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Browsing by Subject "Sparse canonical correlation analysis"
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Item Associating Multi-modal Brain Imaging Phenotypes and Genetic Risk Factors via A Dirty Multi-task Learning Method(IEEE, 2020) Du, Lei; Liu, Fang; Liu, Kefei; Yao, Xiaohui; Risacher, Shannon L.; Han, Junwei; Saykin, Andrew J.; Shen, Li; Radiology and Imaging Sciences, School of MedicineBrain imaging genetics becomes more and more important in brain science, which integrates genetic variations and brain structures or functions to study the genetic basis of brain disorders. The multi-modal imaging data collected by different technologies, measuring the same brain distinctly, might carry complementary information. Unfortunately, we do not know the extent to which the phenotypic variance is shared among multiple imaging modalities, which further might trace back to the complex genetic mechanism. In this paper, we propose a novel dirty multi-task sparse canonical correlation analysis (SCCA) to study imaging genetic problems with multi-modal brain imaging quantitative traits (QTs) involved. The proposed method takes advantages of the multi-task learning and parameter decomposition. It can not only identify the shared imaging QTs and genetic loci across multiple modalities, but also identify the modality-specific imaging QTs and genetic loci, exhibiting a flexible capability of identifying complex multi-SNP-multi-QT associations. Using the state-of-the-art multi-view SCCA and multi-task SCCA, the proposed method shows better or comparable canonical correlation coefficients and canonical weights on both synthetic and real neuroimaging genetic data. In addition, the identified modality-consistent biomarkers, as well as the modality-specific biomarkers, provide meaningful and interesting information, demonstrating the dirty multi-task SCCA could be a powerful alternative method in multi-modal brain imaging genetics.Item Identifying diagnosis-specific genotype–phenotype associations via joint multitask sparse canonical correlation analysis and classification(Oxford, 2020-07-13) Du, Lei; Liu, Fang; Liu, Kefei; Yao, Xiaohui; Risacher, Shannon L; Han, Junwei; Guo, Lei; Saykin, Andrew J; Shen, Li; Radiology and Imaging Sciences, School of MedicineMotivation Brain imaging genetics studies the complex associations between genotypic data such as single nucleotide polymorphisms (SNPs) and imaging quantitative traits (QTs). The neurodegenerative disorders usually exhibit the diversity and heterogeneity, originating from which different diagnostic groups might carry distinct imaging QTs, SNPs and their interactions. Sparse canonical correlation analysis (SCCA) is widely used to identify bi-multivariate genotype–phenotype associations. However, most existing SCCA methods are unsupervised, leading to an inability to identify diagnosis-specific genotype–phenotype associations. Results In this article, we propose a new joint multitask learning method, named MT–SCCALR, which absorbs the merits of both SCCA and logistic regression. MT–SCCALR learns genotype–phenotype associations of multiple tasks jointly, with each task focusing on identifying one diagnosis-specific genotype–phenotype pattern. Meanwhile, MT–SCCALR cannot only select relevant SNPs and imaging QTs for each diagnostic group alone, but also allows the selection of those shared by multiple diagnostic groups. We derive an efficient optimization algorithm whose convergence to a local optimum is guaranteed. Compared with two state-of-the-art methods, MT–SCCALR yields better or similar canonical correlation coefficients and classification performances. In addition, it owns much better discriminative canonical weight patterns of great interest than competitors. This demonstrates the power and capability of MTSCCAR in identifying diagnostically heterogeneous genotype–phenotype patterns, which would be helpful to understand the pathophysiology of brain disorders.Item Multi-task learning based structured sparse canonical correlation analysis for brain imaging genetics(Elsevier, 2022-02) Kim, Mansu; Min, Eun Jeong; Liu, Kefei; Yan, Jingwen; Saykin, Andrew J.; Moore, Jason H.; Long, Qi; Shen, Li; BioHealth Informatics, School of Informatics and ComputingThe advances in technologies for acquiring brain imaging and high-throughput genetic data allow the researcher to access a large amount of multi-modal data. Although the sparse canonical correlation analysis is a powerful bi-multivariate association analysis technique for feature selection, we are still facing major challenges in integrating multi-modal imaging genetic data and yielding biologically meaningful interpretation of imaging genetic findings. In this study, we propose a novel multi-task learning based structured sparse canonical correlation analysis (MTS2CCA) to deliver interpretable results and improve integration in imaging genetics studies. We perform comparative studies with state-of-the-art competing methods on both simulation and real imaging genetic data. On the simulation data, our proposed model has achieved the best performance in terms of canonical correlation coefficients, estimation accuracy, and feature selection accuracy. On the real imaging genetic data, our proposed model has revealed promising features of single-nucleotide polymorphisms and brain regions related to sleep. The identified features can be used to improve clinical score prediction using promising imaging genetic biomarkers. An interesting future direction is to apply our model to additional neurological or psychiatric cohorts such as patients with Alzheimer’s or Parkinson’s disease to demonstrate the generalizability of our method.Item Multi-Task Sparse Canonical Correlation Analysis with Application to Multi-Modal Brain Imaging Genetics(Institute of Electrical and Electronics Engineers, 2021) Du, Lei; Liu, Kefei; Yao, Xiaohui; Risacher, Shannon L.; Han, Junwei; Saykin, Andrew J.; Guo, Lei; Shen, Li; Radiology and Imaging Sciences, School of MedicineBrain imaging genetics studies the genetic basis of brain structures and functionalities via integrating genotypic data such as single nucleotide polymorphisms (SNPs) and imaging quantitative traits (QTs). In this area, both multi-task learning (MTL) and sparse canonical correlation analysis (SCCA) methods are widely used since they are superior to those independent and pairwise univariate analysis. MTL methods generally incorporate a few of QTs and could not select features from multiple QTs; while SCCA methods typically employ one modality of QTs to study its association with SNPs. Both MTL and SCCA are computational expensive as the number of SNPs increases. In this paper, we propose a novel multi-task SCCA (MTSCCA) method to identify bi-multivariate associations between SNPs and multi-modal imaging QTs. MTSCCA could make use of the complementary information carried by different imaging modalities. MTSCCA enforces sparsity at the group level via the G2,1-norm, and jointly selects features across multiple tasks for SNPs and QTs via the ℓ2,1-norm. A fast optimization algorithm is proposed using the grouping information of SNPs. Compared with conventional SCCA methods, MTSCCA obtains better correlation coefficients and canonical weights patterns. In addition, MTSCCA runs very fast and easy-to-implement, indicating its potential power in genome-wide brain-wide imaging genetics.