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Register a new userA Comprehensive Study of Data Augmentation Strategies for Prostate Cancer Detection in Diffusion-weighted MRI using Convolutional Neural Networks
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Data augmentation refers to a group of techniques whose goal is to battle limited amount of available data to improve model generalization and push sample distribution toward the true distribution. While different augmentation strategies and their combinations have been investigated for various computer vision tasks in the context of deep learning, a specific work in the domain of medical imaging is rare and to the best of our knowledge, there has been no dedicated work on exploring the effects of various augmentation methods on the performance of deep learning models in prostate cancer detection. In this work, we have statically applied five most frequently used augmentation techniques (random rotation, horizontal flip, vertical flip, random crop, and translation) to prostate Diffusion-weighted Magnetic Resonance Imaging training dataset of 217 patients separately and evaluated the effect of each method on the accuracy of prostate cancer detection. The augmentation algorithms were applied independently to each data channel and a shallow as well as a deep Convolutional Neural Network (CNN) were trained on the five augmented sets separately. We used Area Under Receiver Operating Characteristic (ROC) curve (AUC) to evaluate the performance of the trained CNNs on a separate test set of 95 patients, using a validation set of 102 patients for finetuning. The shallow network outperformed the deep network with the best 2D slice-based AUC of 0.85 obtained by the rotation method.
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Prostate cancer is one of the most common forms of cancer and the third leading cause of cancer death in North America. As an integrated part of computer-aided detection (CAD) tools, diffusion-weighted magnetic resonance imaging (DWI) has been intensively studied for accurate detection of prostate cancer. With deep convolutional neural networks (CNNs) significant success in computer vision tasks such as object detection and segmentation, different CNNs architectures are increasingly investigated in medical imaging research community as promising solutions for designing more accurate CAD tools for cancer detection. In this work, we developed and implemented an automated CNNs-based pipeline for detection of clinically significant prostate cancer (PCa) for a given axial DWI image and for each patient. DWI images of 427 patients were used as the dataset, which contained 175 patients with PCa and 252 healthy patients. To measure the performance of the proposed pipeline, a test set of 108 (out of 427) patients were set aside and not used in the training phase. The proposed pipeline achieved area under the receiver operating characteristic curve (AUC) of 0.87 (95% Confidence Interval (CI): 0.84-0.90) and 0.84 (95% CI: 0.76-0.91) at slice level and patient level, respectively.
Prediction of Overall Survival (OS) of brain cancer patients from multi-modal MRI is a challenging field of research. Most of the existing literature on survival prediction is based on Radiomic features, which does not consider either non-biological factors or the functional neurological status of the patient(s). Besides, the selection of an appropriate cut-off for survival and the presence of censored data create further problems. Application of deep learning models for OS prediction is also limited due to the lack of large annotated publicly available datasets. In this scenario we analyse the potential of two novel neuroimaging feature families, extracted from brain parcellation atlases and spatial habitats, along with classical radiomic and geometric features; to study their combined predictive power for analysing overall survival. A cross validation strategy with grid search is proposed to simultaneously select and evaluate the most predictive feature subset based on its predictive power. A Cox Proportional Hazard (CoxPH) model is employed for univariate feature selection, followed by the prediction of patient-specific survival functions by three multivariate parsimonious models viz. Coxnet, Random survival forests (RSF) and Survival SVM (SSVM). The brain cancer MRI data used for this research was taken from two open-access collections TCGA-GBM and TCGA-LGG available from The Cancer Imaging Archive (TCIA). Corresponding survival data for each patient was downloaded from The Cancer Genome Atlas (TCGA). A high cross validation $C-index$ score of $0.82pm.10$ was achieved using RSF with the best $24$ selected features. Age was found to be the most important biological predictor. There were $9$, $6$, $6$ and $2$ features selected from the parcellation, habitat, radiomic and region-based feature groups respectively.
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.
The segmentation of prostate whole gland and transition zone in Diffusion Weighted MRI (DWI) are the first step in designing computer-aided detection algorithms for prostate cancer. However, variations in MRI acquisition parameters and scanner manufacturing result in different appearances of prostate tissue in the images. Convolutional neural networks (CNNs) which have shown to be successful in various medical image analysis tasks including segmentation are typically sensitive to the variations in imaging parameters. This sensitivity leads to poor segmentation performance of CNNs trained on a source cohort and tested on a target cohort from a different scanner and hence, it limits the applicability of CNNs for cross-cohort training and testing. Contouring prostate whole gland and transition zone in DWI images are time-consuming and expensive. Thus, it is important to enable CNNs pretrained on images of source domain, to segment images of target domain with minimum requirement for manual segmentation of images from the target domain. In this work, we propose a transfer learning method based on a modified U-net architecture and loss function, for segmentation of prostate whole gland and transition zone in DWIs using a CNN pretrained on a source dataset and tested on the target dataset. We explore the effect of the size of subset of target dataset used for fine-tuning the pre-trained CNN on the overall segmentation accuracy. Our results show that with a fine-tuning data as few as 30 patients from the target domain, the proposed transfer learning-based algorithm can reach dice score coefficient of 0.80 for both prostate whole gland and transition zone segmentation. Using a fine-tuning data of 115 patients from the target domain, dice score coefficient of 0.85 and 0.84 are achieved for segmentation of whole gland and transition zone, respectively, in the target domain.
Acute Lymphoblastic Leukemia (ALL) is a blood cell cancer characterized by numerous immature lymphocytes. Even though automation in ALL prognosis is an essential aspect of cancer diagnosis, it is challenging due to the morphological correlation between malignant and normal cells. The traditional ALL classification strategy demands experienced pathologists to carefully read the cell images, which is arduous, time-consuming, and often suffers inter-observer variations. This article has automated the ALL detection task from microscopic cell images, employing deep Convolutional Neural Networks (CNNs). We explore the weighted ensemble of different deep CNNs to recommend a better ALL cell classifier. The weights for the ensemble candidate models are estimated from their corresponding metrics, such as accuracy, F1-score, AUC, and kappa values. Various data augmentations and pre-processing are incorporated for achieving a better generalization of the network. We utilize the publicly available C-NMC-2019 ALL dataset to conduct all the comprehensive experiments. Our proposed weighted ensemble model, using the kappa values of the ensemble candidates as their weights, has outputted a weighted F1-score of 88.6 %, a balanced accuracy of 86.2 %, and an AUC of 0.941 in the preliminary test set. The qualitative results displaying the gradient class activation maps confirm that the introduced model has a concentrated learned region. In contrast, the ensemble candidate models, such as Xception, VGG-16, DenseNet-121, MobileNet, and InceptionResNet-V2, separately produce coarse and scatter learned areas for most example cases. Since the proposed kappa value-based weighted ensemble yields a better result for the aimed task in this article, it can experiment in other domains of medical diagnostic applications.
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