A novel SCCA approach via truncated ℓ 1-norm and truncated group lasso for brain imaging genetics
Year: 2017
Type: article
Abstract: MOTIVATION: Brain imaging genetics, which studies the linkage between genetic variations and structural or functional measures of the human brain, has become increasingly important in recent years. Discovering the bi-multivariate relationship between genetic markers such as single-nucleotide polymorphisms (SNPs) and neuroimaging quantitative traits (QTs) is one major task in imaging genetics. Sparse Canonical Correlation Analysis (SCCA) has been a popular technique in this area for its powerful capability in identifying bi-multivariate relationships coupled with feature selection. The existing SCCA methods impose either the ℓ1-norm or its variants to induce sparsity. The ℓ0-norm penalty is a perfect sparsity-inducing tool which, however, is an NP-hard problem. RESULTS: In this paper, we propose the truncated ℓ1-norm penalized SCCA to improve the performance and effectiveness of the ℓ1-norm based SCCA methods. Besides, we propose an efficient optimization algorithms to solve this novel SCCA problem. The proposed method is an adaptive shrinkage method via tuning τ. It can avoid the time intensive parameter tuning if given a reasonable small τ. Furthermore, we extend it to the truncated group-lasso (TGL), and propose TGL-SCCA model to improve the group-lasso-based SCCA methods. The experimental results, compared with four benchmark methods, show that our SCCA methods identify better or similar correlation coefficients, and better canonical loading profiles than the competing methods. This demonstrates the effectiveness and efficiency of our methods in discovering interesting imaging genetic associations. AVAILABILITY AND IMPLEMENTATION: The Matlab code and sample data are freely available at http://www.iu.edu/∼shenlab/tools/tlpscca/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics
Language: English
Subfield: Statistics and Probability
Field: Mathematics
Domain: Physical Sciences
Open Access status: bronze
Funders: U.S. Department of Defense, Alzheimer's Association, Bristol-Myers Squibb, Eli Lilly and Company, Pfizer, University of Southern California, Meso Scale Diagnostics, Northwestern University, Alzheimer's Disease Neuroimaging Initiative, BioClinica, Novartis Pharmaceuticals Corporation, Northern California Institute for Research and Education, National Natural Science Foundation of China, Northwestern Polytechnical University, China Postdoctoral Science Foundation, Eisai, Servier, H. Lundbeck A/S, IXICO, Scheme for Promotion of Academic and Research Collaboration, National Institutes of Health, Genentech, University of California, San Diego, Canadian Institutes of Health Research, Fundamental Research Funds for the Central Universities, Natural Science Basic Research Program of Shaanxi Province, National Institute on Aging, National Institute of Biomedical Imaging and Bioengineering, U.S. National Library of Medicine, National Center for Advancing Translational Sciences
Awards: G104586243, G1298807586, Indiana Alzheimer Disease Center, Bioinformatics Strategies for Multidimensional Brain Imaging Genetics, Genetic architecture of memory and executive functioning in Alzheimer's disease, G1554142629, G1593117279, G1654311910, G1711052734, G1880935189, G2100670906, G2152643862, G2189010064, G2340207221, G2423387114, G2471646051, G2522063444, Indiana Clinical and Translational Sciences Institute, G2772251316, G2835601961, G29951154, G3131374986, G3216574877, G3553156159, G3710456697, G3752451908, G3870774570, G3908963977, G4083040189, G4119534169, G43180419, G4475667458, G4501223628, Integrative Bioinformatics Approaches to Human Brain Genomics and Connectomics, THE NCAA-DOD GRAND ALLIANCE: CONCUSSION ASSESSMENT, RESEARCH, AND EDUCATION (CARE) CONSORTIUM, G4696819275, G470063782, G4800177743, G4846477358, G5207404921, G5209990037, G528601746, G5324093878, G5365730499, EFFECTS OF TRAUMATIC BRAIN INJURY (TBI) AND POST TRAUMATIC STRESS DISORDER (PTSD) ON ALZHEIMER'S DISEASE (AD) IN VETERANS USING IMAGING AND BIOMARKERS IN THE AD NEUROIMAGING INITIATIVE (ADNI)", G5654639750, Alzheimer's Disease Neuroimaging Initiative, G5740349702, G5850682332, G613619302, G6173816828, G6412110892, G6447063303, G6719828067, G6792506723, G6798853303, G6899163935, G72415811, G7298697282, G7498691371, Memory Circuitry in MCI and Early Alzheimerâs Disease Prodrome: Molecular Drivers, G764699806, Amyloid Imaging, VMCI, and Analysis for ADNI, G7799614282, G781725486, Metabolic Networks and Pathways in Alzheimer's Disease, G8151151163, G8228018387, G8281378126, G839208290, G8586263799, G8632625050, G8852128998, G8895907669, G8897063270, G8957659042, G9000039018
OpenAlex ID: W2786073924