  Whole slide images (WSI) are microscopy images of stained tissue slides
routinely prepared for diagnosis and treatment selection in medical practice.
WSI are very large (gigapixel size) and complex (made of up to millions of
cells). The current state-of-the-art (SoTA) approach to classify WSI subdivides
them into tiles, encodes them by pre-trained networks and applies Multiple
Instance Learning (MIL) to train for specific downstream tasks. However,
annotated datasets are often small, typically a few hundred to a few thousand
WSI, which may cause overfitting and underperforming models. Conversely, the
number of unannotated WSI is ever increasing, with datasets of tens of
thousands (soon to be millions) of images available. While it has been
previously proposed to use these unannotated data to identify suitable tile
representations by self-supervised learning (SSL), downstream classification
tasks still require full supervision because parts of the MIL architecture is
not trained during tile level SSL pre-training. Here, we propose a strategy of
slide level SSL to leverage the large number of WSI without annotations to
infer powerful slide representations. Applying our method to The Cancer-Genome
Atlas, one of the most widely used data resources in cancer research (16 TB
image data), we are able to downsize the dataset to 23 MB without any loss in
predictive power: we show that a linear classifier trained on top of these
embeddings maintains or improves previous SoTA performances on various
benchmark WSI classification tasks. Finally, we observe that training a
classifier on these representations with tiny datasets (e.g. 50 slides)
improved performances over SoTA by an average of +6.3 AUC points over all
downstream tasks.
