Multi-task feature selection via supervised canonical graph matching for diagnosis of autism spectrum disorder

In this paper, we propose a novel framework for ASD diagnosis using structural magnetic resonance imaging (MRI). Our method deals explicitly with the distributional differences of gray matter (GM) and white matter (WM) features extracted from MR images. We project linearly the GM and WM features onto a canonical space where their correlations are mutually maximized. In this canonical space, features that are highly correlated with the class labels are selected for ASD diagnosis. In addition, graph matching is employed to preserve the geometrical relationships between samples when projected onto the canonical space. Our evaluations based on a public ASD dataset show that the proposed method outperforms all competing methods on all clinically important measures in differentiating ASD patients from healthy individuals

Reduced-Rank Local Distance Metric Learning

Abstract. We propose a new method for local metric learning based on a conical combination of Mahalanobis metrics and pair-wise similarities between the data. Its formulation allows for controlling the rank of the metrics ’ weight matrices. We also offer a convergent algorithm for training the associated model. Experimental results on a collection of classification problems imply that the new method may offer notable performance advantages over alternative metric learning approaches that have recently appeared in the literature

Discriminative multi-task feature selection for multi-modality classification of Alzheimer’s disease

Recently, multi-task based feature selection methods have been used in multi-modality based classification of Alzheimer’s disease (AD) and its prodromal stage, i.e., mild cognitive impairment (MCI). However, in traditional multi-task feature selection methods, some useful discriminative information among subjects is usually not well mined for further improving the subsequent classification performance. Accordingly, in this paper, we propose a discriminative multitask feature selection method to select the most discriminative features for multi-modality based classification of AD/MCI. Specifically, for each modality, we train a linear regression model using the corresponding modality of data, and further enforce the group-sparsity regularization on weights of those regression models for joint selection of common features across multiple modalities. Furthermore, we propose a discriminative regularization term based on the intra-class and inter-class Laplacian matrices to better use the discriminative information among subjects. To evaluate our proposed method, we perform extensive experiments on 202 subjects, including 51 AD patients, 99 MCI patients, and 52 healthy controls (HC), from the baseline MRI and FDG-PET image data of the Alzheimer’s Disease Neuroimaging Initiative (ADNI). The experimental results show that our proposed method not only improves the classification performance, but also has potential to discover the disease-related biomarkers useful for diagnosis of disease, along with the comparison to several state-of-the-art methods for multi-modality based AD/MCI classification

Label-aligned multi-task feature learning for multimodal classification of Alzheimer’s disease and mild cognitive impairment

Multimodal classification methods using different modalities of imaging and non-imaging data have recently shown great advantages over traditional single-modality-based ones for diagnosis and prognosis of Alzheimer’s disease (AD), as well as its prodromal stage, i.e., mild cognitive impairment (MCI). However, to the best of our knowledge, most existing methods focus on mining the relationship across multiple modalities of the same subjects, while ignoring the potentially useful relationship across different subjects. Accordingly, in this paper, we propose a novel learning method for multimodal classification of AD/MCI, by fully exploring the relationships across both modalities and subjects. Specifically, our proposed method includes two subsequent components, i.e., label-aligned multi-task feature selection and multimodal classification. In the first step, the feature selection learning from multiple modalities are treated as different learning tasks and a group sparsity regularizer is imposed to jointly select a subset of relevant features. Furthermore, to utilize the discriminative information among labeled subjects, a new label-aligned regularization term is added into the objective function of standard multi-task feature selection, where label-alignment means that all multi-modality subjects with the same class labels should be closer in the new feature-reduced space. In the second step, a multi-kernel support vector machine (SVM) is adopted to fuse the selected features from multi-modality data for final classification. To validate our method, we perform experiments on the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database using baseline MRI and FDG-PET imaging data. The experimental results demonstrate that our proposed method achieves better classification performance compared with several state-of-the-art methods for multimodal classification of AD/MCI

Multi-target QSAR modelling in the analysis and design of HIV-HCV co-inhibitors: an in-silico study

<p>Abstract</p> <p>Background</p> <p>HIV and HCV infections have become the leading global public-health threats. Even more remarkable, HIV-HCV co-infection is rapidly emerging as a major cause of morbidity and mortality throughout the world, due to the common rapid mutation characteristics of the two viruses as well as their similar complex influence to immunology system. Although considerable progresses have been made on the study of the infection of HIV and HCV respectively, few researches have been conducted on the investigation of the molecular mechanism of their co-infection and designing of the multi-target co-inhibitors for the two viruses simultaneously.</p> <p>Results</p> <p>In our study, a multi-target Quantitative Structure-Activity Relationship (QSAR) study of the inhibitors for HIV-HCV co-infection were addressed with an in-silico machine learning technique, i.e. multi-task learning, to help to guide the co-inhibitor design. Firstly, an integrated dataset with 3 HIV inhibitor subsets targeted on protease, integrase and reverse transcriptase respectively, together with another 6 subsets of 2 HCV inhibitors targeted on NS3 serine protease and NS5B polymerase respectively were compiled. Secondly, an efficient multi-target QSAR modelling of HIV-HCV co-inhibitors was performed by applying an accelerated gradient method based multi-task learning on the whole 9 datasets. Furthermore, by solving the <it>L</it>-1-infinity regularized optimization, the Drug-like index features for compound description were ranked according to their joint importance in multi-target QSAR modelling of HIV and HCV. Finally, a drug structure-activity simulation for investigating the relationships between compound structures and binding affinities was presented based on our multiple target analysis, which is then providing several novel clues for the design of multi-target HIV-HCV co-inhibitors with increasing likelihood of successful therapies on HIV, HCV and HIV-HCV co-infection.</p> <p>Conclusions</p> <p>The framework presented in our study provided an efficient way to identify and design inhibitors that simultaneously and selectively bind to multiple targets from multiple viruses with high affinity, and will definitely shed new lights on the future work of inhibitor synthesis for multi-target HIV, HCV, and HIV-HCV co-infection treatments.</p

An Efficient Primal-Dual Prox Method for Non-Smooth Optimization

We study the non-smooth optimization problems in machine learning, where both the loss function and the regularizer are non-smooth functions. Previous studies on efficient empirical loss minimization assume either a smooth loss function or a strongly convex regularizer, making them unsuitable for non-smooth optimization. We develop a simple yet efficient method for a family of non-smooth optimization problems where the dual form of the loss function is bilinear in primal and dual variables. We cast a non-smooth optimization problem into a minimax optimization problem, and develop a primal dual prox method that solves the minimax optimization problem at a rate of $O(1/T)$ {assuming that the proximal step can be efficiently solved}, significantly faster than a standard subgradient descent method that has an $O(1/\sqrt{T})$ convergence rate. Our empirical study verifies the efficiency of the proposed method for various non-smooth optimization problems that arise ubiquitously in machine learning by comparing it to the state-of-the-art first order methods

Identifying Multimodal Intermediate Phenotypes between Genetic Risk Factors and Disease Status in Alzheimer’s Disease

Neuroimaging genetics has attracted growing attention and interest, which is thought to be a powerful strategy to examine the influence of genetic variants (i.e., single nucleotide polymorphisms (SNPs)) on structures or functions of human brain. In recent studies, univariate or multivariate regression analysis methods are typically used to capture the effective associations between genetic variants and quantitative traits (QTs) such as brain imaging phenotypes. The identified imaging QTs, although associated with certain genetic markers, may not be all disease specific. A useful, but underexplored, scenario could be to discover only those QTs associated with both genetic markers and disease status for revealing the chain from genotype to phenotype to symptom. In addition, multimodal brain imaging phenotypes are extracted from different perspectives and imaging markers consistently showing up in multimodalities may provide more insights for mechanistic understanding of diseases (i.e., Alzheimer’s disease (AD)). In this work, we propose a general framework to exploit multi-modal brain imaging phenotypes as intermediate traits that bridge genetic risk factors and multi-class disease status. We applied our proposed method to explore the relation between the well-known AD risk SNP APOE rs429358 and three baseline brain imaging modalities (i.e., structural magnetic resonance imaging (MRI), fluorodeoxyglucose positron emission tomography (FDG-PET) and F-18 florbetapir PET scans amyloid imaging (AV45)) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. The empirical results demonstrate that our proposed method not only helps improve the performances of imaging genetic associations, but also discovers robust and consistent regions of interests (ROIs) across multi-modalities to guide the disease-induced interpretation