Book ChapterDOI

16 Sep 2018-pp 416-427

TL;DR: This work demonstrates the utility of deep learning and radiomics features for classification of low grade gliomas (LGG) into astrocytoma and oligodendroglioma and achieves a classification accuracy of 90% on the challenge test set.

AbstractDeep learning based techniques have shown to be beneficial for automating various medical image tasks like segmentation of lesions and automation of disease diagnosis. In this work, we demonstrate the utility of deep learning and radiomics features for classification of low grade gliomas (LGG) into astrocytoma and oligodendroglioma. In this study the objective is to use whole-slide H&E stained images and Magnetic Resonance (MR) images of the brain to make a prediction about the class of the glioma. We treat both the pathology and radiology datasets separately for in-depth analysis and then combine the predictions made by the individual models to get the final class label for a patient. The pre-processing of the whole slide images involved region of interest detection, stain normalization and patch extraction. An autoencoder was trained to extract features from each patch and these features are then used to find anomaly patches among the entire set of patches for a single Whole Slide Image. These anomaly patches from all the training slides form the dataset for training the classification model. A deep neural network based classification model was used to classify individual patches among the two classes. For the radiology dataset based analysis, each MRI scan was fed into a pre-processing pipeline which involved skull-stripping, co-registration of MR sequences to T1c, re-sampling of MR volumes to isotropic voxels and segmentation of brain lesion. The lesions in the MR volumes were automatically segmented using a fully convolutional Neural Network (CNN) trained on BraTS-2018 segmentation challenge dataset. From the segmentation maps 64$$\,\times \,$$64$$\,\times \,$$64 cube patches centered around the tumor were extracted from the T1 MR images for extraction of high level radiomic features. These features were then used to train a logistic regression classifier. After developing the two models, we used a confidence based prediction methodology to get the final class labels for each patient. This combined approach achieved a classification accuracy of 90% on the challenge test set (n = 20). These results showcase the emerging role of deep learning and radiomics in analyzing whole-slide images and MR scans for lesion characterization.

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Journal ArticleDOI
TL;DR: The evaluations of the four deep learning-based image analysis methods presented indicate that carefully constructed deep learning algorithms are able to produce high accuracy in the analysis of biomedical image data and the combination of radiographic with histologic image information improves classification performance.
Abstract: Biomedical imaging Is an important source of information in cancer research. Characterizations of cancer morphology at onset, progression, and in response to treatment provide complementary information to that gleaned from genomics and clinical data. Accurate extraction and classification of both visual and latent image features Is an increasingly complex challenge due to the increased complexity and resolution of biomedical image data. In this paper, we present four deep learning-based image analysis methods from the Computational Precision Medicine (CPM) satellite event of the 21st International Medical Image Computing and Computer Assisted Intervention (MICCAI 2018) conference. One method Is a segmentation method designed to segment nuclei in whole slide tissue images (WSIs) of adult diffuse glioma cases. It achieved a Dice similarity coefficient of 0.868 with the CPM challenge datasets. Three methods are classification methods developed to categorize adult diffuse glioma cases into oligodendroglioma and astrocytoma classes using radiographic and histologic image data. These methods achieved accuracy values of 0.75, 0.80, and 0.90, measured as the ratio of the number of correct classifications to the number of total cases, with the challenge datasets. The evaluations of the four methods indicate that (1) carefully constructed deep learning algorithms are able to produce high accuracy in the analysis of biomedical image data and (2) the combination of radiographic with histologic image information improves classification performance.

28 citations

Journal ArticleDOI

TL;DR: This article summarizes the latest studies of deep learning techniques applied to three different kinds of brain cancer medical images (histology, magnetic resonance, and computed tomography) and highlights current challenges in the field for the broader applicability of DCNN in personalized brain cancer care by focusing on two main applications ofDCNNs.
Abstract: In recent years, improved deep learning techniques have been applied to biomedical image processing for the classification and segmentation of different tumors based on magnetic resonance imaging (MRI) and histopathological imaging (H&E) clinical information. Deep Convolutional Neural Networks (DCNNs) architectures include tens to hundreds of processing layers that can extract multiple levels of features in image-based data, which would be otherwise very difficult and time-consuming to be recognized and extracted by experts for classification of tumors into different tumor types, as well as segmentation of tumor images. This article summarizes the latest studies of deep learning techniques applied to three different kinds of brain cancer medical images (histology, magnetic resonance, and computed tomography) and highlights current challenges in the field for the broader applicability of DCNN in personalized brain cancer care by focusing on two main applications of DCNNs: classification and segmentation of brain cancer tumors images.

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### Cites methods from "A Combined Radio-Histological Appro..."

• ...[50] 2018 C lascation – Astrocytoma – Oligodendroglioma H&E Histology; MR FLAIR, T1, T1C, and T2 images A combined DCNNs-based network * Astrocytoma and Oligodendroglioma classification by using DCNN-based model based on both MR and Histological images N/A N/A Private dataset 50 Accuracy: 0....

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• ...[50] put forward a novel DCCN approach by using both H&E WSIs and MR images to classify low-grade gliomas into categories of Astrocytoma and Oligodendroglioma....

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Posted Content
TL;DR: This work investigates a deep learning method combining whole slide images and magnetic resonance images to classify tumors, which comprises a powerful, generic and modular architecture for whole slide image classification.
Abstract: Cancer is a complex disease that provides various types of information depending on the scale of observation. While most tumor diagnostics are performed by observing histopathological slides, radiology images should yield additional knowledge towards the efficacy of cancer diagnostics. This work investigates a deep learning method combining whole slide images and magnetic resonance images to classify tumors. In particular, our solution comprises a powerful, generic and modular architecture for whole slide image classification. Experiments are prospectively conducted on the 2020 Computational Precision Medicine challenge, in a 3-classes unbalanced classification task. We report cross-validation (resp. validation) balanced-accuracy, kappa and f1 of 0.913, 0.897 and 0.951 (resp. 0.91, 0.90 and 0.94). For research purposes, including reproducibility and direct performance comparisons, our finale submitted models are usable off-the-shelf in a Docker image available at this https URL.

1 citations

Book ChapterDOI

21 Jul 2021
TL;DR: This article proposed MG-Net, a self-supervised representation learning framework that leverages multi-modal context using pseudo-imaging data derived from clinical metagenome sequences.
Abstract: The emergence of novel pathogens and zoonotic diseases like the SARS-CoV-2 have underlined the need for developing novel diagnosis and intervention pipelines that can learn rapidly from small amounts of labeled data. Combined with technological advances in next-generation sequencing, metagenome-based diagnostic tools hold much promise to revolutionize rapid point-of-care diagnosis. However, there are significant challenges in developing such an approach, the chief among which is to learn self-supervised representations that can help detect novel pathogen signatures with very low amounts of labeled data. This is particularly a difficult task given that closely related pathogens can share more than $$90\%$$ of their genome structure. In this work, we address these challenges by proposing MG-Net, a self-supervised representation learning framework that leverages multi-modal context using pseudo-imaging data derived from clinical metagenome sequences. We show that the proposed framework can learn robust representations from unlabeled data that can be used for downstream tasks such as metagenome sequence classification with limited access to labeled data. Extensive experiments show that the learned features outperform current baseline metagenome representations, given only 1000 samples per class.
Book ChapterDOI
03 Sep 2020
TL;DR: In this article, a deep learning method combining whole slide images and magnetic resonance images was proposed to classify tumors in a 3-classes unbalanced classification task, achieving a balanced-accuracy of 0.913, 0.897 and 0.951.
Abstract: Cancer is a complex disease that provides various types of information depending on the scale of observation. While most tumor diagnostics are performed by observing histopathological slides, radiology images should yield additional knowledge towards the efficacy of cancer diagnostics. This work investigates a deep learning method combining whole slide images and magnetic resonance images to classify tumors. In particular, our solution comprises a powerful, generic and modular architecture for whole slide image classification. Experiments are prospectively conducted on the 2020 Computational Precision Medicine challenge, in a 3-classes unbalanced classification task. We report cross-validation (resp. validation) balanced-accuracy, kappa and f1 of 0.913, 0.897 and 0.951 (resp. 0.91, 0.90 and 0.94). For research purposes, including reproducibility and direct performance comparisons, our finale submitted models are usable off-the-shelf in a Docker image available at https://hub.docker.com/repository/docker/marvinler/cpm_2020_marvinler.

##### References
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Proceedings ArticleDOI
21 Jul 2017
TL;DR: DenseNet as mentioned in this paper proposes to connect each layer to every other layer in a feed-forward fashion, which can alleviate the vanishing gradient problem, strengthen feature propagation, encourage feature reuse, and substantially reduce the number of parameters.
Abstract: Recent work has shown that convolutional networks can be substantially deeper, more accurate, and efficient to train if they contain shorter connections between layers close to the input and those close to the output. In this paper, we embrace this observation and introduce the Dense Convolutional Network (DenseNet), which connects each layer to every other layer in a feed-forward fashion. Whereas traditional convolutional networks with L layers have L connections—one between each layer and its subsequent layer—our network has L(L+1)/2 direct connections. For each layer, the feature-maps of all preceding layers are used as inputs, and its own feature-maps are used as inputs into all subsequent layers. DenseNets have several compelling advantages: they alleviate the vanishing-gradient problem, strengthen feature propagation, encourage feature reuse, and substantially reduce the number of parameters. We evaluate our proposed architecture on four highly competitive object recognition benchmark tasks (CIFAR-10, CIFAR-100, SVHN, and ImageNet). DenseNets obtain significant improvements over the state-of-the-art on most of them, whilst requiring less memory and computation to achieve high performance. Code and pre-trained models are available at https://github.com/liuzhuang13/DenseNet.

15,769 citations

Proceedings Article
31 Mar 2010
TL;DR: The objective here is to understand better why standard gradient descent from random initialization is doing so poorly with deep neural networks, to better understand these recent relative successes and help design better algorithms in the future.
Abstract: Whereas before 2006 it appears that deep multilayer neural networks were not successfully trained, since then several algorithms have been shown to successfully train them, with experimental results showing the superiority of deeper vs less deep architectures. All these experimental results were obtained with new initialization or training mechanisms. Our objective here is to understand better why standard gradient descent from random initialization is doing so poorly with deep neural networks, to better understand these recent relative successes and help design better algorithms in the future. We first observe the influence of the non-linear activations functions. We find that the logistic sigmoid activation is unsuited for deep networks with random initialization because of its mean value, which can drive especially the top hidden layer into saturation. Surprisingly, we find that saturated units can move out of saturation by themselves, albeit slowly, and explaining the plateaus sometimes seen when training neural networks. We find that a new non-linearity that saturates less can often be beneficial. Finally, we study how activations and gradients vary across layers and during training, with the idea that training may be more difficult when the singular values of the Jacobian associated with each layer are far from 1. Based on these considerations, we propose a new initialization scheme that brings substantially faster convergence. 1 Deep Neural Networks Deep learning methods aim at learning feature hierarchies with features from higher levels of the hierarchy formed by the composition of lower level features. They include Appearing in Proceedings of the 13 International Conference on Artificial Intelligence and Statistics (AISTATS) 2010, Chia Laguna Resort, Sardinia, Italy. Volume 9 of JMLR: WC Weston et al., 2008). Much attention has recently been devoted to them (see (Bengio, 2009) for a review), because of their theoretical appeal, inspiration from biology and human cognition, and because of empirical success in vision (Ranzato et al., 2007; Larochelle et al., 2007; Vincent et al., 2008) and natural language processing (NLP) (Collobert & Weston, 2008; Mnih & Hinton, 2009). Theoretical results reviewed and discussed by Bengio (2009), suggest that in order to learn the kind of complicated functions that can represent high-level abstractions (e.g. in vision, language, and other AI-level tasks), one may need deep architectures. Most of the recent experimental results with deep architecture are obtained with models that can be turned into deep supervised neural networks, but with initialization or training schemes different from the classical feedforward neural networks (Rumelhart et al., 1986). Why are these new algorithms working so much better than the standard random initialization and gradient-based optimization of a supervised training criterion? Part of the answer may be found in recent analyses of the effect of unsupervised pretraining (Erhan et al., 2009), showing that it acts as a regularizer that initializes the parameters in a “better” basin of attraction of the optimization procedure, corresponding to an apparent local minimum associated with better generalization. But earlier work (Bengio et al., 2007) had shown that even a purely supervised but greedy layer-wise procedure would give better results. So here instead of focusing on what unsupervised pre-training or semi-supervised criteria bring to deep architectures, we focus on analyzing what may be going wrong with good old (but deep) multilayer neural networks. Our analysis is driven by investigative experiments to monitor activations (watching for saturation of hidden units) and gradients, across layers and across training iterations. We also evaluate the effects on these of choices of activation function (with the idea that it might affect saturation) and initialization procedure (since unsupervised pretraining is a particular form of initialization and it has a drastic impact).

9,463 citations

Journal ArticleDOI
TL;DR: The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) as mentioned in this paper was organized in conjunction with the MICCAI 2012 and 2013 conferences, and twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low and high grade glioma patients.
Abstract: In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low- and high-grade glioma patients—manually annotated by up to four raters—and to 65 comparable scans generated using tumor image simulation software Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%–85%), illustrating the difficulty of this task We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource

2,695 citations

Journal ArticleDOI
TL;DR: This work uses a simple statistical analysis to impose one image's color characteristics on another by choosing an appropriate source image and applying its characteristic to another image.
Abstract: We use a simple statistical analysis to impose one image's color characteristics on another. We can achieve color correction by choosing an appropriate source image and apply its characteristic to another image.

2,177 citations

Journal ArticleDOI

TL;DR: An efficient and effective dense training scheme which joins the processing of adjacent image patches into one pass through the network while automatically adapting to the inherent class imbalance present in the data, and improves on the state-of-the‐art for all three applications.
Abstract: This work is supported by the EPSRC First Grant scheme (grant ref no. EP/N023668/1) and partially funded under the 7th Framework Programme by the European Commission (TBIcare: http: //www.tbicare.eu/ ; CENTER-TBI: https://www.center-tbi.eu/). This work was further supported by a Medical Research Council (UK) Program Grant (Acute brain injury: heterogeneity of mechanisms, therapeutic targets and outcome effects [G9439390 ID 65883]), the UK National Institute of Health Research Biomedical Research Centre at Cambridge and Technology Platform funding provided by the UK Department of Health. KK is supported by the Imperial College London PhD Scholarship Programme. VFJN is supported by a Health Foundation/Academy of Medical Sciences Clinician Scientist Fellowship. DKM is supported by an NIHR Senior Investigator Award. We gratefully acknowledge the support of NVIDIA Corporation with the donation of two Titan X GPUs for our research.

2,111 citations