TY - JOUR
T1 - Robust group fused lasso for multisample copy number variation detection under uncertainty
AU - Noghabi, Hossein Sharifi
AU - Mohammadi, M.
AU - Tan, Yao Hua
PY - 2016
Y1 - 2016
N2 - One of the most important needs in the post-genome era is providing the researchers with reliable and efficient computational tools to extract and analyse this huge amount of biological data, in which DNA copy number variation (CNV) is a vitally important one. Array-based comparative genomic hybridisation (aCGH) is a common approach in order to detect CNVs. Most of methods for this purpose were proposed for one-dimensional profiles. However, slightly this focus has moved from one- to multi-dimensional signals. In addition, since contamination of these profiles with noise is always an issue, it is highly important to have a robust method for analysing multi-sample aCGH profiles. In this study, the authors propose robust group fused lasso which utilises the robust group total variations. Instead of l2,1 norm, the l1 - l2 M-estimator is used which is more robust in dealing with non-Gaussian noise and high corruption. More importantly, Correntropy (Welsch M-estimator) is also applied for fitting error. Extensive experiments indicate that the proposed method outperforms the state-of-the art algorithms and techniques under a wide range of scenarios with diverse noises.
AB - One of the most important needs in the post-genome era is providing the researchers with reliable and efficient computational tools to extract and analyse this huge amount of biological data, in which DNA copy number variation (CNV) is a vitally important one. Array-based comparative genomic hybridisation (aCGH) is a common approach in order to detect CNVs. Most of methods for this purpose were proposed for one-dimensional profiles. However, slightly this focus has moved from one- to multi-dimensional signals. In addition, since contamination of these profiles with noise is always an issue, it is highly important to have a robust method for analysing multi-sample aCGH profiles. In this study, the authors propose robust group fused lasso which utilises the robust group total variations. Instead of l2,1 norm, the l1 - l2 M-estimator is used which is more robust in dealing with non-Gaussian noise and high corruption. More importantly, Correntropy (Welsch M-estimator) is also applied for fitting error. Extensive experiments indicate that the proposed method outperforms the state-of-the art algorithms and techniques under a wide range of scenarios with diverse noises.
UR - http://www.scopus.com/inward/record.url?scp=84998631580&partnerID=8YFLogxK
U2 - 10.1049/iet-syb.2015.0081
DO - 10.1049/iet-syb.2015.0081
M3 - Article
AN - SCOPUS:84998631580
SN - 1751-8849
VL - 10
SP - 229
EP - 236
JO - IET Systems Biology
JF - IET Systems Biology
IS - 6
ER -