Browsing by Author "Wang, Xiaoqian"

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    Longitudinal Genotype-Phenotype Association Study via Temporal Structure Auto-Learning Predictive Model
    (Springer, 2017-05) Wang, Xiaoqian; Yan, Jingwen; Yao, Xiaohui; Kim, Sungeun; Nho, Kwangsik; Risacher, Shannon L.; Saykin, Andrew J.; Shen, Li; Huang, Heng; Radiology and Imaging Sciences, School of Medicine
    With rapid progress in high-throughput genotyping and neuroimaging, imaging genetics has gained significant attention in the research of complex brain disorders, such as Alzheimer's Disease (AD). The genotype-phenotype association study using imaging genetic data has the potential to reveal genetic basis and biological mechanism of brain structure and function. AD is a progressive neurodegenerative disease, thus, it is crucial to look into the relations between SNPs and longitudinal variations of neuroimaging phenotypes. Although some machine learning models were newly presented to capture the longitudinal patterns in genotype-phenotype association study, most of them required fixed longitudinal structures of prediction tasks and could not automatically learn the interrelations among longitudinal prediction tasks. To address this challenge, we proposed a novel temporal structure auto-learning model to automatically uncover longitudinal genotype-phenotype interrelations and utilized such interrelated structures to enhance phenotype prediction in the meantime. We conducted longitudinal phenotype prediction experiments on the ADNI cohort including 3,123 SNPs and 2 types of biomarkers, VBM and FreeSurfer. Empirical results demonstrated advantages of our proposed model over the counterparts. Moreover, available literature was identified for our top selected SNPs, which demonstrated the rationality of our prediction results. An executable program is available online at https://github.com/littleq1991/sparse_lowRank_regression.
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    Predicting Interrelated Alzheimer's Disease Outcomes via New Self-Learned Structured Low-Rank Model
    (Springer, 2017-06) Wang, Xiaoqian; Liu, Kefei; Yan, Jingwen; Risacher, Shannon L.; Saykin, Andrew J.; Shen, Li; Huang, Heng; ADNI; Radiology and Imaging Sciences, School of Medicine
    Alzheimer's disease (AD) is a progressive neurodegenerative disorder. As the prodromal stage of AD, Mild Cognitive Impairment (MCI) maintains a good chance of converting to AD. How to efficaciously detect this conversion from MCI to AD is significant in AD diagnosis. Different from standard classification problems where the distributions of classes are independent, the AD outcomes are usually interrelated (their distributions have certain overlaps). Most of existing methods failed to examine the interrelations among different classes, such as AD, MCI conversion and MCI non-conversion. In this paper, we proposed a novel self-learned low-rank structured learning model to automatically uncover the interrelations among different classes and utilized such interrelated structures to enhance classification. We conducted experiments on the ADNI cohort data. Empirical results demonstrated advantages of our model.
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    Quantitative trait loci identification for brain endophenotypes via new additive model with random networks
    (Oxford University Press, 2018-09) Wang, Xiaoqian; Chen, Hong; Yan, Jingwen; Nho, Kwangsik; Risacher, Shannon L.; Saykin, Andrew J.; Shen, Li; Huang, Heng; Radiology and Imaging Sciences, School of Medicine
    Motivation: The identification of quantitative trait loci (QTL) is critical to the study of causal relationships between genetic variations and disease abnormalities. We focus on identifying the QTLs associated to the brain endophenotypes in imaging genomics study for Alzheimer's Disease (AD). Existing research works mainly depict the association between single nucleotide polymorphisms (SNPs) and the brain endophenotypes via the linear methods, which may introduce high bias due to the simplicity of the models. Since the influence of QTLs on brain endophenotypes is quite complex, it is desired to design the appropriate non-linear models to investigate the associations of genotypes and endophenotypes. Results: In this paper, we propose a new additive model to learn the non-linear associations between SNPs and brain endophenotypes in Alzheimer's disease. Our model can be flexibly employed to explain the non-linear influence of QTLs, thus is more adaptive for the complex distribution of the high-throughput biological data. Meanwhile, as an important computational learning theory contribution, we provide the generalization error analysis for the proposed approach. Unlike most previous theoretical analysis under independent and identically distributed samples assumption, our error bound is based on m-dependent observations, which is more appropriate for the high-throughput and noisy biological data. Experiments on the data from Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort demonstrate the promising performance of our approach for identifying biological meaningful SNPs.