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Register a new userEvaluating the Robustness of Self-Supervised Learning in Medical Imaging
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Added by
Fernando Navarro
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Self-supervision has demonstrated to be an effective learning strategy when training target tasks on small annotated data-sets. While current research focuses on creating novel pretext tasks to learn meaningful and reusable representations for the target task, these efforts obtain marginal performance gains compared to fully-supervised learning. Meanwhile, little attention has been given to study the robustness of networks trained in a self-supervised manner. In this work, we demonstrate that networks trained via self-supervised learning have superior robustness and generalizability compared to fully-supervised learning in the context of medical imaging. Our experiments on pneumonia detection in X-rays and multi-organ segmentation in CT yield consistent results exposing the hidden benefits of self-supervision for learning robust feature representations.
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Transfer learning is a standard technique to improve performance on tasks with limited data. However, for medical imaging, the value of transfer learning is less clear. This is likely due to the large domain mismatch between the usual natural-image pre-training (e.g. ImageNet) and medical images. However, recent advances in transfer learning have shown substantial improvements from scale. We investigate whether modern methods can change the fortune of transfer learning for medical imaging. For this, we study the class of large-scale pre-trained networks presented by Kolesnikov et al. on three diverse imaging tasks: chest radiography, mammography, and dermatology. We study both transfer performance and critical properties for the deployment in the medical domain, including: out-of-distribution generalization, data-efficiency, sub-group fairness, and uncertainty estimation. Interestingly, we find that for some of these properties transfer from natural to medical images is indeed extremely effective, but only when performed at sufficient scale.
In medical image analysis, the cost of acquiring high-quality data and their annotation by experts is a barrier in many medical applications. Most of the techniques used are based on supervised learning framework and need a large amount of annotated data to achieve satisfactory performance. As an alternative, in this paper, we propose a self-supervised learning approach to learn the spatial anatomical representations from the frames of magnetic resonance (MR) video clips for the diagnosis of knee medical conditions. The pretext model learns meaningful spatial context-invariant representations. The downstream task in our paper is a class imbalanced multi-label classification. Different experiments show that the features learnt by the pretext model provide explainable performance in the downstream task. Moreover, the efficiency and reliability of the proposed pretext model in learning representations of minority classes without applying any strategy towards imbalance in the dataset can be seen from the results. To the best of our knowledge, this work is the first work of its kind in showing the effectiveness and reliability of self-supervised learning algorithms in class imbalanced multi-label classification tasks on MR video. The code for evaluation of the proposed work is available at https://github.com/sadimanna/sslm
Deep learning has demonstrated significant improvements in medical image segmentation using a sufficiently large amount of training data with manual labels. Acquiring well-representative labels requires expert knowledge and exhaustive labors. In this paper, we aim to boost the performance of semi-supervised learning for medical image segmentation with limited labels using a self-ensembling contrastive learning technique. To this end, we propose to train an encoder-decoder network at image-level with small amounts of labeled images, and more importantly, we learn latent representations directly at feature-level by imposing contrastive loss on unlabeled images. This method strengthens intra-class compactness and inter-class separability, so as to get a better pixel classifier. Moreover, we devise a student encoder for online learning and an exponential moving average version of it, called teacher encoder, to improve the performance iteratively in a self-ensembling manner. To construct contrastive samples with unlabeled images, two sampling strategies that exploit structure similarity across medical images and utilize pseudo-labels for construction, termed region-aware and anatomical-aware contrastive sampling, are investigated. We conduct extensive experiments on an MRI and a CT segmentation dataset and demonstrate that in a limited label setting, the proposed method achieves state-of-the-art performance. Moreover, the anatomical-aware strategy that prepares contrastive samples on-the-fly using pseudo-labels realizes better contrastive regularization on feature representations.
Image denoising is of great importance for medical imaging system, since it can improve image quality for disease diagnosis and downstream image analyses. In a variety of applications, dynamic imaging techniques are utilized to capture the time-varying features of the subject, where multiple images are acquired for the same subject at different time points. Although signal-to-noise ratio of each time frame is usually limited by the short acquisition time, the correlation among different time frames can be exploited to improve denoising results with shared information across time frames. With the success of neural networks in computer vision, supervised deep learning methods show prominent performance in single-image denoising, which rely on large datasets with clean-vs-noisy image pairs. Recently, several self-supervised deep denoising models have been proposed, achieving promising results without needing the pairwise ground truth of clean images. In the field of multi-image denoising, however, very few works have been done on extracting correlated information from multiple slices for denoising using self-supervised deep learning methods. In this work, we propose Deformed2Self, an end-to-end self-supervised deep learning framework for dynamic imaging denoising. It combines single-image and multi-image denoising to improve image quality and use a spatial transformer network to model motion between different slices. Further, it only requires a single noisy image with a few auxiliary observations at different time frames for training and inference. Evaluations on phantom and in vivo data with different noise statistics show that our method has comparable performance to other state-of-the-art unsupervised or self-supervised denoising methods and outperforms under high noise levels.
It has been widely recognized that the success of deep learning in image segmentation relies overwhelmingly on a myriad amount of densely annotated training data, which, however, are difficult to obtain due to the tremendous labor and expertise required, particularly for annotating 3D medical images. Although self-supervised learning (SSL) has shown great potential to address this issue, most SSL approaches focus only on image-level global consistency, but ignore the local consistency which plays a pivotal role in capturing structural information for dense prediction tasks such as segmentation. In this paper, we propose a PriorGuided Local (PGL) self-supervised model that learns the region-wise local consistency in the latent feature space. Specifically, we use the spatial transformations, which produce different augmented views of the same image, as a prior to deduce the location relation between two views, which is then used to align the feature maps of the same local region but being extracted on two views. Next, we construct a local consistency loss to minimize the voxel-wise discrepancy between the aligned feature maps. Thus, our PGL model learns the distinctive representations of local regions, and hence is able to retain structural information. This ability is conducive to downstream segmentation tasks. We conducted an extensive evaluation on four public computerized tomography (CT) datasets that cover 11 kinds of major human organs and two tumors. The results indicate that using pre-trained PGL model to initialize a downstream network leads to a substantial performance improvement over both random initialization and the initialization with global consistency-based models. Code and pre-trained weights will be made available at: https://git.io/PGL.
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