Cut instance mixing: A domain-specific data augmentation method applied to gastrointestinal lesion detection.

Early detection of gastrointestinal lesions such as intestinal metaplasia (IM), dysplasia, and polyps remains challenging due to their subtle appearance and the scarcity of well-annotated medical image datasets. To address this limitation, we introduce Cut Instance Mixing (CIM), a domain-specific data augmentation method designed to generate anatomically plausible lesion-containing images through the identification of biologically relevant regions of interest and seamless lesion blending using Poisson image editing and gradient-based mixing. CIM was evaluated across three distinct endoscopic datasets (IM, dysplasia, and polyps) using a ResNet50 classifier and five-fold cross-validation. The proposed method consistently outperformed state-of-the-art augmentation techniques. In IM classification, CIM with α = 0.8 achieved the highest performance (AUC: 0.879, Accuracy: 0.823), surpassing MixUp, CutMix and random copy-paste. In dysplasia detection, CIM reached near-perfect results (AUC: 0.997, Accuracy: 0.966), and demonstrated strong generalization on an external polyp dataset (AUC: 0.830, Accuracy: 0.769). Grad-CAM analyses further confirmed that CIM preserves clinically relevant features, improving model attention on lesion regions. These findings demonstrate that CIM enables the generation of realistic and biologically coherent synthetic samples, effectively mitigating data imbalance and enhancing classification robustness. The method is architecture-agnostic and broadly applicable to tasks requiring anatomically consistent augmentation, providing a promising direction for improving deep learning systems in gastrointestinal imaging.