Domain-Adaptive Pre-training of Self-Supervised Foundation Models for Medical Image Classification in Gastrointestinal Endoscopy

Video capsule endoscopy has transformed gastrointestinal endoscopy (GIE) diagnostics by offering a non-invasive method for capturing detailed images of the gastrointestinal tract, enabling early disease detection. However, its potential is limited by the sheer volume of images generated during the imaging procedure, which can take anywhere from 6-8 hours and often produce up to 1 million images, necessitating automated analysis. Additionally, the variability of these images, combined with the need for expert annotations and the scarcity of large, high-quality labeled datasets, constrains the effectiveness of current medical image analysis models. To address this, we introduce a novel large GIE dataset, called EndoExtend24, created by merging ten existing public and private datasets, ensuring patient integrity across splits. EndoExtend24 includes over 226,000 labeled images, as well as dynamic class mappings, which allow unified training across datasets with differing labeling granularity, supporting up to 123 distinct pathological findings. Further, we propose to leverage domain adaptive pre-training of foundation models trained with self-supervision on generic image data, to adapt them to the task of GIE medical image diagnosis. Specifically, the EVA-02 model, which is based on the ViT architecture and trained on ImageNet-22k with masked image modeling (using EVA-CLIP as a MIM teacher), is pre-trained on the EndoExtend24 dataset to achieve domain adaptation, and finally trained on the Capsule Endoscopy 2024 Challenge dataset. Our model demonstrates robust performance, securing third place in the Capsule Endoscopy 2024 Challenge. We achieved a macro AUC of 0.762 and a balanced accuracy of 37.1% on the test set. These results emphasize the effectiveness of our domain-adaptive pre-training approach and the enriched EndoExtend24 dataset in advancing gastrointestinal endoscopy diagnostics.

Marcel Roth, Micha V. Nowak, Adrian Krenzer, Frank Puppe · 2024