Rare Disease Classification in Video Capsule Endoscopy

Video capsule endoscopy offers a non-invasive way to examine the small bowel, however, the rare but clinically important findings that appear only in less than 1% of labelled frames, provide very less signal for detection. As a result, while models can achieve high overall performance, they almost completely miss these rare findings. We condition each frame's decision on evidence from the rest of that patient's video, not on the frame's own posterior alone, supplying information a single frozen frame can never contain. Building upon Expected Gain Arbitration, a per-frame, macro-F1-optimal correction over the confusion matrix, we further compose it with video-disease-presence conditional resulting in our decoding method Hierarchical Conditional-Expected-gain (HCE). We evaluate HCE on two independent VCE datasets, Kvasir-Capsule and GALAR, against a static temporal-smoothing baseline and an optimal-transport (OT) frame-level correction. HCE significantly improves rare-class recall over a temporal-smoothing baseline on GALAR (2.7--3.1x; 95% CI excludes zero in both scopes) and shows a similar, though not statistically confirmed, gain on Kvasir-Capsule (up to 3.4x). Against OT, HCE still improves rare-class recall in all four evaluation settings (+0.016 to +0.029), and additionally improves macro-F1 and MCC.