Domain adaptation using optimal transport for invariant learning using histopathology datasets

Histopathology is critical for the diagnosis of many diseases, including cancer. These protocols typically require pathologists to manually evaluate slides under a microscope, which is time-consuming and subjective, leading to interest in machine learning to automate analysis. However, computational techniques are limited by batch effects, where technical factors like differences in preparation protocol or scanners can alter the appearance of slides, causing models trained on one institution to fail when generalizing to others. Here, we propose a domain adaptation method that improves the generalization of histopathological models to data from unseen institutions, without the need for labels or retraining in these new settings. Our approach introduces an optimal transport (OT) loss, that extends adversarial methods that penalize models if images from different institutions can be distinguished in their representation space. Unlike previous methods, which operate on single samples, our loss accounts for distributional differences between batches of images. We show that on the Camelyon17 dataset, while both methods can adapt to global differences in color distribution, only our OT loss can reliably classify a cancer phenotype unseen during training. Together, our results suggest that OT improves generalization on rare but critical phenotypes that may only make up a small fraction of the total tiles and variation in a slide.

Hierarchical Optimal Transport for Comparing Histopathology Datasets

Scarcity of labeled histopathology data limits the applicability of deep learning methods to under-profiled cancer types and labels. Transfer learning allows researchers to overcome the limitations of small datasets by pre-training machine learning models on larger datasets similar to the small target dataset. However, similarity between datasets is often determined heuristically. In this paper, we propose a principled notion of distance between histopathology datasets based on a hierarchical generalization of optimal transport distances. Our method does not require any training, is agnostic to model type, and preserves much of the hierarchical structure in histopathology datasets imposed by tiling. We apply our method to H&E stained slides from The Cancer Genome Atlas from six different cancer types. We show that our method outperforms a baseline distance in a cancer-type prediction task. Our results also show that our optimal transport distance predicts difficulty of transferability in a tumor vs.normal prediction setting.