# StRegA: Unsupervised Anomaly Detection in Brain MRIs using a Compact Context-encoding Variational Autoencoder

arXiv: https://arxiv.org/abs/2201.13271 · HTML: https://mlsanity.com/paper/2201.13271/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 49 references that are in the map.
- First posted on arXiv 31 Jan 2022.

## Builds on (most cited first, 17 of 17)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Neural Discrete Representation Learning](https://mlsanity.com/paper/1711.00937/) (2017)
- [Auto-Encoding Variational Bayes](https://mlsanity.com/paper/1312.6114/) (2013)
- [GANomaly: Semi-Supervised Anomaly Detection via Adversarial Training](https://mlsanity.com/paper/1805.06725/) (2018)
- [Adversarial Autoencoders](https://mlsanity.com/paper/1511.05644/) (2015)
- [Unsupervised Anomaly Detection via Variational Auto-Encoder for Seasonal KPIs in Web Applications](https://mlsanity.com/paper/1802.03903/) (2018)
- [Deep Unsupervised Clustering with Gaussian Mixture Variational Autoencoders](https://mlsanity.com/paper/1611.02648/) (2016)
- [Unsupervised Anomaly Localization using Variational Auto-Encoders](https://mlsanity.com/paper/1907.02796/) (2019)
- [Unsupervised Lesion Detection via Image Restoration with a Normative Prior](https://mlsanity.com/paper/2005.00031/) (2020)
- [Context-encoding Variational Autoencoder for Unsupervised Anomaly Detection](https://mlsanity.com/paper/1812.05941/) (2018)
- [Anomaly detection through latent space restoration using vector-quantized variational autoencoders](https://mlsanity.com/paper/2012.06765/) (2020)
- [Robust Anomaly Detection in Images using Adversarial Autoencoders](https://mlsanity.com/paper/1901.06355/) (2019)
- [Scale-Space Autoencoders for Unsupervised Anomaly Segmentation in Brain MRI](https://mlsanity.com/paper/2006.12852/) (2020)
- [Video Anomaly Detection and Localization via Gaussian Mixture Fully Convolutional Variational Autoencoder](https://mlsanity.com/paper/1805.11223/) (2018)
- [Combining GANs and AutoEncoders for Efficient Anomaly Detection](https://mlsanity.com/paper/2011.08102/) (2020)
- [On the Usage of Generative Models for Network Anomaly Detection in Multivariate Time-Series](https://mlsanity.com/paper/2010.08286/) (2020)

## Built on by (most cited first, 6 of 6)

- [Evaluation of pseudo-healthy image reconstruction for anomaly detection with deep generative models: Application to brain FDG PET](https://mlsanity.com/paper/2401.16363/) (2024)
- [Deep Generative Modeling-based Data Augmentation with Demonstration using the BFBT Benchmark Void Fraction Datasets](https://mlsanity.com/paper/2308.10120/) (2023)
- [PULASki: Learning inter-rater variability using statistical distances to improve probabilistic segmentation](https://mlsanity.com/paper/2312.15686/) (2023)
- [Unsupervised Deep Generative Models for Anomaly Detection in Neuroimaging: A Systematic Scoping Review](https://mlsanity.com/paper/2510.14462/) (2025)
- [Transcending the Annotation Bottleneck: AI-Powered Discovery in Biology and Medicine](https://mlsanity.com/paper/2602.20100/) (2026)
- [MIRTO: a registration-gated, multiverse-tested evaluation protocol for unsupervised anomaly segmentation in brain MRI](https://mlsanity.com/paper/2610.02136/) (2026)

## Abstract (arXiv)

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±0.101 while detecting tumours in T2w images of the BraTS dataset and 0.859±0.112 while detecting artificially induced anomalies, while the best performing baseline achieved 0.522±0.135 and 0.783±0.111, respectively.