A deep learning framework for quality assessment and restoration in video endoscopy

Endoscopy is a routine imaging technique used for both diagnosis and minimally invasive surgical treatment. Artifacts such as motion blur, bubbles, specular reflections, floating objects and pixel saturation impede the visual interpretation and the automated analysis of endoscopy videos. Given the widespread use of endoscopy in different clinical applications, we contend that the robust and reliable identification of such artifacts and the automated restoration of corrupted video frames is a fundamental medical imaging problem. Existing state-of-the-art methods only deal with the detection and restoration of selected artifacts. However, typically endoscopy videos contain numerous artifacts which motivates to establish a comprehensive solution. We propose a fully automatic framework that can: 1) detect and classify six different primary artifacts, 2) provide a quality score for each frame and 3) restore mildly corrupted frames. To detect different artifacts our framework exploits fast multi-scale, single stage convolutional neural network detector. We introduce a quality metric to assess frame quality and predict image restoration success. Generative adversarial networks with carefully chosen regularization are finally used to restore corrupted frames. Our detector yields the highest mean average precision (mAP at 5% threshold) of 49.0 and the lowest computational time of 88 ms allowing for accurate real-time processing. Our restoration models for blind deblurring, saturation correction and inpainting demonstrate significant improvements over previous methods. On a set of 10 test videos we show that our approach preserves an average of 68.7% which is 25% more frames than that retained from the raw videos.Comment: 14 page

Novel Deep Learning Models for Medical Imaging Analysis

abstract: Deep learning is a sub-field of machine learning in which models are developed to imitate the workings of the human brain in processing data and creating patterns for decision making. This dissertation is focused on developing deep learning models for medical imaging analysis of different modalities for different tasks including detection, segmentation and classification. Imaging modalities including digital mammography (DM), magnetic resonance imaging (MRI), positron emission tomography (PET) and computed tomography (CT) are studied in the dissertation for various medical applications. The first phase of the research is to develop a novel shallow-deep convolutional neural network (SD-CNN) model for improved breast cancer diagnosis. This model takes one type of medical image as input and synthesizes different modalities for additional feature sources; both original image and synthetic image are used for feature generation. This proposed architecture is validated in the application of breast cancer diagnosis and proved to be outperforming the competing models. Motivated by the success from the first phase, the second phase focuses on improving medical imaging synthesis performance with advanced deep learning architecture. A new architecture named deep residual inception encoder-decoder network (RIED-Net) is proposed. RIED-Net has the advantages of preserving pixel-level information and cross-modality feature transferring. The applicability of RIED-Net is validated in breast cancer diagnosis and Alzheimer’s disease (AD) staging. Recognizing medical imaging research often has multiples inter-related tasks, namely, detection, segmentation and classification, my third phase of the research is to develop a multi-task deep learning model. Specifically, a feature transfer enabled multi-task deep learning model (FT-MTL-Net) is proposed to transfer high-resolution features from segmentation task to low-resolution feature-based classification task. The application of FT-MTL-Net on breast cancer detection, segmentation and classification using DM images is studied. As a continuing effort on exploring the transfer learning in deep models for medical application, the last phase is to develop a deep learning model for both feature transfer and knowledge from pre-training age prediction task to new domain of Mild cognitive impairment (MCI) to AD conversion prediction task. It is validated in the application of predicting MCI patients’ conversion to AD with 3D MRI images.Dissertation/ThesisDoctoral Dissertation Industrial Engineering 201

Computer-aided diagnosis system for bone fracture detection using machine learning algorithms

Diagnostic imaging technology has revolutionized the healthcare industry by allowing more accurate and earlier diagnosis of diseases. This technology reduces the need for invasive procedures such as surgery and enhances the quality of patient care. Several machine learning algorithms like SVM, K-mean clustering and UNET have been demonstrated to be capable of solving classification, detection, and segmentation problems in medical imaging, as well as being used for super-resolution techniques. The purpose of this thesis is to examine machine learning and image processing methods for four key challenges in medical image analysis. The first one is the segmentation of medical images. The second challenge involves implementing super-resolution techniques for medical images. Third, using image processing methods in order to diagnose the abnormalities. The fourth contribution is to enrich the image information by mapping of medical images between different modalities using deep neural models. In this research, all contributions aim at developing an end-to-end model that can detect fractures automatically or be used as a clinical assistant to reduce errors. As the first contribution, the thesis presents a multi-stage novel approach for bone segmentation in X-ray images using faster region-based convolutional neural network (R-CNN) and distance regularized level set evolution (DRLSE) algorithms. A hybrid model utilizing deep neural network (DNN) and image processing techniques are proposed to segment the bones in two stages. Our model is more robust to the changes in X-ray images, as well as applicable to bones that are misplaced. Additionally, we have used transfer learning to reduce the amount of time and effort required to collect and label the data. As the second contribution, DNN models are used to enhance the resolution of medical images. CNN and generative adversarial network have been used as super-resolution techniques to achieve high-resolution medical images. The analysis includes subjective and objective evaluations of different models on regions with or without fractures to compare them with our model. The third contribution involves applying different image analysis methods to X-ray images in order to detect fractures with the minimum amount of human intervention. By using entropy and intensity, we have also attempted to identify regions of interest that have a higher probability of having fractures. We also evaluate the effect of super-resolution technique on the saliency map with and without fractures. Lastly, we present image-to-image mapping by using variational autoencoders and generative adversarial networks to reduce the cost of diagnosis and medical images retrievals. We have attempted to map X-ray images to MRIs in this section in order to fuse the high diagnostic information existing in MRIs, for enhancing the matched X-ray images

Deep learning in diabetic foot ulcers detection: A comprehensive evaluation

There has been a substantial amount of research involving computer methods and technology for the detection and recognition of diabetic foot ulcers (DFUs), but there is a lack of systematic comparisons of state-of-the-art deep learning object detection frameworks applied to this problem. DFUC2020 provided participants with a comprehensive dataset consisting of 2,000 images for training and 2,000 images for testing. This paper summarizes the results of DFUC2020 by comparing the deep learning-based algorithms proposed by the winning teams: Faster R–CNN, three variants of Faster R–CNN and an ensemble method; YOLOv3; YOLOv5; EfficientDet; and a new Cascade Attention Network. For each deep learning method, we provide a detailed description of model architecture, parameter settings for training and additional stages including pre-processing, data augmentation and post-processing. We provide a comprehensive evaluation for each method. All the methods required a data augmentation stage to increase the number of images available for training and a post-processing stage to remove false positives. The best performance was obtained from Deformable Convolution, a variant of Faster R–CNN, with a mean average precision (mAP) of 0.6940 and an F1-Score of 0.7434. Finally, we demonstrate that the ensemble method based on different deep learning methods can enhance the F1-Score but not the mAP

Toward robust deep neural networks

Dans cette thèse, notre objectif est de développer des modèles d’apprentissage robustes et fiables mais précis, en particulier les Convolutional Neural Network (CNN), en présence des exemples anomalies, comme des exemples adversaires et d’échantillons hors distribution –Out-of-Distribution (OOD). Comme la première contribution, nous proposons d’estimer la confiance calibrée pour les exemples adversaires en encourageant la diversité dans un ensemble des CNNs. À cette fin, nous concevons un ensemble de spécialistes diversifiés avec un mécanisme de vote simple et efficace en termes de calcul pour prédire les exemples adversaires avec une faible confiance tout en maintenant la confiance prédicative des échantillons propres élevée. En présence de désaccord dans notre ensemble, nous prouvons qu’une borne supérieure de 0:5 + _0 peut être établie pour la confiance, conduisant à un seuil de détection global fixe de tau = 0; 5. Nous justifions analytiquement le rôle de la diversité dans notre ensemble sur l’atténuation du risque des exemples adversaires à la fois en boîte noire et en boîte blanche. Enfin, nous évaluons empiriquement la robustesse de notre ensemble aux attaques de la boîte noire et de la boîte blanche sur plusieurs données standards. La deuxième contribution vise à aborder la détection d’échantillons OOD à travers un modèle de bout en bout entraîné sur un ensemble OOD approprié. À cette fin, nous abordons la question centrale suivante : comment différencier des différents ensembles de données OOD disponibles par rapport à une tâche de distribution donnée pour sélectionner la plus appropriée, ce qui induit à son tour un modèle calibré avec un taux de détection des ensembles inaperçus de données OOD? Pour répondre à cette question, nous proposons de différencier les ensembles OOD par leur niveau de "protection" des sub-manifolds. Pour mesurer le niveau de protection, nous concevons ensuite trois nouvelles mesures efficaces en termes de calcul à l’aide d’un CNN vanille préformé. Dans une vaste série d’expériences sur les tâches de classification d’image et d’audio, nous démontrons empiriquement la capacité d’un CNN augmenté (A-CNN) et d’un CNN explicitement calibré pour détecter une portion significativement plus grande des exemples OOD. Fait intéressant, nous observons également qu’un tel A-CNN (nommé A-CNN) peut également détecter les adversaires exemples FGS en boîte noire avec des perturbations significatives. En tant que troisième contribution, nous étudions de plus près de la capacité de l’A-CNN sur la détection de types plus larges d’adversaires boîte noire (pas seulement ceux de type FGS). Pour augmenter la capacité d’A-CNN à détecter un plus grand nombre d’adversaires,nous augmentons l’ensemble d’entraînement OOD avec des échantillons interpolés inter-classes. Ensuite, nous démontrons que l’A-CNN, entraîné sur tous ces données, a un taux de détection cohérent sur tous les types des adversaires exemples invisibles. Alors que la entraînement d’un A-CNN sur des adversaires PGD ne conduit pas à un taux de détection stable sur tous les types d’adversaires, en particulier les types inaperçus. Nous évaluons également visuellement l’espace des fonctionnalités et les limites de décision dans l’espace d’entrée d’un CNN vanille et de son homologue augmenté en présence d’adversaires et de ceux qui sont propres. Par un A-CNN correctement formé, nous visons à faire un pas vers un modèle d’apprentissage debout en bout unifié et fiable avec de faibles taux de risque sur les échantillons propres et les échantillons inhabituels, par exemple, les échantillons adversaires et OOD. La dernière contribution est de présenter une application de A-CNN pour l’entraînement d’un détecteur d’objet robuste sur un ensemble de données partiellement étiquetées, en particulier un ensemble de données fusionné. La fusion de divers ensembles de données provenant de contextes similaires mais avec différents ensembles d’objets d’intérêt (OoI) est un moyen peu coûteux de créer un ensemble de données à grande échelle qui couvre un plus large spectre d’OoI. De plus, la fusion d’ensembles de données permet de réaliser un détecteur d’objet unifié, au lieu d’en avoir plusieurs séparés, ce qui entraîne une réduction des coûts de calcul et de temps. Cependant, la fusion d’ensembles de données, en particulier à partir d’un contexte similaire, entraîne de nombreuses instances d’étiquetées manquantes. Dans le but d’entraîner un détecteur d’objet robuste intégré sur un ensemble de données partiellement étiquetées mais à grande échelle, nous proposons un cadre d’entraînement auto-supervisé pour surmonter le problème des instances d’étiquettes manquantes dans les ensembles des données fusionnés. Notre cadre est évalué sur un ensemble de données fusionné avec un taux élevé d’étiquettes manquantes. Les résultats empiriques confirment la viabilité de nos pseudo-étiquettes générées pour améliorer les performances de YOLO, en tant que détecteur d’objet à la pointe de la technologie.In this thesis, our goal is to develop robust and reliable yet accurate learning models, particularly Convolutional Neural Networks (CNNs), in the presence of adversarial examples and Out-of-Distribution (OOD) samples. As the first contribution, we propose to predict adversarial instances with high uncertainty through encouraging diversity in an ensemble of CNNs. To this end, we devise an ensemble of diverse specialists along with a simple and computationally efficient voting mechanism to predict the adversarial examples with low confidence while keeping the predictive confidence of the clean samples high. In the presence of high entropy in our ensemble, we prove that the predictive confidence can be upper-bounded, leading to have a globally fixed threshold over the predictive confidence for identifying adversaries. We analytically justify the role of diversity in our ensemble on mitigating the risk of both black-box and white-box adversarial examples. Finally, we empirically assess the robustness of our ensemble to the black-box and the white-box attacks on several benchmark datasets.The second contribution aims to address the detection of OOD samples through an end-to-end model trained on an appropriate OOD set. To this end, we address the following central question: how to differentiate many available OOD sets w.r.t. a given in distribution task to select the most appropriate one, which in turn induces a model with a high detection rate of unseen OOD sets? To answer this question, we hypothesize that the “protection” level of in-distribution sub-manifolds by each OOD set can be a good possible property to differentiate OOD sets. To measure the protection level, we then design three novel, simple, and cost-effective metrics using a pre-trained vanilla CNN. In an extensive series of experiments on image and audio classification tasks, we empirically demonstrate the abilityof an Augmented-CNN (A-CNN) and an explicitly-calibrated CNN for detecting a significantly larger portion of unseen OOD samples, if they are trained on the most protective OOD set. Interestingly, we also observe that the A-CNN trained on the most protective OOD set (calledA-CNN) can also detect the black-box Fast Gradient Sign (FGS) adversarial examples. As the third contribution, we investigate more closely the capacity of the A-CNN on the detection of wider types of black-box adversaries. To increase the capability of A-CNN to detect a larger number of adversaries, we augment its OOD training set with some inter-class interpolated samples. Then, we demonstrate that the A-CNN trained on the most protective OOD set along with the interpolated samples has a consistent detection rate on all types of unseen adversarial examples. Where as training an A-CNN on Projected Gradient Descent (PGD) adversaries does not lead to a stable detection rate on all types of adversaries, particularly the unseen types. We also visually assess the feature space and the decision boundaries in the input space of a vanilla CNN and its augmented counterpart in the presence of adversaries and the clean ones. By a properly trained A-CNN, we aim to take a step toward a unified and reliable end-to-end learning model with small risk rates on both clean samples and the unusual ones, e.g. adversarial and OOD samples.The last contribution is to show a use-case of A-CNN for training a robust object detector on a partially-labeled dataset, particularly a merged dataset. Merging various datasets from similar contexts but with different sets of Object of Interest (OoI) is an inexpensive way to craft a large-scale dataset which covers a larger spectrum of OoIs. Moreover, merging datasets allows achieving a unified object detector, instead of having several separate ones, resultingin the reduction of computational and time costs. However, merging datasets, especially from a similar context, causes many missing-label instances. With the goal of training an integrated robust object detector on a partially-labeled but large-scale dataset, we propose a self-supervised training framework to overcome the issue of missing-label instances in the merged datasets. Our framework is evaluated on a merged dataset with a high missing-label rate. The empirical results confirm the viability of our generated pseudo-labels to enhance the performance of YOLO, as the current (to date) state-of-the-art object detector