To investigate the impact of OOD radiographs on existing chest X-ray classification models and to increase their robustness against OOD data. The study employed the commonly used chest X-ray classification model, CheXnet, trained on the chest X-ray 14 data set, and tested its robustness against OOD data using three public radiography data sets: IRMA, Bone Age, and MURA, and the ImageNet data set. To detect OOD data for multi-label classification, we proposed in-distribution voting (IDV). The OOD detection performance is measured across data sets using the area under the receiver operating characteristic curve (AUC) analysis and compared with Mahalanobis-based OOD detection, MaxLogit, MaxEnergy and self-supervised OOD detection (SS OOD). Without additional OOD detection, the chest X-ray classifier failed to discard any OOD images, with an AUC of 0.5. The proposed IDV approach trained on ID (chest X-ray 14) and OOD data (IRMA and ImageNet) achieved, on average, 0.999 OOD AUC across the three data sets, surpassing all other OOD detection methods. Mahalanobis-based OOD detection achieved an average OOD detection AUC of 0.982. IDV trained solely with a few thousand ImageNet images had an AUC 0.913, which was higher than MaxLogit (0.726), MaxEnergy (0.724), and SS OOD (0.476). The performance of all tested OOD detection methods did not translate well to radiography data sets, except Mahalanobis-based OOD detection and the proposed IDV method. Training solely on ID data led to incorrect classification of OOD images as ID, resulting in increased false positive rates. IDV substantially improved the model's ID classification performance, even when trained with data that will not occur in the intended use case or test set, without additional inference overhead.
The collection and curation of large-scale medical datasets from multiple institutions is essential for training accurate deep learning models, but privacy concerns often hinder data sharing. Federated learning (FL) is a promising solution that enables privacy-preserving collaborative learning among different institutions, but it generally suffers from performance deterioration due to heterogeneous data distributions and a lack of quality labeled data. In this paper, we present a robust and label-efficient self-supervised FL framework for medical image analysis. Our method introduces a novel Transformer-based self-supervised pre-training paradigm that pre-trains models directly on decentralized target task datasets using masked image modeling, to facilitate more robust representation learning on heterogeneous data and effective knowledge transfer to downstream models. Extensive empirical results on simulated and real-world medical imaging non-IID federated datasets show that masked image modeling with Transformers significantly improves the robustness of models against various degrees of data heterogeneity. Notably, under severe data heterogeneity, our method, without relying on any additional pre-training data, achieves an improvement of 5.06%, 1.53% and 4.58% in test accuracy on retinal, dermatology and chest X-ray classification compared to the supervised baseline with ImageNet pre-training. In addition, we show that our federated self-supervised pre-training methods yield models that generalize better to out-of-distribution data and perform more effectively when fine-tuning with limited labeled data, compared to existing FL algorithms. The code is available at https://github.com/rui-yan/SSL-FL.
Privacy regulations and the physical distribution of heterogeneous data are often primary concerns for the development of deep learning models in a medical context. This paper evaluates the feasibility of differentially private federated learning for chest X-ray classification as a defense against data privacy attacks. To the best of our knowledge, we are the first to directly compare the impact of differentially private training on two different neural network architectures, DenseNet121 and ResNet50. Extending the federated learning environments previously analyzed in terms of privacy, we simulated a heterogeneous and imbalanced federated setting by distributing images from the public CheXpert and Mendeley chest X-ray datasets unevenly among 36 clients. Both non-private baseline models achieved an area under the receiver operating characteristic curve (AUC) of $0.94$ on the binary classification task of detecting the presence of a medical finding. We demonstrate that both model architectures are vulnerable to privacy violation by applying image reconstruction attacks to local model updates from individual clients. The attack was particularly successful during later training stages. To mitigate the risk of privacy breach, we integrated R\'enyi differential privacy with a Gaussian noise mechanism into local model training. We evaluate model performance and attack vulnerability for privacy budgets $\epsilon \in$ {1, 3, 6, 10}. The DenseNet121 achieved the best utility-privacy trade-off with an AUC of $0.94$ for $\epsilon$ = 6. Model performance deteriorated slightly for individual clients compared to the non-private baseline. The ResNet50 only reached an AUC of $0.76$ in the same privacy setting. Its performance was inferior to that of the DenseNet121 for all considered privacy constraints, suggesting that the DenseNet121 architecture is more robust to differentially private training.
While developing artificial intelligence (AI)-based algorithms to solve problems, the amount of data plays a pivotal role - large amount of data helps the researchers and engineers to develop robust AI algorithms. In the case of building AI-based models for problems related to medical imaging, these data need to be transferred from the medical institutions where they were acquired to the organizations developing the algorithms. This movement of data involves time-consuming formalities like complying with HIPAA, GDPR, etc.There is also a risk of patients' private data getting leaked, compromising their confidentiality. One solution to these problems is using the Federated Learning framework. Federated Learning (FL) helps AI models to generalize better and create a robust AI model by using data from different sources having different distributions and data characteristics without moving all the data to a central server. In our paper, we apply the FL framework for training a deep learning model to solve a binary classification problem of predicting the presence or absence of COVID-19. We took three different sources of data and trained individual models on each source. Then we trained an FL model on the complete data and compared all the model performances. We demonstrated that the FL model performs better than the individual models. Moreover, the FL model performed at par with the model trained on all the data combined at a central server. Thus Federated Learning leads to generalized AI models without the cost of data transfer and regulatory overhead.
Deep learning models were frequently reported to learn from shortcuts like dataset biases. As deep learning is playing an increasingly important role in the modern healthcare system, it is of great need to combat shortcut learning in medical data as well as develop unbiased and trustworthy models. In this paper, we study the problem of developing debiased chest X-ray diagnosis models from the biased training data without knowing exactly the bias labels. We start with the observations that the imbalance of bias distribution is one of the key reasons causing shortcut learning, and the dataset biases are preferred by the model if they were easier to be learned than the intended features. Based on these observations, we proposed a novel algorithm, pseudo bias-balanced learning, which first captures and predicts per-sample bias labels via generalized cross entropy loss and then trains a debiased model using pseudo bias labels and bias-balanced softmax function. We constructed several chest X-ray datasets with various dataset bias situations and demonstrated with extensive experiments that our proposed method achieved consistent improvements over other state-of-the-art approaches.
Deep learning methods have shown outstanding classification accuracy in medical imaging problems, which is largely attributed to the availability of large-scale datasets manually annotated with clean labels. However, given the high cost of such manual annotation, new medical imaging classification problems may need to rely on machine-generated noisy labels extracted from radiology reports. Indeed, many Chest X-ray (CXR) classifiers have already been modelled from datasets with noisy labels, but their training procedure is in general not robust to noisy-label samples, leading to sub-optimal models. Furthermore, CXR datasets are mostly multi-label, so current noisy-label learning methods designed for multi-class problems cannot be easily adapted. In this paper, we propose a new method designed for the noisy multi-label CXR learning, which detects and smoothly re-labels samples from the dataset, which is then used to train common multi-label classifiers. The proposed method optimises a bag of multi-label descriptors (BoMD) to promote their similarity with the semantic descriptors produced by BERT models from the multi-label image annotation. Our experiments on diverse noisy multi-label training sets and clean testing sets show that our model has state-of-the-art accuracy and robustness in many CXR multi-label classification benchmarks.
Despite the introduction of vaccines, Coronavirus disease (COVID-19) remains a worldwide dilemma, continuously developing new variants such as Delta and the recent Omicron. The current standard for testing is through polymerase chain reaction (PCR). However, PCRs can be expensive, slow, and/or inaccessible to many people. X-rays on the other hand have been readily used since the early 20th century and are relatively cheaper, quicker to obtain, and typically covered by health insurance. With a careful selection of model, hyperparameters, and augmentations, we show that it is possible to develop models with 83% accuracy in binary classification and 64% in multi-class for detecting COVID-19 infections from chest x-rays.
In recent years, people from all over the world are suffering from one of the most severe diseases in history, known as Coronavirus disease 2019, COVID-19 for short. When the virus reaches the lungs, it has a higher probability to cause lung pneumonia and sepsis. X-ray image is a powerful tool in identifying the typical features of the infection for COVID-19 patients. The radiologists and pathologists observe that ground-glass opacity appears in the chest X-ray for infected patient \cite{cozzi2021ground}, and it could be used as one of the criteria during the diagnosis process. In the past few years, deep learning has proven to be one of the most powerful methods in the field of image classification. Due to significant differences in Chest X-Ray between normal and infected people \cite{rousan2020chest}, deep models could be used to identify the presence of the disease given a patient's Chest X-Ray. Many deep models are complex, and it evolves with lots of input parameters. Designers sometimes struggle with the tuning process for deep models, especially when they build up the model from scratch. Genetic Algorithm, inspired by the biological evolution process, plays a key role in solving such complex problems. In this paper, I proposed a genetic-based approach to optimize the Convolutional Neural Network(CNN) for the Chest X-Ray classification task.
The human gaze is a cost-efficient physiological data that reveals human underlying attentional patterns. The selective attention mechanism helps the cognition system focus on task-relevant visual clues by ignoring the presence of distractors. Thanks to this ability, human beings can efficiently learn from a very limited number of training samples. Inspired by this mechanism, we aim to leverage gaze for medical image analysis tasks with small training data. Our proposed framework includes a backbone encoder and a Selective Attention Network (SAN) that simulates the underlying attention. The SAN implicitly encodes information such as suspicious regions that is relevant to the medical diagnose tasks by estimating the actual human gaze. Then we design a novel Auxiliary Attention Block (AAB) to allow information from SAN to be utilized by the backbone encoder to focus on selective areas. Specifically, this block uses a modified version of a multi-head attention layer to simulate the human visual search procedure. Note that the SAN and AAB can be plugged into different backbones, and the framework can be used for multiple medical image analysis tasks when equipped with task-specific heads. Our method is demonstrated to achieve superior performance on both 3D tumor segmentation and 2D chest X-ray classification tasks. We also show that the estimated gaze probability map of the SAN is consistent with an actual gaze fixation map obtained by board-certified doctors.
Medical images commonly exhibit multiple abnormalities. Predicting them requires multi-class classifiers whose training and desired reliable performance can be affected by a combination of factors, such as, dataset size, data source, distribution, and the loss function used to train the deep neural networks. Currently, the cross-entropy loss remains the de-facto loss function for training deep learning classifiers. This loss function, however, asserts equal learning from all classes, leading to a bias toward the majority class. In this work, we benchmark various state-of-the-art loss functions that are suitable for multi-class classification, critically analyze model performance, and propose improved loss functions. We select a pediatric chest X-ray (CXR) dataset that includes images with no abnormality (normal), and those exhibiting manifestations consistent with bacterial and viral pneumonia. We construct prediction-level and model-level ensembles, respectively, to improve classification performance. Our results show that compared to the individual models and the state-of-the-art literature, the weighted averaging of the predictions for top-3 and top-5 model-level ensembles delivered significantly superior classification performance (p < 0.05) in terms of MCC (0.9068, 95% confidence interval (0.8839, 0.9297)) metric. Finally, we performed localization studies to interpret model behaviors to visualize and confirm that the individual models and ensembles learned meaningful features and highlighted disease manifestations.
A common problem in computer vision -- particularly in medical applications -- is a lack of sufficiently diverse, large sets of training data. These datasets often suffer from severe class imbalance. As a result, networks often overfit and are unable to generalize to novel examples. Generative Adversarial Networks (GANs) offer a novel method of synthetic data augmentation. In this work, we evaluate the use of GAN- based data augmentation to artificially expand the CheXpert dataset of chest radiographs. We compare performance to traditional augmentation and find that GAN-based augmentation leads to higher downstream performance for underrepresented classes. Furthermore, we see that this result is pronounced in low data regimens. This suggests that GAN-based augmentation a promising area of research to improve network performance when data collection is prohibitively expensive.
In many prediction problems, spurious correlations are induced by a changing relationship between the label and a nuisance variable that is also correlated with the covariates. For example, in classifying animals in natural images, the background, which is a nuisance, can predict the type of animal. This nuisance-label relationship does not always hold, and the performance of a model trained under one such relationship may be poor on data with a different nuisance-label relationship. To build predictive models that perform well regardless of the nuisance-label relationship, we develop Nuisance-Randomized Distillation (NURD). We introduce the nuisance-randomized distribution, a distribution where the nuisance and the label are independent. Under this distribution, we define the set of representations such that conditioning on any member, the nuisance and the label remain independent. We prove that the representations in this set always perform better than chance, while representations outside of this set may not. NURD finds a representation from this set that is most informative of the label under the nuisance-randomized distribution, and we prove that this representation achieves the highest performance regardless of the nuisance-label relationship. We evaluate NURD on several tasks including chest X-ray classification where, using non-lung patches as the nuisance, NURD produces models that predict pneumonia under strong spurious correlations.
Radiologists usually observe anatomical regions of chest X-ray images as well as the overall image before making a decision. However, most existing deep learning models only look at the entire X-ray image for classification, failing to utilize important anatomical information. In this paper, we propose a novel multi-label chest X-ray classification model that accurately classifies the image finding and also localizes the findings to their correct anatomical regions. Specifically, our model consists of two modules, the detection module and the anatomical dependency module. The latter utilizes graph convolutional networks, which enable our model to learn not only the label dependency but also the relationship between the anatomical regions in the chest X-ray. We further utilize a method to efficiently create an adjacency matrix for the anatomical regions using the correlation of the label across the different regions. Detailed experiments and analysis of our results show the effectiveness of our method when compared to the current state-of-the-art multi-label chest X-ray image classification methods while also providing accurate location information.
Although deep learning models for chest X-ray interpretation are commonly trained on labels generated by automatic radiology report labelers, the impact of improvements in report labeling on the performance of chest X-ray classification models has not been systematically investigated. We first compare the CheXpert, CheXbert, and VisualCheXbert labelers on the task of extracting accurate chest X-ray image labels from radiology reports, reporting that the VisualCheXbert labeler outperforms the CheXpert and CheXbert labelers. Next, after training image classification models using labels generated from the different radiology report labelers on one of the largest datasets of chest X-rays, we show that an image classification model trained on labels from the VisualCheXbert labeler outperforms image classification models trained on labels from the CheXpert and CheXbert labelers. Our work suggests that recent improvements in radiology report labeling can translate to the development of higher performing chest X-ray classification models.
Multi-label classification of chest X-ray images is frequently performed using discriminative approaches, i.e. learning to map an image directly to its binary labels. Such approaches make it challenging to incorporate auxiliary information such as annotation uncertainty or a dependency among the labels. Building towards this, we propose a novel knowledge graph reformulation of multi-label classification, which not only readily increases predictive performance of an encoder but also serves as a general framework for introducing new domain knowledge. Specifically, we construct a multi-modal knowledge graph out of the chest X-ray images and its labels and pose multi-label classification as a link prediction problem. Incorporating auxiliary information can then simply be achieved by adding additional nodes and relations among them. When tested on a publicly-available radiograph dataset (CheXpert), our relational-reformulation using a naive knowledge graph outperforms the state-of-art by achieving an area-under-ROC curve of 83.5%, an improvement of "sim 1" over a purely discriminative approach.
We propose a highly data-efficient active learning framework for image classification. Our novel framework combines: (1) unsupervised representation learning of a Convolutional Neural Network and (2) the Gaussian Process (GP) method, in sequence to achieve highly data and label efficient classifications. Moreover, both elements are less sensitive to the prevalent and challenging class imbalance issue, thanks to the (1) feature learned without labels and (2) the Bayesian nature of GP. The GP-provided uncertainty estimates enable active learning by ranking samples based on the uncertainty and selectively labeling samples showing higher uncertainty. We apply this novel combination to the severely imbalanced case of COVID-19 chest X-ray classification and the Nerthus colonoscopy classification. We demonstrate that only . 10% of the labeled data is needed to reach the accuracy from training all available labels. We also applied our model architecture and proposed framework to a broader class of datasets with expected success.
The training of deep learning models generally requires a large amount of annotated data for effective convergence and generalisation. However, obtaining high-quality annotations is a laboursome and expensive process due to the need of expert radiologists for the labelling task. The study of semi-supervised learning in medical image analysis is then of crucial importance given that it is much less expensive to obtain unlabelled images than to acquire images labelled by expert radiologists. Essentially, semi-supervised methods leverage large sets of unlabelled data to enable better training convergence and generalisation than using only the small set of labelled images. In this paper, we propose Self-supervised Mean Teacher for Semi-supervised (S$^2$MTS$^2$) learning that combines self-supervised mean-teacher pre-training with semi-supervised fine-tuning. The main innovation of S$^2$MTS$^2$ is the self-supervised mean-teacher pre-training based on the joint contrastive learning, which uses an infinite number of pairs of positive query and key features to improve the mean-teacher representation. The model is then fine-tuned using the exponential moving average teacher framework trained with semi-supervised learning. We validate S$^2$MTS$^2$ on the multi-label classification problems from Chest X-ray14 and CheXpert, and the multi-class classification from ISIC2018, where we show that it outperforms the previous SOTA semi-supervised learning methods by a large margin.
Chest radiography is a relatively cheap, widely available medical procedure that conveys key information for making diagnostic decisions. Chest X-rays are almost always used in the diagnosis of respiratory diseases such as pneumonia or the recent COVID-19. In this paper, we propose a self-supervised deep neural network that is pretrained on an unlabeled chest X-ray dataset. The learned representations are transferred to downstream task - the classification of respiratory diseases. The results obtained on four public datasets show that our approach yields competitive results without requiring large amounts of labeled training data.
Deep neural networks have increasingly been used as an auxiliary tool in healthcare applications, due to their ability to improve performance of several diagnosis tasks. However, these methods are not widely adopted in clinical settings due to the practical limitations in the reliability, generalizability, and interpretability of deep learning based systems. As a result, methods have been developed that impose additional constraints during network training to gain more control as well as improve interpretabilty, facilitating their acceptance in healthcare community. In this work, we investigate the benefit of using Orthogonal Spheres (OS) constraint for classification of COVID-19 cases from chest X-ray images. The OS constraint can be written as a simple orthonormality term which is used in conjunction with the standard cross-entropy loss during classification network training. Previous studies have demonstrated significant benefits in applying such constraints to deep learning models. Our findings corroborate these observations, indicating that the orthonormality loss function effectively produces improved semantic localization via GradCAM visualizations, enhanced classification performance, and reduced model calibration error. Our approach achieves an improvement in accuracy of 1.6% and 4.8% for two- and three-class classification, respectively; similar results are found for models with data augmentation applied. In addition to these findings, our work also presents a new application of the OS regularizer in healthcare, increasing the post-hoc interpretability and performance of deep learning models for COVID-19 classification to facilitate adoption of these methods in clinical settings. We also identify the limitations of our strategy that can be explored for further research in future.
The gold standard for COVID-19 is RT-PCR, testing facilities for which are limited and not always optimally distributed. Test results are delayed, which impacts treatment. Expert radiologists, one of whom is a co-author, are able to diagnose COVID-19 positivity from Chest X-Rays (CXR) and CT scans, that can facilitate timely treatment. Such diagnosis is particularly valuable in locations lacking radiologists with sufficient expertise and familiarity with COVID-19 patients. This paper has two contributions. One, we analyse literature on CXR based COVID-19 diagnosis. We show that popular choices of dataset selection suffer from data homogeneity, leading to misleading results. We compile and analyse a viable benchmark dataset from multiple existing heterogeneous sources. Such a benchmark is important for realistically testing models. Our second contribution relates to learning from imbalanced data. Datasets for COVID X-Ray classification face severe class imbalance, since most subjects are COVID -ve. Twin Support Vector Machines (Twin SVM) and Twin Neural Networks (Twin NN) have, in recent years, emerged as effective ways of handling skewed data. We introduce a state-of-the-art technique, termed as Twin Augmentation, for modifying popular pre-trained deep learning models. Twin Augmentation boosts the performance of a pre-trained deep neural network without requiring re-training. Experiments show, that across a multitude of classifiers, Twin Augmentation is very effective in boosting the performance of given pre-trained model for classification in imbalanced settings.