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      Objective and Automated Detection of Diffuse White Matter Abnormality in Preterm Infants Using Deep Convolutional Neural Networks

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          Abstract

          Diffuse white matter abnormality (DWMA), or diffuse excessive high signal intensity is observed in 50–80% of very preterm infants at term-equivalent age. It is subjectively defined as higher than normal signal intensity in periventricular and subcortical white matter in comparison to normal unmyelinated white matter on T 2-weighted MRI images. Despite the well-documented presence of DWMA, it remains debatable whether DWMA represents pathological tissue injury or a transient developmental phenomenon. Manual tracing of DWMA exhibits poor reliability and reproducibility and unduly increases image processing time. Thus, objective and ideally automatic assessment is critical to accurately elucidate the biologic nature of DWMA. We propose a deep learning approach to automatically identify DWMA regions on T 2-weighted MRI images. Specifically, we formulated DWMA detection as an image voxel classification task; that is, the voxels on T 2-weighted images are treated as samples and exclusively assigned as DWMA or normal white matter voxel classes. To utilize the spatial information of individual voxels, small image patches centered on the given voxels are retrieved. A deep convolutional neural networks (CNN) model was developed to differentiate DWMA and normal voxels. We tested our deep CNN in multiple validation experiments. First, we examined DWMA detection accuracy of our CNN model using computer simulations. This was followed by in vivo assessments in a cohort of very preterm infants ( N = 95) using cross-validation and holdout validation. Finally, we tested our approach on an independent preterm cohort ( N = 28) to externally validate our model. Our deep CNN model achieved Dice similarity index values ranging from 0.85 to 0.99 for DWMA detection in the aforementioned validation experiments. Our proposed deep CNN model exhibited significantly better performance than other popular machine learning models. We present an objective and automated approach for accurately identifying DWMA that may facilitate the clinical diagnosis of DWMA in very preterm infants.

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          Most cited references41

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          Deep convolutional neural networks for multi-modality isointense infant brain image segmentation.

          The segmentation of infant brain tissue images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) plays an important role in studying early brain development in health and disease. In the isointense stage (approximately 6-8 months of age), WM and GM exhibit similar levels of intensity in both T1 and T2 MR images, making the tissue segmentation very challenging. Only a small number of existing methods have been designed for tissue segmentation in this isointense stage; however, they only used a single T1 or T2 images, or the combination of T1 and T2 images. In this paper, we propose to use deep convolutional neural networks (CNNs) for segmenting isointense stage brain tissues using multi-modality MR images. CNNs are a type of deep models in which trainable filters and local neighborhood pooling operations are applied alternatingly on the raw input images, resulting in a hierarchy of increasingly complex features. Specifically, we used multi-modality information from T1, T2, and fractional anisotropy (FA) images as inputs and then generated the segmentation maps as outputs. The multiple intermediate layers applied convolution, pooling, normalization, and other operations to capture the highly nonlinear mappings between inputs and outputs. We compared the performance of our approach with that of the commonly used segmentation methods on a set of manually segmented isointense stage brain images. Results showed that our proposed model significantly outperformed prior methods on infant brain tissue segmentation. In addition, our results indicated that integration of multi-modality images led to significant performance improvement.
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            Deep 3D Convolutional Encoder Networks With Shortcuts for Multiscale Feature Integration Applied to Multiple Sclerosis Lesion Segmentation.

            We propose a novel segmentation approach based on deep 3D convolutional encoder networks with shortcut connections and apply it to the segmentation of multiple sclerosis (MS) lesions in magnetic resonance images. Our model is a neural network that consists of two interconnected pathways, a convolutional pathway, which learns increasingly more abstract and higher-level image features, and a deconvolutional pathway, which predicts the final segmentation at the voxel level. The joint training of the feature extraction and prediction pathways allows for the automatic learning of features at different scales that are optimized for accuracy for any given combination of image types and segmentation task. In addition, shortcut connections between the two pathways allow high- and low-level features to be integrated, which enables the segmentation of lesions across a wide range of sizes. We have evaluated our method on two publicly available data sets (MICCAI 2008 and ISBI 2015 challenges) with the results showing that our method performs comparably to the top-ranked state-of-the-art methods, even when only relatively small data sets are available for training. In addition, we have compared our method with five freely available and widely used MS lesion segmentation methods (EMS, LST-LPA, LST-LGA, Lesion-TOADS, and SLS) on a large data set from an MS clinical trial. The results show that our method consistently outperforms these other methods across a wide range of lesion sizes.
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              Show, Attend and Tell: Neural Image Caption Generation with Visual Attention

              Inspired by recent work in machine translation and object detection, we introduce an attention based model that automatically learns to describe the content of images. We describe how we can train this model in a deterministic manner using standard backpropagation techniques and stochastically by maximizing a variational lower bound. We also show through visualization how the model is able to automatically learn to fix its gaze on salient objects while generating the corresponding words in the output sequence. We validate the use of attention with state-of-the-art performance on three benchmark datasets: Flickr8k, Flickr30k and MS COCO.
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                Author and article information

                Contributors
                Journal
                Front Neurosci
                Front Neurosci
                Front. Neurosci.
                Frontiers in Neuroscience
                Frontiers Media S.A.
                1662-4548
                1662-453X
                18 June 2019
                2019
                : 13
                : 610
                Affiliations
                [1] 1The Perinatal Institute, Cincinnati Children’s Hospital Medical Center , Cincinnati, OH, United States
                [2] 2Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH, United States
                [3] 3Department of Pediatrics, Nationwide Children’s Hospital , Columbus, OH, United States
                [4] 4Department of Radiology, University of Cincinnati College of Medicine , Cincinnati, OH, United States
                [5] 5Department of Electronic Engineering and Computing Systems, University of Cincinnati , Cincinnati, OH, United States
                [6] 6Medpace Inc. , Cincinnati, OH, United States
                [7] 7Department of Physics, University of Cincinnati , Cincinnati, OH, United States
                Author notes

                Edited by: Xi-Nian Zuo, Institute of Psychology (CAS), China

                Reviewed by: Ives R. Levesque, McGill University, Canada; Tolga Cukur, Bilkent University, Turkey

                *Correspondence: Lili He, lili.he@ 123456cchmc.org

                This article was submitted to Brain Imaging Methods, a section of the journal Frontiers in Neuroscience

                Article
                10.3389/fnins.2019.00610
                6591530
                31275101
                e4cee4a3-a8e0-4694-b477-d89bee56c1a8
                Copyright © 2019 Li, Parikh, Wang, Merhar, Chen, Parikh, Holland and He.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 15 February 2019
                : 28 May 2019
                Page count
                Figures: 10, Tables: 5, Equations: 0, References: 56, Pages: 12, Words: 0
                Funding
                Funded by: National Institutes of Health 10.13039/100000002
                Award ID: R21-HD094085
                Award ID: R01-NS094200
                Award ID: R01-NS096037
                Funded by: Cincinnati Children’s Hospital Medical Center 10.13039/100007172
                Award ID: Trustee Award
                Categories
                Neuroscience
                Original Research

                Neurosciences
                diffuse white matter abnormality,very preterm infants,mri,deep learning,convolutional neural networks

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