title: Robust group fused lasso for multisample copy number variation detection under uncertainty.
abstract: 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 ofl2,1norm, thel1-l2M-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.
authors.affiliation: The Center of Excellence of Soft Computing and Intelligent Information Processing (SCIIP), Ferdowsi University of Mashhad, Iran. hossein1990@gmail.com.
authors.forename: Hossein
authors.initials: H
authors.lastname: Sharifi Noghabi
authors.affiliation: Department of Technology, Policy and Management, Delft University of Technology, Netherlands.
authors.forename: Majid
authors.initials: M
authors.lastname: Mohammadi
authors.affiliation: Department of Technology, Policy and Management, Delft University of Technology, Netherlands.
authors.forename: Yao-Hua
authors.initials: YH
authors.lastname: Tan
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000378:metabolism; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D056915:DNA Copy Number Variations; D030541:Databases, Genetic; D005260:Female; D015894:Genome, Human; D006801:Humans; D015233:Models, Statistical; D016011:Normal Distribution; D020641:Polymorphism, Single Nucleotide; D012372:ROC Curve; D059629:Signal-To-Noise Ratio; D012984:Software; D035501:Uncertainty