StRegA: Unsupervised Anomaly Detection in Brain MRIs using a Compact Context-encoding Variational Autoencoder
This work addresses the challenge of detecting diverse brain abnormalities without manual annotations, which is crucial for neuro-radiology, though it is incremental as it builds on existing VAE methods.
The researchers tackled the problem of unsupervised anomaly detection in brain MRIs by proposing a compact context-encoding VAE pipeline (StRegA), which achieved a Dice score of 0.642±0.101 for detecting tumours in clinical data and 0.859±0.112 for artificial anomalies, outperforming baselines.
Expert interpretation of anatomical images of the human brain is the central part of neuro-radiology. Several machine learning-based techniques have been proposed to assist in the analysis process. However, the ML models typically need to be trained to perform a specific task, e.g., brain tumour segmentation or classification. Not only do the corresponding training data require laborious manual annotations, but a wide variety of abnormalities can be present in a human brain MRI - even more than one simultaneously, which renders representation of all possible anomalies very challenging. Hence, a possible solution is an unsupervised anomaly detection (UAD) system that can learn a data distribution from an unlabelled dataset of healthy subjects and then be applied to detect out of distribution samples. Such a technique can then be used to detect anomalies - lesions or abnormalities, for example, brain tumours, without explicitly training the model for that specific pathology. Several Variational Autoencoder (VAE) based techniques have been proposed in the past for this task. Even though they perform very well on controlled artificially simulated anomalies, many of them perform poorly while detecting anomalies in clinical data. This research proposes a compact version of the "context-encoding" VAE (ceVAE) model, combined with pre and post-processing steps, creating a UAD pipeline (StRegA), which is more robust on clinical data, and shows its applicability in detecting anomalies such as tumours in brain MRIs. The proposed pipeline achieved a Dice score of 0.642$\pm$0.101 while detecting tumours in T2w images of the BraTS dataset and 0.859$\pm$0.112 while detecting artificially induced anomalies, while the best performing baseline achieved 0.522$\pm$0.135 and 0.783$\pm$0.111, respectively.