Hierarchical Optimal Transport for Comparing Histopathology Datasets

Anna Yeaton, Rahul G Krishnan, Rebecca Mieloszyk, David Alvarez-Melis, Grace Huynh

Keywords: Histopathology, domain adaptation, transfer learning, optimal transport

TL;DR: Optimal transport provides a distance between slides and between histopathology datasets, improves upon baseline methods, and correlates with difficulty of transfer learning.

Abstract: 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.

Registration: I acknowledge that publication of this at MIDL and in the proceedings requires at least one of the authors to register and present the work during the conference.

Authorship: I confirm that I am the author of this work and that it has not been submitted to another publication before.

Paper Type: both

Primary Subject Area: Transfer Learning and Domain Adaptation

Secondary Subject Area: Application: Histopathology

Confidentiality And Author Instructions: I read the call for papers and author instructions. I acknowledge that exceeding the page limit and/or altering the latex template can result in desk rejection.

Code And Data: https://github.com/ayeaton/HHOT

Community Implementations: [ 1 code implementation](https://www.catalyzex.com/paper/hierarchical-optimal-transport-for-comparing/code)