Journal article
Pattern Discovery in Brain Imaging Genetics via SCCA Modeling with a Generic Non-convex Penalty
Scientific reports, Vol.7(1), 14052
10/25/2017
DOI: 10.1038/s41598-017-13930-y
PMCID: PMC5656688
PMID: 29070790
Abstract
Brain imaging genetics intends to uncover associations between genetic markers and neuroimaging quantitative traits. Sparse canonical correlation analysis (SCCA) can discover bi-multivariate associations and select relevant features, and is becoming popular in imaging genetic studies. The L1-norm function is not only convex, but also singular at the origin, which is a necessary condition for sparsity. Thus most SCCA methods impose. l(1)-norm onto the individual feature or the structure level of features to pursuit corresponding sparsity. However, the. 1-norm penalty over-penalizes large coefficients and may incurs estimation bias. A number of non-convex penalties are proposed to reduce the estimation bias in regression tasks. But using them in SCCA remains largely unexplored. In this paper, we design a unified non-convex SCCA model, based on seven non-convex functions, for unbiased estimation and stable feature selection simultaneously. We also propose an efficient optimization algorithm. The proposed method obtains both higher correlation coefficients and better canonical loading patterns. Specifically, these SCCA methods with non-convex penalties discover a strong association between the APOE e4 rs429358 SNP and the hippocampus region of the brain. They both are Alzheimer's disease related biomarkers, indicating the potential and power of the non-convex methods in brain imaging genetics.
Details
- Title: Subtitle
- Pattern Discovery in Brain Imaging Genetics via SCCA Modeling with a Generic Non-convex Penalty
- Creators
- Lei Du - Northwestern Polytechnical UniversityKefei Liu - Indiana University – Purdue University IndianapolisXiaohui Yao - Indiana University – Purdue University IndianapolisJingwen Yan - Indiana University – Purdue University IndianapolisShannon L. Risacher - Indiana University – Purdue University IndianapolisJunwei Han - Northwestern Polytechnical UniversityLei Guo - Northwestern Polytechnical UniversityAndrew J. Saykin - Indiana University – Purdue University IndianapolisLi Shen - Indiana University – Purdue University IndianapolisAlzheimer’s Disease Neuroimaging Initiative
- Contributors
- Hristina Koleva (Contributor) - University of Iowa, Psychiatry
- Resource Type
- Journal article
- Publication Details
- Scientific reports, Vol.7(1), 14052
- DOI
- 10.1038/s41598-017-13930-y
- PMID
- 29070790
- PMCID
- PMC5656688
- NLM abbreviation
- Sci Rep
- ISSN
- 2045-2322
- eISSN
- 2045-2322
- Publisher
- Springer Nature
- Number of pages
- 14
- Grant note
- National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute on Aging (NIA); NIH National Institute of Biomedical Imaging & Bioengineering (NIBIB) Eli Lilly and Company; Eli Lilly Fujirebio Araclon Biotech CereSpir, Inc. Lundbeck; Lundbeck Corporation Johnson & Johnson Pharmaceutical Research & Development LLC.; Johnson & Johnson; Johnson & Johnson USA U01 AG024904 / Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Neurological Disorders & Stroke (NINDS) U01 AG024904; R01 EB022574; R01 LM011360; P30 AG10133; R01 AG19771; UL1 TR001108; R01 AG 042437; R01 AG046171; R01 AG040770 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA Biogen Piramal Imaging Servier Eisai Inc.; Eisai Co Ltd Alzheimer's Association IXICO Ltd. Pfizer Inc.; Pfizer Janssen Alzheimer Immunotherapy Research & Development, LLC. 3102016OQD0065 / Fundamental Research Funds for the Central Universities Transition Therapeutics Alzheimer's Drug Discovery Foundation Novartis Pharmaceuticals Corporation; Novartis Northwestern Polytechnical University 2017M613202 / China Postdoctoral Science Foundation Foundation for the National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA 61602384 / National Natural Science Foundation of China; National Natural Science Foundation of China (NSFC) R01LM011360 / NATIONAL LIBRARY OF MEDICINE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM) W81XWH-12-2-0012 / DOD ADNI (Department of Defense) BioClinica, Inc. P41EB015922 / NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Biomedical Imaging & Bioengineering (NIBIB) Cogstate; CogState Limited GE Healthcare; General Electric Meso Scale Diagnostics, LLC. F. Hoffmann-La Roche Ltd; Hoffmann-La Roche AbbVie EuroImmun P30AG008051 / NATIONAL INSTITUTE ON AGING; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute on Aging (NIA) W81XWH-12-2-0012; W81XWH-14-2-0151; W81XWH-13-1-0259 / Department of Defense; United States Department of Defense Merck Co., Inc.; Merck & Company Lumosity Canadian Institutes of Health Research; Canadian Institutes of Health Research (CIHR) NeuroRx Research Takeda Pharmaceutical Company; Takeda Pharmaceutical Company Ltd Bristol-Myers Squibb Company; Bristol-Myers Squibb UL1TR002369 / NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Center for Advancing Translational Sciences (NCATS) 14132004 / National Collegiate Athletic Association at Indiana University company Genentech, Inc. Neurotrack Technologies Elan Pharmaceuticals, Inc. 2017JQ6001 / Natural Science Basic Research Plan in Shaanxi Province of China
- Language
- English
- Date published
- 10/25/2017
- Academic Unit
- Psychiatry
- Record Identifier
- 9984293755802771
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