CHR-DE using a non-convex regularization (local search) with differential evolution (global search) in a wrapper-embedded memetic framework. The complex harmonic regularization (CHR) can approximate to the combination and ℓ<subscript>q</subscript> (1 ≤ q < 2) for selecting biomarkers in group. And differential evolution (DE) is utilized to globally optimize the CHR’s hyperparameters, which make CHR-DE achieve strong capability of selecting groups of genes in high-dimensional biological data. We also developed an efficient path seeking algorithm to optimize this penalized model. The proposed method is evaluated on synthetic and three gene expression datasets: breast cancer, hepatocellular carcinoma and colorectal cancer. The experimental results demonstrate that CHR-DE is a more effective tool for feature selection and learning prediction. [ABSTRACT FROM AUTHOR]
- Subjects :
- BIOLOGICAL tags
CARCINOGENS
INCURABLE diseases
ONCOLOGY
ETIOLOGY of diseases
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 14
- Issue :
- 2
- Database :
- Complementary Index
- Journal :
- PLoS ONE
- Publication Type :
- Academic Journal
- Accession number :
- 134708681
- Full Text :
- https://doi.org/10.1371/journal.pone.0210786