Modeling the Density of Pixel-level Self-supervised Embeddings for Unsupervised Pathology Segmentation in Medical CT

Accurate detection of all pathological findings in 3D medical images remains a significant challenge, as supervised models are limited to detecting only the few pathology classes annotated in existing datasets. To address this, we frame pathology detection as an unsupervised visual anomaly segmentation (UVAS) problem, leveraging the inherent rarity of pathological patterns compared to healthy ones. We enhance the existing density-based UVAS framework with two key innovations: (1) dense self-supervised learning for feature extraction, eliminating the need for supervised pretraining, and (2) learned, masking-invariant dense features as conditioning variables, replacing hand-crafted positional encodings. Trained on over 30,000 unlabeled 3D CT volumes, our fully self-supervised model, Screener, outperforms existing UVAS methods on four large-scale test datasets comprising 1,820 scans with diverse pathologies. Furthermore, in a low-shot supervised fine-tuning setting, Screener surpasses existing self-supervised pretraining methods, establishing it as a state-of-the-art foundation for pathology segmentation. The code and pretrained models are available at https://github.com/mishgon/screener.