Authors:Christian Zöllner (1), Mozzam Motiwala (1), Aysel Ahadova (1), Gerrit Anders (4), Robert Hüneburg (2 and 3), Jacob Nattermann (2 and 3), Matthias Kloor (1) ((1) Department of Applied Tumor Biology Institute of Pathology Heidelberg University Hospital, (2) National Center for Hereditary Tumor Syndromes University Hospital Bonn, (3) Department of Internal Medicine I University Hospital Bonn, (4) Leibniz Institut für Wissensmedien)
Abstract:Training of neural networks for histopathology classification tasks typically relies on data encoding into latent space, which reduces complexity and improves performance. There are several encoder networks available, either pretrained on general image datasets such as ImageNET, or specifically on histopathological images. Training of encoder networks should be adapted to downstream tasks, allowing encoding of biologic/diagnostic content while rendering networks invariant to label-irrelevant transformations.
This paper investigates the effect of classical image transformation on the latent space, using networks provided by Lunit Inc. and Bioptimus, both focusing on pathological images, and by Meta Research Team. We assess variance of embeddings resulting from standard data transformations by comparing original and transformed image embeddings and by contrasting them with random, unrelated embeddings, using image tiles from hematoxylin/eosin-stained sections available in a colorectal tissue dataset and the publicly accessible TCGA dataset.
Our findings show that embeddings of original and transformed images are closer to each other than to random embeddings, indicating robustness to transformations. However, they are not fully invariant, revealing that the encoder networks do not completely neutralize transformation effects in latent space, explaining why transformation-mediated augmentation of datasets can improve performance. Significant differences were observed between general and histopathology-specific encoder networks.
From: Christian Zöllner [view email]
[v1]
Tue, 23 Jun 2026 11:06:00 UTC (3,268 KB)
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