Self-supervised pretraining followed by supervised fine-tuning has seen success in image recognition, especially when labeled examples are scarce, but has received limited attention in medical image analysis. This paper studies the effectiveness of self-supervised learning as a pretraining strategy for medical image classification. We conduct experiments on two distinct tasks: dermatology skin condition classification from digital camera images and multi-label chest X-ray classification, and demonstrate that self-supervised learning on ImageNet, followed by additional self-supervised learning on unlabeled domain-specific medical images significantly improves the accuracy of medical image classifiers. We introduce a novel Multi-Instance Contrastive Learning (MICLe) method that uses multiple images of the underlying pathology per patient case, when available, to construct more informative positive pairs for self-supervised learning. Combining our contributions, we achieve an improvement of 6.7% in top-1 accuracy and an improvement of 1.1% in mean AUC on dermatology and chest X-ray classification respectively, outperforming strong supervised baselines pretrained on ImageNet. In addition, we show that big self-supervised models are robust to distribution shift and can learn efficiently with a small number of labeled medical images.
Machine learning models in health care are often deployed in settings where it is important to protect patient privacy. In such settings, methods for differentially private (DP) learning provide a general-purpose approach to learn models with privacy guarantees. Modern methods for DP learning ensure privacy through mechanisms that censor information judged as too unique. The resulting privacy-preserving models, therefore, neglect information from the tails of a data distribution, resulting in a loss of accuracy that can disproportionately affect small groups. In this paper, we study the effects of DP learning in health care. We use state-of-the-art methods for DP learning to train privacy-preserving models in clinical prediction tasks, including x-ray classification of images and mortality prediction in time series data. We use these models to perform a comprehensive empirical investigation of the tradeoffs between privacy, utility, robustness to dataset shift, and fairness. Our results highlight lesser-known limitations of methods for DP learning in health care, models that exhibit steep tradeoffs between privacy and utility, and models whose predictions are disproportionately influenced by large demographic groups in the training data. We discuss the costs and benefits of differentially private learning in health care.
Modern deep learning systems for medical image classification have demonstrated exceptional capabilities for distinguishing between image based medical categories. However, they are severely hindered by their ina-bility to explain the reasoning behind their decision making. This is partly due to the uninterpretable continuous latent representations of neural net-works. Emergent languages (EL) have recently been shown to enhance the capabilities of neural networks by equipping them with symbolic represen-tations in the framework of referential games. Symbolic representations are one of the cornerstones of highly explainable good old fashioned AI (GOFAI) systems. In this work, we demonstrate for the first time, the emer-gence of deep symbolic representations of emergent language in the frame-work of image classification. We show that EL based classification models can perform as well as, if not better than state of the art deep learning mod-els. In addition, they provide a symbolic representation that opens up an entire field of possibilities of interpretable GOFAI methods involving symbol manipulation. We demonstrate the EL classification framework on immune cell marker based cell classification and chest X-ray classification using the CheXpert dataset. Code is available online at https://github.com/AriChow/EL.
Deep generative models have enabled the automated synthesis of high-quality data for diverse applications. However, the most effective generative models are specialized to data from a single domain (e.g., images or text). Real-world applications such as healthcare require multi-modal data from multiple domains (e.g., both images and corresponding text), which are difficult to acquire due to limited availability and privacy concerns and are much harder to synthesize. To tackle this joint synthesis challenge, we propose an End-to-end MultImodal X-ray genERative model (EMIXER) for jointly synthesizing x-ray images and corresponding free-text reports, all conditional on diagnosis labels. EMIXER is an conditional generative adversarial model by 1) generating an image based on a label, 2) encoding the image to a hidden embedding, 3) producing the corresponding text via a hierarchical decoder from the image embedding, and 4) a joint discriminator for assessing both the image and the corresponding text. EMIXER also enables self-supervision to leverage vast amount of unlabeled data. Extensive experiments with real X-ray reports data illustrate how data augmentation using synthesized multimodal samples can improve the performance of a variety of supervised tasks including COVID-19 X-ray classification with very limited samples. The quality of generated images and reports are also confirmed by radiologists. We quantitatively show that EMIXER generated synthetic datasets can augment X-ray image classification, report generation models to achieve 5.94% and 6.9% improvement on models trained only on real data samples. Taken together, our results highlight the promise of state of generative models to advance clinical machine learning.
Automated diagnostic assistants in healthcare necessitate accurate AI models that can be trained with limited labeled data, can cope with severe class imbalances and can support simultaneous prediction of multiple disease conditions. To this end, we present a deep learning framework that utilizes a number of key components to enable robust modeling in such challenging scenarios. Using an important use-case in chest X-ray classification, we provide several key insights on the effective use of data augmentation, self-training via distillation and confidence tempering for small data learning in medical imaging. Our results show that using 85% lesser labeled data, we can build predictive models that match the performance of classifiers trained in a large-scale data setting.
We consider the problem of classifying a medical image dataset when we have a limited amounts of labels. This is very common yet challenging setting as labelled data is expensive, time consuming to collect and may require expert knowledge. The current classification go-to of deep supervised learning is unable to cope with such a problem setup. However, using semi-supervised learning, one can produce accurate classifications using a significantly reduced amount of labelled data. Therefore, semi-supervised learning is perfectly suited for medical image classification. However, there has almost been no uptake of semi-supervised methods in the medical domain. In this work, we propose an all-in-one framework for deep semi-supervised classification focusing on graph based approaches, which up to our knowledge it is the first time that an approach with minimal labels has been shown to such an unprecedented scale with medical data. We introduce the concept of hybrid models by defining a classifier as a combination between an energy-based model and a deep net. Our energy functional is built on the Dirichlet energy based on the graph p-Laplacian. Our framework includes energies based on the $\ell_1$ and $\ell_2$ norms. We then connected this energy model to a deep net to generate a much richer feature space to construct a stronger graph. Our framework can be set to be adapted to any complex dataset. We demonstrate, through extensive numerical comparisons, that our approach readily compete with fully-supervised state-of-the-art techniques for the applications of Malaria Cells, Mammograms and Chest X-ray classification whilst using only 20% of labels.
Over the last years, Deep Learning has been successfully applied to a broad range of medical applications. Especially in the context of chest X-ray classification, results have been reported which are on par, or even superior to experienced radiologists. Despite this success in controlled experimental environments, it has been noted that the ability of Deep Learning models to generalize to data from a new domain (with potentially different tasks) is often limited. In order to address this challenge, we investigate techniques from the field of Continual Learning (CL) including Joint Training (JT), Elastic Weight Consolidation (EWC) and Learning Without Forgetting (LWF). Using the ChestX-ray14 and the MIMIC-CXR datasets, we demonstrate empirically that these methods provide promising options to improve the performance of Deep Learning models on a target domain and to mitigate effectively catastrophic forgetting for the source domain. To this end, the best overall performance was obtained using JT, while for LWF competitive results could be achieved - even without accessing data from the source domain.
The task of classifying X-ray data is a problem of both theoretical and clinical interest. Whilst supervised deep learning methods rely upon huge amounts of labelled data, the critical problem of achieving a good classification accuracy when an extremely small amount of labelled data is available has yet to be tackled. In this work, we introduce a novel semi-supervised framework for X-ray classification which is based on a graph-based optimisation model. To the best of our knowledge, this is the first method that exploits graph-based semi-supervised learning for X-ray data classification. Furthermore, we introduce a new multi-class classification functional with carefully selected class priors which allows for a smooth solution that strengthens the synergy between the limited number of labels and the huge amount of unlabelled data. We demonstrate, through a set of numerical and visual experiments, that our method produces highly competitive results on the ChestX-ray14 data set whilst drastically reducing the need for annotated data.
Recently, there have been several successful deep learning approaches for automatically classifying chest X-ray images into different disease categories. However, there is not yet a comprehensive vulnerability analysis of these models against the so-called adversarial perturbations/attacks, which makes deep models more trustful in clinical practices. In this paper, we extensively analyzed the performance of two state-of-the-art classification deep networks on chest X-ray images. These two networks were attacked by three different categories (ten methods in total) of adversarial methods (both white- and black-box), namely gradient-based, score-based, and decision-based attacks. Furthermore, we modified the pooling operations in the two classification networks to measure their sensitivities against different attacks, on the specific task of chest X-ray classification.
The increased availability of X-ray image archives (e.g. the ChestX-ray14 dataset from the NIH Clinical Center) has triggered a growing interest in deep learning techniques. To provide better insight into the different approaches, and their applications to chest X-ray classification, we investigate a powerful network architecture in detail: the ResNet-50. Building on prior work in this domain, we consider transfer learning with and without fine-tuning as well as the training of a dedicated X-ray network from scratch. To leverage the high spatial resolution of X-ray data, we also include an extended ResNet-50 architecture, and a network integrating non-image data (patient age, gender and acquisition type) in the classification process. In a concluding experiment, we also investigate multiple ResNet depths (i.e. ResNet-38 and ResNet-101). In a systematic evaluation, using 5-fold re-sampling and a multi-label loss function, we compare the performance of the different approaches for pathology classification by ROC statistics and analyze differences between the classifiers using rank correlation. Overall, we observe a considerable spread in the achieved performance and conclude that the X-ray-specific ResNet-38, integrating non-image data yields the best overall results. Furthermore, class activation maps are used to understand the classification process, and a detailed analysis of the impact of non-image features is provided.