Bi-level gene selection of cancer by combining clustering and sparse learning

The diagnosis of cancer based on gene expression profile data has attracted extensive attention in the field of biomedical science. This type of data usually has the characteristics of high dimensionality and noise. In this paper, a hybrid gene selection method based on clustering and sparse learning is proposed to choose the key genes with high precision. We first propose a filter method, which combines the k-means clustering algorithm and signal-to-noise ratio ranking method, and then, a weighted gene co-expression network has been applied to the reduced data set to identify modules corresponding to biological pathways. Moreover, we choose the key genes by using group bridge and sparse group lasso as wrapper methods. Finally, we conduct some numerical experiments on six cancer datasets. The numerical results show that our proposed method has achieved good performance in gene selection and cancer classification.

Logistic regression with adaptive sparse group lasso penalty and its application in acute leukemia diagnosis

Cancer diagnosis based on gene expression profile data has attracted extensive attention in computational biology and medicine. It suffers from three challenges in practical applications: noise, gene grouping, and adaptive gene selection. This paper aims to solve the above problems by developing the logistic regression with adaptive sparse group lasso penalty (LR-ASGL). A noise information processing method for cancer gene expression profile data is first presented via robust principal component analysis. Genes are then divided into groups by performing weighted gene co-expression network analysis on the clean matrix. By approximating the relative value of the noise size, gene reliability criterion and robust evaluation criterion are proposed. Finally, LR-ASGL is presented for simultaneous cancer diagnosis and adaptive gene selection. The performance of the proposed method is compared with the other four methods in three simulation settings: Gaussian noise, uniformly distributed noise, and mixed noise. The acute leukemia data are adopted as an experimental example to demonstrate the advantages of LR-ASGL in prediction and gene selection.

Fused Group Lasso Regularized Multi-Task Feature Learning and Its Application to the Cognitive Performance Prediction of Alzheimer's Disease

Alzheimer's disease (AD) is characterized by gradual neurodegeneration and loss of brain function, especially for memory during early stages. Regression analysis has been widely applied to AD research to relate clinical and biomarker data such as predicting cognitive outcomes from MRI measures. Recently, multi-task based feature learning (MTFL) methods with sparsity-inducing [Formula: see text]-norm have been widely studied to select a discriminative feature subset from MRI features by incorporating inherent correlations among multiple clinical cognitive measures. However, existing MTFL assumes the correlation among all tasks is uniform, and the task relatedness is modeled by encouraging a common subset of features via sparsity-inducing regularizations that neglect the inherent structure of tasks and MRI features. To address this issue, we proposed a fused group lasso regularization to model the underlying structures, involving 1) a graph structure within tasks and 2) a group structure among the image features. To this end, we present a multi-task feature learning framework with a mixed norm of fused group lasso and [Formula: see text]-norm to model these more flexible structures. For optimization, we employed the alternating direction method of multipliers (ADMM) to efficiently solve the proposed non-smooth formulation. We evaluated the performance of the proposed method using the Alzheimer's Disease Neuroimaging Initiative (ADNI) datasets. The experimental results demonstrate that incorporating the two prior structures with fused group lasso norm into the multi-task feature learning can improve prediction performance over several competing methods, with estimated correlations of cognitive functions and identification of cognition-relevant imaging markers that are clinically and biologically meaningful.

Modeling Alzheimer's disease cognitive scores using multi-task sparse group lasso

Alzheimer's disease (AD) is a severe neurodegenerative disorder characterized by loss of memory and reduction in cognitive functions due to progressive degeneration of neurons and their connections, eventually leading to death. In this paper, we consider the problem of simultaneously predicting several different cognitive scores associated with categorizing subjects as normal, mild cognitive impairment (MCI), or Alzheimer's disease (AD) in a multi-task learning framework using features extracted from brain images obtained from ADNI (Alzheimer's Disease Neuroimaging Initiative). To solve the problem, we present a multi-task sparse group lasso (MT-SGL) framework, which estimates sparse features coupled across tasks, and can work with loss functions associated with any Generalized Linear Models. Through comparisons with a variety of baseline models using multiple evaluation metrics, we illustrate the promising predictive performance of MT-SGL on ADNI along with its ability to identify brain regions more likely to help the characterization Alzheimer's disease progression.

A Dirichlet-tree multinomial regression model for associating dietary nutrients with gut microorganisms

Understanding the factors that alter the composition of the human microbiota may help personalized healthcare strategies and therapeutic drug targets. In many sequencing studies, microbial communities are characterized by a list of taxa, their counts, and their evolutionary relationships represented by a phylogenetic tree. In this article, we consider an extension of the Dirichlet multinomial distribution, called the Dirichlet-tree multinomial distribution, for multivariate, over-dispersed, and tree-structured count data. To address the relationships between these counts and a set of covariates, we propose the Dirichlet-tree multinomial regression model for which we develop a penalized likelihood method for estimating parameters and selecting covariates. For efficient optimization, we adopt the accelerated proximal gradient approach. Simulation studies are presented to demonstrate the good performance of the proposed procedure. An analysis of a data set relating dietary nutrients with bacterial counts is used to show that the incorporation of the tree structure into the model helps increase the prediction power.