CheXbreak: Misclassification Identification for Deep Learning Models Interpreting Chest X-rays

A major obstacle to the integration of deep learning models for chest x-ray interpretation into clinical settings is the lack of understanding of their failure modes. In this work, we first investigate whether there are patient subgroups that chest x-ray models are likely to misclassify. We find that patient age and the radiographic finding of lung lesion, pneumothorax or support devices are statistically relevant features for predicting misclassification for some chest x-ray models. Second, we develop misclassification predictors on chest x-ray models using their outputs and clinical features. We find that our best performing misclassification identifier achieves an AUROC close to 0.9 for most diseases. Third, employing our misclassification identifiers, we develop a corrective algorithm to selectively flip model predictions that have high likelihood of misclassification at inference time. We observe F1 improvement on the prediction of Consolidation (0.008 [95\% CI 0.005, 0.010]) and Edema (0.003, [95\% CI 0.001, 0.006]). By carrying out our investigation on ten distinct and high-performing chest x-ray models, we are able to derive insights across model architectures and offer a generalizable framework applicable to other medical imaging tasks.

VisualCheXbert: Addressing the Discrepancy Between Radiology Report Labels and Image Labels

Automatic extraction of medical conditions from free-text radiology reports is critical for supervising computer vision models to interpret medical images. In this work, we show that radiologists labeling reports significantly disagree with radiologists labeling corresponding chest X-ray images, which reduces the quality of report labels as proxies for image labels. We develop and evaluate methods to produce labels from radiology reports that have better agreement with radiologists labeling images. Our best performing method, called VisualCheXbert, uses a biomedically-pretrained BERT model to directly map from a radiology report to the image labels, with a supervisory signal determined by a computer vision model trained to detect medical conditions from chest X-ray images. We find that VisualCheXbert outperforms an approach using an existing radiology report labeler by an average F1 score of 0.14 (95% CI 0.12, 0.17). We also find that VisualCheXbert better agrees with radiologists labeling chest X-ray images than do radiologists labeling the corresponding radiology reports by an average F1 score across several medical conditions of between 0.12 (95% CI 0.09, 0.15) and 0.21 (95% CI 0.18, 0.24).

CheXseen: Unseen Disease Detection for Deep Learning Interpretation of Chest X-rays

We systematically evaluate the performance of deep learning models in the presence of diseases not labeled for or present during training. First, we evaluate whether deep learning models trained on a subset of diseases (seen diseases) can detect the presence of any one of a larger set of diseases. We find that models tend to falsely classify diseases outside of the subset (unseen diseases) as "no disease". Second, we evaluate whether models trained on seen diseases can detect seen diseases when co-occurring with diseases outside the subset (unseen diseases). We find that models are still able to detect seen diseases even when co-occurring with unseen diseases. Third, we evaluate whether feature representations learned by models may be used to detect the presence of unseen diseases given a small labeled set of unseen diseases. We find that the penultimate layer of the deep neural network provides useful features for unseen disease detection. Our results can inform the safe clinical deployment of deep learning models trained on a non-exhaustive set of disease classes.

MedAug: Contrastive learning leveraging patient metadata improves representations for chest X-ray interpretation

Self-supervised contrastive learning between pairs of multiple views of the same image has been shown to successfully leverage unlabeled data to produce meaningful visual representations for both natural and medical images. However, there has been limited work on determining how to select pairs for medical images, where availability of patient metadata can be leveraged to improve representations. In this work, we develop a method to select positive pairs coming from views of possibly different images through the use of patient metadata. We compare strategies for selecting positive pairs for chest X-ray interpretation including requiring them to be from the same patient, imaging study or laterality. We evaluate downstream task performance by fine-tuning the linear layer on 1% of the labeled dataset for pleural effusion classification. Our best performing positive pair selection strategy, which involves using images from the same patient from the same study across all lateralities, achieves a performance increase of 3.4% and 14.4% in mean AUC from both a previous contrastive method and ImageNet pretrained baseline respectively. Our controlled experiments show that the keys to improving downstream performance on disease classification are (1) using patient metadata to appropriately create positive pairs from different images with the same underlying pathologies, and (2) maximizing the number of different images used in query pairing. In addition, we explore leveraging patient metadata to select hard negative pairs for contrastive learning, but do not find improvement over baselines that do not use metadata. Our method is broadly applicable to medical image interpretation and allows flexibility for incorporating medical insights in choosing pairs for contrastive learning.

CheXternal: Generalization of Deep Learning Models for Chest X-ray Interpretation to Photos of Chest X-rays and External Clinical Settings

Recent advances in training deep learning models have demonstrated the potential to provide accurate chest X-ray interpretation and increase access to radiology expertise. However, poor generalization due to data distribution shifts in clinical settings is a key barrier to implementation. In this study, we measured the diagnostic performance for 8 different chest X-ray models when applied to (1) smartphone photos of chest X-rays and (2) external datasets without any finetuning. All models were developed by different groups and submitted to the CheXpert challenge, and re-applied to test datasets without further tuning. We found that (1) on photos of chest X-rays, all 8 models experienced a statistically significant drop in task performance, but only 3 performed significantly worse than radiologists on average, and (2) on the external set, none of the models performed statistically significantly worse than radiologists, and five models performed statistically significantly better than radiologists. Our results demonstrate that some chest X-ray models, under clinically relevant distribution shifts, were comparable to radiologists while other models were not. Future work should investigate aspects of model training procedures and dataset collection that influence generalization in the presence of data distribution shifts.

CheXseg: Combining Expert Annotations with DNN-generated Saliency Maps for X-ray Segmentation

Medical image segmentation models are typically supervised by expert annotations at the pixel-level, which can be expensive to acquire. In this work, we propose a method that combines the high quality of pixel-level expert annotations with the scale of coarse DNN-generated saliency maps for training multi-label semantic segmentation models. We demonstrate the application of our semi-supervised method, which we call CheXseg, on multi-label chest x-ray interpretation. We find that CheXseg improves upon the performance (mIoU) of fully-supervised methods that use only pixel-level expert annotations by 13.4% and weakly-supervised methods that use only DNN-generated saliency maps by 91.2%. Furthermore, we implement a semi-supervised method using knowledge distillation and find that though it is outperformed by CheXseg, it exceeds the performance (mIoU) of the best fully-supervised method by 4.83%. Our best method is able to match radiologist agreement on three out of ten pathologies and reduces the overall performance gap by 71.6% as compared to weakly-supervised methods.

CheXtransfer: Performance and Parameter Efficiency of ImageNet Models for Chest X-Ray Interpretation

Deep learning methods for chest X-ray interpretation typically rely on pretrained models developed for ImageNet. This paradigm assumes that better ImageNet architectures perform better on chest X-ray tasks and that ImageNet-pretrained weights provide a performance boost over random initialization. In this work, we compare the transfer performance and parameter efficiency of 16 popular convolutional architectures on a large chest X-ray dataset (CheXpert) to investigate these assumptions. First, we find no relationship between ImageNet performance and CheXpert performance for both models without pretraining and models with pretraining. Second, we find that, for models without pretraining, the choice of model family influences performance more than size within a family for medical imaging tasks. Third, we observe that ImageNet pretraining yields a statistically significant boost in performance across architectures, with a higher boost for smaller architectures. Fourth, we examine whether ImageNet architectures are unnecessarily large for CheXpert by truncating final blocks from pretrained models, and find that we can make models 3.25x more parameter-efficient on average without a statistically significant drop in performance. Our work contributes new experimental evidence about the relation of ImageNet to chest x-ray interpretation performance.