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Register a new userQuantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathology
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Added by
David Tellez
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Stain variation is a phenomenon observed when distinct pathology laboratories stain tissue slides that exhibit similar but not identical color appearance. Due to this color shift between laboratories, convolutional neural networks (CNNs) trained with images from one lab often underperform on unseen images from the other lab. Several techniques have been proposed to reduce the generalization error, mainly grouped into two categories: stain color augmentation and stain color normalization. The former simulates a wide variety of realistic stain variations during training, producing stain-invariant CNNs. The latter aims to match training and test color distributions in order to reduce stain variation. For the first time, we compared some of these techniques and quantified their effect on CNN classification performance using a heterogeneous dataset of hematoxylin and eosin histopathology images from 4 organs and 9 pathology laboratories. Additionally, we propose a novel unsupervised method to perform stain color normalization using a neural network. Based on our experimental results, we provide practical guidelines on how to use stain color augmentation and stain color normalization in future computational pathology applications.
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Explainability of deep learning methods is imperative to facilitate their clinical adoption in digital pathology. However, popular deep learning methods and explainability techniques (explainers) based on pixel-wise processing disregard biological entities notion, thus complicating comprehension by pathologists. In this work, we address this by adopting biological entity-based graph processing and graph explainers enabling explanations accessible to pathologists. In this context, a major challenge becomes to discern meaningful explainers, particularly in a standardized and quantifiable fashion. To this end, we propose herein a set of novel quantitative metrics based on statistics of class separability using pathologically measurable concepts to characterize graph explainers. We employ the proposed metrics to evaluate three types of graph explainers, namely the layer-wise relevance propagation, gradient-based saliency, and graph pruning approaches, to explain Cell-Graph representations for Breast Cancer Subtyping. The proposed metrics are also applicable in other domains by using domain-specific intuitive concepts. We validate the qualitative and quantitative findings on the BRACS dataset, a large cohort of breast cancer RoIs, by expert pathologists.
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Recently, cyber-attacks have been extensively seen due to the everlasting increase of malware in the cyber world. These attacks cause irreversible damage not only to end-users but also to corporate computer systems. Ransomware attacks such as WannaCry and Petya specifically targets to make critical infrastructures such as airports and rendered operational processes inoperable. Hence, it has attracted increasing attention in terms of volume, versatility, and intricacy. The most important feature of this type of malware is that they change shape as they propagate from one computer to another. Since standard signature-based detection software fails to identify this type of malware because they have different characteristics on each contaminated computer. This paper aims at providing an image augmentation enhanced deep convolutional neural network (CNN) models for the detection of malware families in a metamorphic malware environment. The main contributions of the papers model structure consist of three components, including image generation from malware samples, image augmentation, and the last one is classifying the malware families by using a convolutional neural network model. In the first component, the collected malware samples are converted binary representation to 3-channel images using windowing technique. The second component of the system create the augmented version of the images, and the last component builds a classification model. In this study, five different deep convolutional neural network model for malware family detection is used.
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