@inproceedings{d45fb4d14e5643afb10a430af0b9b010,
title = "Detecting genetic risk factors for Alzheimer's disease in whole genome sequence data via Lasso screening",
abstract = "Genetic factors play a key role in Alzheimer's disease (AD). The Alzheimer's Disease Neuroimaging Initiative (ADNI) whole genome sequence (WGS) data offers new power to investigate mechanisms of AD by combining entire genome sequences with neuroimaging and clinical data. Here we explore the ADNI WGS SNP (single nucleotide polymorphism) data in depth and extract approximately six million valid SNP features. We investigate imaging genetics associations using Lasso regression - a widely used sparse learning technique. To solve the large-scale Lasso problem more efficiently, we employ a highly efficient screening rule for Lasso - called dual polytope projections (DPP) - to remove irrelevant features from the optimization problem. Experiments demonstrate that the DPP can effectively identify irrelevant features and leads to a 400× speedup. This allows us for the first time to run the compute-intensive model selection procedure called stability selection to rank SNPs that may affect the brain and AD risk.",
keywords = "Alzheimer's Disease, Lasso, Lasso Screening, Whole Genome Sequence",
author = "Tao Yang and Jie Wang and Qian Sun and Hibar, {Derrek P.} and Neda Jahanshad and Li Liu and Yalin Wang and Liang Zhan and Thompson, {Paul M.} and Jieping Ye",
note = "Publisher Copyright: {\textcopyright} 2015 IEEE.; 12th IEEE International Symposium on Biomedical Imaging, ISBI 2015 ; Conference date: 16-04-2015 Through 19-04-2015",
year = "2015",
month = jul,
day = "21",
doi = "10.1109/ISBI.2015.7164036",
language = "English (US)",
series = "Proceedings - International Symposium on Biomedical Imaging",
publisher = "IEEE Computer Society",
pages = "985--989",
booktitle = "2015 IEEE 12th International Symposium on Biomedical Imaging, ISBI 2015",
}