The sparse group lasso for high-dimensional integrative linear discriminant analysis with application to alzheimer's disease prediction

2020 ◽  
Vol 90 (17) ◽  
pp. 3218-3231
Author(s):  
Hao Chen ◽  
Yong He ◽  
Jiadong Ji ◽  
Yufeng Shi
2007 ◽  
Vol 3 ◽  
pp. 117693510700300 ◽  
Author(s):  
Nadège Dossat ◽  
Alain Mangé ◽  
Jérôme Solassol ◽  
William Jacot ◽  
Ludovic Lhermitte ◽  
...  

A key challenge in clinical proteomics of cancer is the identification of biomarkers that could allow detection, diagnosis and prognosis of the diseases. Recent advances in mass spectrometry and proteomic instrumentations offer unique chance to rapidly identify these markers. These advances pose considerable challenges, similar to those created by microarray-based investigation, for the discovery of pattern of markers from high-dimensional data, specific to each pathologic state (e.g. normal vs cancer). We propose a three-step strategy to select important markers from high-dimensional mass spectrometry data using surface enhanced laser desorption/ionization (SELDI) technology. The first two steps are the selection of the most discriminating biomarkers with a construction of different classifiers. Finally, we compare and validate their performance and robustness using different supervised classification methods such as Support Vector Machine, Linear Discriminant Analysis, Quadratic Discriminant Analysis, Neural Networks, Classification Trees and Boosting Trees. We show that the proposed method is suitable for analysing high-throughput proteomics data and that the combination of logistic regression and Linear Discriminant Analysis outperform other methods tested.


2020 ◽  
Vol 2020 ◽  
pp. 1-23
Author(s):  
Xiaoli Liu ◽  
Jianzhong Wang ◽  
Fulong Ren ◽  
Jun Kong

As the largest cause of dementia, Alzheimer’s disease (AD) has brought serious burdens to patients and their families, mostly in the financial, psychological, and emotional aspects. In order to assess the progression of AD and develop new treatment methods for the disease, it is essential to infer the trajectories of patients’ cognitive performance over time to identify biomarkers that connect the patterns of brain atrophy and AD progression. In this article, a structured regularized regression approach termed group guided fused Laplacian sparse group Lasso (GFL-SGL) is proposed to infer disease progression by considering multiple prediction of the same cognitive scores at different time points (longitudinal analysis). The proposed GFL-SGL simultaneously exploits the interrelated structures within the MRI features and among the tasks with sparse group Lasso (SGL) norm and presents a novel group guided fused Laplacian (GFL) regularization. This combination effectively incorporates both the relatedness among multiple longitudinal time points with a general weighted (undirected) dependency graphs and useful inherent group structure in features. Furthermore, an alternating direction method of multipliers- (ADMM-) based algorithm is also derived to optimize the nonsmooth objective function of the proposed approach. Experiments on the dataset from Alzheimer’s Disease Neuroimaging Initiative (ADNI) show that the proposed GFL-SGL outperformed some other state-of-the-art algorithms and effectively fused the multimodality data. The compact sets of cognition-relevant imaging biomarkers identified by our approach are consistent with the results of clinical studies.


2018 ◽  
Vol 28 (08) ◽  
pp. 1850017 ◽  
Author(s):  
Chen Fang ◽  
Chunfei Li ◽  
Mercedes Cabrerizo ◽  
Armando Barreto ◽  
Jean Andrian ◽  
...  

Over the past few years, several approaches have been proposed to assist in the early diagnosis of Alzheimer’s disease (AD) and its prodromal stage of mild cognitive impairment (MCI). Using multimodal biomarkers for this high-dimensional classification problem, the widely used algorithms include Support Vector Machines (SVM), Sparse Representation-based classification (SRC), Deep Belief Networks (DBN) and Random Forest (RF). These widely used algorithms continue to yield unsatisfactory performance for delineating the MCI participants from the cognitively normal control (CN) group. A novel Gaussian discriminant analysis-based algorithm is thus introduced to achieve a more effective and accurate classification performance than the aforementioned state-of-the-art algorithms. This study makes use of magnetic resonance imaging (MRI) data uniquely as input to two separate high-dimensional decision spaces that reflect the structural measures of the two brain hemispheres. The data used include 190 CN, 305 MCI and 133 AD subjects as part of the AD Big Data DREAM Challenge #1. Using 80% data for a 10-fold cross-validation, the proposed algorithm achieved an average F1 score of 95.89% and an accuracy of 96.54% for discriminating AD from CN; and more importantly, an average F1 score of 92.08% and an accuracy of 90.26% for discriminating MCI from CN. Then, a true test was implemented on the remaining 20% held-out test data. For discriminating MCI from CN, an accuracy of 80.61%, a sensitivity of 81.97% and a specificity of 78.38% were obtained. These results show significant improvement over existing algorithms for discriminating the subtle differences between MCI participants and the CN group.


2012 ◽  
Vol 42 (2) ◽  
pp. 209-231 ◽  
Author(s):  
Masashi Hyodo ◽  
Takayuki Yamada ◽  
Tetsuo Himeno ◽  
Takashi Seo

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