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Register a new userA Multi-task Deep Feature Selection Method for Brain Imaging Genetics
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Using brain imaging quantitative traits (QTs) to identify the genetic risk factors is an important research topic in imaging genetics. Many efforts have been made via building linear models, e.g. linear regression (LR), to extract the association between imaging QTs and genetic factors such as single nucleotide polymorphisms (SNPs). However, to the best of our knowledge, these linear models could not fully uncover the complicated relationship due to the locis elusive and diverse impacts on imaging QTs. Though deep learning models can extract the nonlinear relationship, they could not select relevant genetic factors. In this paper, we proposed a novel multi-task deep feature selection (MTDFS) method for brain imaging genetics. MTDFS first adds a multi-task one-to-one layer and imposes a hybrid sparsity-inducing penalty to select relevant SNPs making significant contributions to abnormal imaging QTs. It then builds a multi-task deep neural network to model the complicated associations between imaging QTs and SNPs. MTDFS can not only extract the nonlinear relationship but also arms the deep neural network with the feature selection capability. We compared MTDFS to both LR and single-task DFS (DFS) methods on the real neuroimaging genetic data. The experimental results showed that MTDFS performed better than both LR and DFS in terms of the QT-SNP relationship identification and feature selection. In a word, MTDFS is powerful for identifying risk loci and could be a great supplement to the method library for brain imaging genetics.
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Functional brain network has been widely studied to understand the relationship between brain organization and behavior. In this paper, we aim to explore the functional connectivity of brain network under a emph{multi-step} cognitive task involving with consecutive behaviors, and further understand the effect of behaviors on the brain organization. The functional brain networks are constructed base on a high spatial and temporal resolution fMRI dataset and analyzed via complex network based approach. We find that at voxel level the functional brain network shows robust small-worldness and scale-free characteristics, while its assortativity and rich-club organization are slightly restricted to order of behaviors performed. More interestingly, the functional connectivity of brain network in activated ROIs strongly correlates with behaviors and behaves obvious differences restricted to order of behaviors performed. These empirical results suggest that the brain organization has the generic properties of small-worldness and scale-free characteristics, and its diverse function connectivity emerging from activated ROIs is strongly driven by these behavioral activities via the plasticity of brain.
Three-dimensional imaging plays an important role in imaging applications where it is necessary to record depth. The number of applications that use depth imaging is increasing rapidly, and examples include self-driving autonomous vehicles and auto-focus assist on smartphone cameras. Light detection and ranging (LIDAR) via single-photon sensitive detector (SPAD) arrays is an emerging technology that enables the acquisition of depth images at high frame rates. However, the spatial resolution of this technology is typically low in comparison to the intensity images recorded by conventional cameras. To increase the native resolution of depth images from a SPAD camera, we develop a deep network built specifically to take advantage of the multiple features that can be extracted from a cameras histogram data. The network is designed for a SPAD camera operating in a dual-mode such that it captures alternate low resolution depth and high resolution intensity images at high frame rates, thus the system does not require any additional sensor to provide intensity images. The network then uses the intensity images and multiple features extracted from downsampled histograms to guide the upsampling of the depth. Our network provides significant image resolution enhancement and image denoising across a wide range of signal-to-noise ratios and photon levels. We apply the network to a range of 3D data, demonstrating denoising and a four-fold resolution enhancement of depth.
In this paper, we propose a novel weighted combination feature selection method using bootstrap and fuzzy sets. The proposed method mainly consists of three processes, including fuzzy sets generation using bootstrap, weighted combination of fuzzy sets and feature ranking based on defuzzification. We implemented the proposed method by combining four state-of-the-art feature selection methods and evaluated the performance based on three publicly available biomedical datasets using five-fold cross validation. Based on the feature selection results, our proposed method produced comparable (if not better) classification accuracies to the best of the individual feature selection methods for all evaluated datasets. More importantly, we also applied standard deviation and Pearsons correlation to measure the stability of the methods. Remarkably, our combination method achieved significantly higher stability than the four individual methods when variations and size reductions were introduced to the datasets.
In recent years, deep neural networks have achieved state-of-the-art performance in a variety of recognition and segmentation tasks in medical imaging including brain tumor segmentation. We investigate that segmenting a brain tumor is facing to the imbalanced data problem where the number of pixels belonging to the background class (non tumor pixel) is much larger than the number of pixels belonging to the foreground class (tumor pixel). To address this problem, we propose a multi-task network which is formed as a cascaded structure. Our model consists of two targets, i.e., (i) effectively differentiate the brain tumor regions and (ii) estimate the brain tumor mask. The first objective is performed by our proposed contextual brain tumor detection network, which plays a role of an attention gate and focuses on the region around brain tumor only while ignoring the far neighbor background which is less correlated to the tumor. The second objective is built upon a 3D atrous residual network and under an encode-decode network in order to effectively segment both large and small objects (brain tumor). Our 3D atrous residual network is designed with a skip connection to enables the gradient from the deep layers to be directly propagated to shallow layers, thus, features of different depths are preserved and used for refining each other. In order to incorporate larger contextual information from volume MRI data, our network utilizes the 3D atrous convolution with various kernel sizes, which enlarges the receptive field of filters. Our proposed network has been evaluated on various datasets including BRATS2015, BRATS2017 and BRATS2018 datasets with both validation set and testing set. Our performance has been benchmarked by both region-based metrics and surface-based metrics. We also have conducted comparisons against state-of-the-art approaches.
Resting-state functional magnetic resonance imaging (rs-fMRI)-derived functional connectivity patterns have been extensively utilized to delineate global functional organization of the human brain in health, development, and neuropsychiatric disorders. In this paper, we investigate how functional connectivity in males and females differs in an age prediction framework. We first estimate functional connectivity between regions-of-interest (ROIs) using distance correlation instead of Pearsons correlation. Distance correlation, as a multivariate statistical method, explores spatial relations of voxel-wise time courses within individual ROIs and measures both linear and nonlinear dependence, capturing more complex information of between-ROI interactions. Then, a novel non-convex multi-task learning (NC-MTL) model is proposed to study age-related gender differences in functional connectivity, where age prediction for each gender group is viewed as one task. Specifically, in the proposed NC-MTL model, we introduce a composite regularizer with a combination of non-convex $ell_{2,1-2}$ and $ell_{1-2}$ regularization terms for selecting both common and task-specific features. Finally, we validate the proposed NC-MTL model along with distance correlation based functional connectivity on rs-fMRI of the Philadelphia Neurodevelopmental Cohort for predicting ages of both genders. The experimental results demonstrate that the proposed NC-MTL model outperforms other competing MTL models in age prediction, as well as characterizing developmental gender differences in functional connectivity patterns.
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