Unets have become the standard method for semantic segmentation of medical images, along with fully convolutional networks (FCN). Unet++ was introduced as a variant of Unet, in order to solve some of the problems facing Unet and FCNs. Unet++ provided networks with an ensemble of variable depth Unets, hence eliminating the need for professionals estimating the best suitable depth for a task. While Unet and all its variants, including Unet++ aimed at providing networks that were able to train well without requiring large quantities of annotated data, none of them attempted to eliminate the need for pixel-wise annotated data altogether. Obtaining such data for each disease to be diagnosed comes at a high cost. Hence such data is scarce. In this paper we use contrastive learning to train Unet++ for semantic segmentation of medical images using medical images from various sources including magnetic resonance imaging (MRI) and computed tomography (CT), without the need for pixel-wise annotations. Here we describe the architecture of the proposed model and the training method used. This is still a work in progress and so we abstain from including results in this paper. The results and the trained model would be made available upon publication or in subsequent versions of this paper on arxiv.
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Automatic Target Recognition (ATR) algorithms classify a given Synthetic Aperture Radar (SAR) image into one of the known target classes using a set of training images available for each class. Recently, learning methods have shown to achieve state-of-the-art classification accuracy if abundant training data is available, sampled uniformly over the classes, and their poses. In this paper, we consider the task of ATR with a limited set of training images. We propose a data augmentation approach to incorporate domain knowledge and improve the generalization power of a data-intensive learning algorithm, such as a Convolutional neural network (CNN). The proposed data augmentation method employs a limited persistence sparse modeling approach, capitalizing on commonly observed characteristics of wide-angle synthetic aperture radar (SAR) imagery. Specifically, we exploit the sparsity of the scattering centers in the spatial domain and the smoothly-varying structure of the scattering coefficients in the azimuthal domain to solve the ill-posed problem of over-parametrized model fitting. Using this estimated model, we synthesize new images at poses and sub-pixel translations not available in the given data to augment CNN's training data. The experimental results show that for the training data starved region, the proposed method provides a significant gain in the resulting ATR algorithm's generalization performance.
Object detectors trained with weak annotations are affordable alternatives to fully-supervised counterparts. However, there is still a significant performance gap between them. We propose to narrow this gap by fine-tuning a base pre-trained weakly-supervised detector with a few fully-annotated samples automatically selected from the training set using ``box-in-box'' (BiB), a novel active learning strategy designed specifically to address the well-documented failure modes of weakly-supervised detectors. Experiments on the VOC07 and COCO benchmarks show that BiB outperforms other active learning techniques and significantly improves the base weakly-supervised detector's performance with only a few fully-annotated images per class. BiB reaches 97% of the performance of fully-supervised Fast RCNN with only 10% of fully-annotated images on VOC07. On COCO, using on average 10 fully-annotated images per class, or equivalently 1% of the training set, BiB also reduces the performance gap (in AP) between the weakly-supervised detector and the fully-supervised Fast RCNN by over 70%, showing a good trade-off between performance and data efficiency. Our code is publicly available at //github.com/huyvvo/BiB.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
Applying artificial intelligence techniques in medical imaging is one of the most promising areas in medicine. However, most of the recent success in this area highly relies on large amounts of carefully annotated data, whereas annotating medical images is a costly process. In this paper, we propose a novel method, called FocalMix, which, to the best of our knowledge, is the first to leverage recent advances in semi-supervised learning (SSL) for 3D medical image detection. We conducted extensive experiments on two widely used datasets for lung nodule detection, LUNA16 and NLST. Results show that our proposed SSL methods can achieve a substantial improvement of up to 17.3% over state-of-the-art supervised learning approaches with 400 unlabeled CT scans.
Image segmentation is a key topic in image processing and computer vision with applications such as scene understanding, medical image analysis, robotic perception, video surveillance, augmented reality, and image compression, among many others. Various algorithms for image segmentation have been developed in the literature. Recently, due to the success of deep learning models in a wide range of vision applications, there has been a substantial amount of works aimed at developing image segmentation approaches using deep learning models. In this survey, we provide a comprehensive review of the literature at the time of this writing, covering a broad spectrum of pioneering works for semantic and instance-level segmentation, including fully convolutional pixel-labeling networks, encoder-decoder architectures, multi-scale and pyramid based approaches, recurrent networks, visual attention models, and generative models in adversarial settings. We investigate the similarity, strengths and challenges of these deep learning models, examine the most widely used datasets, report performances, and discuss promising future research directions in this area.
Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research.
In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-S{\o}rensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.
Deep Convolutional Neural Networks have pushed the state-of-the art for semantic segmentation provided that a large amount of images together with pixel-wise annotations is available. Data collection is expensive and a solution to alleviate it is to use transfer learning. This reduces the amount of annotated data required for the network training but it does not get rid of this heavy processing step. We propose a method of transfer learning without annotations on the target task for datasets with redundant content and distinct pixel distributions. Our method takes advantage of the approximate content alignment of the images between two datasets when the approximation error prevents the reuse of annotation from one dataset to another. Given the annotations for only one dataset, we train a first network in a supervised manner. This network autonomously learns to generate deep data representations relevant to the semantic segmentation. Then the images in the new dataset, we train a new network to generate a deep data representation that matches the one from the first network on the previous dataset. The training consists in a regression between feature maps and does not require any annotations on the new dataset. We show that this method reaches performances similar to a classic transfer learning on the PASCAL VOC dataset with synthetic transformations.
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